ESEfinder


Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang and Adrian R. Krainer





Initially only the high-scores (values above the selected threshold) are displayed in a table format, divided by matrix used.

If multiple sequences were submitted, multiple tables are provided.

The threshold applied is indicated for each matrix.

Clicking the button will open a new window with a table comprising all matrix scores referring to that sequence, with no threshold applied.

Clicking the button will open a new window with a graphic representation of the high scores.

EXAMPLE OF OUTPUT:

ESEfinder Analysis Results

Thu Feb 13 17:02:53 2003

Protein: SF2/ASF SC35 SRp40 SRp55

Seqence ID: Seq#1 BRCA1 wt
Sequence:
ATGCTGAGTTTGTGTGTGAACGGACACTGAAATATTTTCTAGGAATTGCG
GGAGGAAAATGGGTAGTTAGCTATTTCT

Length=78

Threshold applied
  SF2/ASF
Thr=1.956		     SC35
Thr=2.383		     SRp40
Thr=2.67		     SRp55
Thr=2.676		  
Position Motif Score       Position Motif Score       Position Motif Score       Position Motif Score      
4
23
50		 CTGAGTT
GACACTG
GGGAGGA		 2.142950
2.164970
3.714214		 22
43		 GGACACTG
GAATTGCG		 4.968561
2.530293		 36 TTTCTAG 4.151518 11
13
47
60		 TGTGTG
TGTGTG
TGCGGG
TGGGTA		 2.820871
2.820871
3.558695
2.708481

Seqence ID: Seq#2 BRCA1 E1694X
Sequence:
ATGCTTAGTTTGTGTGTGAACGGACACTGAAATATTTTCTAGGAATTGCG
GGAGGAAAATGGGTAGTTAGCTATTTCT

Length=78

Threshold applied
  SF2/ASF
Thr=1.956		     SC35
Thr=2.383		     SRp40
Thr=2.67		     SRp55
Thr=2.676		  
Position Motif Score       Position Motif Score       Position Motif Score       Position Motif Score      
23
50		 GACACTG
GGGAGGA		 2.164970
3.714214		 22
43		 GGACACTG
GAATTGCG		 4.968561
2.530293		 36 TTTCTAG 4.151518 2
11
13
47
60		 TGCTTA
TGTGTG
TGTGTG
TGCGGG
TGGGTA		 3.466667
2.820871
2.820871
3.558695
2.708481

Thank you for using ESE Finder!

 

A NEW WINDOW WITH THE ENTIRE SET OF SCORES FOR THE SELECTED SEQUENCE WILL OPEN.

 

Sequence ID: Seq#1 BRCA1 WT
All Scores
  SF2/ASF     SC35     SRp40     SRp55  
Position Motif Score             Position Motif Score             Position Motif Score             Position Motif Score            
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72		 ATGCTGA
TGCTGAG
GCTGAGT
CTGAGTT
TGAGTTT
GAGTTTG
AGTTTGT
GTTTGTG
TTTGTGT
TTGTGTG
TGTGTGT
GTGTGTG
TGTGTGA
GTGTGAA
TGTGAAC
GTGAACG
TGAACGG
GAACGGA
AACGGAC
ACGGACA
CGGACAC
GGACACT
GACACTG
ACACTGA
CACTGAA
ACTGAAA
CTGAAAT
TGAAATA
GAAATAT
AAATATT
AATATTT
ATATTTT
TATTTTC
ATTTTCT
TTTTCTA
TTTCTAG
TTCTAGG
TCTAGGA
CTAGGAA
TAGGAAT
AGGAATT
GGAATTG
GAATTGC
AATTGCG
ATTGCGG
TTGCGGG
TGCGGGA
GCGGGAG
CGGGAGG
GGGAGGA
GGAGGAA
GAGGAAA
AGGAAAA
GGAAAAT
GAAAATG
AAAATGG
AAATGGG
AATGGGT
ATGGGTA
TGGGTAG
GGGTAGT
GGTAGTT
GTAGTTA
TAGTTAG
AGTTAGC
GTTAGCT
TTAGCTA
TAGCTAT
AGCTATT
GCTATTT
CTATTTC
TATTTCT		 -0.802126
-3.168125
-4.809234
2.142950
-7.024210
-3.055857
-4.001171
-4.322554
-5.579483
-3.631949
-4.904181
-2.258769
-4.550941
-1.989695
-9.335317
-2.185219
0.154582
1.104103
-4.213166
-5.897824
1.111260
-4.193708
2.164970
-3.468842
0.956366
-7.961609
-0.234370
-3.762392
-2.752938
-5.673978
-3.223108
-6.796502
-7.972679
-7.254210
-4.364837
-6.615732
-3.185302
-1.000984
-2.933881
-4.970911
-1.606545
-3.115994
-4.479470
-4.585616
-2.983996
-0.054598
-0.321314
-3.777116
-0.263451
3.714214
-3.835886
-3.244491
-1.711013
-3.200160
-2.668772
-1.476621
-2.007879
-2.092045
-2.917573
-5.791675
-1.009508
-0.822840
-5.973092
-4.886745
-5.854570
-1.955850
-4.822545
-3.055881
-3.811185
-4.020685
-6.144716
-6.576988		 1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71		 ATGCTGAG
TGCTGAGT
GCTGAGTT
CTGAGTTT
TGAGTTTG
GAGTTTGT
AGTTTGTG
GTTTGTGT
TTTGTGTG
TTGTGTGT
TGTGTGTG
GTGTGTGA
TGTGTGAA
GTGTGAAC
TGTGAACG
GTGAACGG
TGAACGGA
GAACGGAC
AACGGACA
ACGGACAC
CGGACACT
GGACACTG
GACACTGA
ACACTGAA
CACTGAAA
ACTGAAAT
CTGAAATA
TGAAATAT
GAAATATT
AAATATTT
AATATTTT
ATATTTTC
TATTTTCT
ATTTTCTA
TTTTCTAG
TTTCTAGG
TTCTAGGA
TCTAGGAA
CTAGGAAT
TAGGAATT
AGGAATTG
GGAATTGC
GAATTGCG
AATTGCGG
ATTGCGGG
TTGCGGGA
TGCGGGAG
GCGGGAGG
CGGGAGGA
GGGAGGAA
GGAGGAAA
GAGGAAAA
AGGAAAAT
GGAAAATG
GAAAATGG
AAAATGGG
AAATGGGT
AATGGGTA
ATGGGTAG
TGGGTAGT
GGGTAGTT
GGTAGTTA
GTAGTTAG
TAGTTAGC
AGTTAGCT
GTTAGCTA
TTAGCTAT
TAGCTATT
AGCTATTT
GCTATTTC
CTATTTCT		 -0.953327
-2.583471
-2.499387
-6.117111
-1.795063
-3.516036
2.225263
-2.202658
-1.187285
-5.990942
-0.539607
-2.131028
-2.012614
-2.192189
-1.258708
-1.994153
-2.992015
-0.016143
-1.628218
-6.097903
-4.763975
4.968561
-1.106249
-1.494733
0.183969
-5.636057
-3.429356
-4.791516
-1.914222
-1.364387
-3.676763
-1.938039
-2.151473
2.042998
0.202439
-1.170634
-0.634126
-4.187132
-5.391111
-4.973930
-2.507559
-4.325592
2.530293
0.321279
-2.450477
-3.136123
-1.132224
-5.084615
-4.740194
-1.840052
-0.904647
-2.137127
-5.338619
0.993624
-2.139450
-3.364642
-3.295948
-1.191223
-4.603612
-7.219907
0.265351
0.107995
-1.416210
-5.113459
-0.392519
1.189332
-4.966779
-2.562615
0.007147
-3.599919
-2.858921		 1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72		 ATGCTGA
TGCTGAG
GCTGAGT
CTGAGTT
TGAGTTT
GAGTTTG
AGTTTGT
GTTTGTG
TTTGTGT
TTGTGTG
TGTGTGT
GTGTGTG
TGTGTGA
GTGTGAA
TGTGAAC
GTGAACG
TGAACGG
GAACGGA
AACGGAC
ACGGACA
CGGACAC
GGACACT
GACACTG
ACACTGA
CACTGAA
ACTGAAA
CTGAAAT
TGAAATA
GAAATAT
AAATATT
AATATTT
ATATTTT
TATTTTC
ATTTTCT
TTTTCTA
TTTCTAG
TTCTAGG
TCTAGGA
CTAGGAA
TAGGAAT
AGGAATT
GGAATTG
GAATTGC
AATTGCG
ATTGCGG
TTGCGGG
TGCGGGA
GCGGGAG
CGGGAGG
GGGAGGA
GGAGGAA
GAGGAAA
AGGAAAA
GGAAAAT
GAAAATG
AAAATGG
AAATGGG
AATGGGT
ATGGGTA
TGGGTAG
GGGTAGT
GGTAGTT
GTAGTTA
TAGTTAG
AGTTAGC
GTTAGCT
TTAGCTA
TAGCTAT
AGCTATT
GCTATTT
CTATTTC
TATTTCT		 -0.273530
-2.399717
-1.333269
-5.481014
-0.871477
-5.708351
-1.606131
-4.501006
0.613287
-3.558190
0.103796
-6.062528
0.103796
-6.989545
1.320792
-0.975433
2.196855
-3.382945
-5.076832
-1.745693
-2.179103
0.311162
-6.170750
2.647323
-6.583315
-0.446379
-1.471734
-0.470452
-3.210964
-3.780845
-4.258239
-2.071913
-2.485128
-1.402261
-3.560820
4.151518
1.232164
-1.228193
-1.572797
-3.224996
-4.128868
-0.838780
-1.919643
-3.284018
0.454153
0.848990
-3.553316
-3.635445
0.813041
-6.115600
-4.229931
-5.729334
-2.674149
-1.520071
-2.038221
1.193320
-1.931122
-4.699825
-6.329237
0.356181
-4.376646
-6.576626
-2.866324
-1.749294
0.178694
-4.350208
-1.853237
-1.746398
-4.731230
-3.446244
0.160110
-2.307300		 1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73		 ATGCTG
TGCTGA
GCTGAG
CTGAGT
TGAGTT
GAGTTT
AGTTTG
GTTTGT
TTTGTG
TTGTGT
TGTGTG
GTGTGT
TGTGTG
GTGTGA
TGTGAA
GTGAAC
TGAACG
GAACGG
AACGGA
ACGGAC
CGGACA
GGACAC
GACACT
ACACTG
CACTGA
ACTGAA
CTGAAA
TGAAAT
GAAATA
AAATAT
AATATT
ATATTT
TATTTT
ATTTTC
TTTTCT
TTTCTA
TTCTAG
TCTAGG
CTAGGA
TAGGAA
AGGAAT
GGAATT
GAATTG
AATTGC
ATTGCG
TTGCGG
TGCGGG
GCGGGA
CGGGAG
GGGAGG
GGAGGA
GAGGAA
AGGAAA
GGAAAA
GAAAAT
AAAATG
AAATGG
AATGGG
ATGGGT
TGGGTA
GGGTAG
GGTAGT
GTAGTT
TAGTTA
AGTTAG
GTTAGC
TTAGCT
TAGCTA
AGCTAT
GCTATT
CTATTT
TATTTC
ATTTCT		 -5.184310
2.652795
-4.897574
-4.044608
1.435138
-5.209255
-1.369876
-6.207977
0.516899
-4.909171
2.820871
-7.718439
2.820871
-5.522603
1.613738
-5.253385
-0.980963
-4.302870
2.461332
-3.722232
-1.336133
-3.722232
-3.056990
-4.261817
1.213386
-2.577009
-3.640105
-1.778727
-0.395614
-5.969474
-1.080988
-5.059581
-0.889525
-1.910537
-5.190042
-0.389001
-2.840582
-0.905633
-0.317619
-0.505384
-4.587995
-1.982790
-3.488998
-1.029097
-3.975081
-4.111407
3.558695
-3.218631
-2.125545
-2.921391
0.007834
-3.314652
-2.392159
-2.392159
-5.196655
-0.871193
-3.380377
-0.488436
-4.491974
2.708481
-6.408036
-2.208693
-3.678102
-0.204151
-3.975081
-1.951590
-3.474039
-0.204151
-3.221149
-3.698793
-4.003555
1.671550
-7.076817

Thank you for using ESE Finder!

 


web site created and mantained by Luca Cartegni (cartegni@cshl.edu). CGI-scripts implemented by Jinhua Wang (wang@cshl.edu)

 

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