GLAM2: Gapped Local Alignment of Motifs

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

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_	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.

logo with ssc
Score: 1277.07

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [EW]DE[ARV][KRL]R[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]DA?NG[NV][QAL].{0,8}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.
Click here to with double the “maximum number of iterations without improvement” to find it.

logo with ssc
Score: 1274.78

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [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]?.{0,8}NG[QV][ALV]K[ILV]SDFGL[AS]K

logo with ssc
Score: 1271.80

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [AV][KRL][MR].{0,1}[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[APRE]?[LN]G[NV].{0,8}[ALV]K[ILV]SDFGL[AS]KF[LS]R

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Score: 1257.40

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [KRL]R[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]?.{0,8}NG[QV][ALV]K[ILV]SDFGL[AS]KF[LS]R?D

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Score: 1254.89

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].{0,8}D?[AR][KN]G[NV][QI]?[ALV]K[ILV]SDFGL[AS]KF[LS]R

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Score: 1234.81

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [YI][AT]LQ[IL][AI]N[AG][LV][AE]Y[ICL]H.{0,2}S[KR]P?G[IV][LVY]HRD[ILV]KP[SED]N[IL]L[LV]D.{0,5}[APR]?[KN]G[NV].{0,1}[QI]?[ALV]K[ILV][SG]D?FGL[AS]KFLR

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Score: 982.689

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: [PKR]G[IV][LVY]HR?D[ILV]KP[SED]N[IL]L[LV]D[PL]?[ARL]?NG[QV][AL].{0,7}K[ILV]SDFGL[AS]K?.{0,6}R[DK]?[PV]?[GSR][KE][SDT][AHRV]?[SG]?[HL][IVL]?[HST][TY]R[CEV].{0,13}G?TP[GR]Y

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Score: 946.651

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: S[NTY]V?[CV].{0,1}G?TPRY[MRV][AS]PE[LV]LL.{0,8}G.{0,3}EY[STG][AE][AEK][SV]D[IV][YW]S[FL]G[CV][ILV]L[FM]E[IL][IML][AT]G[KSY][LP]P?F[DP][EG][LS][NR]L?[MQV]T[LQ]

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Score: 659.250

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: V[FY][RY][AG][IK][CN]?[LT]?E[DT]G[ET][EQ][AV]A[IV]KK.{0,30}[FL][QR][GH][KR]R[VY]?[KE][FQ]?[NLF]K?RE[IV].[LV][ML][GK][PR][LV]?[DK].{0,1}HPN[ILV][IV]E[IYL][ILY]G[VY]FF[ES]

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Score: 380.013

against sequence databases using GLAM2SCAN.

Regular Expression for Motif: K..[PKF]S[DF]P?PRF[PS]AGA[KT]?[DPR][LV]I[SG]?KR[ICL][KL]E.[SDN]?PSERP[ST].{0,1}[IA]AE[IL]LE[DH][PEL][RW]FKE?KR