matrix-clustering deor

matrix-clustering  -v 1 -max_matrices 300 -matrix Collection_1 $RSAT/public_html/tmp/www-data/2026/07/02/matrix-clustering_2026-07-02.140117_qoCFYw/matrix-clustering_query_matrices.meme meme -hclust_method average -calc sum -title deor -metric_build_tree Ncor -lth w 5 -lth cor 0.4 -lth Ncor 0.4 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2026/07/02/matrix-clustering_2026-07-02.140117_qoCFYw/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 = 0.4
cor = 0.4

Individual Motif View

Motif id	Motif name	Cluster	Collection	Width	IC	Number of sites	Consensus	Consensus (Rev)
Collection_1_m35_VQSEATRR_RhaR	VQSEATRR_RhaR	cluster_1	Collection_1	34	12.57	21	++++YRATCRWWWWYGATYRW+++++++++++++	+++++++++++++wyrATCrwwwwyGATyr++++
Collection_1_m15_VETGTTRK_SrlR	VETGTTRK_SrlR	cluster_14	Collection_1	29	24.51	5	AwCTTTCAhhhhhhhhhhhhhATCTTTCA	TGAAAGATDDDDDDDDDDDDDTGAAAGWT
Collection_1_m23_IESISTRR_FruR	IESISTRR_FruR	cluster_1	Collection_1	34	20.08	6	++++WWAWCWATCAWWWWCWWTCA++++++++++	++++++++++TGAwwGwwwwTGATwGwTww++++
Collection_1_m49_VKSDMTRR_LacR	VKSDMTRR_LacR	cluster_6	Collection_1	22	20.52	5	+++wTGTTTktTwTTGTTTTtT	AAAAAACAAWAAMAAACAW+++
Collection_1_m40_SKSESTRR_FruR	SKSESTRR_FruR	cluster_1	Collection_1	34	22.81	3	++++TGAmwGTTkTTrmmbGTTTT++++++++++	++++++++++AAAACVKKYAAMAACWKTCA++++
Collection_1_m20_QPSTRK_MntR_2	QPSTRK_MntR_2	cluster_18	Collection_1	22	24.95	4	TwwyTTAGmCTAGkCTAArwwA	TWWYTTAGMCTAGKCTAARWWA
Collection_1_m51_VESSVTRN_AgaR2	VESSVTRN_AgaR2	cluster_3	Collection_1	25	15.51	4	STTTCGnnnnnnnnnnnnnCGAAAS	STTTCGNNNNNNNNNNNNNCGAAAS
Collection_1_m17_AKTTMGRQ_AzrR	AKTTMGRQ_AzrR	cluster_12	Collection_1	20	19.50	8	CYTTAYwwdRYhwwRTAARG	CYTTAYWWDRYHWWRTAARG
Collection_1_m28_VESSVTRS_AgaR2	VESSVTRS_AgaR2	cluster_3	Collection_1	25	14.39	4	YTTTCRnnnnnnnnnnnnnYGAAAR	YTTTCRNNNNNNNNNNNNNYGAAAR
Collection_1_m44_VPSEATRR_RhaR	VPSEATRR_RhaR	cluster_1	Collection_1	34	11.29	13	++++YRATCRWWWWYGATYRW+++++++++++++	+++++++++++++wYRATCrwwwwYGATYR++++
Collection_1_m50_VNSDMTRR_LacR	VNSDMTRR_LacR	cluster_6	Collection_1	22	20.15	6	+++TTGTTTrTTwTTGTTTkTT	AAMAAACAAWAAYAAACAA+++
Collection_1_m1_IDSTQTRR_CsqR	IDSTQTRR_CsqR	cluster_17	Collection_1	24	25.36	34	AAAAAkTGACrssyGTCAmTTTTT	AAAAAKTGACRSSYGTCAMTTTTT
Collection_1_m22_IQSEATRR_RhaR	IQSEATRR_RhaR	cluster_1	Collection_1	34	14.15	6	++++YRATCRWWWWYGATYRW+++++++++++++	+++++++++++++wyrATCrwwwwyGATyr++++
Collection_1_m18_SASLQARR_SufR	SASLQARR_SufR	cluster_5	Collection_1	24	24.61	8	TTDRRCAACRYHDRYGTTGYYHAA	TTdRRCAACRYhdRYGTTGYYhAA
Collection_1_m38_LESESTRR_FruR	LESESTRR_FruR	cluster_1	Collection_1	34	18.27	19	++++TGAwAGAwwwTGmTwGAmww++++++++++	++++++++++WWKTCWAKCAWWWTCTWTCA++++
Collection_1_m13_VGSEATRR_RhaR	VGSEATRR_RhaR	cluster_1	Collection_1	34	11.75	5	++++YRATCRWTTTYGATCRT+++++++++++++	+++++++++++++ayGAtCraaawyGATyr++++
Collection_1_m30_TESRETRR_FucR	TESRETRR_FucR	cluster_7	Collection_1	36	27.19	10	wTGmCCGwWTdmramdAWWThktykhAWwCGGkCAw	WTGMCCGWWTDMRAMDAWWTHKTYKHAWWCGGKCAW
Collection_1_m31_VKSEVTRS_RhaR	VKSEVTRS_RhaR	cluster_4	Collection_1	20	12.57	10	+TKTCRATTTTTKWCRA+++	+++TyGwmAaaaaTyGAmA+
Collection_1_m19_MKSMITRR_RhaR	MKSMITRR_RhaR	cluster_6	Collection_1	22	18.93	13	TTdTSATWAATTwATSAYAA++	++TTRTSATWAATTWATSAHAA
Collection_1_m9_LQSASTRR_FruR	LQSASTRR_FruR	cluster_1	Collection_1	34	26.65	29	++++TGAtTGTTTTTGAwTGwwwwTGrwarawww	WWWTYTWYCAWWWWCAWTCAAAAACAATCA++++
Collection_1_m11_VSTEETRR_RhaR	VSTEETRR_RhaR	cluster_6	Collection_1	22	16.52	23	++WAAAWWCAAAMAWAAACAAA	TTTGTTTwtKTTTGwWTttw++
Collection_1_m27_LDSESTRR_FruR	LDSESTRR_FruR	cluster_1	Collection_1	34	18.64	8	++++TGRwAGWwwdTGmWwGAmwd++++++++++	++++++++++HWKTCWWKCAHWWWCTWYCA++++
Collection_1_m12_LDSKNTRR_IolR	LDSKNTRR_IolR	cluster_6	Collection_1	22	17.07	32	TTTTGRTTATTTTTTKRTWAW+	+wTWAyMAAAAaATaAYCAAaA
Collection_1_m7_IQSESTRR_FruR	IQSESTRR_FruR	cluster_1	Collection_1	34	21.20	48	+wwwTGAtTGwTWwTGAAtGwwTwTGAwTgw+++	+++WCAWTCAWAWWCATTCAWWAWCAATCAWWW+
Collection_1_m29_VDSEVTRK_GlmR	VDSEVTRK_GlmR	cluster_2	Collection_1	19	21.52	26	AwSTTTCGAwTCGAAASwT	AWSTTTCGAWTCGAAASWT
Collection_1_m24_TNSDMTRR_LacR	TNSDMTRR_LacR	cluster_6	Collection_1	22	16.81	4	++++AAACAYWWWHMAACA+++	+++TGTTKdwWWRTGTTT++++
Collection_1_m26_AVSPQARR_SufR	AVSPQARR_SufR	cluster_5	Collection_1	24	23.50	10	TTTAACAACHAWWTDGTTGTTAAA	TTTAACAAChawwtdGTTGTTAAA
Collection_1_m10_TESRDTRR_GlcR	TESRDTRR_GlcR	cluster_8	Collection_1	20	23.27	4	RCTTAwAWTyACTTAwwRAT	ATYWWTAAGTRAWTWTAAGY
Collection_1_m34_ITSAMTRR_GalR	ITSAMTRR_GalR	cluster_9	Collection_1	17	5.44	38	ckrwsmksssmkswymg	CKRWSMKSSSMKSWYMG
Collection_1_m42_VKSEVTRN_RhaR	VKSEVTRN_RhaR	cluster_4	Collection_1	20	14.09	4	+TKTCRANNNNTKTCRA+++	+++TyGAmAnnnnTyGAmA+
Collection_1_m16_VESEVTRK_GlmR	VESEVTRK_GlmR	cluster_2	Collection_1	19	20.24	6	AwsTTTCGawtCGAAAswT	AWSTTTCGAWTCGAAASWT
Collection_1_m25_AQTPQARR_SufR	AQTPQARR_SufR	cluster_5	Collection_1	24	19.99	22	WwwAACAACAwwwwTGTTGTTwwW	WWWAACAACAWWWWTGTTGTTWWW
Collection_1_m41_NC1]MTRR_GalR	NC1]MTRR_GalR	cluster_9	Collection_1	17	9.53	4	WkrwbmKnnnMkvwymW	WKRWBMKNNNMKVWYMW
Collection_1_m4_TESPQTRR_GlpR	TESPQTRR_GlpR	cluster_10	Collection_1	22	16.00	84	wwATGwKCGwwwwCGMwCATww	WWATGWKCGWWWWCGMWCATWW
Collection_1_m21_VNSKVTRK_PflR	VNSKVTRK_PflR	cluster_2	Collection_1	19	17.57	6	TAMTTTCRWWYGAAAKTA+	+TAmTTTCrwwyGAAAkTA
Collection_1_m43_VKSTSTRR_FucR	VKSTSTRR_FucR	cluster_11	Collection_1	19	22.87	4	AyTTGAAyAwTrTTCAArT	AYTTGAAYAWTRTTCAART
Collection_1_m2_LKSEMTRR_DeoR	LKSEMTRR_DeoR	cluster_10	Collection_1	22	14.35	50	twwTGTkAktwwamTmACAwwa	TWWTGTKAKTWWAMTMACAWWA
Collection_1_m48_AQSTRTYR_SO1758	AQSTRTYR_SO1758	cluster_13	Collection_1	20	24.46	14	ACTGACAkSATSmTGTCAGT	ACTGACAKSATSMTGTCAGT
Collection_1_m33_VKSTTARD_SufR	VKSTTARD_SufR	cluster_15	Collection_1	19	18.98	4	ddKyTATTGwCAATArMhh	DDKYTATTGWCAATARMHH
Collection_1_m5_VESPATRR_UlaR	VESPATRR_UlaR	cluster_1	Collection_1	34	16.97	22	DWWTAWTCAAAWTTAATCWYWWT+++++++++++	+++++++++++awwrWGATTaaWTTTGAWTAwwh
Collection_1_m8_ISSEMTYR_CutR	ISSEMTYR_CutR	cluster_8	Collection_1	20	17.93	10	+AAWATGTGAAAAWRTG+++	+++CAywTTTTCACATWTT+
Collection_1_m47_VASEATRR_RhaR_2	VASEATRR_RhaR_2	cluster_1	Collection_1	34	12.46	8	++++YGAKCRWNNNYGATYRW+++++++++++++	+++++++++++++wyrATCrnnnwyGmTCr++++
Collection_1_m46_LQSESTRR_FruR	LQSESTRR_FruR	cluster_1	Collection_1	34	18.44	6	++++TGawTGwwTTTGrTTGwwwT++++++++++	++++++++++AWWWCAAYCAAAWWCAWTCA++++
Collection_1_m45_VESRDTRR_GlcR	VESRDTRR_GlcR	cluster_8	Collection_1	20	18.15	4	rCTTAThhhhACTTATW+++	+++WATAAGTDDDDATAAGY
Collection_1_m36_VASTVTRN_AgaR	VASTVTRN_AgaR	cluster_2	Collection_1	19	9.53	6	++MWWWCRWWWYGWWWK++	++mwwwcrwwwygwwwk++
Collection_1_m39_AQSPQARR_SufR	AQSPQARR_SufR	cluster_5	Collection_1	24	20.72	28	TTWARCAACAMWWKTGTTGYTWAA	TTWArCAACamwwktGTTGyTWAA
Collection_1_m32_ALSPQARR_SufR	ALSPQARR_SufR	cluster_5	Collection_1	24	25.10	12	TTwAACAACAwmkwTGTTGTTwAA	TTWAACAACAWMKWTGTTGTTWAA
Collection_1_m37_VNSKVTRK_PflR	VNSKVTRK_PflR	cluster_16	Collection_1	21	16.83	56	wCGwAAtwrWwWywaTTwCGw	WCGWAATWRWWWYWATTWCGW
Collection_1_m3_TESKETRR_FucR	TESKETRR_FucR	cluster_7	Collection_1	36	22.69	74	aTGmCCGTTTTarwwwwwwwwwwytAAAACGGkCAt	ATGMCCGTTTTARWWWWWWWWWWYTAAAACGGKCAT
Collection_1_m14_VASEVTRS_AgaR	VASEVTRS_AgaR	cluster_4	Collection_1	20	18.96	6	CTTTCAAAMASTTTC+++++	+++++GAAAsTkTTTGAAAG
Collection_1_m6_VNSTVTRN_AgaR	VNSTVTRN_AgaR	cluster_4	Collection_1	20	16.39	81	MAAWMRAAAYRAAAYGAAAG	CTTTCRTTTyrTTTYkwTTk

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: deor (02/07/2026 14:01)

Command

Results Summary

Clusters Summary Table

Individual Cluster View

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

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Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

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Branch Motifs

Branch Motifs

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Branch Motifs

Definitions

Individual Motif View

Heatmap View

Exported files