# RSAT - matrix-clustering result

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

## Results Summary

Nb Input motifs | Nb Input collections | Nb Clusters Found | Download Root motifs | Complete results [zip] | Parameters used
Linkage method | Similarity metric | Thresholds to partition the tree
60 | 1 | 19 | Download | Download |
average | Ncor | Ncor = 0.55 cor = 0.6

| Logo Forest (dynamic browsing) Logo Forest (rapid overview - low image quality) cluster_1 cluster_2 cluster_3 cluster_4 cluster_5 cluster_6 cluster_7 cluster_8 cluster_9 cluster_10 cluster_11 cluster_12 cluster_13 cluster_14 cluster_15 cluster_16 cluster_17 cluster_18 cluster_19
Clusters Summary ## Clusters Summary Table
Root Motif | Root Motif (Reverse) | Cluster ID | # Motifs | Motif_Name::Collection | Number of Motifs by Collection | Root Motif (transfac Format)
--- | --- | --- | --- | --- | --- | ---
| cluster_1 | 7 | QPKSF_ArsR::Collection_1:: QSRSF_ArsR::Collection_1:: QSKSF_ArsR::Collection_1:: QSKSY_ArsR::Collection_1:: QSRSR_SahR::Collection_1:: QNSSH_SahR::Collection_1:: QSGSH_SahR::Collection_1:: | Collection_1::7_motifs | Show matrix
|  | cluster_2 | 8 | FSTSK_ArsR::Collection_1:: QSKSR_ArsR2::Collection_1:: ISTSK_ArsR::Collection_1:: MSTSR_ArsR::Collection_1:: VSTSK_ArsR::Collection_1:: MSTSK_ArsR::Collection_1:: KPSSH_SdpR::Collection_1:: KPSSQ_SdpR::Collection_1:: | Collection_1::8_motifs | Show matrix
|  | cluster_3 | 12 | QSLSH_CzcR2::Collection_1:: QSVSH_CzcR2::Collection_1:: QSTSH_CzrA::Collection_1:: ESASH_SmtB::Collection_1:: QSNSH_CzrA::Collection_1:: QTTSH_CzrA::Collection_1:: QSSSH_CzrA::Collection_1:: QSASH_CzrA::Collection_1:: QPRSR_SahR::Collection_1:: QPASQ_AseR::Collection_1:: QPSSQ_AseR::Collection_1:: QPKSR_ArsR::Collection_1:: | Collection_1::12_motifs | Show matrix
|  | cluster_4 | 9 | QKALE_Phr::Collection_1:: QKAIG_Phr::Collection_1:: QKAIE_Phr::Collection_1:: PKALE_Phr::Collection_1:: PKAIS_Phr::Collection_1:: PKAIE_Phr::Collection_1:: PKVIE_Phr::Collection_1:: PKVLE_Phr::Collection_1:: PKAID_Phr::Collection_1:: | Collection_1::9_motifs | Show matrix
|  | cluster_5 | 3 | KSTSH_YczG::Collection_1:: QQTSF_YdfF::Collection_1:: PQTSF_YdfF::Collection_1:: | Collection_1::3_motifs | Show matrix
|  | cluster_6 | 2 | RTNSN_CadR::Collection_1:: RSNSN_CadR::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_7 | 3 | QSTSQ_YbzH::Collection_1:: QPTSY_Caur_3587::Collection_1:: QPTSH_ArsR::Collection_1:: | Collection_1::3_motifs | Show matrix
|  | cluster_8 | 2 | ASNSF_ArsR3_2::Collection_1:: GTNSF_ArsR3::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_9 | 2 | QSASQ_HlyU::Collection_1:: ASASQ_YgaV::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_10 | 2 | VPTSA_Cg1831::Collection_1:: LPTSA_Cg1831::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_11 | 2 | PSTSH_DMR_39480::Collection_1:: ASTSK_Ddes_1264::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_12 | 1 | VSASH_SmtB::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_13 | 1 | QPLSQ_Znr::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_14 | 1 | ASHSQ_SutR::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_15 | 1 | QPLSQ_Znr::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_16 | 1 | RTASH_DESPIG_02495::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_17 | 1 | AAGRR_SufR::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_18 | 1 | QPRST_SamR::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_19 | 1 | KSTSQ_DMR_45340::Collection_1 | Collection_1 : 1 motif | Show matrix

- Note: by default the table displays the first 50 clusters. Click on the Show X entries button to display more (or less) clusters.
- Click on the column names to change the order of the data.
- Use the Search window to find your motif (s) of interest.

Individual Cluster View

## Individual Cluster View

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cluster_1
cluster_2
cluster_3
cluster_4
cluster_5
cluster_6
cluster_7
cluster_8
cluster_9
cluster_10
cluster_11
cluster_12
cluster_13
cluster_14
cluster_15
cluster_16
cluster_17
cluster_18
cluster_19
Display Logo Trees
cluster_1
cluster_2
cluster_3
cluster_4
cluster_5
cluster_6
cluster_7
cluster_8
cluster_9
cluster_10
cluster_11
cluster_12
cluster_13
cluster_14
cluster_15
cluster_16
cluster_17
cluster_18
cluster_19
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | -A T A T C A A A A w w T T T T G A T A T- |  |  | Collection_1::2_motifs | PSSM | 22.96 | 42
Node 2 | ---A T C A A r w w w w y T T G A T--- |  |  | Collection_1::2_motifs | PSSM | 13.28 | 32
Node 3 | ---A T C A A r w w w w y T T G A T--- |  |  | Collection_1::3_motifs | PSSM | 12.37 | 38
Node 4 | -A T A T C A A r a w w t y T T G A T A T- |  |  | Collection_1::3_motifs | PSSM | 16.91 | 108
Node 5 | T A w A T C A A a w w w w t T T G A T w T A |  |  | Collection_1::4_motifs | PSSM | 18.05 | 232
Node 6 | T A w A T C A A a w w w w t T T G A T w T A |  |  | Collection_1::7_motifs | PSSM | 17.57 | 270

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | -A T T T k G C y A w w T r G C m A A A T- |  |  | Collection_1::2_motifs | PSSM | 14.36 | 36
Node 2 | -A T T T k G C y A w w T r G C m A A A T- |  |  | Collection_1::3_motifs | PSSM | 14.56 | 44
Node 3 | -A T T T k G C y A w w T r G C m A A A T- |  |  | Collection_1::4_motifs | PSSM | 13.99 | 56
Node 4 | -A T T T k G C y A w w T r G C m A A A T- |  |  | Collection_1::5_motifs | PSSM | 13.49 | 64
Node 5 | -A T T T k G C h A w w T d G C m A A A T- |  |  | Collection_1::6_motifs | PSSM | 13.57 | 72
Node 6 | T A T T T A G A y A w w T r T C T A A A T A |  |  | Collection_1::2_motifs | PSSM | 21.28 | 164
Node 7 | T A T T T A G a y A w w T r t C T A A A T A |  |  | Collection_1::8_motifs | PSSM | 17.11 | 236

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | --C A T A T G A A y A w w T r T T C A T A T G-- |  |  | Collection_1::2_motifs | PSSM | 21.28 | 60
Node 2 | A A y A y m T G A A y A w w T r T T C A k r T r T T |  |  | Collection_1::2_motifs | PSSM | 22.58 | 44
Node 3 | ---A T A T G w W w W y r W w W w C A T A T--- |  |  | Collection_1::2_motifs | PSSM | 19.40 | 14
Node 4 | --C A T A T G A A y A w w T r T T C A T A T G-- |  |  | Collection_1::3_motifs | PSSM | 20.78 | 68
Node 5 | --t A T A T A y G h w W W w d C r T A T A T a-- |  |  | Collection_1::2_motifs | PSSM | 16.37 | 88
Node 6 | A A y A T A T G A A y A w w T r T T C A T A T r T T |  |  | Collection_1::5_motifs | PSSM | 22.57 | 112
Node 7 | a w t A T A T A w G y a w w t r C w T A T A T a w t |  |  | Collection_1::3_motifs | PSSM | 13.74 | 140
Node 8 | A A y A T A T G A A y A w w T r T T C A T A T r T T |  |  | Collection_1::6_motifs | PSSM | 18.88 | 152
Node 9 | A A y A T A T G A A y A w w T r T T C A T A T r T T |  |  | Collection_1::8_motifs | PSSM | 18.50 | 166
Node 10 | a w t A y A T A A r g A t a T c y T T A T r T a w t |  |  | Collection_1::4_motifs | PSSM | 15.91 | 330
Node 11 | a A y A T A T r A r s A w w T s y T y A T A T r T t |  |  | Collection_1::12_motifs | PSSM | 15.31 | 496

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | T W w w r T A A C w w w w w G T T A y w w W A |  |  | Collection_1::2_motifs | PSSM | 20.64 | 28
Node 2 | d w y m C T A A C w t w a w G T T A G k r w h |  |  | Collection_1::2_motifs | PSSM | 17.46 | 12
Node 3 | T T T a r T w A C h w w w d G T w A y t A A A |  |  | Collection_1::3_motifs | PSSM | 15.89 | 202
Node 4 | w w T A C T A A C t w w w a G T T A G T A w w |  |  | Collection_1::3_motifs | PSSM | 18.05 | 16
Node 5 | a w y A C T A A C w w w w w G T T A G T r w t |  |  | Collection_1::4_motifs | PSSM | 15.30 | 26
Node 6 | r w y A C T A A C y w w w r G T T A G T r w y |  |  | Collection_1::5_motifs | PSSM | 15.27 | 32
Node 7 | r w t a C T A A C w w w w w G T T A G t a w y |  |  | Collection_1::6_motifs | PSSM | 15.25 | 36
Node 8 | T T T a s T w A C h w w w d G T w A s t A A A |  |  | Collection_1::9_motifs | PSSM | 14.68 | 238

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | -T T C r A T k A T m A T y G A A- |  |  | Collection_1::2_motifs | PSSM | 16.29 | 20
Node 2 | G T T C G A w k A T m w T C G A A C |  |  | Collection_1::3_motifs | PSSM | 18.47 | 36

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | K T C A G C r y r y G C T G A M |  |  | Collection_1::2_motifs | PSSM | 13.29 | 36

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | A T A T Y G A y r a t y r T C R A T A T |  |  | Collection_1::2_motifs | PSSM | 12.77 | 80
Node 2 | A T A T y G A y r w w y r T C r A T A T |  |  | Collection_1::3_motifs | PSSM | 12.51 | 94

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | Y A r K w C A A Y d w w h R T T G w M y T R |  |  | Collection_1::2_motifs | PSSM | 17.49 | 8

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | y t T A w w T T A G w w w w w w C T A A w w T A a r |  |  | Collection_1::2_motifs | PSSM | 15.07 | 192

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | A s T C A A W y R v b Y r W T T G A s T |  |  | Collection_1::2_motifs | PSSM | 20.62 | 8

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | k A k T T C G w m A y r T k w C G A A m T m |  |  | Collection_1::2_motifs | PSSM | 18.91 | 8

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y r m T T G A w y A r y T r w T C A A k y r |  |  | Collection_1 : 1 motif | PSSM | 23.23 | 4

cluster_13

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w y y A G C A m k m k T G C T r r w |  |  | Collection_1 : 1 motif | PSSM | 13.33 | 8

cluster_14

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | A T G A T G r w w y C A T C A T |  |  | Collection_1 : 1 motif | PSSM | 18.51 | 10

cluster_15

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | C A T G C r y s a t s r y G C A T G |  |  | Collection_1 : 1 motif | PSSM | 16.70 | 20

cluster_16

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | t a A A A C T A r w w w w y T A G T T T t a C C A C: C o l l e c t i o n_1_m 8_R T A S H_D E S P I G_0 2 4 9 5 C C i d: C o l l e c t i o n_1_m 8_R T A S H_D E S P I G_0 2 4 9 5 C C m e r g e d_I D: R T A S H_D E S P I G_0 2 4 9 5 C C m e r g e d_A C: C o l l e c t i o n_1:::R T A S H_D E S P I G_0 2 4 9 5 |  |  | Collection_1 : 1 motif | PSSM | 19.95 | 6

cluster_17

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T T A s r m m A C A h W W d T G T k k y s T A A |  |  | Collection_1 : 1 motif | PSSM | 22.71 | 8

cluster_18

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | A T C y c T t y A T C s s G A T r a A g r G A T |  |  | Collection_1 : 1 motif | PSSM | 19.38 | 34

cluster_19

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T w G T T C s k w w w w w m s G A A C w A |  |  | Collection_1 : 1 motif | PSSM | 21.49 | 4

- Each cluster has a different color.
- Click on the upper buttons to display separately the information of each cluster.
- Click on the circles at each tree to display its corresponding merged motifs.

### Definitions

- Logo tree.
  This results shows the hierarchical tree with its logo alignment of one cluster.
  The logos are shown in Forward (left logo) and Reverse (right logo) orientation.
- Branch-motifs.
  On the trees are displayed the branch number that is the number in which the motifs were incorporated in the tree.
  The Branch-Motifs table shows the logo in both orientations and the link to the file in TRANSFAC format with the branch-motif.

Individual Motif View ## Individual Motif View
Motif id | Motif name | Cluster | Collection | Width | IC | Number of sites | Consensus | Consensus (Rev) | Logo | Logo (Rev)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
Collection_1_m34_QPRSR_SahR | QPRSR_SahR | cluster_3 | Collection_1 | 26 | 20.12 | 190 | +++A Y A T A A A G A T A T C T T T A T R T+++ | +++A y A T A A A G A T A T C T T T A T r T+++ |  |
Collection_1_m37_VSTSK_ArsR | VSTSK_ArsR | cluster_2 | Collection_1 | 22 | 15.09 | 14 | +a T T T k G C y A w w T r G C m A A A t+ | +A T T T K G C Y A W W T R G C M A A A T+ |  |
Collection_1_m54_QPKSF_ArsR | QPKSF_ArsR | cluster_1 | Collection_1 | 22 | 12.16 | 6 | +++A T C A A W T K M A W T T G A T+++ | +++A T C A A w t k m a w T T G A T+++ |  |
Collection_1_m31_ESASH_SmtB | ESASH_SmtB | cluster_3 | Collection_1 | 26 | 22.06 | 32 | A A y A y c T G A A y A r y T r T T C A g r T r T T | A A Y A Y C T G A A Y A R Y T R T T C A G R T R T T |  |
Collection_1_m3_QPASQ_AseR | QPASQ_AseR | cluster_3 | Collection_1 | 26 | 13.83 | 52 | A W T A Y A T A A G Y M W W K R C T T A T R T A W T | a w t A y A T A A G y m w w k r C T T A T r T a w t |  |
Collection_1_m41_KSTSH_YczG | KSTSH_YczG | cluster_5 | Collection_1 | 18 | 21.00 | 16 | G T T C G A W D A T H W T C G A A C | G T T C G A W d A T h W T C G A A C |  |
Collection_1_m4_QSASQ_HlyU | QSASQ_HlyU | cluster_9 | Collection_1 | 26 | 14.24 | 150 | ++T A w A T T A G w w w w w w C T A A T w T A++ | ++T A W A T T A G W W W W W W C T A A T W T A++ |  |
Collection_1_m29_LPTSA_Cg1831 | LPTSA_Cg1831 | cluster_10 | Collection_1 | 20 | 26.34 | 4 | A s T C A A A T G A T C A T T T G A s T | A S T C A A A T G A T C A T T T G A S T |  |
Collection_1_m21_ISTSK_ArsR | ISTSK_ArsR | cluster_2 | Collection_1 | 22 | 14.81 | 12 | +R T T T K S M H A W W T D K S M A A A Y+ | +r T T T k s m h A w w T d k s m A A A y+ |  |
Collection_1_m27_PSTSH_DMR_39480 | PSTSH_DMR_39480 | cluster_11 | Collection_1 | 22 | 22.70 | 4 | k W d T T C G A M A b v T K T C G A A h W m | K W D T T C G A M A B V T K T C G A A H W M |  |
Collection_1_m52_PKALE_Phr | PKALE_Phr | cluster_4 | Collection_1 | 23 | 23.40 | 4 | N W W M C T A A C W T W A W G T T A G K W W N | n w W M C T A A C w T w A w G T T A G K W w n |  |
Collection_1_m8_RTASH_DESPIG_02495 | RTASH_DESPIG_02495 | cluster_16 | Collection_1 | 22 | 19.95 | 6 | t a A A A C T A r w w w w y T A G T T T t a | T A A A A C T A R W W W W Y T A G T T T T A |  |
Collection_1_m1_QPKSR_ArsR | QPKSR_ArsR | cluster_3 | Collection_1 | 26 | 16.57 | 84 | ++t A T A T A y G a w w w w t C r T A T A T a++ | ++T A T A T A Y G A W W W W T C R T A T A T A++ |  |
Collection_1_m22_QPTSY_Caur_3587 | QPTSY_Caur_3587 | cluster_7 | Collection_1 | 20 | 20.51 | 6 | A t A T T G A A w w w w T T C A A T a T | A T A T T G A A W W W W T T C A A T A T |  |
Collection_1_m20_QPLSQ_Znr | QPLSQ_Znr | cluster_13 | Collection_1 | 18 | 13.33 | 8 | w y y A G C A m k m k T G C T r r w | W Y Y A G C A M K M K T G C T R R W |  |
Collection_1_m19_QPSSQ_AseR | QPSSQ_AseR | cluster_3 | Collection_1 | 26 | 25.74 | 4 | ++T A T A T W A R y A W W T r Y T W A T A T A++ | ++T A T A T W A R Y A W W T R Y T W A T A T A++ |  |
Collection_1_m53_PKAID_Phr | PKAID_Phr | cluster_4 | Collection_1 | 23 | 16.20 | 8 | d w y A c T A A C w w w w w G T T A g T r w h | D W Y A C T A A C W W W W W G T T A G T R W H |  |
Collection_1_m60_ASTSK_Ddes_1264 | ASTSK_Ddes_1264 | cluster_11 | Collection_1 | 22 | 24.09 | 4 | Y A T T T C G T Y v h d b R A C G A A A T R | Y A T T T C G T Y V H D B R A C G A A A T R |  |
Collection_1_m2_KPSSH_SdpR | KPSSH_SdpR | cluster_2 | Collection_1 | 22 | 21.45 | 160 | T A T T T A G A y A w w T r T C T A A A T A | T A T T T A G A Y A W W T R T C T A A A T A |  |
Collection_1_m48_MSTSK_ArsR | MSTSK_ArsR | cluster_2 | Collection_1 | 22 | 14.97 | 22 | +A T T T K G C y A w w T r G C M A A A T+ | +A T T T K G C Y A W W T R G C M A A A T+ |  |
Collection_1_m33_QSASH_CzrA | QSASH_CzrA | cluster_3 | Collection_1 | 26 | 21.27 | 56 | ++C A T A T G A A y A w w T r T T C A T A T G++ | ++C A T A T G A A Y A W W T R T T C A T A T G++ |  |
Collection_1_m35_QSTSQ_YbzH | QSTSQ_YbzH | cluster_7 | Collection_1 | 20 | 19.22 | 14 | A T A T C G W A A T A T T W C G A T A T | A T A T C G w a A T A T t w C G A T A T |  |
Collection_1_m13_RTNSN_CadR | RTNSN_CadR | cluster_6 | Collection_1 | 16 | 16.73 | 4 | K W C A S C A b v T G S T G W M | K W C A S C A B V T G S T G W M |  |
Collection_1_m39_KPSSQ_SdpR | KPSSQ_SdpR | cluster_2 | Collection_1 | 22 | 21.58 | 4 | +A W T T A r k W A W W T W m y T A A W T+ | +A W T T A R K W A W W T W M Y T A A W T+ |  |
Collection_1_m25_PKAIS_Phr | PKAIS_Phr | cluster_4 | Collection_1 | 23 | 21.93 | 6 | R W T R S T A A C Y A W T R G T T A S Y A W Y | r w T r s T A A C y A w T r G T T A s y A w y |  |
Collection_1_m26_VPTSA_Cg1831 | VPTSA_Cg1831 | cluster_10 | Collection_1 | 20 | 22.18 | 4 | A s T C A A w C r s s y G w T T G A s T | A S T C A A W C R S S Y G W T T G A S T |  |
Collection_1_m40_QSNSH_CzrA | QSNSH_CzrA | cluster_3 | Collection_1 | 26 | 29.89 | 12 | W A T A T A T G A A y A w w T r T T C A T A T A T W | W A T A T A T G A A Y A W W T R T T C A T A T A T W |  |
Collection_1_m47_QSRSR_SahR | QSRSR_SahR | cluster_1 | Collection_1 | 22 | 15.96 | 66 | +A T A T C A A G W T A W C T T G A T A T+ | +A T A T C A A g w T A w c T T G A T A T+ |  |
Collection_1_m50_QSLSH_CzcR2 | QSLSH_CzcR2 | cluster_3 | Collection_1 | 26 | 23.57 | 4 | +++A T A T G A w w A y r T w w T C A T A T+++ | +++A T A T G A W W A Y R T W W T C A T A T+++ |  |
Collection_1_m11_AAGRR_SufR | AAGRR_SufR | cluster_17 | Collection_1 | 24 | 22.71 | 8 | T T A s r m m A C A h W W d T G T k k y s T A A | T T A S R M M A C A H W W D T G T K K Y S T A A |  |
Collection_1_m43_QKALE_Phr | QKALE_Phr | cluster_4 | Collection_1 | 23 | 15.84 | 174 | T T T A R T W A C Y W W W R G T W A Y T A A A | T T T A r T w A C y w w w r G T w A y T A A A |  |
Collection_1_m51_PQTSF_YdfF | PQTSF_YdfF | cluster_5 | Collection_1 | 18 | 16.65 | 14 | +T T C r A Y k A T m R T y G A A+ | +T T C R A Y K A T M R T Y G A A+ |  |
Collection_1_m55_QKAIE_Phr | QKAIE_Phr | cluster_4 | Collection_1 | 23 | 20.59 | 20 | T w w w r T A A C w w w w w G T T A y w w w A | T W W W R T A A C W W W W W G T T A Y W W W A |  |
Collection_1_m44_QQTSF_YdfF | QQTSF_YdfF | cluster_5 | Collection_1 | 18 | 17.61 | 6 | +T T C r A T k w w m A T y G A A+ | +T T C R A T K W W M A T Y G A A+ |  |
Collection_1_m7_ASASQ_YgaV | ASASQ_YgaV | cluster_9 | Collection_1 | 26 | 18.06 | 42 | y t T A a T T w A G w w w w w w C T w A A t T A a r | Y T T A A T T W A G W W W W W W C T W A A T T A A R |  |
Collection_1_m18_QKAIG_Phr | QKAIG_Phr | cluster_4 | Collection_1 | 23 | 23.40 | 8 | W T W w r T A A C w w w w w G T T A y w W A W | W T W W R T A A C W W W W W G T T A Y W W A W |  |
Collection_1_m57_QSGSH_SahR | QSGSH_SahR | cluster_1 | Collection_1 | 22 | 22.93 | 38 | +A T A T C A A A A w w T T T T G A T A T+ | +A T A T C A A A A W W T T T T G A T A T+ |  |
Collection_1_m12_QTTSH_CzrA | QTTSH_CzrA | cluster_3 | Collection_1 | 26 | 23.08 | 8 | ++Y A T A T G W K Y A T A T R M W C A T A T R++ | ++y A T A T G w k y A T A T r m w C A T A T r++ |  |
Collection_1_m42_QSKSF_ArsR | QSKSF_ArsR | cluster_1 | Collection_1 | 22 | 13.38 | 26 | +++A T C A A r w w w w y T T G A T+++ | +++A T C A A R W W W W Y T T G A T+++ |  |
Collection_1_m6_QSTSH_CzrA | QSTSH_CzrA | cluster_3 | Collection_1 | 26 | 15.52 | 40 | +W H A T A T T D A Y A W W T R T H A A T A T D W+ | +W h A T A T t d a y A w w T r t h a A T A T d W+ |  |
Collection_1_m45_MSTSR_ArsR | MSTSR_ArsR | cluster_2 | Collection_1 | 22 | 18.81 | 8 | +A Y T T K D Y H A W W T D R H M A A R T+ | +A Y T T K d Y h A w w T d R h M A A R T+ |  |
Collection_1_m5_QSKSY_ArsR | QSKSY_ArsR | cluster_1 | Collection_1 | 22 | 20.31 | 124 | T W M A T C A A A W W W W T T T G A T K W A | T w m A T C A A a w w w w t T T G A T k w A |  |
Collection_1_m14_ASNSF_ArsR3_2 | ASNSF_ArsR3_2 | cluster_8 | Collection_1 | 22 | 19.50 | 4 | Y A v K h C A A Y r h d y R T T G d M b T R | Y A V K H C A A Y R H D Y R T T G D M B T R |  |
Collection_1_m32_QSRSF_ArsR | QSRSF_ArsR | cluster_1 | Collection_1 | 22 | 15.96 | 6 | +++A T C A A m w w w w k T T G A T+++ | +++A T C A A M W W W W K T T G A T+++ |  |
Collection_1_m16_QSSSH_CzrA | QSSSH_CzrA | cluster_3 | Collection_1 | 26 | 24.35 | 4 | ++y R T A T G A A y R W W Y r T T C A T A Y r++ | ++Y R T A T G A A Y R W W Y R T T C A T A Y R++ |  |
Collection_1_m59_QSVSH_CzcR2 | QSVSH_CzcR2 | cluster_3 | Collection_1 | 26 | 19.61 | 10 | +++A T A T G T T r w y r w y A A C A T A T+++ | +++A T A T G T T R W Y R W Y A A C A T A T+++ |  |
Collection_1_m28_QPRST_SamR | QPRST_SamR | cluster_18 | Collection_1 | 24 | 19.38 | 34 | A T C y c T t y A T C s s G A T r a A g r G A T | A T C Y C T T Y A T C S S G A T R A A G R G A T |  |
Collection_1_m46_QPLSQ_Znr | QPLSQ_Znr | cluster_15 | Collection_1 | 18 | 16.70 | 20 | C A T G C r y s a t s r y G C A T G | C A T G C R Y S A T S R Y G C A T G |  |
Collection_1_m56_QNSSH_SahR | QNSSH_SahR | cluster_1 | Collection_1 | 22 | 24.52 | 4 | +A T A T C A A A R h d Y T T T G A T A T+ | +A T A T C A A A R H D Y T T T G A T A T+ |  |
Collection_1_m36_FSTSK_ArsR | FSTSK_ArsR | cluster_2 | Collection_1 | 22 | 19.50 | 8 | +R Y T T G S H M A W W T K D S C A A R Y+ | +R y T T G S h m A W W T k d S C A A r Y+ |  |
Collection_1_m10_PKVIE_Phr | PKVIE_Phr | cluster_4 | Collection_1 | 23 | 26.17 | 4 | W Y T A C T A A C Y W W W R G T T A G T A R W | W Y T A C T A A C y w w w r G T T A G T A R W |  |
Collection_1_m9_GTNSF_ArsR3 | GTNSF_ArsR3 | cluster_8 | Collection_1 | 22 | 21.24 | 4 | Y W W K K C A A Y w W W w R T T G M M W W R | Y W W K K C A A Y W W W W R T T G M M W W R |  |
Collection_1_m17_PKVLE_Phr | PKVLE_Phr | cluster_4 | Collection_1 | 23 | 24.09 | 4 | d w T m C T A A C W Y w R W G T T A G k A w h | D W T M C T A A C W Y W R W G T T A G K A W H |  |
Collection_1_m15_PKAIE_Phr | PKAIE_Phr | cluster_4 | Collection_1 | 23 | 16.10 | 10 | M A S A Y T A A C W W W W W G T T A R T S T K | m a s A Y T A A C w w w w w G T T A R T s t k |  |
Collection_1_m58_RSNSN_CadR | RSNSN_CadR | cluster_6 | Collection_1 | 16 | 13.45 | 32 | T T C A G C r y r y G C T G A A | T T C A G C R Y R Y G C T G A A |  |
Collection_1_m24_QPTSH_ArsR | QPTSH_ArsR | cluster_7 | Collection_1 | 20 | 12.97 | 74 | A T A T y G A y r r y y r T C r A T A T | A T A T Y G A Y R R Y Y R T C R A T A T |  |
Collection_1_m23_QSKSR_ArsR2 | QSKSR_ArsR2 | cluster_2 | Collection_1 | 22 | 14.16 | 8 | +A T T T K K M H A D H T D K M M A A A T+ | +A T T T k K m h A d h T d k M m A A A T+ |  |
Collection_1_m49_KSTSQ_DMR_45340 | KSTSQ_DMR_45340 | cluster_19 | Collection_1 | 21 | 21.49 | 4 | T w G T T C s k w w w w w m s G A A C w A | T W G T T C S K W W W W W M S G A A C W A |  |
Collection_1_m38_ASHSQ_SutR | ASHSQ_SutR | cluster_14 | Collection_1 | 16 | 18.51 | 10 | A T G A T G r W W y C A T C A T | A T G A T G R W W Y C A T C A T |  |
Collection_1_m30_VSASH_SmtB | VSASH_SmtB | cluster_12 | Collection_1 | 22 | 23.23 | 4 | y r M T T G A W Y A R Y T R W T C A A K y r | Y R M T T G A W Y A R Y T R W T C A A K Y R |  |
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Additional Files

## 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.

- References
  1. Castro-Mondragon JA et al. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. doi: 10.1093/nar/gkx314; Nucleic Acids Research (2017)
  2. Last RSAT release: Nguyen NTT et al. RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research (2018).
- Additional Information
  - Jacques van Helden course
- Contact
  - Jaime Castro-Mondragon - j.a.c.mondragon@ncmm.uio.no
  - Morgane Thomas-Chollier - mthomas@biologie.ens.fr
  - Jacques van Helden - Jacques.van-Helden@univ-amu.fr