GLAM2: Gapped Local Alignment of Motifs

Version 1056
bin/glam2 -Q -O . -M -A 'meme@nbcr.net' -X '' -z 2 -a 2 -b 50 -w 20 -r 10 -n 2000 -D 0.1 -E 2 -I 0.02 -J 1 p sequences

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
At1g01140.1_ 114 L K E D E A R R Y F Q Q L I N A V D Y C H . . . S R G V Y H R D L K P E N L I L D A N G . . . . . . . . V L K V S D F G L S A 165 + 118.
At1g01140.2_ 114 L K E D E A R R Y F Q Q L I N A V D Y C H . . . S R G V Y H R D L K P E N L I L D A N G . . . . . . . . V L K V S D F G L S A 165 + 118.
At1g01140.3_ 114 L K E D E A R R Y F Q Q L I N A V D Y C H . . . S R G V Y H R D L K P E N L I L D A N G . . . . . . . . V L K V S D F G L S A 165 + 118.
At1g01450.1_ 121 L S L P V A V D L M L Q I A L G M E Y L H . . . S K R I Y H G E L N P S N I L V K P R S N Q S G D G Y L L G K I F G F G L N S 180 + 41.2
At1g01540.1_ 249 L T W D I R M N I I L G M A K G L A Y L H E G L E P K V V H R D I K S S N I L L D R Q W . . . . . . . . N A K V S D F G L A K 303 + 105.
At1g01540.2_ 249 L T W D I R M N I I L G M A K G L A Y L H E G L E P K V V H R D I K S S N I L L D R Q W . . . . . . . . N A K V S D F G L A K 303 + 105.
At1g01560.1_ 138 L T D D H S R F F L Y Q L L R G L K Y V H . . . S A N V L H R D L K P S N L L L N A N C . . . . . . . . D L K I G D F G L A R 189 + 82.7
At1g01740.1_ 149 M K W A M R L R V A L Y I S E A L E Y C S N N . G H T L Y H . D L N A Y R V L F D E E C . . . . . . . . N P R L S T F G L M K 201 + 9.84
At1g02970.1_ 344 V S E R E I L V I M H Q I A K A L H F V H . . . E K G I A H L D V K P D N I Y I K N G . . . . . . . . . V C K L G D F G C A T 394 + 71.9
At1g03740.1_ 309 F T E P Q V K C Y M R Q L L S G L E H C H . . . S R G V L H R D I K G S N L L I D S K G . . . . . . . . V L K I A D F G L A T 360 + 98.9
At1g03920.1_ 232 L S E D E A K F Y I A E S V L A I E S I H . . . N R N Y I H R D I K P D N L L L D R Y G . . . . . . . . H L R L S D F G L C K 283 + 77.0
At1g03930.1_ 100 L S L K T V L M L A D Q L I N R V E F M H . . . T R G F L H R D I K P D N F L M G L G R K A N . . . . . Q V Y I I D F G L G K 154 + 89.5
At1g04210.1_ 899 V P M D L A L S I A R D I S G A L M E L H . . . S K D I I H R D I K S E N V L I D L D N Q S A N G E P . I V K L C D F D R A V 957 + 55.1
At1g04440.1_ 100 F S L K T V L M L A D Q M I N R V E Y M H . . . V K G F L H R D I K P D N F L M G L G R K A N . . . . . Q V Y I I D Y G L A K 154 + 88.7
At1g04700.1_ 867 L D R R K K L M I T L D S A F G M E Y L H . . . M K N I V H F D L K C D N L L V N L R D P Q R P . . . . I C K V G D F G L S R 922 + 69.8
At1g05100.1_ 102 I D E A R V V K Y T R Q I L L G L E Y I H N . . S K G I A H C D I K G S N V L V G E N G . . . . . . . . E A K I A D F G C A K 154 + 84.4
At1g05700.1_ 653 L S W R Q R L Q I A L D A A Q G L E Y L H C G C K P P I V H R D V K T S N I L L N E K N . . . . . . . . R A K L A D F G L S R 707 + 81.7
At1g06390.1_ 166 M P I F Y V K L Y T Y Q I F R G L A Y I H T . . V P G V C H R D V K P Q N L L V D P L T H . . . . . . . Q V K L C D F G S A K 219 + 106.
At1g06390.2_ 166 M P I F Y V K L Y T Y Q I F R G L A Y I H T . . V P G V C H R D V K P Q N L L V D P L T H . . . . . . . Q V K L C D F G S A K 219 + 106.
Score: 1289.52
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: L[KST][EW]DE[ARV][KRL]R[YI][AT]LQ[IL][AI]N[AG][LV][AE]Y[ICL]H.{0,3}S[PKR]G[IV][LVY]HR?D[ILV]KP[SED]N[IL]L[LV]D[AL].{1,10}[QV][ALV]K[ILV]SDFGL[AS]K

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.
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Score: 1252.93
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [KRL]R[YI][AT]LQ[IL][AI]N[AG][LV][AE]Y[ICL]H.{0,3}S[PKR]G[IV][LVY]HR?D[ILV]KP[SED]N[IL]L[LV]DP?[ARL]?NG.{0,7}[QV][ALV]K[ILV]SDFGL[AS]KF[LS]R
Score: 1240.60
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [KRL]R[YI][AT]LQ[IL][AI]N[AG][LV][AE]Y[ICL]H[TN]?S[KR]?G.{0,4}[IV][LVY]HR?D[ILV]KP[SED]N[IL]L[LV]DA?NG[NV][QAL].{0,8}K[ILV]SDFGL[AS]KF[LS]R
Score: 1234.97
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [YI][AT]LQ[IL][AI]N[AG][LV][AE]Y[ICL]HS.{0,3}[PKR]G[IV][LVY]HR?D[ILV]KP[SED]N[IL]L[LV]D[AL].{0,9}G[QV][ALV]K[ILV]SDFGL[AS]KF[LS]R.{0,19}[STG][HEL][LPS][HSV]
Score: 913.469
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [LT]S[NTY]V[CT].{0,1}G?TPRY[MRV]?APE?[LV]L?[LF]?N[ACD]?[KT][GH]Y.{0,4}[TG]A[AE].{0,7}[SV]D?[IV][YW]S[FL]G[CV][ILV]L[FM]E[IL][IML][AT]G[KSY][LN]?P[FL]F?[DP][EG]S[NR]
Score: 699.274
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [VY]VG[PT][PF][DR]Y[MR]?APELL.[GKT]G.{0,8}I?C?[EK]Y[GST][AE][EKS][CSV]DP?[IW][YWF]S[FL]G[AC][LV]LMI?E[IL][IL][LT]G[KS][NP][PL][FI]?[PT]G[LS][SR]
Score: 673.886
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [GKT]GYE?Y[STG][AE][AEK][SV]D[IV][YW]S[FL]G[CV][ILV]L[FM]E[IL][IML][AT]G[KSY][LN]?P[FL][DF][EP][GLS]RL[MQ][TV]LQ
Score: 458.308
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: RHQ[DT]V?[KRE][EQ][FL][AK][RV].{0,1}E[ILV]E[LV][ML][GKR]R[LV]?[DKR].{0,1}HPN[ILV][IV]?E[IYL][ILY]G[VY]F.[ES]
Score: 299.297
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: L[IL][GKS]Y[CFT][DS]?[ERV]E[EGK].[YF]?[LNR].{0,2}[HY][KS]?[ML]V[EMY][ED][YLF][MV][DPR].{0,2}[EGS][TD][ML]
Score: 214.607
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: DV[DS]DE[DS]I?T[IEG]?NH[SCV][DF][SF]?[AS]TFS[LN]?S?[EK]E[CSV]?[RL]V[TL][AEN]K