MEME

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use MEME in your research, please cite the following paper:
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.

Discovered Motifs   |   Block diagrams of Motifs   |   Program information   |   Explanation

Discovered Motifs

Motif Overview

Motif 1
  • 1.1e-269
  • 40 sites
Motif 1 Logo
Motif 2
  • 6.9e-182
  • 37 sites
Motif 2 Logo
Motif 3
  • 1.4e-156
  • 25 sites
Motif 3 Logo
Motif 4
  • 7.8e-122
  • 27 sites
Motif 4 Logo
Motif 5
  • 1.3e-092
  • 19 sites
Motif 5 Logo
Motif 6
  • 4.8e-059
  • 13 sites
Motif 6 Logo
Motif 7
  • 2.6e-059
  • 28 sites
Motif 7 Logo
Motif 8
  • 7.4e-053
  • 8 sites
Motif 8 Logo
Motif 9
  • 5.3e-047
  • 13 sites
Motif 9 Logo
Motif 10
  • 5.5e-043
  • 40 sites
Motif 10 Logo
Motif 11
  • 4.6e-046
  • 24 sites
Motif 11 Logo
Motif 12
  • 1.3e-041
  • 10 sites
Motif 12 Logo
Motif 13
  • 4.0e-032
  • 24 sites
Motif 13 Logo
Motif 14
  • 2.0e-031
  • 21 sites
Motif 14 Logo
Motif 15
  • 6.6e-030
  • 5 sites
Motif 15 Logo
Motif 16
  • 1.8e-029
  • 5 sites
Motif 16 Logo
Motif 17
  • 1.9e-027
  • 7 sites
Motif 17 Logo
Motif 18
  • 6.1e-021
  • 6 sites
Motif 18 Logo
Motif 19
  • 2.4e-020
  • 8 sites
Motif 19 Logo
Motif 20
  • 6.1e-018
  • 31 sites
Motif 20 Logo

Further Analysis

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Motif 1

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Summary

Sequence Logo

E-value 1.1e-269
Width 10
Sites 40
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

IWFQNRRMKW

Further Analysis

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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1514 4 1.24e-13 RQIK IWFQNRRMKW KKTYADFIAS
1513 4 1.24e-13 RQIK IWFQNRRMKW KKDIMGEWGN
1512 4 1.24e-13 RQIK IWFQNRRMKW KK
1511 4 1.24e-13 RQIK IWFQNRRMKW KA
1510 4 1.24e-13 RQIK IWFQNRRMKW K
1509 4 1.24e-13 RQIK IWFQNRRMKW AK
1508 4 1.24e-13 RQIK IWFQNRRMKW
1487 4 1.24e-13 RQIA IWFQNRRMKW KK
1483 4 1.24e-13 RQAK IWFQNRRMKW KK
1437 4 1.24e-13 RHIK IWFQNRRMKW KK
1431 4 1.24e-13 RAIK IWFQNRRMKW KK
1420 3 1.24e-13 QIK IWFQNRRMKW KK
1225 1 1.24e-13 K IWFQNRRMKW KK
1199 0 1.24e-13 IWFQNRRMKW KK
1195 2 1.24e-13 IK IWFQNRRMKW KK
1043 5 1.24e-13 CRQIK IWFQNRRMKW KK
1031 4 1.24e-13 AQIK IWFQNRRMKW KK
1020 12 1.24e-13 ALCPPERQIK IWFQNRRMKW KKEN
1019 12 1.24e-13 ALCLTERQIK IWFQNRRMKW KKEN
1501 4 4.82e-13 RQIK IWFQNRAMKW KK
1491 4 4.82e-13 RQIK IFFQNRRMKW KK
1515 4 7.85e-13 RQIR IWFQNRRMRW RR
1498 4 8.45e-13 RQIK IWFQNARMKW KK
1494 4 1.06e-12 RQIK IWFPNRRMKW KK
1042 5 1.06e-12 CRQIK IWFPNRRMKW KKC
1505 4 2.15e-12 RQIK IWFQNRRMAW KK
1493 4 2.15e-12 RQIK IWFANRRMKW KK
1488 4 2.15e-12 RQIK AWFQNRRMKW KK
1035 12 2.15e-12 ALCLTERQIK IWFANRRMKW KKEN
1561 46 3.18e-12 ALSLSERQIK IWFQNRRMKS KKDR
1496 4 5.37e-12 RQIK IWFQARRMKW KK
1492 4 5.37e-12 RQIK IWAQNRRMKW KK
1507 4 6.96e-12 RQIK IWFQNRRMKA KK
1489 4 9.05e-12 RQIK IAFQNRRMKW KK
1319 10 9.05e-12 LIRLWSHLIH IWFQNRRLKW KKK
1503 4 1.31e-11 RQIK IWFQNRRAKW KK
1490 4 2.01e-11 RQIK IFFQNRRMKF KK
1499 4 2.48e-10 RQIK IWFQNMRRKW KK
1071 47 6.02e-09 ELGLNEAQIK IWFQNKRAKI KKST
1543 4 9.06e-09 RVIR VWFQNKRCKD KK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1019 1.24e-13
1020 1.24e-13
1031 1.24e-13
1035 2.15e-12
1042 1.06e-12
1043 1.24e-13
1071 6.02e-09
1195 1.24e-13
1199 1.24e-13
1225 1.24e-13
1319 9.05e-12
1420 1.24e-13
1431 1.24e-13
1437 1.24e-13
1483 1.24e-13
1487 1.24e-13
1488 2.15e-12
1489 9.05e-12
1490 2.01e-11
1491 4.82e-13
1492 5.37e-12
1493 2.15e-12
1494 1.06e-12
1496 5.37e-12
1498 8.45e-13
1499 2.48e-10
1501 4.82e-13
1503 1.31e-11
1505 2.15e-12
1507 6.96e-12
1508 1.24e-13
1509 1.24e-13
1510 1.24e-13
1511 1.24e-13
1512 1.24e-13
1513 1.24e-13
1514 1.24e-13
1515 7.85e-13
1543 9.06e-09
1561 3.18e-12
 
0
10
20
30
40
50
60

Time 18.3 secs.

Motif 2

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Summary

Sequence Logo

E-value 6.9e-182
Width 10
Sites 37
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[ML]IIFR[ID][LA][IA]SH

Further Analysis

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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1366 0 2.32e-14 MIIFRDLISH
1370 0 1.16e-13 MIIFRILISH KK
1367 0 4.74e-13 MIIFRIAASH KK
1384 0 4.90e-13 MIIYRDLISH
1386 0 1.38e-12 MIIYRIAASH KK
1365 0 1.38e-12 MIIFRALISH KK
1318 0 2.86e-12 LIIFRILISH RR
1317 0 2.86e-12 LIIFRILISH R
1316 0 2.86e-12 LIIFRILISH KK
1315 0 2.86e-12 LIIFRILISH K
1314 0 2.86e-12 LIIFRILISH HH
1313 0 2.86e-12 LIIFRILISH
1629 0 4.64e-12 WIIFRIAASH KK
1364 0 4.64e-12 MIIFRAAASH KK
1372 0 4.92e-12 MIISRDLISH
1368 0 4.92e-12 MIIFRIAATH KK
1377 0 7.04e-12 MIIYRALISH KK
1079 0 7.04e-12 FIIFRIAASH KK
1312 0 8.25e-12 LIIFRIAASH KK
1369 0 9.28e-12 MIIFRIAAYH KK
1362 0 1.02e-11 MIIFAIAASH KK
1628 0 1.42e-11 WIIFRALISH KK
1363 0 1.42e-11 MIIFKIAASH KK
1375 0 2.10e-11 MIIYRAEISH
1627 0 2.79e-11 WIIFRAAASH KK
1630 0 2.97e-11 WIIFRIAATH KK
1311 0 4.25e-11 LIIFAILISH KK
1631 0 5.06e-11 WIIFRIAAYH KK
1626 0 7.77e-11 WIIFKIAASH KK
1310 0 8.44e-11 LIIFAIAASH KK
1039 0 9.37e-11 CIISRDLISH
1419 0 1.49e-10 QIISRDLISH
1385 0 1.61e-10 MIIYRDLISK K
1379 0 7.29e-10 MIIYRDKKSH
1371 0 1.13e-09 MIIRRDLISE
1444 7 9.23e-09 RILQQLL FIHFRIGCRH SRI
1443 7 9.23e-09 RILQQLL FIHFRIGCRH

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1039 9.37e-11
1079 7.04e-12
1310 8.44e-11
1311 4.25e-11
1312 8.25e-12
1313 2.86e-12
1314 2.86e-12
1315 2.86e-12
1316 2.86e-12
1317 2.86e-12
1318 2.86e-12
1362 1.02e-11
1363 1.42e-11
1364 4.64e-12
1365 1.38e-12
1366 2.32e-14
1367 4.74e-13
1368 4.92e-12
1369 9.28e-12
1370 1.16e-13
1371 1.13e-09
1372 4.92e-12
1375 2.10e-11
1377 7.04e-12
1379 7.29e-10
1384 4.90e-13
1385 1.61e-10
1386 1.38e-12
1419 1.49e-10
1443 9.23e-09
1444 9.23e-09
1626 7.77e-11
1627 2.79e-11
1628 1.42e-11
1629 4.64e-12
1630 2.97e-11
1631 5.06e-11
 
0
5
10
15
20

Time 35.3 secs.

Motif 3

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Summary

Sequence Logo

E-value 1.4e-156
Width 10
Sites 25
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

LWMRWYSPTT

Further Analysis

Submit this motif to  
      
      
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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1477 1 2.80e-14 R LWMRWYSPTT RRYG
1476 1 2.80e-14 R LWMRWYSPTT RRYA
1475 1 2.80e-14 R LWMRWYSPTT RRAG
1474 1 2.80e-14 R LWMRWYSPTT RAYG
1473 1 2.80e-14 R LWMRWYSPTT ARYG
1262 1 2.80e-14 K LWMRWYSPTT RRYG
1028 1 2.80e-14 A LWMRWYSPTT RRYG
1479 1 5.51e-14 R LWMRWYSPWT RRYG
1478 1 5.51e-14 R LWMRWYSPWT RRWG
1263 1 5.51e-14 K LWMRWYSPWT RRYG
1433 1 9.52e-14 R AWMRWYSPTT RRYG
1467 1 1.46e-13 R LWMAWYSPTT RRYG
1470 1 3.14e-13 R LWMRWYAPTT RRYG
1261 1 3.14e-13 K LWMRWYSATT RRYG
1471 1 4.05e-13 R LWMRWYSPAT RRYG
1472 1 5.03e-13 R LWMRWYSPTA RRYG
1469 1 1.02e-12 R LWMRWASPTT RRYG
1468 1 1.78e-12 R LWMRAYSPTT RRYG
1459 1 1.78e-12 R LAMRWYSPTT RRYG
1466 1 3.47e-12 R LWARWYSPTT RRYG
1481 1 4.24e-12 R LYMRYYSPTT RRYG
1460 1 5.50e-12 R LFMRFYSPTT RRYG
1465 1 1.62e-11 R LVMRVYSPTT RRYG
1462 1 4.96e-11 R LLMRLYSPTT RRYG
1461 1 7.49e-11 R LIMRIYSPTT RRYG

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1028 2.80e-14
1261 3.14e-13
1262 2.80e-14
1263 5.51e-14
1433 9.52e-14
1459 1.78e-12
1460 5.50e-12
1461 7.49e-11
1462 4.96e-11
1465 1.62e-11
1466 3.47e-12
1467 1.46e-13
1468 1.78e-12
1469 1.02e-12
1470 3.14e-13
1471 4.05e-13
1472 5.03e-13
1473 2.80e-14
1474 2.80e-14
1475 2.80e-14
1476 2.80e-14
1477 2.80e-14
1478 5.51e-14
1479 5.51e-14
1481 4.24e-12
 
0
2
4
6
8
10
12
14

Time 51.5 secs.

Motif 4

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Summary

Sequence Logo

E-value 7.8e-122
Width 10
Sites 27
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[CS]RWRWK[CS][CS]KK

Further Analysis

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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1356 2 1.03e-12 MD CRWRWKCCKK
1267 3 1.03e-12 KMD CRWRWKCCKK
1215 2 1.03e-12 KD CRWRWKCCKK
1214 1 1.03e-12 K CRWRWKCCKK
1057 1 1.03e-12 D CRWRWKCCKK
1045 0 1.03e-12 CRWRWKCCKK
1269 3 3.45e-12 KMD CRWRWKCSKK
1048 0 3.45e-12 CRWRWKCSKK
1579 0 5.72e-12 SRWRWKCCKK
1274 3 5.72e-12 KMD SRWRWKCCKK
1271 3 7.99e-12 KMD CRWRWKSCKK
1580 0 1.71e-11 SRWRWKCSKK
1275 3 1.71e-11 KMD SRWRWKCSKK
1044 0 1.71e-11 CRWRFKCCKK
1041 0 1.78e-11 CRFRWKCCKK
1272 3 2.29e-11 KMD CRWRWKSSKK
1049 0 2.29e-11 CRWRWKSSKK
1581 0 2.79e-11 SRWRWKSCKK
1276 3 2.79e-11 KMD SRWRWKSCKK
1266 3 3.24e-11 KMD CRWRPKCCKK
1212 3 3.24e-11 KCG CRWRWKCGCK K
1047 0 3.24e-11 CRWRWKCGCK K
1297 0 6.74e-11 KRWRWKCCKK
1582 0 8.30e-11 SRWRWKSSKK
1277 3 8.30e-11 KMD SRWRWKSSKK
1040 0 2.76e-10 CRFRFKCCKK
1265 3 2.99e-09 KMD CRPRPKCCKK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1040 2.76e-10
1041 1.78e-11
1044 1.71e-11
1045 1.03e-12
1047 3.24e-11
1048 3.45e-12
1049 2.29e-11
1057 1.03e-12
1212 3.24e-11
1214 1.03e-12
1215 1.03e-12
1265 2.99e-09
1266 3.24e-11
1267 1.03e-12
1269 3.45e-12
1271 7.99e-12
1272 2.29e-11
1274 5.72e-12
1275 1.71e-11
1276 2.79e-11
1277 8.30e-11
1297 6.74e-11
1356 1.03e-12
1579 5.72e-12
1580 1.71e-11
1581 2.79e-11
1582 8.30e-11
 
0
2
4
6
8
10
12
14

Time 67.3 secs.

Motif 5

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Summary

Sequence Logo

E-value 1.3e-092
Width 10
Sites 19
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

IRKQAHAHSK

Further Analysis

Submit this motif to  
      
      
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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1339 8 1.11e-12 LLIILRRR IRKQAHAHSK
1330 8 1.11e-12 LLIILRRA IRKQAHAHSK
1329 8 1.11e-12 LLIILRAR IRKQAHAHSK
1328 8 1.11e-12 LLIILARR IRKQAHAHSK
1327 8 1.11e-12 LLIIARRR IRKQAHAHSK
1326 8 1.11e-12 LLIALRRR IRKQAHAHSK
1322 8 1.11e-12 LLAILRRR IRKQAHAHSK
1304 8 1.11e-12 LAIILRRR IRKQAHAHSK
1196 5 1.11e-12 ILRRR IRKQAHAHSK
1025 8 1.11e-12 ALIILRRR IRKQAHAHSK
1001 8 1.11e-12 AAAAARRR IRKQAHAHSK
1332 9 2.91e-12 LLIILRRRI ARKQAHAHSK
1331 8 2.91e-12 LLIILRRR ARKQAHAHSK
1337 8 6.26e-12 LLIILRRR IRKQAHAHAK
1338 8 1.21e-11 LLIILRRR IRKQAHAHSA
1333 8 1.21e-11 LLIILRRR IRAQAHAHSK
1336 8 2.47e-11 LLIILRRR IRKQAHAASK
1335 8 2.47e-11 LLIILRRR IRKQAAAHSK
1334 8 3.06e-11 LLIILRRR IRKAAHAHSK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1001 1.11e-12
1025 1.11e-12
1196 1.11e-12
1304 1.11e-12
1322 1.11e-12
1326 1.11e-12
1327 1.11e-12
1328 1.11e-12
1329 1.11e-12
1330 1.11e-12
1331 2.91e-12
1332 2.91e-12
1333 1.21e-11
1334 3.06e-11
1335 2.47e-11
1336 2.47e-11
1337 6.26e-12
1338 1.21e-11
1339 1.11e-12
 
0
2
4
6
8
10
12
14
16
18

Time 83.2 secs.

Motif 6

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Summary

Sequence Logo

E-value 4.8e-059
Width 10
Sites 13
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

VALLPAVLLA

Further Analysis

Submit this motif to  
      
      
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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1634 6 1.95e-12 WRFKAA VALLPAVLLA LLAP
1455 15 1.95e-12 QRRRPPQCAA VALLPAVLLA LLAP
1013 2 1.95e-12 AA VALLPAVLLA LLAVTDQLGE
1012 2 1.95e-12 AA VALLPAVLLA LLAPVQRKRQ
1011 2 1.95e-12 AA VALLPAVLLA LLAPSGASGL
1010 2 1.95e-12 AA VALLPAVLLA LLAPRRRRRR
1009 2 1.95e-12 AA VALLPAVLLA LLAPRKKRRQ
1008 2 1.95e-12 AA VALLPAVLLA LLAPRKKRRQ
1007 2 1.95e-12 AA VALLPAVLLA LLAPEILLPN
1006 2 1.95e-12 AA VALLPAVLLA LLAP
1005 2 1.95e-12 AA VALLPAVLLA LLAKKNNLKE
1004 2 1.95e-12 AA VALLPAVLLA LLAKKNNLKD
1003 2 1.95e-12 AA VALLPAVLLA LLAK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1003 1.95e-12
1004 1.95e-12
1005 1.95e-12
1006 1.95e-12
1007 1.95e-12
1008 1.95e-12
1009 1.95e-12
1010 1.95e-12
1011 1.95e-12
1012 1.95e-12
1013 1.95e-12
1455 1.95e-12
1634 1.95e-12
 
0
5
10
15
20
25
30
35
40

Time 99.1 secs.

Motif 7

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Summary

Sequence Logo

E-value 2.6e-059
Width 10
Sites 28
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[IL][NA]LKALAA[LA][AL]

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1344 10 8.58e-12 LNSAGYLLGK INLKALAALA KKIL
1325 4 8.58e-12 LLGK INLKALAALA KKIL
1197 0 8.58e-12 INLKALAALA KKIL
1179 7 8.58e-12 GWTLNSK INLKALAALA KKIL
1175 13 8.58e-12 LNSAGYLLGK INLKALAALA KKLL
1174 13 8.58e-12 LNSAGYLLGK INLKALAALA KKIL
1172 13 8.58e-12 LNPPGYLLGK INLKALAALA KKIL
1171 13 8.58e-12 LNPAGYLLGK INLKALAALA KKIL
1104 2 8.58e-12 GK INLKALAALA KKIL
1017 7 8.58e-12 AGYLLGK INLKALAALA KKILTYADFI
1016 7 8.58e-12 AGYLLGK INLKALAALA KKIL
1176 13 8.12e-10 LNSAGYLLGK INLKAPAALA KKIL
1346 8 1.74e-09 LNSAGYLL GKLKALAALA KIL
1345 8 1.74e-09 LNSAGYLL GKLKALAALA K
1177 11 1.74e-09 WTLNSAGYLL GKLKALAALA KKIL
1018 5 1.74e-09 AGYLL GKLKALAALA KKIL
1072 5 6.23e-09 ELALE LALEALEAAL ELA
1246 5 2.11e-08 KLALK LALKALQAAL QLA
1120 0 2.11e-08 GLLEALAELL EGLRKRLRKF
1245 5 2.34e-08 KLALK LALKALKAAL KLAGC
1244 5 2.34e-08 KLALK LALKALKAAL KLA
1243 5 2.34e-08 KLALK LALKALKAAL K
1241 1 2.34e-08 K LALKALKAAL KLA
1343 6 2.60e-08 LNSAGY LLGKALAALA KKIL
1358 4 7.71e-08 MGLG LHLLVLAAAL QGAWSQPKKK
1357 4 7.71e-08 MGLG LHLLVLAAAL QGAKKKRKV
1623 19 3.72e-07 AEALAEHLAE ALAEALEALA A
1015 8 1.00e-06 AEKVDPVK LNLTLSAAAE ALTGLGDK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1015 1.00e-06
1016 8.58e-12
1017 8.58e-12
1018 1.74e-09
1072 6.23e-09
1104 8.58e-12
1120 2.11e-08
1171 8.58e-12
1172 8.58e-12
1174 8.58e-12
1175 8.58e-12
1176 8.12e-10
1177 1.74e-09
1179 8.58e-12
1197 8.58e-12
1241 2.34e-08
1243 2.34e-08
1244 2.34e-08
1245 2.34e-08
1246 2.11e-08
1325 8.58e-12
1343 2.60e-08
1344 8.58e-12
1345 1.74e-09
1346 1.74e-09
1357 7.71e-08
1358 7.71e-08
1623 3.72e-07
 
0
5
10
15
20
25
30
35

Time 114.4 secs.

Motif 8

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Summary

Sequence Logo

E-value 7.4e-053
Width 10
Sites 8
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

DVRSVTTEIN

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1597 11 3.84e-15 KRRITPKKVI DVRSVTTEIN T
1595 11 3.84e-15 KRRITPKDVI DVRSVTTEIN T
1592 11 3.84e-15 KRRITPDDVI DVRSVTTEIN T
1591 12 3.84e-15 AARITPKDVI DVRSVTTEIN T
1589 11 3.84e-15 ARRITPKDVI DVRSVTTEIN T
1185 17 3.84e-15 KRRITPKDVI DVRSVTTEIN T
1594 11 4.24e-15 KRRITPKDVI DVESVTTEIN T
1596 11 4.22e-13 KRRITPKDVI DVRSVTTKIN T

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1185 3.84e-15
1589 3.84e-15
1591 3.84e-15
1592 3.84e-15
1594 4.24e-15
1595 3.84e-15
1596 4.22e-13
1597 3.84e-15
 
0
5
10
15
20
25

Time 129.1 secs.

Motif 9

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Summary

Sequence Logo

E-value 5.3e-047
Width 10
Sites 13
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

HHCRSKAKRS

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1577 3 1.18e-12 SRR HHCRSKAKRS AHH
1566 3 1.18e-12 SRA HHCRSKAKRS RHH
1553 3 1.18e-12 SAR HHCRSKAKRS RHH
1519 2 1.18e-12 RR HHCRSKAKRS R
1161 3 1.18e-12 GRR HHCRSKAKRS RHH
1576 3 8.13e-12 SRR HHCRSKAKRA RHH
1572 3 8.13e-12 SRR HHCRAKAKRS RHH
1575 3 8.86e-12 SRR HHCRSKAKAS RHH
1574 3 1.62e-11 SRR HHCRSKAARS RHH
1573 3 1.62e-11 SRR HHCRSAAKRS RHH
1570 3 3.42e-11 SRR HACRSKAKRS RHH
1567 3 3.42e-11 SRR AHCRSKAKRS RHH
1571 3 1.25e-10 SRR HHARSKAKRS RHH

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1161 1.18e-12
1519 1.18e-12
1553 1.18e-12
1566 1.18e-12
1567 3.42e-11
1570 3.42e-11
1571 1.25e-10
1572 8.13e-12
1573 1.62e-11
1574 1.62e-11
1575 8.86e-12
1576 8.13e-12
1577 1.18e-12
 
0
2
4
6
8
10
12
14
16

Time 143.6 secs.

Motif 10

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Summary

Sequence Logo

E-value 5.5e-043
Width 9
Sites 40
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

RKKRRQRRR

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1646 2 2.08e-08 YG RKKRRQRRR
1455 0 2.08e-08 RKKRRQRRR PPQCAAVALL
1454 0 2.08e-08 RKKRRQRRR
1307 6 2.08e-08 LGISYG RKKRRQRRR PPQ
1217 16 2.08e-08 TWWTEWSQPG RKKRRQRRR PPQ
1182 3 2.08e-08 GYG RKKRRQRRR G
1150 1 2.08e-08 G RKKRRQRRR PWQ
1149 1 2.08e-08 G RKKRRQRRR PPQTYADFIA
1147 1 2.08e-08 G RKKRRQRRR PPQC
1146 1 2.08e-08 G RKKRRQRRR PPQ
1145 1 2.08e-08 G RKKRRQRRR PP
1144 1 2.08e-08 G RKKRRQRRR C
1143 1 2.08e-08 G RKKRRQRRR
1081 11 2.08e-08 ITKALGISYG RKKRRQRRR PPQ
1009 16 2.08e-08 PAVLLALLAP RKKRRQRRR PPQC
1008 16 2.08e-08 PAVLLALLAP RKKRRQRRR PPQ
1446 0 3.89e-08 RKARRQRRR
1142 1 1.32e-07 G RKKRRQRRP PQC
1450 0 1.43e-07 RKKRRQARR
1453 0 1.73e-07 RKKRRQRRA
1432 0 1.73e-07 RAKRRQRRR
1451 0 2.00e-07 RKKRRQRAR
1140 1 2.00e-07 G RKKRRQRAR PPQC
1601 1 2.04e-07 T RQARRNRRR RWRERQRGC
1600 1 2.04e-07 T RQARRNRRR RWRERQR
1485 0 2.04e-07 RQARRNRRR C
1484 0 2.04e-07 RQARRNRRR ALWKTLLKKV
1645 3 2.44e-07 YGR KKKRRQRRR
1448 0 2.86e-07 RKKRAQRRR
1447 0 2.86e-07 RKKARQRRR
1023 0 3.37e-07 AKKRRQRRR
1181 3 4.19e-07 GYG RKKRRGRRR THRLPRRRRR
1449 0 1.01e-06 RKKRRARRR
1138 1 2.55e-06 G RKKRRQARA PPQC
1141 1 2.76e-06 G RKKRRQRPP QC
1650 2 6.82e-06 YG RRARRRRRR
1398 0 7.24e-06 NRARRNRRR VR
1651 2 1.99e-05 YG RRRRRRRRR
1532 0 1.99e-05 RRRRRRRRR
1165 1 1.99e-05 G RRRRRRRRR PPQ

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1008 2.08e-08
1009 2.08e-08
1023 3.37e-07
1081 2.08e-08
1138 2.55e-06
1140 2.00e-07
1141 2.76e-06
1142 1.32e-07
1143 2.08e-08
1144 2.08e-08
1145 2.08e-08
1146 2.08e-08
1147 2.08e-08
1149 2.08e-08
1150 2.08e-08
1165 1.99e-05
1181 4.19e-07
1182 2.08e-08
1217 2.08e-08
1307 2.08e-08
1398 7.24e-06
1432 1.73e-07
1446 3.89e-08
1447 2.86e-07
1448 2.86e-07
1449 1.01e-06
1450 1.43e-07
1451 2.00e-07
1453 1.73e-07
1454 2.08e-08
1455 2.08e-08
1484 2.04e-07
1485 2.04e-07
1532 1.99e-05
1600 2.04e-07
1601 2.04e-07
1645 2.44e-07
1646 2.08e-08
1650 6.82e-06
1651 1.99e-05
 
0
5
10
15
20
25
30

Time 158.1 secs.

Motif 11

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Summary

Sequence Logo

E-value 4.6e-046
Width 7
Sites 24
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

I[TI][YP][RKA]D[LV]I

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1383 1 4.99e-09 M IIYRDLI S
1382 1 4.99e-09 M IIYRDLI A
1381 1 4.99e-09 M IIYRDLI
1194 0 4.99e-09 IIYRDLI SH
1021 1 4.99e-09 A IIYRDLI S
1373 1 6.28e-09 M IIYADLI S
1596 4 7.49e-09 TKRR ITPKDVI DVRSVTTKIN
1595 4 7.49e-09 TKRR ITPKDVI DVRSVTTEIN
1594 4 7.49e-09 TKRR ITPKDVI DVESVTTEIN
1593 4 7.49e-09 TKRR ITPKDVI DV
1592 4 7.49e-09 TKRR ITPDDVI DVRSVTTEIN
1591 5 7.49e-09 TKAAR ITPKDVI DVRSVTTEIN
1589 4 7.49e-09 TARR ITPKDVI DVRSVTTEIN
1185 10 7.49e-09 HHHHHHTKRR ITPKDVI DVRSVTTEIN
1017 20 3.73e-08 KALAALAKKI LTYADFI ASGRTGRRNA
1378 1 4.19e-08 M IIYRDAI S
1360 1 5.61e-08 M IAYRDLI S
1149 12 5.61e-08 KKRRQRRRPP QTYADFI ASGRTGRRNA
1380 1 1.30e-07 M IIYRDLA S
1514 15 1.68e-07 WFQNRRMKWK KTYADFI ASGRTGRRNA
1352 1 1.88e-07 M AIYRDLI S
1361 1 2.21e-07 M IIARDLI S
1536 10 2.61e-07 RRRRRRRRRR RTYADFI ASGRTGRRNA
1376 1 6.62e-07 M IIYRALI S

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1017 3.73e-08
1021 4.99e-09
1149 5.61e-08
1185 7.49e-09
1194 4.99e-09
1352 1.88e-07
1360 5.61e-08
1361 2.21e-07
1373 6.28e-09
1376 6.62e-07
1378 4.19e-08
1380 1.30e-07
1381 4.99e-09
1382 4.99e-09
1383 4.99e-09
1514 1.68e-07
1536 2.61e-07
1589 7.49e-09
1591 7.49e-09
1592 7.49e-09
1593 7.49e-09
1594 7.49e-09
1595 7.49e-09
1596 7.49e-09
 
0
5
10
15
20
25
30
35

Time 172.7 secs.

Motif 12

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Summary

Sequence Logo

E-value 1.3e-041
Width 10
Sites 10
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

G[WG]T[LC]N[SPT][AP]G[YC]L

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1178 0 5.14e-14 GWTLNSAGYL LGPHAVGNHR
1177 0 5.14e-14 GWTLNSAGYL LGKLKALAAL
1176 0 5.14e-14 GWTLNSAGYL LGKINLKAPA
1175 0 5.14e-14 GWTLNSAGYL LGKINLKALA
1174 0 5.14e-14 GWTLNSAGYL LGKINLKALA
1173 0 5.14e-14 GWTLNSAGYL LGKFLPLILR
1171 0 4.78e-13 GWTLNPAGYL LGKINLKALA
1172 0 6.72e-13 GWTLNPPGYL LGKINLKALA
1122 10 7.21e-11 GLPVCGETCV GGTCNTPGCT CSWPKCTRN
1121 10 2.08e-10 GLPVCGETCV GGTCNTPGCK CSWPVCTRN

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1121 2.08e-10
1122 7.21e-11
1171 4.78e-13
1172 6.72e-13
1173 5.14e-14
1174 5.14e-14
1175 5.14e-14
1176 5.14e-14
1177 5.14e-14
1178 5.14e-14
 
0
5
10
15
20
25
30

Time 186.4 secs.

Motif 13

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Summary

Sequence Logo

E-value 4.0e-032
Width 10
Sites 24
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[AG]L[WF][RK][AT]L[WL][RK][KLS][LV]

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1128 4 1.31e-10 GLWR ALWRALWRSL WKSKRKV
1127 4 1.31e-10 GLWR ALWRALWRSL WKLKWKV
1126 4 1.31e-10 GLWR ALWRALWRSL WKLKRKV
1125 4 1.31e-10 GLWR ALWRALWRSL WKKKRKV
1133 0 6.20e-10 GLWRALWRLL RSLWRLLWSQ
1132 0 6.20e-10 GLWRALWRLL RSLWRLLWRA
1131 0 6.20e-10 GLWRALWRLL RSLWRLLWKA
1130 0 1.23e-09 GLWRALWRGL RSLWKLKRKV
1129 0 1.23e-09 GLWRALWRGL RSLWKKKRKV
1389 11 3.10e-09 VKSKIGSWIL VLFVAMWSDV GLCKKRPKP
1354 9 3.51e-09 MANLGYWLL ALFVTMWTDV GLCKKRPKP
1124 0 3.92e-09 GLWRALWRAL RSLWKLKRKV
1029 0 6.63e-09 ALWMTLLKKV LKAAAKAALN
1614 7 8.34e-09 VKRKKKP ALWKTLLKKV LKA
1484 9 8.34e-09 RQARRNRRR ALWKTLLKKV LKA
1404 7 8.34e-09 PKKKRKV ALWKTLLKKV LKA
1027 0 8.34e-09 ALWKTLLKKV LKAPKKKRKV
1026 0 8.34e-09 ALWKTLLKKV LKA
1117 0 2.30e-08 GLFRALLRLL RSLWRLLLRA
1353 9 2.75e-08 MANLGCWML VLFVATWSDL GLCKKRPKP
1116 0 4.17e-08 GLFKALLKLL KSLWKLLLKA
1264 3 5.17e-07 KLW SAWPSLWSSL WKP
1480 0 5.54e-07 RLWRALPRVL RRLLRP
1115 7 5.54e-07 GLFEALL ELLESLWELL LEA

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1026 8.34e-09
1027 8.34e-09
1029 6.63e-09
1115 5.54e-07
1116 4.17e-08
1117 2.30e-08
1124 3.92e-09
1125 1.31e-10
1126 1.31e-10
1127 1.31e-10
1128 1.31e-10
1129 1.23e-09
1130 1.23e-09
1131 6.20e-10
1132 6.20e-10
1133 6.20e-10
1264 5.17e-07
1353 2.75e-08
1354 3.51e-09
1389 3.10e-09
1404 8.34e-09
1480 5.54e-07
1484 8.34e-09
1614 8.34e-09
 
0
5
10
15
20
25
30

Time 200.5 secs.

Motif 14

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Summary

Sequence Logo

E-value 2.0e-031
Width 9
Sites 21
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

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   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

P[PR]P[LV]P[FL]P[PR]P

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1609 3 4.79e-11 VHL PPPVHLPPP VHLPPP
1608 3 4.79e-11 VHL PPPVHLPPP
1607 3 7.71e-11 VEL PPPVELPPP VELPPP
1612 3 2.74e-10 VKL PPPVKLPPP VKLPPP
1611 3 2.74e-10 VKL PPPVKLPPP
1523 14 4.35e-10 PRPPRLPRPR PRPLPFPRP G
1463 6 4.35e-10 RLPRPR PRPLPFPRP G
1415 4 4.35e-10 PRPR PRPLPFPRP G
1414 2 4.35e-10 PR PRPLPFPRP G
1413 10 4.35e-10 PRPPRLPRPR PRPLPFPRP G
1412 0 4.35e-10 PRPLPFPRP G
1409 8 4.35e-10 PPRLPRPR PRPLPFPRP G
1620 3 5.83e-10 VRL PPPVRLPPP VRLPPP
1619 3 5.83e-10 VRL PPPVRLPPP
1050 3 7.13e-08 CSI PPEVKFNPF VYLI
1522 6 9.49e-08 RRIRPR PPRLPRPRP RP
1521 6 9.49e-08 RRIRPR PPRLPRPRP
1187 0 1.11e-07 HPGSPFPPE HRP
1426 2 1.58e-07 QS PTDFTFPNP L
1562 2 3.70e-07 SL GWMLPFSPP F
1661 3 9.62e-06 YSH IATLPFTPT

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1050 7.13e-08
1187 1.11e-07
1409 4.35e-10
1412 4.35e-10
1413 4.35e-10
1414 4.35e-10
1415 4.35e-10
1426 1.58e-07
1463 4.35e-10
1521 9.49e-08
1522 9.49e-08
1523 4.35e-10
1562 3.70e-07
1607 7.71e-11
1608 4.79e-11
1609 4.79e-11
1611 2.74e-10
1612 2.74e-10
1619 5.83e-10
1620 5.83e-10
1661 9.62e-06
 
0
5
10
15
20

Time 213.6 secs.

Motif 15

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Summary

Sequence Logo

E-value 6.6e-030
Width 10
Sites 5
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

DSDCPGACIC

Further Analysis

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Data Formats

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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1101 13 1.39e-15 CPKILKKCRR DSDCPGACIC RGNGYCGSGS
1100 13 1.39e-15 CPKILKACRR DSDCPGACIC RGNGYCGSGS
1099 13 1.39e-15 CPKILAKCRR DSDCPGACIC RGNGYCGSGS
1098 13 1.39e-15 CPKILAACRR DSDCPGACIC RGNGYCGSGS
1097 13 1.39e-15 CPAILKKCRR DSDCPGACIC RGNGYCGSGS

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1097 1.39e-15
1098 1.39e-15
1099 1.39e-15
1100 1.39e-15
1101 1.39e-15
 
0
5
10
15
20
25
30

Time 226 secs.

Motif 16

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Summary

Sequence Logo

E-value 1.8e-029
Width 10
Sites 5
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GNGYCGSGSD

Further Analysis

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Data Formats

View the motif in PSPM Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1101 24 1.65e-15 SDCPGACICR GNGYCGSGSD
1100 24 1.65e-15 SDCPGACICR GNGYCGSGSD
1099 24 1.65e-15 SDCPGACICR GNGYCGSGSD
1098 24 1.65e-15 SDCPGACICR GNGYCGSGSD
1097 24 1.65e-15 SDCPGACICR GNGYCGSGSD

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1097 1.65e-15
1098 1.65e-15
1099 1.65e-15
1100 1.65e-15
1101 1.65e-15
 
0
5
10
15
20
25
30

Time 238.2 secs.

Motif 17

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Summary

Sequence Logo

E-value 1.9e-027
Width 9
Sites 7
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

QWQRNMRKV

Further Analysis

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Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
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Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1429 0 2.00e-12 QWQRNMRKV RGPPVSCIKR
1428 0 2.00e-12 QWQRNMRKV R
1211 3 2.00e-12 KCF QWQRNMRKV RGPPVSSIKR
1210 3 2.00e-12 KCF QWQRNMRKV RGPPVSCIKR
1209 3 2.00e-12 KCF QWQRNMRKV RGPPVSC
1208 3 2.00e-12 KCF QWQRNMRKV R
1086 1 2.00e-12 F QWQRNMRKV RGPPVS

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1086 2.00e-12
1208 2.00e-12
1209 2.00e-12
1210 2.00e-12
1211 2.00e-12
1428 2.00e-12
1429 2.00e-12
 
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Time 250.8 secs.

Motif 18

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Summary

Sequence Logo

E-value 6.1e-021
Width 10
Sites 6
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

FGKADCDRPP

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1255 10 4.69e-14 KLIKGRTPIK FGKADCDRPP KHSQNGMGK
1254 10 4.69e-14 KLIKGRTPIK FGKADCDRPP KHSQNGM
1253 10 4.69e-14 KLIKGRTPIK FGKADCDRPP KHSQNGK
1252 10 4.69e-14 KLIKGRTPIK FGKADCDRPP KHSGK
1221 7 4.69e-14 KGRTPIK FGKADCDRPP KHSQNGMGK
1256 10 7.29e-10 KLIKGRTPIK FGKARCRRPP KHSGK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1221 4.69e-14
1252 4.69e-14
1253 4.69e-14
1254 4.69e-14
1255 4.69e-14
1256 7.29e-10
 
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Time 263.1 secs.

Motif 19

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Summary

Sequence Logo

E-value 2.4e-020
Width 10
Sites 8
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

KKTTTKPTKK

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1292 9 6.04e-12 KRIPNKKPG KKTTTKPTKK PTIKTTKKDL
1291 9 6.04e-12 KRIPNKKPG KKTTTKPTKK PTIKTTKKDL
1290 9 6.04e-12 KRIPNKKPG KKTTTKPTKK PTIKTTKK
1289 9 6.04e-12 KRIPNKKPG KKTTTKPTKK PTIK
1288 9 6.04e-12 KRIPNKKPG KKTTTKPTKK
1236 0 6.04e-12 KKTTTKPTKK
1233 4 6.04e-12 KKPG KKTTTKPTKK PTIKTTKK
1232 4 6.04e-12 KKPG KKTTTKPTKK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1232 6.04e-12
1233 6.04e-12
1236 6.04e-12
1288 6.04e-12
1289 6.04e-12
1290 6.04e-12
1291 6.04e-12
1292 6.04e-12
 
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35

Time 275.1 secs.

Motif 20

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Summary

Sequence Logo

E-value 6.1e-018
Width 10
Sites 31
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GR[QA][AL]R[RI]A[AG]RR

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1157 0 4.10e-10 GRQLRIAGRR LRRRSR
1156 0 4.10e-10 GRQLRIAGRR LRGRSR
1159 0 5.55e-10 GRQLRRAGRR LRRRSR
1158 0 5.55e-10 GRQLRRAGRR LRGRSR
1644 1 3.78e-09 Y GRAARRAARR
1550 6 4.43e-09 RVTSWL GRQLRIAGKR LEGRSK
1548 6 4.43e-09 RVRSWL GRQLRIAGKR LEGRSK
1538 7 4.43e-09 RRVTSWL GRQLRIAGKR LEGRSK
1486 11 4.43e-09 QGAARVTSWL GRQLRIAGKR LEGRSK
1155 0 4.43e-09 GRQLRIAGKR LRGRSK
1154 0 4.43e-09 GRQLRIAGKR LEGRSK
1643 1 1.68e-08 Y EREARRAARR
1648 1 2.64e-08 Y GRRARRAARR
1641 1 3.04e-08 Y AREARRAARR
1640 1 3.04e-08 Y ARAARRAARR
1402 1 3.04e-08 P ARAARRAARR
1323 19 3.79e-08 QCRICMRNFS TRQARRNHRR RHRR
1002 13 3.79e-08 ACRICMRNFS TRQARRNHRR RHRR
1656 1 9.97e-08 Y PRAARRAARR
1654 1 1.10e-07 Y KRAARRAARR
1436 7 1.51e-07 RGSRRAV TRAQRRDGRR RRRSRRESYS
1642 1 2.14e-07 Y ARKARRAARR
1280 2 2.47e-07 KM TRAQRRAAAR RNRWTARGC
1260 2 2.47e-07 KL TRAQRRAAAR KNKRNTRGC
1655 1 6.15e-07 Y KRKARRAARR
1649 1 1.65e-06 Y GRRARRRARR
1659 1 3.38e-06 Y RRAARRAARA
1569 0 4.10e-06 SRRARRSPRH LGSG
1458 7 4.10e-06 RKKRRRE SRRARRSPRH L
1568 0 5.93e-06 SRRARRSPRE SGKKRKRKR
1639 1 4.59e-05 Y ARAAARQARA

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1002 3.79e-08
1154 4.43e-09
1155 4.43e-09
1156 4.10e-10
1157 4.10e-10
1158 5.55e-10
1159 5.55e-10
1260 2.47e-07
1280 2.47e-07
1323 3.79e-08
1402 3.04e-08
1436 1.51e-07
1458 4.10e-06
1486 4.43e-09
1538 4.43e-09
1548 4.43e-09
1550 4.43e-09
1568 5.93e-06
1569 4.10e-06
1639 4.59e-05
1640 3.04e-08
1641 3.04e-08
1642 2.14e-07
1643 1.68e-08
1644 3.78e-09
1648 2.64e-08
1649 1.65e-06
1654 1.10e-07
1655 6.15e-07
1656 9.97e-08
1659 3.38e-06
 
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Time 286.9 secs.

All Motifs

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Combined Block Diagrams

Non-overlapping sites with a p-value better than 0.0001.
The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. The motif blocks have tool tips with more information.

Motif 1
Motif 2
Motif 3
Motif 4
Motif 5
Motif 6
Motif 7
Motif 8
Motif 9
Motif 10
Motif 11
Motif 12
Motif 13
Motif 14
Motif 15
Motif 16
Motif 17
Motif 18
Motif 19
Motif 20
Name Combined p-value Motif Location
1001 7.74e-04
1002 6.77e-05
1003 1.35e-07
1004 6.48e-07
1005 5.91e-07
1006 1.01e-07
1007 6.35e-10
1008 2.03e-10
1009 3.04e-10
1010 3.03e-07
1011 1.56e-07
1012 4.27e-07
1013 3.63e-08
1015 1.96e-04
1016 5.70e-05
1017 1.43e-07
1018 1.91e-03
1019 4.46e-04
1020 5.46e-04
1021 1.00e-05
1023 7.41e-05
1025 1.99e-04
1026 4.69e-04
1027 1.65e-03
1028 3.28e-05
1029 3.84e-07
1031 6.69e-03
1032 9.08e-07
1035 1.94e-03
1039 4.65e-07
1040 7.28e-04
1041 5.05e-04
1042 2.01e-02
1043 8.41e-03
1044 6.58e-04
1045 4.12e-04
1047 1.95e-02
1048 5.78e-04
1049 3.64e-04
1050 4.07e-04
1057 1.14e-03
1060 2.01e-03
1071 2.89e-03
1072 6.06e-06
1079 2.69e-08
1081 1.42e-02
1086 3.34e-04
1090 1.06e-02
1094 2.64e-07
1097 1.51e-16
1098 9.65e-18
1099 5.66e-16
1100 2.40e-16
1101 2.76e-15
1104 8.56e-06
1115 1.24e-03
1116 9.43e-02
1117 7.47e-02
1120 1.44e-03
1121 1.41e-05
1122 1.67e-05
1124 1.25e-02
1125 1.26e-02
1126 1.34e-02
1127 1.71e-02
1128 3.42e-03
1129 4.55e-02
1130 4.58e-02
1131 6.71e-02
1132 6.97e-02
1133 4.58e-02
1138 4.17e-02
1140 2.49e-01
1141 2.44e-01
1142 6.53e-02
1143 3.38e-02
1144 1.20e-01
1145 7.97e-02
1146 1.13e-01
1147 1.31e-01
1148 5.75e-01
1149 4.66e-05
1150 2.19e-01
1154 4.24e-04
1155 3.02e-03
1156 3.37e-03
1157 4.00e-03
1158 2.34e-03
1159 2.24e-03
1161 2.58e-04
1165 7.27e-01
1171 2.19e-12
1172 2.58e-12
1173 1.78e-05
1174 4.55e-13
1175 3.57e-13
1176 3.96e-12
1177 2.90e-10
1178 2.98e-07
1179 3.50e-08
1181 4.98e-01
1182 1.75e-01
1185 1.76e-12
1187 4.86e-02
1194 1.90e-06
1195 3.22e-03
1196 6.60e-04
1197 1.35e-06
1199 9.81e-04
1205 1.10e-01
1208 4.69e-04
1209 1.24e-03
1210 3.70e-05
1211 1.83e-04
1212 3.33e-02
1214 5.11e-03
1215 1.42e-03
1217 4.59e-03
1221 9.46e-06
1222 1.53e-01
1225 2.16e-03
1232 1.89e-04
1233 5.14e-03
1234 8.62e-02
1236 1.93e-04
1239 6.21e-02
1240 3.08e-02
1241 1.01e-03
1243 1.95e-02
1244 8.90e-03
1245 1.52e-02
1246 2.78e-03
1247 9.79e-02
1249 3.90e-03
1252 2.75e-06
1253 8.86e-06
1254 8.86e-06
1255 1.85e-05
1256 2.46e-04
1260 2.33e-02
1261 1.42e-05
1262 7.68e-05
1263 2.71e-03
1264 2.44e-02
1265 3.04e-03
1266 6.72e-04
1267 5.18e-04
1269 1.43e-04
1271 1.52e-03
1272 5.39e-04
1274 4.61e-03
1275 1.48e-03
1276 8.04e-03
1277 3.77e-03
1280 1.57e-02
1288 1.59e-03
1289 4.79e-03
1290 9.51e-03
1291 4.31e-03
1292 3.67e-03
1297 4.59e-03
1302 5.98e-01
1304 5.08e-04
1307 1.13e-01
1310 5.82e-08
1311 4.79e-06
1312 4.41e-08
1313 5.76e-06
1314 2.12e-06
1315 1.92e-06
1316 1.98e-06
1317 7.54e-06
1318 5.25e-06
1319 5.57e-03
1322 1.31e-03
1323 9.31e-05
1325 1.52e-05
1326 8.22e-04
1327 1.35e-04
1328 9.87e-05
1329 7.94e-06
1330 3.27e-06
1331 6.30e-05
1332 1.58e-04
1333 1.80e-04
1334 3.31e-04
1335 3.61e-04
1336 2.75e-04
1337 2.79e-04
1338 1.91e-04
1339 1.99e-04
1343 2.16e-04
1344 2.10e-05
1345 2.42e-03
1346 4.33e-03
1352 1.44e-04
1353 1.16e-04
1354 5.65e-05
1356 5.34e-04
1357 1.08e-03
1358 3.01e-03
1360 4.47e-05
1361 2.25e-04
1362 1.35e-08
1363 1.33e-07
1364 4.61e-10
1365 3.63e-09
1366 2.64e-09
1367 5.40e-09
1368 3.92e-08
1369 2.93e-07
1370 2.09e-07
1371 3.96e-06
1372 4.33e-08
1373 1.22e-05
1374 1.24e-03
1375 1.68e-07
1376 5.80e-04
1377 1.09e-09
1378 4.42e-05
1379 2.08e-04
1380 1.21e-04
1381 9.98e-09
1382 8.37e-06
1383 9.55e-06
1384 4.05e-10
1385 3.38e-09
1386 1.31e-09
1389 9.72e-05
1398 2.55e-01
1402 2.82e-04
1404 1.05e-02
1409 2.44e-01
1412 1.43e-02
1413 3.04e-01
1414 1.22e-01
1415 2.65e-01
1419 1.07e-06
1420 4.46e-03
1421 3.78e-03
1426 3.00e-04
1428 3.03e-05
1429 1.39e-05
1431 5.93e-03
1432 4.05e-05
1433 9.52e-05
1436 6.79e-02
1437 6.79e-03
1443 8.72e-02
1444 6.86e-02
1446 1.20e-05
1447 1.32e-04
1448 6.65e-05
1449 2.28e-04
1450 7.42e-05
1451 7.14e-05
1453 2.85e-05
1454 8.87e-06
1455 2.69e-11
1458 2.35e-01
1459 1.30e-03
1460 1.45e-04
1461 2.89e-04
1462 1.07e-03
1463 2.07e-01
1465 3.25e-05
1466 1.23e-03
1467 2.15e-05
1468 8.89e-06
1469 3.56e-04
1470 4.72e-04
1471 1.57e-04
1472 1.17e-04
1473 3.82e-06
1474 1.14e-05
1475 5.62e-05
1476 4.06e-05
1477 6.00e-05
1478 1.87e-03
1479 2.26e-03
1480 7.41e-02
1481 2.49e-04
1483 5.67e-03
1484 5.13e-06
1485 4.25e-02
1486 7.07e-03
1487 3.29e-03
1488 5.24e-03
1489 1.70e-02
1490 4.74e-02
1491 1.34e-02
1492 1.25e-02
1493 1.69e-02
1494 2.46e-02
1496 2.18e-02
1498 1.60e-03
1499 1.73e-02
1501 1.42e-03
1503 3.08e-02
1505 4.22e-03
1507 1.31e-02
1508 2.75e-03
1509 6.77e-03
1510 4.99e-03
1511 6.86e-03
1512 6.97e-03
1513 7.03e-06
1514 7.18e-08
1515 8.69e-03
1517 1.11e-01
1519 2.53e-04
1521 6.28e-01
1522 7.49e-01
1523 3.71e-01
1530 6.94e-01
1532 1.86e-03
1533 9.20e-01
1534 9.63e-01
1535 9.92e-01
1536 1.20e-02
1538 9.22e-03
1543 3.28e-02
1544 1.88e-01
1545 1.35e-01
1548 6.88e-03
1550 7.32e-03
1553 4.73e-05
1561 2.53e-04
1562 1.76e-04
1566 1.04e-04
1567 3.40e-04
1568 2.17e-01
1569 3.92e-02
1570 1.43e-03
1571 2.21e-03
1572 7.23e-04
1573 2.82e-05
1574 4.15e-04
1575 4.60e-05
1576 9.13e-04
1577 1.22e-04
1579 8.41e-04
1580 9.69e-04
1581 4.38e-04
1582 4.63e-04
1589 1.47e-13
1591 1.73e-14
1592 3.10e-13
1593 1.98e-03
1594 3.03e-14
1595 3.35e-13
1596 3.10e-11
1597 3.66e-10
1600 1.43e-02
1601 2.31e-02
1607 2.93e-04
1608 7.12e-05
1609 1.12e-03
1611 2.38e-03
1612 2.19e-02
1614 1.50e-02
1619 4.20e-03
1620 2.86e-02
1623 3.07e-03
1624 7.79e-02
1626 9.68e-07
1627 3.73e-09
1628 3.56e-08
1629 7.06e-08
1630 3.81e-07
1631 2.88e-06
1634 1.58e-07
1639 1.04e-03
1640 1.66e-04
1641 1.05e-04
1642 4.38e-04
1643 9.48e-05
1644 4.56e-05
1645 4.56e-01
1646 1.25e-01
1647 3.64e-01
1648 9.53e-04
1649 2.89e-02
1650 1.32e-01
1651 5.61e-01
1654 1.51e-03
1655 3.79e-03
1656 1.74e-03
1659 1.19e-02
1660 8.57e-01
1661 3.12e-02
 
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Motif 1
Motif 2
Motif 3
Motif 4
Motif 5
Motif 6
Motif 7
Motif 8
Motif 9
Motif 10
Motif 11
Motif 12
Motif 13
Motif 14
Motif 15
Motif 16
Motif 17
Motif 18
Motif 19
Motif 20
Top
MEME version
4.7.0 (Release date: Wed Sep 28 17:30:10 EST 2011)
Reference
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
show training set...
Command line summary

Letter frequencies in dataset
A: 0.087   C: 0.020   D: 0.018   E: 0.019   F: 0.027   G: 0.047   H: 0.023   I: 0.054   K: 0.139   L: 0.094   M: 0.017   N: 0.024   P: 0.051   Q: 0.033   R: 0.179   S: 0.045   T: 0.039   V: 0.027   W: 0.037   Y: 0.020

Background letter frequencies (from dataset with add-one prior applied):
A: 0.087   C: 0.020   D: 0.018   E: 0.019   F: 0.027   G: 0.047   H: 0.023   I: 0.054   K: 0.139   L: 0.094   M: 0.017   N: 0.024   P: 0.051   Q: 0.033   R: 0.179   S: 0.045   T: 0.039   V: 0.027   W: 0.037   Y: 0.020

Stopping Reason
Stopped because nmotifs = 20 reached. Program ran on webs.iiitd.edu.in.
show model parameters...

Explanation of MEME Results

Top

The MEME results consist of

  • The overview of all discovered motifs.
  • Information on each of the motifs MEME discovered, including:
    1. A summary table showing the width, number of contributing sites, log likelihood ratio, statistical significance, information content and relative entropy of the motif.
    2. A sequence LOGO.
    3. Downloadable LOGO files suitable for publication.
    4. A regular expression describing the motif.
    5. Some further analysis that can be performed on the motif.
    6. A list of data formats describing the motif.
    7. The contributing sites of the motif sorted by p-value and aligned with each other.
    8. The block diagrams of the contributing sites of the motif within each sequence in the training set.
  • A combined block diagram showing an optimized (non-overlapping) tiling of all of the motifs onto each of the sequences in the training set.
  • The version of MEME and the date it was released.
  • The reference to cite if you use MEME in your research.
  • A description of the sequences you submitted (the "training set") showing the name, "weight" and length of each sequence.
  • The command line summary detailing the parameters with which you ran MEME.
  • The reason why MEME stopped and the name of the CPU on which it ran.
  • This explanation of how to interpret MEME results.

Motifs

For each motif that it discovers in the training set, MEME prints the following information:

Summary Table

This summary table gives the main attributes of the motif.

E-value
The statistical significance of the motif. MEME usually finds the most statistically significant (low E-value) motifs first. The E-value of a motif is based on its log likelihood ratio, width, sites, the background letter frequencies (given in the command line summary), and the size of the training set. The E-value is an estimate of the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and site count, that one would find in a similarly sized set of random sequences. (In random sequences each position is independent with letters chosen according to the background letter frequencies.)
Width
The width of the motif. Each motif describes a pattern of a fixed with as no gaps are allowed in MEME motifs.
Sites
The number of sites contributing to the construction of the motif.
Log Likelihood Ratio
The log likelihood ratio of the motif.The log likelihood ratio is the logarithm of the ratio of the probability of the occurrences of the motif given the motif model (likelihood given the motif) versus their probability given the background model (likelihood given the null model). (Normally the background model is a 0-order Markov model using the background letter frequencies, but higher order Markov models may be specified via the -bfile option to MEME.)
Information Content
The information content of the motif in bits. It is equal to the sum of the uncorrected information content, R(), in the columns of the LOGO. This is equal relative entropy of the motif relative to a uniform background frequency model.
Relative Entropy
The relative entropy of the motif, computed in bits and relative to the background letter frequencies given in the command line summary. It is equal to the log-likelihood ratio (llr) divided by the number of contributing sites of the motif times 1/ln(2),

re = llr / (sites * ln(2)).
Sequence LOGO

MEME motifs are represented by position-specific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif. These are displayed as "sequence LOGOS", containing stacks of letters at each position in the motif. The total height of the stack is the "information content" of that position in the motif in bits. The height of the individual letters in a stack is the probability of the letter at that position multiplied by the total information content of the stack.

Note: The MEME LOGO differs from those produced by the Weblogo program because a small-sample correction is NOT applied. However, MEME LOGOs in PNG and encapsulated postscript (EPS) formats with small-sample correction (SSC) are available by clicking on the download button with "SSC" set to "on" under Download LOGO. The MEME LOGOs without small sample correction are similarly available. Error bars are included in the LOGOs with small-sample correction.

Modern web browsers supporting the canvas element and it's text manipulation functions as described in the html 5 standard, can render the sequence LOGOs without needing the images. The browsers which work with this feature are:

  • Firefox 3.5 and above
  • Safari 4 and above
  • Google Chrome 4 and above

Unfortunately Internet Explorer 8 does not support any html 5 features.

The information content of each motif position is computed as described in the paper by Schneider and Stephens, "Sequence Logos: A New Way to Display Consensus Sequences" but the small-sample correction, e(n), is set to zero for the LOGO displayed in the MEME output. The corrected information content of position i is given by

            R(i) for amino acids   = log2(20) - (H(i) + e(n))   (1a) 
            R(i) for nucleic acids =    2    - (H(i) + e(n))    (1b)
          

where H(i) is the entropy of position i,

            H(l) = - (Sum f(a,i) * log2[ f(a,i) ]).             (2)
          

Here, f(a,i) is the frequency of base or amino acid a at position i, and e(n) is the small-sample correction for an alignment of n letters. The height of letter a in column i is given by

            height = f(a,i) * R(i)                              (3)
          

The approximation for the small-sample correction, e(n), is given by:

            e(n) = (s-1) / (2 * ln(2) * n),                     (4)
          

where s is 4 for nucleotides, 20 for amino acids, and n is the number of sequences in the alignment.

The letters in the logos are colored as follows.
For DNA sequences, the letter categories contain one letter each.

NUCLEIC ACIDS COLOR
A RED
C BLUE
G ORANGE
T GREEN

For proteins, the categories are based on the biochemical properties of the various amino acids.

AMINO ACIDS COLOR PROPERTIES
A, C, F, I, L, V, W and M BLUE Most hydrophobic[Kyte and Doolittle, 1982]
NQST GREEN Polar, non-charged, non-aliphatic residues
DE MAGENTA Acidic
KR RED Positively charged
H PINK  
G ORANGE  
P YELLOW  
Y TURQUOISE  

J. Kyte and R. Doolittle, 1982. "A Simple Method for Displaying the Hydropathic Character of a Protein", J. Mol Biol. 157, 105-132.

Note: the "text" output format of MEME preserves the historical MEME format where LOGOS are replaced by a simplified probability matrix, a relative entropy plot, and a multi-level consensus sequence.

Download LOGO

Logos can be generated on the fly by the meme webservice and you may specify a number of options to customize them to your needs. The options are:

Orientation
Only valid for nucleotide motifs. Generate the standard view or the reverse complemented view of the motif.
SSC
Use small sample correction and show errorbars on the image. Small sample correction is used by the Weblogo program.
Format
The format of the generated image. If the image is to be used on the web then png is recommend. If the image is to be published then eps is recommended.
Width
The width of the generated image in centimetres.
Height
The height of the generated image in centimetres.

Regular Expression

This is a regular expression (RE) describing the motif. In each column, all letters with observed frequencies greater than 0.2 are shown; less-frequent letters are not included in the RE. MEME regular expressions are interpreted as follows: single letters match that letter; groups of letters in square brackets match any of the letters in the group. Regular expressions can be used for searching for the motif in sequences (using, for example, PatMatch) but the search accuracy will usually be better with the PSSM (using, for example MAST.)

Further Analysis

Either as a group or individually the motifs have a number of options for further analysis.

MAST
Finds the best matching positions for a set of motifs in each sequence provided to it, ranked by the combined score of each sequence. For more information about MAST please read the introduction.
FIMO
Finds all matches for a motif. For more information about FIMO please read the introduction.
TOMTOM
Compares a single motif to a database of motifs. For more information about TOMTOM please read the introduction.
GOMO
Identifies possible roles of DNA binding motifs. For more information about GOMO please read the introduction.
BLOCKS
Submit to Blocks Multiple Alignment Processor where you can do several things like create phylogeny trees and search the blocks against a database of other blocks (protein only). For more information about BLOCKS Multiple Alignment Processor please visit the website.
Data Formats

The extracted data is avaliable in the following formats.

PSPM Format
The motif itself is a position-specific probability matrix giving, for each position in the pattern, the observed frequency ("probability") of each possible letter. The probability matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The motif is preceded by a line starting with "letter-probability matrix:" and containing the length of the alphabet, width of the motif, number of occurrences of the motif, and the E-value of the motif.
Note: Earlier versions of MEME gave the posterior probabilities--the probability after applying a prior on letter frequencies--rather than the observed frequencies. These versions of MEME also gave the number of possible positions for the motif rather than the actual number of occurrences. The output from these earlier versions of MEME can be distinguished by "n=" rather than "nsites=" in the line preceding the matrix.
PSSM Format
The position-specific scoring matrix corresponding to the motif is printed for use by database search programs such as MAST. This matrix is a log-odds matrix calculated by taking 100 times the log (base 2) of the ratio p/f at each position in the motif where p is the probability of a particular letter at that position in the motif, and f is the background frequency of the letter (given in the command line summary section.) This is the same matrix that is used above in computing the p-values of the occurrences of the motif in the Sites and Block Diagrams sections. The scoring matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The scoring matrix is preceded by a line starting with "log-odds matrix:" and containing the length of the alphabet, width of the motif, number of characters in the training set, the scoring threshold (obsolete) and the motif E-value.
Note: The probability p used to compute the PSSM is not exactly the same as the corresponding value in the Position Specific Probability Matrix (PSPM). The values of p used to compute the PSSM take into account the motif prior, whereas the values in the PSPM are just the observed frequencies of letters in the motif sites.
BLOCKS Format
For use with BLOCKS tools.
FASTA Format
The FASTA format as described here.
Raw Format
Just the sites of the sequences that contributed to the motif. One site per line.
Sites

MEME displays the occurrences (sites) of the motif in the training set. The sites are shown aligned with each other, and the ten sequence positions preceding and following each site are also shown. Each site is identified by the name of the sequence where it occurs, the strand (if both strands of DNA sequences are being used), and the position in the sequence where the site begins. When the DNA strand is specified, '+' means the sequence in the training set, and '-' means the reverse complement of the training set sequence. (For '-' strands, the 'start' position is actually the position on the positive strand where the site ends.) The sites are listed in order of increasing statistical significance (p-value). The p-value of a site is computed from the the match score of the site with the position specific scoring matrix for the motif. The p-value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. (This is referred to as the position p-value by the MAST algorithm.)

Block Diagrams

The occurrences of the motif in the training set sequences are shown as coloured blocks on a line. One diagram is printed for each sequence showing all the sites contributating to that motif in that sequence. The sequences are listed in the same order as in the input to make it easier to compare multiple block diagrams. Additionally the best p-value for the sequence/motif combination is listed though this may not be in ascending order as with the sites. The p-value of an occurrence is the probability of a single random subsequence the length of the motif, generated according to the 0-order background model, having a score at least as high as the score of the occurrence. When the DNA strand is specified '+', it means the motif appears from left to right on the sequence, and '-' means the motif appears from right to left on the complementary strand. A sequence position scale is shown at the end of each table of block diagrams.

Combined Block Diagrams

The motif occurrences shown in the motif summary may not be exactly the same as those reported in each motif section because only motifs with a position p-value of 0.0001 that don't overlap other, more significant motif occurrences are shown.

See the documentation for MAST output for the definition of position and combined p-values.