Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3433
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50596
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:14462 original size:9 final size:9
Alignment explanation
Indices: 14448--14551 Score: 59
Period size: 9 Copynumber: 11.3 Consensus size: 9
14438 TTTTGGTTAA
14448 AAATTACCC
1 AAATTACCC
14457 AAATTACCC
1 AAATTACCC
14466 AAATTACCC
1 AAATTACCC
* *
14475 -GATTAACC
1 AAATTACCC
*
14483 GAATTACCC
1 AAATTACCC
* * *
14492 -GATTAACT
1 AAATTACCC
* **
14500 GAATTAATC
1 AAATTACCC
*
14509 GAATTACCC
1 AAATTACCC
14518 GAAAATTACCC
1 --AAATTACCC
*
14529 GAATTACCC
1 AAATTACCC
14538 GAAAATTACCC
1 --AAATTACCC
14549 AAA
1 AAA
14552 AAGTTCAGTG
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
8 11 0.15
9 47 0.64
11 16 0.22
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (9 bp):
AAATTACCC
Found at i:14487 original size:17 final size:17
Alignment explanation
Indices: 14467--14505 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
14457 AAATTACCCA
14467 AATTACCCGATTAACCG
1 AATTACCCGATTAACCG
*
14484 AATTACCCGATTAACTG
1 AATTACCCGATTAACCG
14501 AATTA
1 AATTA
14506 ATCGAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (17 bp):
AATTACCCGATTAACCG
Found at i:14553 original size:11 final size:11
Alignment explanation
Indices: 14510--14552 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
14500 GAATTAATCG
14510 AATTACCCGAA
1 AATTACCCGAA
14521 AATTACCCG--
1 AATTACCCGAA
14530 AATTACCCGAA
1 AATTACCCGAA
14541 AATTACCC-AA
1 AATTACCCGAA
14551 AA
1 AA
14553 AGTTCAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.30
10 4 0.13
11 17 0.57
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (11 bp):
AATTACCCGAA
Found at i:19449 original size:24 final size:24
Alignment explanation
Indices: 19404--19449 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
19394 AGAACAATCC
* * *
19404 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAACAGCTT
*
19428 CAAAAGCAAATGAATGAACAGC
1 CAAAAGCAAATGAAGGAACAGC
19450 AAAAGATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAACAGCTT
Found at i:27631 original size:45 final size:44
Alignment explanation
Indices: 27580--28044 Score: 305
Period size: 45 Copynumber: 10.7 Consensus size: 44
27570 GATCGCATTT
*
27580 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAGTAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAA-CA
**
27625 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AACA
* * * * ***
27670 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAACA
* * * * *
27715 A-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA--AACCTC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAC-A
* * * * * *
27757 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG-CATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
* * *
27798 AGTCTTATCTCCCTGAAGTTGCAATGGAGTAGACTAAGTAAAGAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAA-CA
* * * ***
27843 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAACA
* * * * * *
27888 A-TCCTATCTCCCTGAAGTTGCAG-AGAGCAGA-T-TG-CATCT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
* *
27927 AGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAAAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGT-AAACA
* * * ***
27972 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAACA
*
28017 A-TCCTATCTCCCTGAAGTTGCAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
28045 TGGATTAAAA
Statistics
Matches: 327, Mismatches: 69, Indels: 49
0.73 0.16 0.11
Matches are distributed among these distances:
39 3 0.01
40 41 0.13
41 16 0.05
42 7 0.02
43 16 0.05
44 99 0.30
45 132 0.40
46 13 0.04
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
Found at i:27725 original size:44 final size:44
Alignment explanation
Indices: 27582--28053 Score: 332
Period size: 44 Copynumber: 10.8 Consensus size: 44
27572 TCGCATTTAG
* * ***
27582 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACT-AAGTAAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-CAA
* * ** *
27626 GTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCCGAC-AA
* *
27672 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
* * * *
27716 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC-TCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-A
* * * *
27760 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CG-C-ATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-C-AA
* * * ** *
27800 TCTTATCTCCCTGAAGTTGCAATGGAGTAGACT-AAGTAAAGAAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--CCGACAA
*
27845 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
* * *
27889 TCCTATCTCCCTGAAGTTGCAG-AGAGCAGATT---G-C-ATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-C-AA
* * *** *
27929 TTTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAAAAAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--CCGACAA
*
27974 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
* **
28018 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
28054 ACCTTAGATC
Statistics
Matches: 337, Mismatches: 63, Indels: 55
0.74 0.14 0.12
Matches are distributed among these distances:
38 1 0.00
39 3 0.01
40 43 0.13
41 15 0.04
42 2 0.01
43 18 0.05
44 120 0.36
45 119 0.35
46 14 0.04
47 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
Found at i:27870 original size:129 final size:129
Alignment explanation
Indices: 27714--28039 Score: 519
Period size: 129 Copynumber: 2.5 Consensus size: 129
27704 TAAAGCCGAC
* * * * * *
27714 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC-TCAGATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-ATCCTATCTCCCTGAAGTT
* *
27778 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGTAGACTAAGTAAAGAA
65 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAAAAA
*
27843 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
* * *
27908 CAGAGAGCAGATTGCATCTAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAAAA
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAAAAA
*
27972 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
28037 CAG
66 CAG
28040 TGGAGTGGAT
Statistics
Matches: 182, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
129 180 0.99
130 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (129 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAAAAA
Found at i:28027 original size:173 final size:172
Alignment explanation
Indices: 27496--28135 Score: 639
Period size: 173 Copynumber: 3.7 Consensus size: 172
27486 GTGGCCAAAT
* * * * * ** *
27496 AATCCTATCTCCTTGAAGTTGCAATGGAGCGGATTAAAACC-TCAGATCTTATCTCTTTGAAGTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGACA-ATCCTATCTCCCTGAAGTT
* * *
27560 GCAGAGAGCAGATCGCATTTAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAGTAAAGCA
65 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAACA
* * *
27625 AGTCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGC
130 AGTCTTATCTC-CCTGAAGTTGCAGTGAAGCAGACT-AAGAAGAC
* * * *
27669 AAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTT
1 -AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGACAATCCTATCTCCCTGAAGTT
* * *** * * * * *
27734 GCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG--C
65 GCAG-AGAGCAGA-TCGCATCT-AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
* * * * * *
27794 ATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGTAGACTAAGTAAAGAA
126 AACAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAG--AAGAC
* * *
27843 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGACAATCCTATCTCCCTGAAGTTG
* * *
27908 CAGAGAGCAGATTGCATCTAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAAAAA
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAACAA
* * **
27973 ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGAC
131 GTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACT-AAGAAGAC
** * * * * *
28016 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTA-GATCTTATTTCTCTGAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-GACAATCCTATCTCCCTGAAGTT
* *
28080 GCAGAGAGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCATACTA
65 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
28136 GCAGATCAAG
Statistics
Matches: 381, Mismatches: 70, Indels: 31
0.79 0.15 0.06
Matches are distributed among these distances:
169 20 0.05
170 9 0.02
171 5 0.01
172 10 0.03
173 202 0.53
174 90 0.24
175 12 0.03
176 4 0.01
177 8 0.02
178 21 0.06
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (172 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGACAATCCTATCTCCCTGAAGTTG
CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAACAA
GTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGAAGAC
Found at i:28803 original size:6 final size:6
Alignment explanation
Indices: 28792--28827 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
28782 CTGTCATCTA
28792 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
28828 ATACTGATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:29715 original size:22 final size:22
Alignment explanation
Indices: 29673--29715 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29663 TACGTATATT
*
29673 TATTTATAATATTGTAATTTAA
1 TATTTATAATATTATAATTTAA
*
29695 TATTTAT-ATATATATATTTTA
1 TATTTATAATAT-TATAATTTA
29716 TGTATCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTTATAATATTATAATTTAA
Found at i:29718 original size:55 final size:55
Alignment explanation
Indices: 29616--29719 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 55
29606 TTAATTAGTT
* *
29616 TTTATTTATATATATTTATTTATTTATTTAACAAATATTTTTATATGTACGTATA
1 TTTATTTATATATATTTATTTATATATTTAACAAATATATTTATATGTACGTATA
* *
29671 TTTATTTATA-ATATTGTAATTTA-ATATTTATATATATATATTT-TATGTA
1 TTTATTTATATATATT-T-ATTTATATATTTA-ACAAATATATTTATATGTA
29720 TCCATTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
54 5 0.12
55 23 0.55
56 14 0.33
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (55 bp):
TTTATTTATATATATTTATTTATATATTTAACAAATATATTTATATGTACGTATA
Found at i:32175 original size:23 final size:23
Alignment explanation
Indices: 32149--32204 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
32139 TTTTTGTGCA
32149 TTTTT-ATATTGTTTTGCTATCG
1 TTTTTAATATTGTTTTGCTATCG
* * *
32171 TTTTTAATGTTGTTTTGCTGTTG
1 TTTTTAATATTGTTTTGCTATCG
32194 TTTTTAATATT
1 TTTTTAATATT
32205 ATTTGGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.66
Consensus pattern (23 bp):
TTTTTAATATTGTTTTGCTATCG
Found at i:33540 original size:17 final size:18
Alignment explanation
Indices: 33518--33589 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 18
33508 CCAAATAAGT
33518 AATAAA-TAATAAAATAA
1 AATAAACTAATAAAATAA
*
33535 AATAAAGTAAT-AAATAA
1 AATAAACTAATAAAATAA
* * *
33552 AGTAAACAAAGAAAATAA
1 AATAAACTAATAAAATAA
33570 TAA-AAA-TAATAAAAATAA
1 -AATAAACTAAT-AAAATAA
33588 AA
1 AA
33590 ATTGGGTTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
17 23 0.52
18 20 0.45
19 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (18 bp):
AATAAACTAATAAAATAA
Found at i:33571 original size:21 final size:21
Alignment explanation
Indices: 33521--33574 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
33511 AATAAGTAAT
*
33521 AAATAATAAAATAAAATAAAG
1 AAATAATAAAATAAAACAAAG
* *
33542 TAATAAATAAAGT-AAACAAAG
1 AAAT-AATAAAATAAAACAAAG
33563 AAAATAATAAAA
1 -AAATAATAAAA
33575 ATAATAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (21 bp):
AAATAATAAAATAAAACAAAG
Found at i:33575 original size:9 final size:9
Alignment explanation
Indices: 33563--33587 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33553 GTAAACAAAG
33563 AAAATAATA
1 AAAATAATA
33572 AAAATAATA
1 AAAATAATA
33581 AAAATAA
1 AAAATAA
33588 AAATTGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAATA
Found at i:33582 original size:25 final size:26
Alignment explanation
Indices: 33510--33589 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 26
33500 ATTAATATCC
33510 AAATAAGTAATAAATAATAAAATAAAAT
1 AAATAA-TAA-AAATAATAAAATAAAAT
* *
33538 AAAGTAATAAATAA-AGTAAACA-AAGA-
1 AAA-TAATAAA-AATAATAAA-ATAAAAT
33564 AAATAATAAAAATAATAAAAATAAAA
1 AAATAATAAAAATAAT-AAAATAAAA
33590 ATTGGGTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
24 2 0.05
25 10 0.24
26 9 0.21
27 9 0.21
28 9 0.21
29 3 0.07
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (26 bp):
AAATAATAAAAATAATAAAATAAAAT
Found at i:35066 original size:21 final size:20
Alignment explanation
Indices: 35042--35087 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
35032 TGGAATTTTT
* *
35042 ACATTTGTGTTGCATTTGAAG
1 ACATTTATGATGCATTTG-AG
*
35063 ACATTTATGATGTATTTGAG
1 ACATTTATGATGCATTTGAG
35083 ACATT
1 ACATT
35088 GTTTGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (20 bp):
ACATTTATGATGCATTTGAG
Found at i:36341 original size:31 final size:30
Alignment explanation
Indices: 36247--36349 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 30
36237 TTTGGAAATT
* * * *
36247 TTACATTT-TATCTATTAATTCAATAGAAG
1 TTACATTTATATATTTTAATTCCATGGAAG
* **
36276 TTACATTT-TATAGATTTAATTCCATTTAAG
1 TTACATTTATATA-TTTTAATTCCATGGAAG
*
36306 TTACATTTATATATTTTAATTTGCATGGAAG
1 TTACATTTATATATTTTAA-TTCCATGGAAG
36337 TTACA-TTATATAT
1 TTACATTTATATAT
36350 GGAGTTTATA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
29 11 0.18
30 33 0.54
31 17 0.28
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.49
Consensus pattern (30 bp):
TTACATTTATATATTTTAATTCCATGGAAG
Found at i:39090 original size:13 final size:13
Alignment explanation
Indices: 39072--39098 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39062 TTTAATTTTC
39072 AAAATTTAAAAAA
1 AAAATTTAAAAAA
39085 AAAATTTAAAAAA
1 AAAATTTAAAAAA
39098 A
1 A
39099 TAAAAATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATTTAAAAAA
Found at i:39136 original size:30 final size:30
Alignment explanation
Indices: 39102--39203 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
39092 AAAAAAATAA
*
39102 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-CT
* *
39132 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTCT
* * *
39162 AAATTTCACTTAGACCCCTAAACCTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTC-TCT
39192 AAATTTCATTTT
1 AAATTTCATTTT
39204 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
30 59 0.97
31 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTCT
Found at i:40414 original size:21 final size:20
Alignment explanation
Indices: 40390--40434 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40380 GATTTGTGTT
*
40390 AAATACAGTATTTTTAAAGAA
1 AAAT-CAGTATTTTTAAAAAA
* *
40411 AAATCATTTTTTTTAAAAAA
1 AAATCAGTATTTTTAAAAAA
40431 AAAT
1 AAAT
40435 TCATGTCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
AAATCAGTATTTTTAAAAAA
Found at i:40570 original size:16 final size:16
Alignment explanation
Indices: 40522--40570 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
40512 TTTCTTTCTA
*
40522 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
40538 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
40555 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
40571 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:40607 original size:20 final size:20
Alignment explanation
Indices: 40569--40605 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
40559 ATTCGTGTTT
40569 TCGTGTTTTCAAAAAAAATC
1 TCGTGTTTTCAAAAAAAATC
40589 TCGTG-TTTCAAAAAAAA
1 TCGTGTTTTCAAAAAAAA
40606 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (20 bp):
TCGTGTTTTCAAAAAAAATC
Found at i:40707 original size:18 final size:18
Alignment explanation
Indices: 40686--41119 Score: 202
Period size: 18 Copynumber: 25.0 Consensus size: 18
40676 AAATTTTGTG
40686 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
40704 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
40722 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
40740 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
40757 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT--TCAAAAA
* *
40777 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
40795 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
40812 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
40830 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
40846 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
40864 TTCTCGCGTTTAAAAAAAA
1 TTTTCGTGTTT-TCAAAAA
**
40883 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
40901 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
40915 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
40930 ---TCGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
40945 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
40962 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
40979 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
40996 TTCCCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
41015 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* * *
41033 ATTTCATTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
41052 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
41069 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
41085 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
41103 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
41120 AAAACTTTCG
Statistics
Matches: 314, Mismatches: 66, Indels: 73
0.69 0.15 0.16
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 6 0.02
15 6 0.02
16 21 0.07
17 103 0.33
18 118 0.38
19 33 0.11
20 20 0.06
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:40767 original size:17 final size:17
Alignment explanation
Indices: 40686--41119 Score: 190
Period size: 17 Copynumber: 25.0 Consensus size: 17
40676 AAATTTTGTG
40686 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
40704 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
*
40722 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTG-TTTCAAAAA
* * *
40740 TTCTGGCGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
*
40757 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT---CAAAAA
* *
40777 TTTACGTGTTTTCACAAA
1 TTTTCGTG-TTTCAAAAA
*
40795 TTTTCGTGTTTCACAAA
1 TTTTCGTGTTTCAAAAA
*
40812 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
40830 -CTCCAGTGTTTC-AAAG
1 TTTTC-GTGTTTCAAAAA
* *
40846 TTTCCATGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
40864 TTCTCGCGTTTAAAAAAAA
1 TTTTCGTGTTT--CAAAAA
**
40883 AATTCGTGTTTCAAAATA
1 TTTTCGTGTTTCAAAA-A
* **
40901 TTCTCGCATTTC---AA
1 TTTTCGTGTTTCAAAAA
***
40915 TTTT--TGTTTTTTAAA
1 TTTTCGTGTTTCAAAAA
40930 ---TCGTGTTTCAAAAAA
1 TTTTCGTGTTTC-AAAAA
* * *
40945 ATGTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
*
40962 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
* * *
40979 TTTCCCTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
**
40996 TTCCCGTGTTTCAAAAAAA
1 TTTTCGTGTTTC--AAAAA
* * *
41015 ATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTCAA-AAA
* * *
41033 ATTTCATTTTTTCTAAAAA
1 TTTTC-GTGTTTC-AAAAA
*
41052 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
*
41069 TTTTCGTGTTT-ACAAA
1 TTTTCGTGTTTCAAAAA
*
41085 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* *
41103 TTCTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
41120 AAAACTTTCG
Statistics
Matches: 314, Mismatches: 72, Indels: 61
0.70 0.16 0.14
Matches are distributed among these distances:
12 4 0.01
14 9 0.03
15 6 0.02
16 15 0.05
17 121 0.39
18 103 0.33
19 39 0.12
20 14 0.04
21 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTTCGTGTTTCAAAAA
Found at i:40829 original size:55 final size:53
Alignment explanation
Indices: 40686--40829 Score: 171
Period size: 55 Copynumber: 2.7 Consensus size: 53
40676 AAATTTTGTG
** *
40686 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAGAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCACAAA
* * * **
40740 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTT--GTGTTTTCACAAA
* *
40795 TTTTCGTGTTTCACAAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAA
40830 CTCCAGTGTT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
53 28 0.38
54 5 0.07
55 40 0.55
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (53 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCACAAA
Found at i:40839 original size:73 final size:73
Alignment explanation
Indices: 40699--40840 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 73
40689 TCGTGTTTTC
* * * * *
40699 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAGAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCACAAATTCTCGCGTTTCAAAAATCTCCGT
40764 GTTTAAAA
66 GTTTAAAA
* *
40772 AAAAATTTACGTGTTTTCACAAAT-TTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCC
1 AAAAATTTACGTGTTTTCAAAAATCTTT-GTGTTTTCACAAATTCTCGCG-TTTCAAAAATCTCC
40834 AGTGTTT
64 -GTGTTT
40841 CAAAGTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
72 19 0.32
73 40 0.68
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (73 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCACAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAAA
Done.