Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2907_ERROPOS15385168
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: 86094
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1105 original size:3 final size:3
Alignment explanation
Indices: 1097--1125 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1087 GATTTAGTCC
1097 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1126 CCTATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5536 original size:23 final size:24
Alignment explanation
Indices: 5500--5550 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
5490 AAGTGTGTTA
* **
5500 TAATTTAATATTATTTTATAGATT
1 TAATTAAATATTATAATATAGATT
*
5524 TAATTAAAT-TTATAATATATATT
1 TAATTAAATATTATAATATAGATT
5547 TAAT
1 TAAT
5551 GTAGAGGCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TAATTAAATATTATAATATAGATT
Found at i:7573 original size:20 final size:19
Alignment explanation
Indices: 7511--7573 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
7501 AAACTATTTG
7511 TTTTTGAA-TTTTTATGATT
1 TTTTTGAATTTTTTAT-ATT
* * **
7530 TTTTTTACATATTTTATAAA
1 TTTTTGA-ATTTTTTATATT
7550 TTTTTGAATGTTTTTATATT
1 TTTTTGAAT-TTTTTATATT
7570 TTTT
1 TTTT
7574 AAATTATTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 8 0.24
20 19 0.58
21 6 0.18
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (19 bp):
TTTTTGAATTTTTTATATT
Found at i:11785 original size:5 final size:6
Alignment explanation
Indices: 11767--11804 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
11757 TAAATCTATG
11767 TCTTTT TCTTTTT TCTTTT TCTTTT TCTTTT TCATTTT
1 TCTTTT TC-TTTT TCTTTT TCTTTT TCTTTT TC-TTTT
11805 AACTTGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 20 0.67
7 10 0.33
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:15259 original size:13 final size:13
Alignment explanation
Indices: 15230--15258 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15220 ACTATAAATC
15230 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
15243 TTTTCTTTT-TTT
1 TTTTCTTTTCTTT
15255 TTTT
1 TTTT
15259 TTCCCGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:18746 original size:98 final size:98
Alignment explanation
Indices: 18581--18817 Score: 242
Period size: 98 Copynumber: 2.4 Consensus size: 98
18571 GTGCACATTC
* * * * ** * * * *
18581 CCTTTTCAAATGGTATACACGAAGTATACATACCCTTTTCA-ATTTGTACACACAAAGTGCACAT
1 CCTTTTCAAGTGATATACACAAAGTATACCTTTCATTTTCATA-TGGTATACACAAAGTACACAT
* * * * * **
18645 AACCTTTTCAAGTATACACATATAGTGTACCTTT
65 AACCTTTCCAAGTATACACACAAAATGTACATAG
* * *
18679 TCTTTTCAAGTGATATACACAAAGTATACCTTTCATTTTCATATGGTATACACAAAGTATACCTA
1 CCTTTTCAAGTGATATACACAAAGTATACCTTTCATTTTCATATGGTATACACAAAGTACACATA
*
18744 ACCTTTCCAAGTGTACACACAAAATGTACATAG
66 ACCTTTCCAAGTATACACACAAAATGTACATAG
* * *
18777 CCTTTTCATGTGGTATACACAAAGTATACCTTTCCTTTTCA
1 CCTTTTCAAGTGATATACACAAAGTATACCTTTCATTTTCA
18818 CATTCAATAG
Statistics
Matches: 113, Mismatches: 25, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
98 112 0.99
99 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (98 bp):
CCTTTTCAAGTGATATACACAAAGTATACCTTTCATTTTCATATGGTATACACAAAGTACACATA
ACCTTTCCAAGTATACACACAAAATGTACATAG
Found at i:18764 original size:65 final size:65
Alignment explanation
Indices: 18581--18817 Score: 219
Period size: 65 Copynumber: 3.6 Consensus size: 65
18571 GTGCACATTC
* * * * * *
18581 CCTTTTCAAATGGTATACACGAAGTATACATACCCTTTTCAATTTGTACACACAAAGTGCACATA
1 CCTTTTCATATGGTATACACAAAGTATACCTAACCTTTTCAA-GTGTACACACAAAGTGTACATA
18646 A
65 A
* *** * * *
18647 CCTTTTCA-A--GTATACACATATAGTGTACCTTTTCTTTTCAAGTGATATACACAAAGTATACC
1 CCTTTTCATATGGTATACACA-A-AGTATACCTAACCTTTTCAAGTG-TACACACAAAGTGTACA
**
18709 TTT
63 TAA
* * * *
18712 CATTTTCATATGGTATACACAAAGTATACCTAACCTTTCCAAGTGTACACACAAAATGTACATAG
1 CCTTTTCATATGGTATACACAAAGTATACCTAACCTTTTCAAGTGTACACACAAAGTGTACATAA
* **
18777 CCTTTTCATGTGGTATACACAAAGTATACCTTTCCTTTTCA
1 CCTTTTCATATGGTATACACAAAGTATACCTAACCTTTTCA
18818 CATTCAATAG
Statistics
Matches: 135, Mismatches: 30, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
63 8 0.06
64 3 0.02
65 87 0.64
66 27 0.20
67 1 0.01
68 9 0.07
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (65 bp):
CCTTTTCATATGGTATACACAAAGTATACCTAACCTTTTCAAGTGTACACACAAAGTGTACATAA
Found at i:18814 original size:33 final size:33
Alignment explanation
Indices: 18581--18817 Score: 169
Period size: 33 Copynumber: 7.2 Consensus size: 33
18571 GTGCACATTC
* * * **
18581 CCTTTTCAAATGGTATACACGAAGTATACATAC
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* * * ** * **
18614 CCTTTTCAATTTGTACACACAAAGTGCACATAA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
*
18647 CCTTTTCAA---GTATACACATATAGTGTACCTTT
1 CCTTTTCAAGTGGTATACACA-A-AGTATACCTTT
* *
18679 TCTTTTCAAGTGATATACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* **
18712 CATTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTTCA-AGTGGTATACACAAAGTATACCTTT
* * * * * **
18745 CCTTTCCAAGT-GTACACACAAAATGTACATAG
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
*
18777 CCTTTTCATGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
18810 CCTTTTCA
1 CCTTTTCA
18818 CATTCAATAG
Statistics
Matches: 161, Mismatches: 35, Indels: 16
0.76 0.17 0.08
Matches are distributed among these distances:
30 8 0.05
31 1 0.01
32 41 0.25
33 101 0.63
34 2 0.01
35 8 0.05
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (33 bp):
CCTTTTCAAGTGGTATACACAAAGTATACCTTT
Found at i:18856 original size:29 final size:29
Alignment explanation
Indices: 18810--18878 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
18800 GTATACCTTT
*
18810 CCTTTTCACATTCAATAGTCGAAGCTATC
1 CCTTTTCACATTCAATAGCCGAAGCTATC
* *
18839 CCTTTTCACATTCGATAGCCGAAGTTATC
1 CCTTTTCACATTCAATAGCCGAAGCTATC
*
18868 CTTTTTCACAT
1 CCTTTTCACAT
18879 GGTACACACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (29 bp):
CCTTTTCACATTCAATAGCCGAAGCTATC
Found at i:19576 original size:21 final size:22
Alignment explanation
Indices: 19530--19572 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
19520 TGTAAAAGTG
*
19530 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
19552 ATTTC-CTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
19572 A
1 A
19573 ATTTACACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:19943 original size:16 final size:16
Alignment explanation
Indices: 19913--19957 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
19903 TATATTAGGA
*
19913 CTTATCACTTTTAAT-
1 CTTATAACTTTTAATC
*
19928 TTTATAACTATTTAATC
1 CTTATAACT-TTTAATC
19945 CTTATAACTTTTA
1 CTTATAACTTTTA
19958 GAATTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (16 bp):
CTTATAACTTTTAATC
Found at i:20445 original size:15 final size:15
Alignment explanation
Indices: 20425--20460 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20415 CAAAATTAAT
20425 ATTTTTACAACATTC
1 ATTTTTACAACATTC
* *
20440 ATTTTTATAATATTC
1 ATTTTTACAACATTC
20455 ATTTTT
1 ATTTTT
20461 CTTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTACAACATTC
Found at i:24459 original size:21 final size:21
Alignment explanation
Indices: 24435--24478 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
24425 TTATAACAAC
24435 ATTTCTCACAGTGATAATCAT
1 ATTTCTCACAGTGATAATCAT
24456 ATTTCTCACAGTGATAATCAT
1 ATTTCTCACAGTGATAATCAT
24477 AT
1 AT
24479 GTATAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (21 bp):
ATTTCTCACAGTGATAATCAT
Found at i:27373 original size:26 final size:26
Alignment explanation
Indices: 27344--27451 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
27334 TGATACAAAT
27344 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
27370 TGATAATTGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27396 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
27422 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27448 TGAT
1 TGAT
27452 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:35540 original size:26 final size:26
Alignment explanation
Indices: 35508--35615 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
35498 TGGTACAAAT
* *
35508 TGATAATGGGTTAGGTAAATGTTACA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
35534 TAATAAT-GGATTAGGTAAATATTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
35560 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
35586 TGATAATAGTTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
35612 TGAT
1 TGAT
35616 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
25 2 0.03
26 70 0.95
27 2 0.03
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:43724 original size:18 final size:18
Alignment explanation
Indices: 43701--43738 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
43691 CCATGTGTTA
43701 GACACAAGGATTGAATAT
1 GACACAAGGATTGAATAT
43719 GACACAAGGATTGAATAT
1 GACACAAGGATTGAATAT
43737 GA
1 GA
43739 GGCGGAGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (18 bp):
GACACAAGGATTGAATAT
Found at i:53537 original size:13 final size:14
Alignment explanation
Indices: 53502--53539 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
53492 CACTGTTTCT
*
53502 GAAAA-ATTGATTA
1 GAAAATATTTATTA
53515 GAAAATATTTATTA
1 GAAAATATTTATTA
53529 -AAAATATTTAT
1 GAAAATATTTAT
53540 GAAGTTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (14 bp):
GAAAATATTTATTA
Found at i:54102 original size:31 final size:32
Alignment explanation
Indices: 54053--54116 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
54043 ATATTAAATA
*
54053 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
54084 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATATTTAT-TAATTAAATATATTAAATTATG
54116 A
1 A
54117 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:55052 original size:15 final size:15
Alignment explanation
Indices: 55029--55076 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
55019 TATCAAATTT
55029 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
55044 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
55059 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
55073 ATAT
1 ATAT
55077 AATATATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:55605 original size:18 final size:19
Alignment explanation
Indices: 55584--55624 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
55574 AATGAAATGA
55584 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
55602 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
55621 GAAA
1 GAAA
55625 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:57387 original size:30 final size:28
Alignment explanation
Indices: 57338--57399 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 28
57328 TATATATAAT
*
57338 TTAATTATACAATATATTATTGAATT-AA
1 TTAATTATAAAATATATTA-TGAATTAAA
57366 TTAATTATAAATATCATATTATGAATTAAA
1 TTAATTATAAA-AT-ATATTATGAATTAAA
57396 TTAA
1 TTAA
57400 ATTAAAGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 10 0.33
29 8 0.27
30 12 0.40
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (28 bp):
TTAATTATAAAATATATTATGAATTAAA
Found at i:57392 original size:25 final size:27
Alignment explanation
Indices: 57338--57394 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
57328 TATATATAAT
*
57338 TTAATTATACAATATATTATTGAATTAA
1 TTAATTATACAATATATTATT-AATGAA
57366 TTAATTATA-AATATCA-TATT-ATGAA
1 TTAATTATACAATAT-ATTATTAATGAA
57391 TTAA
1 TTAA
57395 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
27 9 0.33
28 10 0.37
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (27 bp):
TTAATTATACAATATATTATTAATGAA
Found at i:57523 original size:16 final size:16
Alignment explanation
Indices: 57504--57553 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
57494 AAATATATAT
57504 TTATTATTTATCATTA
1 TTATTATTTATCATTA
*
57520 TTATTATTCTATCA-AA
1 TTATTATT-TATCATTA
*
57536 TTATAATTTAT-ATTA
1 TTATTATTTATCATTA
57551 TTA
1 TTA
57554 AATTATTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 16 0.55
17 5 0.17
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTTATCATTA
Found at i:58695 original size:23 final size:21
Alignment explanation
Indices: 58676--58750 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
58666 CAGGCACTTT
58676 ATGTGTCGTATATCAAGCACCTC
1 ATGTGTCG--TATCAAGCACCTC
*
58699 GTGTGTCGTATCAAGCACCTC
1 ATGTGTCGTATCAAGCACCTC
* * * * * *
58720 GTGTATCATTTCTAGCA-CTT
1 ATGTGTCGTATCAAGCACCTC
58740 ATGTGTCGTAT
1 ATGTGTCGTAT
58751 ACTGATCAGG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
20 9 0.21
21 26 0.62
23 7 0.17
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (21 bp):
ATGTGTCGTATCAAGCACCTC
Found at i:58710 original size:21 final size:22
Alignment explanation
Indices: 58677--58723 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 22
58667 AGGCACTTTA
58677 TGTGTCGTATATCAAGCACCTCG
1 TGTGTCG-ATATCAAGCACCTCG
58700 TGTGTCG-TATCAAGCACCTCG
1 TGTGTCGATATCAAGCACCTCG
58721 TGT
1 TGT
58724 ATCATTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.71
23 7 0.29
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (22 bp):
TGTGTCGATATCAAGCACCTCG
Found at i:58736 original size:21 final size:21
Alignment explanation
Indices: 58685--58737 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
58675 TATGTGTCGT
*
58685 ATATCAAGCACCTCGTGTGTC
1 ATATCAAGCACCTCGTGTATC
*
58706 GTATCAAGCACCTCGTGTATC
1 ATATCAAGCACCTCGTGTATC
* *
58727 ATTTCTAGCAC
1 ATATCAAGCAC
58738 TTATGTGTCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (21 bp):
ATATCAAGCACCTCGTGTATC
Found at i:61572 original size:13 final size:11
Alignment explanation
Indices: 61542--61567 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61532 TAGCTGGCAA
61542 ATATCTTGTAG
1 ATATCTTGTAG
61553 ATATCTTGTAG
1 ATATCTTGTAG
61564 ATAT
1 ATAT
61568 ATCTTTCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (11 bp):
ATATCTTGTAG
Found at i:62643 original size:25 final size:25
Alignment explanation
Indices: 62614--62664 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
62604 CAAAGGAAAA
**
62614 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
62639 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
62664 T
1 T
62665 TTATAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:64990 original size:18 final size:18
Alignment explanation
Indices: 64944--64990 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 18
64934 TTATCGTTGA
64944 ATTTATCAT-TTTA-AAT
1 ATTTATCATATTTATAAT
64960 ATTT-T--TA-TTATAAT
1 ATTTATCATATTTATAAT
64974 ATTTATCATATTTATAA
1 ATTTATCATATTTATAA
64991 ATAAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
13 4 0.16
14 7 0.28
15 2 0.08
16 4 0.16
17 2 0.08
18 6 0.24
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATCATATTTATAAT
Found at i:73667 original size:55 final size:55
Alignment explanation
Indices: 73599--73706 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
73589 CGTGCCCTTA
*
73599 GCCCGTGTGCAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCAC
1 GCCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCAC
*
73654 GCCCGTGTACAACACTGACTTTAAAACATGGCCATGACACACGCCCGTGTGGC
1 GCCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGC
73707 CTACCTGTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (55 bp):
GCCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCAC
Found at i:73717 original size:55 final size:55
Alignment explanation
Indices: 73600--73733 Score: 193
Period size: 55 Copynumber: 2.5 Consensus size: 55
73590 GTGCCCTTAG
* *
73600 CCCGTGTGCAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCACG
1 CCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCACA
*
73655 CCCGTGTACAACACTGACTTTAAAACATGGCCATGACACACGCCCGTGTGGC-CTA
1 CCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCAC-A
*
73710 CCTGTGTACTAA-ACTGAC-TTAAAA
1 CCCGTGTAC-AACACTGACTTTAAAA
73734 TTTTAAGTGT
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
54 7 0.10
55 64 0.88
56 2 0.03
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
CCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCACA
Found at i:73901 original size:13 final size:13
Alignment explanation
Indices: 73883--73917 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
73873 CTAGGCACAC
*
73883 GCCCGTGTGCCTT
1 GCCCGTGTGCATT
73896 GCCCGTGTGCATT
1 GCCCGTGTGCATT
*
73909 ACCCGTGTG
1 GCCCGTGTG
73918 GACCAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.34, G:0.31, T:0.29
Consensus pattern (13 bp):
GCCCGTGTGCATT
Found at i:74768 original size:47 final size:47
Alignment explanation
Indices: 74565--74882 Score: 231
Period size: 47 Copynumber: 6.7 Consensus size: 47
74555 GGGATAAGTT
* *
74565 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGAG
1 GCCGATG-CATGTCCCAGACA-GGTCTTACACTAGCTATCATCGTCGAG
* * * * *
74614 GCCGATGCCATGTCTCAGACATGGTTTTACACTAGCTCTCATATGTACG-T
1 GCCGATG-CATGTCCCAGACA-GGTCTTACACTAGCTATCAT-CGT-CGAG
* * * * *
74664 GCTGATGCATGTCCCGGACATGTCTTACACTAG-TA-CAAC-TCTTA-
1 GCCGATGCATGTCCCAGACAGGTCTTACACTAGCTATCATCGTC-GAG
* *
74708 GCCGATGCATGTCCCAGACACGTCTTACACTGGCTATCATCGTCGAG
1 GCCGATGCATGTCCCAGACAGGTCTTACACTAGCTATCATCGTCGAG
* * * * *
74755 GCCGATACGTGTCCCAGACATGTCTTACACTAG-TACTCATC-TCTAC
1 GCCGATGCATGTCCCAGACAGGTCTTACACTAGCTA-TCATCGTCGAG
* * ** *
74801 GCCGATGCCATGTCCCAGACATGGTCTTATACTGGC-ATTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACA-GGTCTTACACTAGCTA-TCATCGTCGAG
* * *
74849 GCCAATGCATGTCCTAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACAGGTCTTACACTAGC
74883 ACACAAGTAA
Statistics
Matches: 213, Mismatches: 43, Indels: 29
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.00
44 30 0.14
45 2 0.01
46 28 0.13
47 61 0.29
48 32 0.15
49 50 0.23
50 7 0.03
51 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACAGGTCTTACACTAGCTATCATCGTCGAG
Found at i:74857 original size:141 final size:140
Alignment explanation
Indices: 74573--74879 Score: 336
Period size: 141 Copynumber: 2.2 Consensus size: 140
74563 TTGCCGATGC
* * *
74573 CATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCTCAGACATGG
1 CATGTCCCAGACA-CGTCTTACACTGGCTATCATCATCGAGGCCGATGACATGTCCCAGACATGG
* * * * *
74638 TTTTACACTAGCTCTCATATGTACGTGCTGATGCATGTCCCGGACATGTCTTACACTAGTACAAC
65 TCTTACACTAGCTCTCATATCTACG-GCCGATGCATGTCCCAGACATGTCTTACACTAGTACAAA
* *
74703 TCTTAGCCGATG
129 TCGTAGCCAATG
* *
74715 CATGTCCCAGACACGTCTTACACTGGCTATCATCGTCGAGGCCGAT-ACGTGTCCCAGACAT-GT
1 CATGTCCCAGACACGTCTTACACTGGCTATCATCATCGAGGCCGATGACATGTCCCAGACATGGT
* * * *
74778 CTTACACTAG-TACTCATCTCTAC-GCCGATGCCATGTCCCAGACATGGTCTTATACTGGCATTC
66 CTTACACTAGCT-CTCATATCTACGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAG--TAC
*
74841 ATAAT-GTGGCCAATG
126 A-AATCGTAGCCAATG
* *
74856 CATGTCCTAGACATGTCTTACACT
1 CATGTCCCAGACACGTCTTACACT
74880 AGCACACAAG
Statistics
Matches: 140, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
137 6 0.04
138 14 0.10
139 30 0.21
140 12 0.09
141 63 0.45
142 15 0.11
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (140 bp):
CATGTCCCAGACACGTCTTACACTGGCTATCATCATCGAGGCCGATGACATGTCCCAGACATGGT
CTTACACTAGCTCTCATATCTACGGCCGATGCATGTCCCAGACATGTCTTACACTAGTACAAATC
GTAGCCAATG
Found at i:74868 original size:94 final size:91
Alignment explanation
Indices: 74565--74881 Score: 318
Period size: 94 Copynumber: 3.4 Consensus size: 91
74555 GGGATAAGTT
* * *
74565 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCTC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAG-TATCATC-TCTA-GCCGATGCCATGTCCC
* * *
74630 AGACATGGTTTTACACTAGCTCTCATATGTACG
61 AGACATGGTCTTACACTGGCTATCATATGT--G
* * *
74663 TGCTGATGCATGTCCCGGACATGTCTTACACTAGTA-CAACTCTTAGCCGATG-CATGTCCCAGA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGTATCATCTC-TAGCCGATGCCATGTCCCAGA
* * *
74726 CA-CGTCTTACACTGGCTATCATCGTCGAG
64 CATGGTCTTACACTGGCTATCAT-AT-GTG
* *
74755 GCCGATACGTGTCCCAGACATGTCTTACACTAGTACTCATCTCTACGCCGATGCCATGTCCCAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGTA-TCATCTCTA-GCCGATGCCATGTCCCAGA
*
74820 CATGGTCTTATACTGGC-ATTCATAATGTG
64 CATGGTCTTACACTGGCTA-TCAT-ATGTG
* *
74849 GCCAATGCATGTCCTAGACATGTCTTACACTAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAG
74882 CACACAAGTA
Statistics
Matches: 183, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
91 31 0.17
92 19 0.10
93 25 0.14
94 55 0.30
95 21 0.11
96 2 0.01
97 11 0.06
98 13 0.07
99 6 0.03
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (91 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGTATCATCTCTAGCCGATGCCATGTCCCAGACA
TGGTCTTACACTGGCTATCATATGTG
Found at i:78474 original size:51 final size:49
Alignment explanation
Indices: 78344--78588 Score: 301
Period size: 49 Copynumber: 4.9 Consensus size: 49
78334 TCTATTATGA
*
78344 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
78393 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * ** *
78443 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGCTA
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-AATT
* * *
78494 GGTCATGTGTGTAGTACTAAGTACAGGCTACTACGTGTACCGGATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
78543 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
78589 GCTTTGGCTA
Statistics
Matches: 163, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
49 82 0.50
50 42 0.26
51 39 0.24
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:81873 original size:6 final size:6
Alignment explanation
Indices: 81864--81889 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
81854 TATATACTGT
81864 ATACAC ATACAC ATACAC ATACAC AT
1 ATACAC ATACAC ATACAC ATACAC AT
81890 GTACTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
ATACAC
Found at i:81913 original size:6 final size:6
Alignment explanation
Indices: 81902--81933 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
81892 ACTCTCTTTC
81902 CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CC
1 CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CC
81934 GTTTGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.53, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCAAT
Found at i:86015 original size:3 final size:3
Alignment explanation
Indices: 86007--86038 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
85997 TCTAAACCCA
86007 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
86039 ACAACTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.