GLAM2: Gapped Local Alignment of Motifs

Version 1056
../../../INSTALLED/bin/glam2 -Q -O . -z 2 -a 2 -b 50 -w 20 -r 10 -n 1000 -D 0.1 -E 2 -I 0.02 -J 1 p ../../../tests/lipocalin.s

If you use this program in your research, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008.

Best Motif Found:

NAME START SITES END STRAND MARGINAL SCORE
ICYA_MANSE 13 K P V N D F D L S A F A G A W H E I A K 32 + 33.3
LACB_BOVIN 21 Q T M K G L D I Q K V A G T W Y S L A M 40 + 18.8
BBP_PIEBR 12 K P V D N F D W S N Y H G K W W E V A K 31 + 27.9
RETB_BOVIN 10 R V K E N F D K A R F A G T W Y A M A K 29 + 25.5
MUP2_MOUSE 23 S T G R N F N V E K I N G E W H T I I L 42 + 13.4
Score: 80.3660
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against sequence databases using GLAM2SCAN.

Replicates:

Check that at least some of these are similar to the best motif found.
If not, there may well be an even better motif: re-run GLAM2 with more iterations to find it.

Score: 80.3660
logo with ssc
against sequence databases using GLAM2SCAN.
Score: 79.9988
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against sequence databases using GLAM2SCAN.
Score: 77.7514
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against sequence databases using GLAM2SCAN.
Score: 77.2641
logo with ssc
against sequence databases using GLAM2SCAN.
Score: 74.8248
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against sequence databases using GLAM2SCAN.
Score: 71.6171
logo with ssc
against sequence databases using GLAM2SCAN.
Score: 70.9453
logo with ssc
against sequence databases using GLAM2SCAN.
Score: 69.1736
logo with ssc
against sequence databases using GLAM2SCAN.
Score: 37.0388
logo with ssc
against sequence databases using GLAM2SCAN.