GLAM2: Gapped Local Alignment of Motifs

Version 1056
glam2 -O glam2_example_output_files -M p At.faa

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.[full text]

Best Motif Found:

NAME START SITES END STRAND MARGINAL SCORE
At1g01140.1_ 116 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 + 120.
At1g01140.2_ 116 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 + 120.
At1g01140.3_ 116 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 + 120.
At1g01450.1_ 123 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 + 44.0
At1g01540.1_ 251 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 + 106.
At1g01540.2_ 251 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 + 106.
At1g01560.1_ 140 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 + 84.9
At1g01740.1_ 151 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 + 12.2
At1g02970.1_ 346 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 + 69.3
At1g03740.1_ 311 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 + 100.
At1g03920.1_ 234 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 + 79.2
At1g03930.1_ 102 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 + 86.4
At1g04210.1_ 901 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 + 49.6
At1g04440.1_ 102 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 + 81.5
At1g04700.1_ 869 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 + 65.3
At1g05100.1_ 104 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 + 90.7
At1g05700.1_ 655 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 + 78.3
At1g06390.1_ 168 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 + 105.
At1g06390.2_ 168 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 + 105.
with double the "maximum number of iterations without improvement" to find it.

Score: 1277.07
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [EW]DE[ARV][RLK]R[YI][AT]LQ[LI][IA]N[AG][VL][EA]Y[CLI]HS.{0,3}[RKP]G[VI][YVL]HR?D[LIV]KP[ESD]N[LI]L[LV]DA?NG[VN][LQA].{0,8}K[VIL]SDFGL[SA]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.
Click here to with double the "maximum number of iterations without improvement" to find it.

Score: 1271.22
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [ARV][RLK]R[YI][AT]LQ[LI][IA]N[AG][VL][EA]Y[CLI]HS.{0,3}[RKP]G[VI][YVL]HR?D[LIV]KP[ESD]N[LI]L[LV]D[AL]?.{0,8}NG[VQ][LAV]K[VIL]SDFGL[SA]KF[SL]R
with double the "maximum number of iterations without improvement" to find it.

Score: 1250.03
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [RLK]R[YI][AT]LQ[LI][IA]N[AG][VL][EA]Y[CLI]H.{0,3}S[RKP]G[VI][YVL]HR?D[LIV]KP[ESD]N[LI]L[LV]D[AL]?.{0,8}[NK]G[VN]Q?[LAV]K[VIL]SDFGL[SA]KF[SL]R
with double the "maximum number of iterations without improvement" to find it.

Score: 946.511
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: V[CV]G?TPRY[VRM][AS]PE?[VL]?LLG.{0,9}[KT][GE]Y[DL]?[GST][AE][AKE][SV]D[VI][WY]S[FL]G[VC][IVL]L[FM]E[LI][MLI][AT]G[YKS][LP]P?F[DP][EG][SL][NR]?L[MQV][TD][LQ]
with double the "maximum number of iterations without improvement" to find it.

Score: 922.481
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: S[TNY][VLI][CTV].{0,5}G?TPRY[VRM]?APE?[VL]L?.{0,8}A[KT][GE][LF]?Y[IV]?[DE]?[GT][AS][AE][KR]?[SV]D[VI][WY]S[FL]G[VC][IVL]L[FM]E[LI][MLI][AT]G[YKS][LN]?P[FL][DF][EP][SGL]R
with double the "maximum number of iterations without improvement" to find it.

Score: 887.989
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: S[TY][LVI][CTV].{0,5}G?TPR.{0,2}Y[VRM]APE[VL]L.?[TG][KGA][GS]Y?[DNY]?[GET].{0,9}[AKE][SV]D[VI][WY]S[FL]G[VC][IVL]L[FM]E[LI][MLI][AT]G[YKS][LN]?P[LIY]?F[DP][EG]S[NR]L[MQV]
with double the "maximum number of iterations without improvement" to find it.

Score: 848.504
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [LV][LTS]Y.[AV]?[CV]G?T[PL].Y[VRM]AP?E?[VYL]L.[TG][KA]?G.{0,8}H[YL][GT][AE]?[AKE][SV]D[VI][WYF]SFG[VC][IVL]LFE[LI][MLI][AT]G?[YK][LN]?P[FLI]?[DF][EP][SG][RL]
with double the "maximum number of iterations without improvement" to find it.

Score: 680.611
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: VFR[HGD][KQE]?R[VR][EK]FLK?RE[IV]S[VL][ML][KG]R[LV].{0,1}[KD]H[PD]N[VI][VI][ER][IL]?[ILY]G[VY]FF[SDE]G[TE].{0,13}FLY[IL]V[LMY]E[LFY][VM][DP][GN]G?[TS]L
with double the "maximum number of iterations without improvement" to find it.

Score: 383.331
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [NP][LSQ][MGSI][TQ][LAG]Y[KP].{0,3}[IEW][CFYH]?[KLG][AV].{0,2}E?[FV][SEP][CVE]?[PLM][PGV]?[WR].{0,2}[FRL][SHP][QKP][GNS][AL]K[RD][VL][IL][KG][RY][ICL]L?.{0,1}[ES][PGR][NDS]P[IRS][TL][RL][IV]?[SYT].{0,1}[IA][AFL][EM][LA][LN][EGDA][DNH][ELP][WF]F
with double the "maximum number of iterations without improvement" to find it.

Score: 281.318
logo with ssc
against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [FL][SG][GS][SA][RK]..{0,2}K?[ARG]?[TE][PG].[VI]?S[RH].{0,5}RV[GTS][NR][YW][EY][MTR][LA][RP]EL?.{0,2}GA[GT][NE][FGY]