matrix-clustering arsr

matrix-clustering  -v 1 -max_matrices 300 -matrix Collection_1 $RSAT/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.100155_pz7tbJ/matrix-clustering_query_matrices.meme meme -hclust_method average -calc sum -title arsr -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.55 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.100155_pz7tbJ/matrix-clustering

Results Summary

Nb Input motifs

Nb Input collections

Nb Clusters Found

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Root motifs

Complete results [zip]

Parameters used

Linkage method

Similarity metric

Thresholds to partition the tree

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average

Ncor

Ncor = 0.55
cor = 0.6

Individual Motif View

Motif id	Motif name	Cluster	Collection	Width	IC	Number of sites	Consensus	Consensus (Rev)
Collection_1_m34_QPRSR_SahR	QPRSR_SahR	cluster_3	Collection_1	26	20.12	190	+++AYATAAAGATATCTTTATRT+++	+++AyATAAAGATATCTTTATrT+++
Collection_1_m37_VSTSK_ArsR	VSTSK_ArsR	cluster_2	Collection_1	22	15.09	14	+aTTTkGCyAwwTrGCmAAAt+	+ATTTKGCYAWWTRGCMAAAT+
Collection_1_m54_QPKSF_ArsR	QPKSF_ArsR	cluster_1	Collection_1	22	12.16	6	+++ATCAAWTKMAWTTGAT+++	+++ATCAAwtkmawTTGAT+++
Collection_1_m31_ESASH_SmtB	ESASH_SmtB	cluster_3	Collection_1	26	22.06	32	AAyAycTGAAyAryTrTTCAgrTrTT	AAYAYCTGAAYARYTRTTCAGRTRTT
Collection_1_m3_QPASQ_AseR	QPASQ_AseR	cluster_3	Collection_1	26	13.83	52	AWTAYATAAGYMWWKRCTTATRTAWT	awtAyATAAGymwwkrCTTATrTawt
Collection_1_m41_KSTSH_YczG	KSTSH_YczG	cluster_5	Collection_1	18	21.00	16	GTTCGAWDATHWTCGAAC	GTTCGAWdAThWTCGAAC
Collection_1_m4_QSASQ_HlyU	QSASQ_HlyU	cluster_9	Collection_1	26	14.24	150	++TAwATTAGwwwwwwCTAATwTA++	++TAWATTAGWWWWWWCTAATWTA++
Collection_1_m29_LPTSA_Cg1831	LPTSA_Cg1831	cluster_10	Collection_1	20	26.34	4	AsTCAAATGATCATTTGAsT	ASTCAAATGATCATTTGAST
Collection_1_m21_ISTSK_ArsR	ISTSK_ArsR	cluster_2	Collection_1	22	14.81	12	+RTTTKSMHAWWTDKSMAAAY+	+rTTTksmhAwwTdksmAAAy+
Collection_1_m27_PSTSH_DMR_39480	PSTSH_DMR_39480	cluster_11	Collection_1	22	22.70	4	kWdTTCGAMAbvTKTCGAAhWm	KWDTTCGAMABVTKTCGAAHWM
Collection_1_m52_PKALE_Phr	PKALE_Phr	cluster_4	Collection_1	23	23.40	4	NWWMCTAACWTWAWGTTAGKWWN	nwWMCTAACwTwAwGTTAGKWwn
Collection_1_m8_RTASH_DESPIG_02495	RTASH_DESPIG_02495	cluster_16	Collection_1	22	19.95	6	taAAACTArwwwwyTAGTTTta	TAAAACTARWWWWYTAGTTTTA
Collection_1_m1_QPKSR_ArsR	QPKSR_ArsR	cluster_3	Collection_1	26	16.57	84	++tATATAyGawwwwtCrTATATa++	++TATATAYGAWWWWTCRTATATA++
Collection_1_m22_QPTSY_Caur_3587	QPTSY_Caur_3587	cluster_7	Collection_1	20	20.51	6	AtATTGAAwwwwTTCAATaT	ATATTGAAWWWWTTCAATAT
Collection_1_m20_QPLSQ_Znr	QPLSQ_Znr	cluster_13	Collection_1	18	13.33	8	wyyAGCAmkmkTGCTrrw	WYYAGCAMKMKTGCTRRW
Collection_1_m19_QPSSQ_AseR	QPSSQ_AseR	cluster_3	Collection_1	26	25.74	4	++TATATWARyAWWTrYTWATATA++	++TATATWARYAWWTRYTWATATA++
Collection_1_m53_PKAID_Phr	PKAID_Phr	cluster_4	Collection_1	23	16.20	8	dwyAcTAACwwwwwGTTAgTrwh	DWYACTAACWWWWWGTTAGTRWH
Collection_1_m60_ASTSK_Ddes_1264	ASTSK_Ddes_1264	cluster_11	Collection_1	22	24.09	4	YATTTCGTYvhdbRACGAAATR	YATTTCGTYVHDBRACGAAATR
Collection_1_m2_KPSSH_SdpR	KPSSH_SdpR	cluster_2	Collection_1	22	21.45	160	TATTTAGAyAwwTrTCTAAATA	TATTTAGAYAWWTRTCTAAATA
Collection_1_m48_MSTSK_ArsR	MSTSK_ArsR	cluster_2	Collection_1	22	14.97	22	+ATTTKGCyAwwTrGCMAAAT+	+ATTTKGCYAWWTRGCMAAAT+
Collection_1_m33_QSASH_CzrA	QSASH_CzrA	cluster_3	Collection_1	26	21.27	56	++CATATGAAyAwwTrTTCATATG++	++CATATGAAYAWWTRTTCATATG++
Collection_1_m35_QSTSQ_YbzH	QSTSQ_YbzH	cluster_7	Collection_1	20	19.22	14	ATATCGWAATATTWCGATAT	ATATCGwaATATtwCGATAT
Collection_1_m13_RTNSN_CadR	RTNSN_CadR	cluster_6	Collection_1	16	16.73	4	KWCASCAbvTGSTGWM	KWCASCABVTGSTGWM
Collection_1_m39_KPSSQ_SdpR	KPSSQ_SdpR	cluster_2	Collection_1	22	21.58	4	+AWTTArkWAWWTWmyTAAWT+	+AWTTARKWAWWTWMYTAAWT+
Collection_1_m25_PKAIS_Phr	PKAIS_Phr	cluster_4	Collection_1	23	21.93	6	RWTRSTAACYAWTRGTTASYAWY	rwTrsTAACyAwTrGTTAsyAwy
Collection_1_m26_VPTSA_Cg1831	VPTSA_Cg1831	cluster_10	Collection_1	20	22.18	4	AsTCAAwCrssyGwTTGAsT	ASTCAAWCRSSYGWTTGAST
Collection_1_m40_QSNSH_CzrA	QSNSH_CzrA	cluster_3	Collection_1	26	29.89	12	WATATATGAAyAwwTrTTCATATATW	WATATATGAAYAWWTRTTCATATATW
Collection_1_m47_QSRSR_SahR	QSRSR_SahR	cluster_1	Collection_1	22	15.96	66	+ATATCAAGWTAWCTTGATAT+	+ATATCAAgwTAwcTTGATAT+
Collection_1_m50_QSLSH_CzcR2	QSLSH_CzcR2	cluster_3	Collection_1	26	23.57	4	+++ATATGAwwAyrTwwTCATAT+++	+++ATATGAWWAYRTWWTCATAT+++
Collection_1_m11_AAGRR_SufR	AAGRR_SufR	cluster_17	Collection_1	24	22.71	8	TTAsrmmACAhWWdTGTkkysTAA	TTASRMMACAHWWDTGTKKYSTAA
Collection_1_m43_QKALE_Phr	QKALE_Phr	cluster_4	Collection_1	23	15.84	174	TTTARTWACYWWWRGTWAYTAAA	TTTArTwACywwwrGTwAyTAAA
Collection_1_m51_PQTSF_YdfF	PQTSF_YdfF	cluster_5	Collection_1	18	16.65	14	+TTCrAYkATmRTyGAA+	+TTCRAYKATMRTYGAA+
Collection_1_m55_QKAIE_Phr	QKAIE_Phr	cluster_4	Collection_1	23	20.59	20	TwwwrTAACwwwwwGTTAywwwA	TWWWRTAACWWWWWGTTAYWWWA
Collection_1_m44_QQTSF_YdfF	QQTSF_YdfF	cluster_5	Collection_1	18	17.61	6	+TTCrATkwwmATyGAA+	+TTCRATKWWMATYGAA+
Collection_1_m7_ASASQ_YgaV	ASASQ_YgaV	cluster_9	Collection_1	26	18.06	42	ytTAaTTwAGwwwwwwCTwAAtTAar	YTTAATTWAGWWWWWWCTWAATTAAR
Collection_1_m18_QKAIG_Phr	QKAIG_Phr	cluster_4	Collection_1	23	23.40	8	WTWwrTAACwwwwwGTTAywWAW	WTWWRTAACWWWWWGTTAYWWAW
Collection_1_m57_QSGSH_SahR	QSGSH_SahR	cluster_1	Collection_1	22	22.93	38	+ATATCAAAAwwTTTTGATAT+	+ATATCAAAAWWTTTTGATAT+
Collection_1_m12_QTTSH_CzrA	QTTSH_CzrA	cluster_3	Collection_1	26	23.08	8	++YATATGWKYATATRMWCATATR++	++yATATGwkyATATrmwCATATr++
Collection_1_m42_QSKSF_ArsR	QSKSF_ArsR	cluster_1	Collection_1	22	13.38	26	+++ATCAArwwwwyTTGAT+++	+++ATCAARWWWWYTTGAT+++
Collection_1_m6_QSTSH_CzrA	QSTSH_CzrA	cluster_3	Collection_1	26	15.52	40	+WHATATTDAYAWWTRTHAATATDW+	+WhATATtdayAwwTrthaATATdW+
Collection_1_m45_MSTSR_ArsR	MSTSR_ArsR	cluster_2	Collection_1	22	18.81	8	+AYTTKDYHAWWTDRHMAART+	+AYTTKdYhAwwTdRhMAART+
Collection_1_m5_QSKSY_ArsR	QSKSY_ArsR	cluster_1	Collection_1	22	20.31	124	TWMATCAAAWWWWTTTGATKWA	TwmATCAAawwwwtTTGATkwA
Collection_1_m14_ASNSF_ArsR3_2	ASNSF_ArsR3_2	cluster_8	Collection_1	22	19.50	4	YAvKhCAAYrhdyRTTGdMbTR	YAVKHCAAYRHDYRTTGDMBTR
Collection_1_m32_QSRSF_ArsR	QSRSF_ArsR	cluster_1	Collection_1	22	15.96	6	+++ATCAAmwwwwkTTGAT+++	+++ATCAAMWWWWKTTGAT+++
Collection_1_m16_QSSSH_CzrA	QSSSH_CzrA	cluster_3	Collection_1	26	24.35	4	++yRTATGAAyRWWYrTTCATAYr++	++YRTATGAAYRWWYRTTCATAYR++
Collection_1_m59_QSVSH_CzcR2	QSVSH_CzcR2	cluster_3	Collection_1	26	19.61	10	+++ATATGTTrwyrwyAACATAT+++	+++ATATGTTRWYRWYAACATAT+++
Collection_1_m28_QPRST_SamR	QPRST_SamR	cluster_18	Collection_1	24	19.38	34	ATCycTtyATCssGATraAgrGAT	ATCYCTTYATCSSGATRAAGRGAT
Collection_1_m46_QPLSQ_Znr	QPLSQ_Znr	cluster_15	Collection_1	18	16.70	20	CATGCrysatsryGCATG	CATGCRYSATSRYGCATG
Collection_1_m56_QNSSH_SahR	QNSSH_SahR	cluster_1	Collection_1	22	24.52	4	+ATATCAAARhdYTTTGATAT+	+ATATCAAARHDYTTTGATAT+
Collection_1_m36_FSTSK_ArsR	FSTSK_ArsR	cluster_2	Collection_1	22	19.50	8	+RYTTGSHMAWWTKDSCAARY+	+RyTTGShmAWWTkdSCAArY+
Collection_1_m10_PKVIE_Phr	PKVIE_Phr	cluster_4	Collection_1	23	26.17	4	WYTACTAACYWWWRGTTAGTARW	WYTACTAACywwwrGTTAGTARW
Collection_1_m9_GTNSF_ArsR3	GTNSF_ArsR3	cluster_8	Collection_1	22	21.24	4	YWWKKCAAYwWWwRTTGMMWWR	YWWKKCAAYWWWWRTTGMMWWR
Collection_1_m17_PKVLE_Phr	PKVLE_Phr	cluster_4	Collection_1	23	24.09	4	dwTmCTAACWYwRWGTTAGkAwh	DWTMCTAACWYWRWGTTAGKAWH
Collection_1_m15_PKAIE_Phr	PKAIE_Phr	cluster_4	Collection_1	23	16.10	10	MASAYTAACWWWWWGTTARTSTK	masAYTAACwwwwwGTTARTstk
Collection_1_m58_RSNSN_CadR	RSNSN_CadR	cluster_6	Collection_1	16	13.45	32	TTCAGCryryGCTGAA	TTCAGCRYRYGCTGAA
Collection_1_m24_QPTSH_ArsR	QPTSH_ArsR	cluster_7	Collection_1	20	12.97	74	ATATyGAyrryyrTCrATAT	ATATYGAYRRYYRTCRATAT
Collection_1_m23_QSKSR_ArsR2	QSKSR_ArsR2	cluster_2	Collection_1	22	14.16	8	+ATTTKKMHADHTDKMMAAAT+	+ATTTkKmhAdhTdkMmAAAT+
Collection_1_m49_KSTSQ_DMR_45340	KSTSQ_DMR_45340	cluster_19	Collection_1	21	21.49	4	TwGTTCskwwwwwmsGAACwA	TWGTTCSKWWWWWMSGAACWA
Collection_1_m38_ASHSQ_SutR	ASHSQ_SutR	cluster_14	Collection_1	16	18.51	10	ATGATGrWWyCATCAT	ATGATGRWWYCATCAT
Collection_1_m30_VSASH_SmtB	VSASH_SmtB	cluster_12	Collection_1	22	23.23	4	yrMTTGAWYARYTRWTCAAKyr	YRMTTGAWYARYTRWTCAAKYR

Click on the column names to change the order of the data.
Write the name of one cluster, collection or a pattern in the Search window.

Exported files

File	Description
Pairwise comparison	This table shows the pairwise comparison between all the input motifs using different metrics. This is the compare-matrices result.
Matrix description	This table shows information of each input motif.
Cluster-wise Motif Files [zip]	One TRANSFAC file is generated for each cluster including all the input motifs grouped in the corresponding cluster.
Root motifs	A file with the root matrix of each cluster.
Motif collections per cluster	A tab separated file containing the counts of motif of each collection on each cluster.
Clusters	A tab separated file containing the clusters and their correspondng motifs.
Central motifs IDs	A tab separated file containing the central motif, that one who is the most similar to all the others motif in the same cluster.
Central motifs (in TRANSFAC format)	A transfac file containing the central motif, that one who is the most similar to all the others motif within the same cluster.
Input motifs	The input motifs analyzed with matrix-clustering.

RSAT - matrix-clustering result

Analysis: arsr (18/06/2026 10:02)

Command

Results Summary

Clusters Summary Table

Individual Cluster View

Branch Motifs

Branch Motifs

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Branch Motifs

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Definitions

Individual Motif View

Heatmap View

Exported files