# RSAT - matrix-clustering result

### Analysis: test (15/09/2025 17:00)

## 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
56 | 3 | 21 | Download | Download |
average | Ncor | Ncor = 0.4 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 cluster_20 cluster_21
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 | 17 | assembly_12::2:: assembly_3::3:: assembly_7::2:: assembly_2::3:: assembly_2::1:: assembly_9::2:: assembly_4::2:: assembly_19::2:: assembly_6::2:: assembly_4::1:: assembly_2::2:: assembly_3::1:: assembly_15::3:: assembly_1::3:: assembly_8::3:: assembly_3::2:: assembly_5::2:: | 3::5_motifs 1::3_motifs 2::9_motifs | Show matrix
|  | cluster_2 | 5 | assembly_6::3:: assembly_13::1:: assembly_7::1:: assembly_12::1:: assembly_4::3:: | 1::3_motifs 3::2_motifs | Show matrix
|  | cluster_3 | 2 | assembly_5::1:: assembly_11::2:: | 1::1_motif 2::1_motif | Show matrix
|  | cluster_4 | 3 | assembly_10::1:: assembly_1::1:: assembly_1::2:: | 2::1_motif 1::2_motifs | Show matrix
|  | cluster_5 | 2 | assembly_14::1:: assembly_11::3:: | 3::1_motif 1::1_motif | Show matrix
|  | cluster_6 | 2 | assembly_17::2:: assembly_12::3:: | 2::1_motif 3::1_motif | Show matrix
|  | cluster_7 | 3 | assembly_10::2:: assembly_13::3:: assembly_5::3:: | 2::1_motif 3::2_motifs | Show matrix
|  | cluster_8 | 4 | assembly_9::1:: assembly_10::3:: assembly_6::1:: assembly_16::2:: | 2::1_motif 3::1_motif 1::2_motifs | Show matrix
|  | cluster_9 | 2 | assembly_15::2:: assembly_14::3:: | 2::1_motif 3::1_motif | Show matrix
|  | cluster_10 | 2 | assembly_15::1:: assembly_16::3:: | 3::1_motif 1::1_motif | Show matrix
|  | cluster_11 | 2 | assembly_18::1:: assembly_8::2:: | 2::1_motif 1::1_motif | Show matrix
|  | cluster_12 | 3 | assembly_14::2:: assembly_20::1:: assembly_9::3:: | 1::1_motif 3::1_motif 2::1_motif | Show matrix
|  | cluster_13 | 1 | assembly_16::1 | 1 : 1 motif | Show matrix
|  | cluster_14 | 1 | assembly_17::1 | 1 : 1 motif | Show matrix
|  | cluster_15 | 1 | assembly_8::1 | 1 : 1 motif | Show matrix
|  | cluster_16 | 1 | assembly_19::1 | 1 : 1 motif | Show matrix
|  | cluster_17 | 1 | assembly_18::2 | 2 : 1 motif | Show matrix
|  | cluster_18 | 1 | assembly_7::3 | 3 : 1 motif | Show matrix
|  | cluster_19 | 1 | assembly_11::1 | 1 : 1 motif | Show matrix
|  | cluster_20 | 1 | assembly_20::2 | 2 : 1 motif | Show matrix
|  | cluster_21 | 1 | assembly_13::2 | 2 : 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
cluster_20
cluster_21
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
cluster_20
cluster_21
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | ---w w G T G A A G a w----- |  |  | 3::1_motif 2::1_motif | PSSM | 8.53 | 574
Node 2 | ---w r G A G A A G A s a w--- |  |  | 2::1_motif 3::1_motif | PSSM | 7.47 | 1172
Node 3 | w w T T c A A G A A G a A v a w-- |  |  | 2::2_motifs | PSSM | 7.84 | 1254
Node 4 | -r a m G A A G A A G A r r a a-- |  |  | 3::2_motifs | PSSM | 8.54 | 1518
Node 5 | w w w T c A A G A A G A A a w--- |  |  | 2::1_motif 1::1_motif | PSSM | 7.73 | 2665
Node 6 | a r r m G A A G A A G A r r a a-- |  |  | 3::3_motifs | PSSM | 8.66 | 2135
Node 7 | w w w T c A A G A A G A A a w w-- |  |  | 2::3_motifs 1::1_motif | PSSM | 7.69 | 3919
Node 8 | a r r w G A A G A A G A r r a r r a |  |  | 3::3_motifs 1::1_motif | PSSM | 8.64 | 2679
Node 9 | w w w T c A A G A A G A A a w w-- |  |  | 1::1_motif 2::4_motifs | PSSM | 7.54 | 4191
Node 10 | w w a r c m A G A A G A c w w--- |  |  | 2::2_motifs | PSSM | 7.38 | 742
Node 11 | w w t T c A A G A A g a a a w w-- |  |  | 1::1_motif 2::5_motifs | PSSM | 7.15 | 5748
Node 12 | a r a a g A A G A A G A r r a r r a |  |  | 3::3_motifs 1::1_motif 2::2_motifs | PSSM | 7.87 | 3421
Node 13 | w w w t s A A G A A g A a r a r r a |  |  | 1::2_motifs 3::3_motifs 2::7_motifs | PSSM | 6.81 | 9169
Node 14 | ---w w G w G A A G A s a w--- |  |  | 2::2_motifs 3::2_motifs | PSSM | 6.87 | 1746
Node 15 | w w w t s A A G A A g A a r a w a a |  |  | 3::3_motifs 1::3_motifs 2::7_motifs | PSSM | 6.72 | 9488
Node 16 | w w w w s A A G A A G A a r a w a a |  |  | 3::5_motifs 1::3_motifs 2::9_motifs | PSSM | 6.32 | 11234

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w k g A G C T T C C w w |  |  | 1::2_motifs | PSSM | 8.11 | 257
Node 2 | w w k g A G C T T C c w w |  |  | 3::1_motif 1::2_motifs | PSSM | 7.33 | 484
Node 3 | w w a c A G w T T C w w- |  |  | 3::1_motif 1::1_motif | PSSM | 7.05 | 1221
Node 4 | w w a s A G h T T C h w w |  |  | 1::3_motifs 3::2_motifs | PSSM | 6.30 | 1705

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | h d C C G G C G A w d |  |  | 1::1_motif 2::1_motif | PSSM | 6.37 | 488

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | -w w r c A G A G A G A c w w w |  |  | 2::1_motif 1::1_motif | PSSM | 7.79 | 851
Node 2 | r a r r c A G A G A G A c w d w |  |  | 2::1_motif 1::2_motifs | PSSM | 7.89 | 1795

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w a A s A A A G w w |  |  | 3::1_motif 1::1_motif | PSSM | 8.02 | 1511

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w a A C G A m C w w |  |  | 2::1_motif 3::1_motif | PSSM | 7.93 | 267

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w G A G C A A s a w w |  |  | 3::2_motifs | PSSM | 6.30 | 1420
Node 2 | w w r A G C A A C A w w |  |  | 2::1_motif 3::2_motifs | PSSM | 5.95 | 3295

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | ---w w w G C A G C A r w w-- |  |  | 2::1_motif 1::1_motif | PSSM | 5.95 | 1285
Node 2 | ---w w w G C A G C A r a w r- |  |  | 2::1_motif 1::1_motif 3::1_motif | PSSM | 5.79 | 1382
Node 3 | w a A d w w G C A G C A r m a w w |  |  | 2::1_motif 3::1_motif 1::2_motifs | PSSM | 6.52 | 1733

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w m A C G T G G C w w |  |  | 2::1_motif 3::1_motif | PSSM | 6.24 | 730

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w G A C A g A A a w |  |  | 3::1_motif 1::1_motif | PSSM | 5.87 | 3517

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w T m T G A G A w w |  |  | 2::1_motif 1::1_motif | PSSM | 6.10 | 2683

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w T C A A g A C w w- |  |  | 3::1_motif 1::1_motif | PSSM | 6.19 | 2581
Node 2 | w w T C A A g A C w w w |  |  | 1::1_motif 3::1_motif 2::1_motif | PSSM | 6.06 | 2785

cluster_13

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C A A A A G w w |  |  | 1 : 1 motif | PSSM | 8.61 | 1043

cluster_14

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A G G A C A w d |  |  | 1 : 1 motif | PSSM | 8.62 | 263

cluster_15

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A C C A C A A w w |  |  | 1 : 1 motif | PSSM | 6.45 | 3312

cluster_16

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w t C T G C A A w w |  |  | 1 : 1 motif | PSSM | 8.62 | 326

cluster_17

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w A A C A G C T w w |  |  | 2 : 1 motif | PSSM | 6.31 | 1344

cluster_18

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | a w A G A G C C w w |  |  | 3 : 1 motif | PSSM | 8.54 | 127

cluster_19

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w T G A G C T G A w w |  |  | 1 : 1 motif | PSSM | 7.57 | 422

cluster_20

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C T T G G A w w |  |  | 2 : 1 motif | PSSM | 8.57 | 277

cluster_21

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | r w G G A G G A d d |  |  | 2 : 1 motif | PSSM | 8.69 | 201

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3_m2_assembly_2 | assembly_2 | cluster_1 | 3 | 18 | 7.76 | 647 | +++W R G A G A A G A G W W+++ | +++w w C T C T T C T C y w+++ |  |
3_m7_assembly_7 | assembly_7 | cluster_18 | 3 | 10 | 8.54 | 127 | a w A G A G C C w w | W W G G C T C T W T |  |
2_m9_assembly_9 | assembly_9 | cluster_1 | 2 | 18 | 7.12 | 1557 | W W K T T C T T G A A W W+++++ | +++++w w T T C A A G A A m w w |  |
2_m5_assembly_5 | assembly_5 | cluster_1 | 2 | 18 | 8.93 | 263 | w a A g c A A G A A G A c w a+++ | +++T W G T C T T C T T G C T T W |  |
3_m11_assembly_11 | assembly_11 | cluster_5 | 3 | 10 | 8.60 | 560 | a a A C A A A G w w | W W C T T T G T T T |  |
2_m8_assembly_8 | assembly_8 | cluster_11 | 2 | 11 | 8.60 | 524 | +w a A T G A G A w w | W W T C T C A T T W+ |  |
1_m15_assembly_15 | assembly_15 | cluster_10 | 1 | 11 | 6.56 | 2682 | w w G A C A G A A a a | T T T T C T G T C W W |  |
2_m1_assembly_1 | assembly_1 | cluster_4 | 2 | 16 | 8.45 | 354 | +a a a c A G A G A G A c T w w | W W A G T C T C T C T G T T T+ |  |
2_m14_assembly_14 | assembly_14 | cluster_12 | 2 | 12 | 7.73 | 204 | W W G G C G T T G A W R | y w T C A A C G C C w w |  |
2_m16_assembly_16 | assembly_16 | cluster_8 | 2 | 17 | 6.23 | 891 | +++w w T G C A G C A w w+++ | +++W W T G C T G C A W W+++ |  |
1_m4_assembly_4 | assembly_4 | cluster_1 | 1 | 18 | 7.72 | 2191 | +w w T c A A G A A G A A a w+++ | +++W T T T C T T C T T G A W W+ |  |
2_m17_assembly_17 | assembly_17 | cluster_6 | 2 | 10 | 8.61 | 169 | w a A C G A A C w w | W W G T T C G T T W |  |
1_m12_assembly_12 | assembly_12 | cluster_2 | 1 | 13 | 8.53 | 620 | ++w a A G A T T C w w+ | +W W G A A T C T T W++ |  |
2_m18_assembly_18 | assembly_18 | cluster_17 | 2 | 11 | 6.31 | 1344 | w w A A C A G C T w w | W W A G C T G T T W W |  |
1_m3_assembly_3 | assembly_3 | cluster_1 | 1 | 18 | 9.31 | 544 | +T Y Y T C Y T C T T C T T C A W H | d w t G A A G A A G A r G A r r a+ |  |
3_m13_assembly_13 | assembly_13 | cluster_7 | 3 | 12 | 6.42 | 947 | w w G A G C A A C w w+ | +W W G T T G C T C W W |  |
1_m19_assembly_19 | assembly_19 | cluster_16 | 1 | 10 | 8.62 | 326 | w t C T G C A A w w | W W T T G C A G A W |  |
1_m14_assembly_14 | assembly_14 | cluster_5 | 1 | 10 | 8.76 | 951 | w a A G A A A G w w | W W C T T T C T T W |  |
1_m1_assembly_1 | assembly_1 | cluster_4 | 1 | 16 | 7.92 | 497 | +w d G c A G A G A G A c w w+ | +W W G T C T C T C T G C H W+ |  |
2_m15_assembly_15 | assembly_15 | cluster_9 | 2 | 11 | 6.43 | 621 | w m A C G T G G C w w | W W G C C A C G T K W |  |
3_m6_assembly_6 | assembly_6 | cluster_2 | 3 | 13 | 7.61 | 227 | W W G G A G C T T C W W+ | +w w G A A G C T C C w w |  |
3_m10_assembly_10 | assembly_10 | cluster_8 | 3 | 17 | 7.74 | 97 | ++++Y W T C T G C G G C T R+ | +y a G C C G C A G A w r++++ |  |
1_m8_assembly_8 | assembly_8 | cluster_15 | 1 | 11 | 6.45 | 3312 | w a A C C A C A A w w | W W T T G T G G T T W |  |
1_m5_assembly_5 | assembly_5 | cluster_3 | 1 | 11 | 6.25 | 412 | h d C C G G C G A w w | W W T C G C C G G H D |  |
1_m9_assembly_9 | assembly_9 | cluster_8 | 1 | 17 | 8.94 | 351 | W W T G C T G C T G T T T C T T W | w a A G A A A c A G c A g c A w w |  |
2_m12_assembly_12 | assembly_12 | cluster_1 | 2 | 18 | 8.59 | 289 | +++W W G T G A A G A W+++++ | +++++w t C T T C A C w w+++ |  |
1_m17_assembly_17 | assembly_17 | cluster_14 | 1 | 10 | 8.62 | 263 | w a A G G A C A w d | H W T G T C C T T W |  |
2_m19_assembly_19 | assembly_19 | cluster_1 | 2 | 18 | 8.23 | 795 | w w T T c A A G A A G A A m w w++ | ++W W K T T C T T C T T G A A W W |  |
2_m3_assembly_3 | assembly_3 | cluster_1 | 2 | 18 | 7.45 | 479 | +w w a m C A G A A G A c w w+++ | +++W W G T C T T C T G K T W W+ |  |
1_m18_assembly_18 | assembly_18 | cluster_11 | 1 | 11 | 6.29 | 2159 | w w T C T G A G A w w | W W T C T C A G A W W |  |
1_m16_assembly_16 | assembly_16 | cluster_13 | 1 | 10 | 8.61 | 1043 | w w C A A A A G w w | W W C T T T T G W W |  |
2_m4_assembly_4 | assembly_4 | cluster_1 | 2 | 18 | 8.41 | 272 | D W T T C A A G A A G C T W W+++ | +++w w A G C T T C T T G A A w h |  |
1_m2_assembly_2 | assembly_2 | cluster_1 | 1 | 18 | 8.88 | 319 | T W T G A K C T T C T T C T C W W+ | +w w G A G A A G A A G m T c A w a |  |
1_m7_assembly_7 | assembly_7 | cluster_2 | 1 | 13 | 8.95 | 105 | w w T G A G C T T C C w w | W W G G A A G C T C A W W |  |
1_m11_assembly_11 | assembly_11 | cluster_19 | 1 | 12 | 7.57 | 422 | w w T G A G C T G A w w | W W T C A G C T C A W W |  |
2_m20_assembly_20 | assembly_20 | cluster_20 | 2 | 10 | 8.57 | 277 | w w C T T G G A w w | W W T C C A A G W W |  |
2_m10_assembly_10 | assembly_10 | cluster_7 | 2 | 12 | 6.34 | 1875 | +W W T G T T G C T T W | w a A G C A A C A w w+ |  |
3_m15_assembly_15 | assembly_15 | cluster_1 | 3 | 18 | 9.27 | 617 | a r r A G A A G A A G A r r a+++ | +++T Y Y T C T T C T T C T Y Y T |  |
2_m6_assembly_6 | assembly_6 | cluster_1 | 2 | 18 | 8.10 | 459 | w w T T c A A G A A G m A r a w++ | ++W T Y T K C T T C T T G A A W W |  |
3_m4_assembly_4 | assembly_4 | cluster_2 | 3 | 13 | 7.83 | 601 | w w A C A G T T T C w w+ | +W W G A A A C T G T W W |  |
3_m12_assembly_12 | assembly_12 | cluster_6 | 3 | 10 | 8.58 | 98 | w a A C G A C C a w | W T G G T C G T T W |  |
1_m13_assembly_13 | assembly_13 | cluster_2 | 1 | 13 | 8.36 | 152 | W W G G A G C T T C C W W | w w G G A A G C T c c w w |  |
3_m3_assembly_3 | assembly_3 | cluster_1 | 3 | 18 | 8.49 | 285 | +++W W G T G A A G W W+++++ | +++++w w C T T C A C w w+++ |  |
1_m20_assembly_20 | assembly_20 | cluster_12 | 1 | 12 | 6.36 | 2293 | w w T C A A G A C w w+ | +W W G T C T T G A W W |  |
3_m14_assembly_14 | assembly_14 | cluster_9 | 3 | 11 | 8.55 | 109 | +m w C G T G A C w w | W W G T C A C G W K+ |  |
3_m1_assembly_1 | assembly_1 | cluster_1 | 3 | 18 | 8.38 | 732 | +R A M G A A G A A G A R R A+++ | +++t y y T C T T C T T C k t y+ |  |
1_m6_assembly_6 | assembly_6 | cluster_8 | 1 | 17 | 7.18 | 394 | +++d a A G C A G C A G m w++ | ++W K C T G C T G C T T H+++ |  |
1_m10_assembly_10 | assembly_10 | cluster_4 | 1 | 16 | 8.47 | 944 | Y T S T C T C T C T S T C T Y+ | +r a g A s A G A G A G A s a r |  |
3_m8_assembly_8 | assembly_8 | cluster_1 | 3 | 18 | 8.97 | 786 | +R A M G A A G A A G A M G A A++ | ++t t c k T C T T C T T C k t y+ |  |
3_m5_assembly_5 | assembly_5 | cluster_7 | 3 | 12 | 7.69 | 473 | w w G A G C A A G A a w | W T T C T T G C T C W W |  |
3_m9_assembly_9 | assembly_9 | cluster_12 | 3 | 12 | 8.72 | 288 | +w w C A A C A C w w+ | +W W G T G T T G W W+ |  |
2_m7_assembly_7 | assembly_7 | cluster_1 | 2 | 18 | 7.83 | 525 | +++W W G A G A A G A C A W+++ | +++w t g T C T T C T C w w+++ |  |
2_m2_assembly_2 | assembly_2 | cluster_1 | 2 | 18 | 8.38 | 474 | w w t T C A A G A A G A m a w+++ | +++W T K T C T T C T T G A A W W |  |
2_m11_assembly_11 | assembly_11 | cluster_3 | 2 | 11 | 8.46 | 76 | +r r C G G C G A k d | H M T C G C C G Y Y+ |  |
2_m13_assembly_13 | assembly_13 | cluster_21 | 2 | 10 | 8.69 | 201 | r w G G A G G A d d | H H T C C T C C W Y |  |
3_m16_assembly_16 | assembly_16 | cluster_10 | 3 | 11 | 6.37 | 835 | w w G A C A C A G w w | W W C T G T G T C W W |  |
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.
Heatmap View ## Heatmap View Distance table | PDF

Cluster composition by collection
Collections Overlap

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.
Collections Complementarity | A dynamic heatmap showing how many motifs contribute each collection to each 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