Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018220.1 Corchorus olitorius cultivar O-4 contig18253, whole genome shotgun sequence
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: 24081
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2628 original size:21 final size:21
Alignment explanation
Indices: 2603--2643 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2593 TTAGAAACCC
2603 TAGTACCACTTAG-ATCCAATT
1 TAGTACCACTT-GTATCCAATT
2624 TAGTACCACTTGTATCCAAT
1 TAGTACCACTTGTATCCAAT
2644 AGGGCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (21 bp):
TAGTACCACTTGTATCCAATT
Found at i:3779 original size:21 final size:21
Alignment explanation
Indices: 3753--3794 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3743 TTCAACAGAC
3753 CAAGTCCTAGGCAGGAGTTGT
1 CAAGTCCTAGGCAGGAGTTGT
* *
3774 CAAGTCTTGGGCAGGAGTTGT
1 CAAGTCCTAGGCAGGAGTTGT
3795 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (21 bp):
CAAGTCCTAGGCAGGAGTTGT
Found at i:3805 original size:71 final size:71
Alignment explanation
Indices: 3681--3865 Score: 271
Period size: 71 Copynumber: 2.6 Consensus size: 71
3671 TTTTCCGCAA
* ** *
3681 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTAGATAGGACTTGTTCTGAATTTTCTTCCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTC
3746 AACAGAC
65 AACAGAC
* * * * *
3753 CAAGTCCTAGGCAGGAGTTGTCAAGTCTTGGGCAGGAGTTGTTTTGATTTTTCTTCCGTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
3818 ACAGAC
66 ACAGAC
*
3824 CAGGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
3866 CCTGTTTTTA
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 80 0.80
72 20 0.20
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
ACAGAC
Found at i:3853 original size:21 final size:21
Alignment explanation
Indices: 3827--3866 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3817 AACAGACCAG
*
3827 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
3848 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
3867 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:4053 original size:21 final size:21
Alignment explanation
Indices: 4029--4068 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4019 CTCTTGTCAT
* *
4029 TGGACCTATTGGCATCTTTAA
1 TGGACCAAATGGCATCTTTAA
*
4050 TGGATCAAATGGCATCTTT
1 TGGACCAAATGGCATCTTT
4069 GGCAACTCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (21 bp):
TGGACCAAATGGCATCTTTAA
Found at i:4871 original size:6 final size:6
Alignment explanation
Indices: 4864--4906 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
4854 ATAGTTCAAT
* *
4864 TCCAAT TCCAAT TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA T
4907 ATTAGTCATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (6 bp):
TCCAAA
Found at i:5441 original size:2 final size:2
Alignment explanation
Indices: 5434--5470 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5424 CAAAATCCCT
* *
5434 TA TA TA TA TA TA TA CA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5471 TAACAAAGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5454 original size:12 final size:12
Alignment explanation
Indices: 5437--5470 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
5427 AATCCCTTAT
5437 ATATATATATAC
1 ATATATATATAC
5449 ATATATATATAC
1 ATATATATATAC
5461 ATATATATAT
1 ATATATATAT
5471 TAACAAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATATATATAC
Found at i:5523 original size:17 final size:18
Alignment explanation
Indices: 5493--5531 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
5483 GCAAATACTT
5493 TACCAAAGCTAAACACTA
1 TACCAAAGCTAAACACTA
*
5511 TACCAAA-CTAAACACTT
1 TACCAAAGCTAAACACTA
5528 TACC
1 TACC
5532 GAGCTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.21
Consensus pattern (18 bp):
TACCAAAGCTAAACACTA
Found at i:7143 original size:18 final size:18
Alignment explanation
Indices: 7120--7154 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7110 TTTTGTCAGC
7120 AATGATGATATGGCACCT
1 AATGATGATATGGCACCT
*
7138 AATGATGCTATGGCACC
1 AATGATGATATGGCACC
7155 AAATCACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (18 bp):
AATGATGATATGGCACCT
Found at i:8034 original size:34 final size:30
Alignment explanation
Indices: 7956--8040 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 30
7946 TGGAGGATTT
*
7956 AAAAGCTTTAATGTAGAGA-AATAGAGAGA
1 AAAAGCTTTAATGTAGAGAGAGTAGAGAGA
*
7985 AAAAGCTTTAGTGTAGAGAGAGTAGAGAGA
1 AAAAGCTTTAATGTAGAGAGAGTAGAGAGA
*
8015 GAAAGAGGGTTTTAATGTAGAGAGAG
1 -AAA-A--GCTTTAATGTAGAGAGAG
8041 AGTGTGGAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 18 0.38
30 9 0.19
31 3 0.06
32 1 0.02
34 16 0.34
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.21
Consensus pattern (30 bp):
AAAAGCTTTAATGTAGAGAGAGTAGAGAGA
Found at i:9721 original size:162 final size:161
Alignment explanation
Indices: 9433--9760 Score: 541
Period size: 162 Copynumber: 2.0 Consensus size: 161
9423 GTATCATGAT
* * * *
9433 AATAAAGACAAGGTGTGAACTATAGCTTGTCTCAATCATCGGCGGCACGGTGCCTTGCCATGCCT
1 AATAAAGACAAGGTGAGAACTATAGCTTGTCTCAATCACCGGCGGCACGATGCCTTGCCATCCCT
* *
9498 TGATGATGGTAATCAATGCATCATACAAGGAAGACTAGGTGTGAGCTATAGTGGTTTTCTCAATC
66 TGATGATGGTAATCAATACATCATACAAGGAAGACTAGGTGTGAGCTATAGTGGGTTTCTCAATC
9563 ACCAATGCCTTGCCACATAGTGGGCCTTTGTA
131 ACCAATGCCTTGCCACATAGTGGG-CTTTGTA
* * * *
9595 AATAGAGACATGGTGAGAACTATAGGTTGTCTCAATCACCGGCGGCATGATGCCTTGCCATCCCT
1 AATAAAGACAAGGTGAGAACTATAGCTTGTCTCAATCACCGGCGGCACGATGCCTTGCCATCCCT
9660 TGATGATGGTGAA-CAATACATCATACAAGGAAGACTAGGTGTGAGCTATAGTGGGTTTCTCAAT
66 TGATGATGGT-AATCAATACATCATACAAGGAAGACTAGGTGTGAGCTATAGTGGGTTTCTCAAT
9724 CACCAATGCCTTGCCACATAGTGGGCTTTGTA
130 CACCAATGCCTTGCCACATAGTGGGCTTTGTA
9756 AATAA
1 AATAA
9761 GGTGAGAGAC
Statistics
Matches: 154, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
161 11 0.07
162 141 0.92
163 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (161 bp):
AATAAAGACAAGGTGAGAACTATAGCTTGTCTCAATCACCGGCGGCACGATGCCTTGCCATCCCT
TGATGATGGTAATCAATACATCATACAAGGAAGACTAGGTGTGAGCTATAGTGGGTTTCTCAATC
ACCAATGCCTTGCCACATAGTGGGCTTTGTA
Found at i:9796 original size:59 final size:59
Alignment explanation
Indices: 9722--9931 Score: 393
Period size: 59 Copynumber: 3.6 Consensus size: 59
9712 GGGTTTCTCA
*
9722 ATCACCAATGCCTTGCCACATAGTGGGCTTTGTAAATAAGGTGAGAGACATATTGCTCG
1 ATCACCAATGTCTTGCCACATAGTGGGCTTTGTAAATAAGGTGAGAGACATATTGCTCG
*
9781 ATCACCAATGTCTTGCCACGTAGTGGGCTTTGTAAATAAGGTGAGAGACATATTGCTCG
1 ATCACCAATGTCTTGCCACATAGTGGGCTTTGTAAATAAGGTGAGAGACATATTGCTCG
*
9840 ATCACCAATGTCTTGCCACGTAGTGGGCTTTGTAAATAAGGTGAGAGACATATTGCTCG
1 ATCACCAATGTCTTGCCACATAGTGGGCTTTGTAAATAAGGTGAGAGACATATTGCTCG
9899 ATCACCAATGTCTTGCCACATAGTGGGCTTTGT
1 ATCACCAATGTCTTGCCACATAGTGGGCTTTGT
9932 TATGAACCAC
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 148 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (59 bp):
ATCACCAATGTCTTGCCACATAGTGGGCTTTGTAAATAAGGTGAGAGACATATTGCTCG
Found at i:10190 original size:133 final size:133
Alignment explanation
Indices: 9936--10334 Score: 618
Period size: 133 Copynumber: 3.0 Consensus size: 133
9926 CTTTGTTATG
* *
9936 AACCACGGGGGATTTACCATTCTAGGCCAGCCACCATGATTTAAGCTACCTCTTGATATATACGG
1 AACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTTAAGCTACCTCTTGATATAT--GG
*
10001 GTTCTTACAATCAAATGGTGACCGCCATTGTTGGAGTTACCACCGCAATGGCTCGTTTAAGGGAG
64 GTTCTTACAATCAAATGGTGACCGCCATTGTTAGAGTTACCACCGCAATGGCTCGTTTAAGGGAG
10066 AATGA
129 AATGA
10071 AACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTTAAGCTACCTCTTGATATATGGGT
1 AACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTTAAGCTACCTCTTGATATATGGGT
* * *
10136 TCTTACAATCAAATGGTGACCGTCATTGCTAGAGTTACCATCGCAATGGCTCGTTTAAGGGAGAA
66 TCTTACAATCAAATGGTGACCGCCATTGTTAGAGTTACCACCGCAATGGCTCGTTTAAGGGAGAA
*
10201 GGA
131 TGA
* * * * *
10204 AACCATCGGGGATTTACCATTCTAGGTCGGTCATCATGATTTAAGCTACCTCTTGATATATAGGT
1 AACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTTAAGCTACCTCTTGATATATGGGT
* * * * * *
10269 TCTTATAATCAAATGGTGACCGCCATTGTTTGAGTTACCACCACAATGGTTTGTTTAAAGGAGAA
66 TCTTACAATCAAATGGTGACCGCCATTGTTAGAGTTACCACCGCAATGGCTCGTTTAAGGGAGAA
10334 T
131 T
10335 AAAAAATACT
Statistics
Matches: 242, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 183 0.76
135 59 0.24
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (133 bp):
AACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTTAAGCTACCTCTTGATATATGGGT
TCTTACAATCAAATGGTGACCGCCATTGTTAGAGTTACCACCGCAATGGCTCGTTTAAGGGAGAA
TGA
Found at i:10576 original size:19 final size:19
Alignment explanation
Indices: 10531--10576 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
10521 TAATCATTTG
*
10531 TGAA-TAATGGGGTTTCAA
1 TGAAGTAATGGGCTTTCAA
* *
10549 TG-GGTAATGGGCTTTTAA
1 TGAAGTAATGGGCTTTCAA
10567 TGAAGTAATG
1 TGAAGTAATG
10577 CCCCTTCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.35
Consensus pattern (19 bp):
TGAAGTAATGGGCTTTCAA
Found at i:13501 original size:2 final size:2
Alignment explanation
Indices: 13489--13533 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
13479 TAAGGATCAT
*
13489 TA TA CA TA TA TA TA TA TA TA TA TA TGA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
13531 TA T
1 TA T
13534 GTCATTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14518 original size:42 final size:42
Alignment explanation
Indices: 14459--14539 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
14449 GCTAAGTCTT
14459 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
* * *
14501 GAAAATTCTTTGTAAATTAAGAAATGCTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATC
14540 CTGATTCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
Found at i:14672 original size:56 final size:56
Alignment explanation
Indices: 14605--14718 Score: 176
Period size: 56 Copynumber: 2.0 Consensus size: 56
14595 TTTATTCTGT
* *
14605 AGAACAATTAAGTAGTGATAAGGGG-TAAGAATTTATTATAACATTTATTGTGTGAA
1 AGAACAATTAAGTAGAGATAGGGGGAT-AGAATTTATTATAACATTTATTGTGTGAA
* *
14661 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAACAATTAAGTAGAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
14717 AG
1 AG
14719 GAAATGGATA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 52 0.98
57 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (56 bp):
AGAACAATTAAGTAGAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
Found at i:15608 original size:37 final size:38
Alignment explanation
Indices: 15510--15597 Score: 121
Period size: 37 Copynumber: 2.4 Consensus size: 38
15500 TGGTGACTGA
* *
15510 ATGGGAACTTTCCC-AGTTT--GAAAACTTAAAAGCTG
1 ATGGGAACTTTCCCAAATTTAAAAAAACTTAAAAGCTG
15545 ATGGGAACTTTCCCAAATTTAAAAAAACTTAAAA-CTG
1 ATGGGAACTTTCCCAAATTTAAAAAAACTTAAAAGCTG
*
15582 GTGGGAACTTTCCCAA
1 ATGGGAACTTTCCCAA
15598 TTAGAGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
35 14 0.30
36 4 0.09
37 18 0.38
38 11 0.23
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (38 bp):
ATGGGAACTTTCCCAAATTTAAAAAAACTTAAAAGCTG
Found at i:16415 original size:4 final size:4
Alignment explanation
Indices: 16391--16438 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
16381 AAAAAATATG
*
16391 AAGA AAAA AAGA AA-A AA-A AAGA AAGA AAGA AAGA AAGA AAGA AA-A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
16436 AAG
1 AAG
16439 CACCTAGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 9 0.22
4 31 0.77
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:17753 original size:1 final size:1
Alignment explanation
Indices: 17749--17779 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
17739 AAGGTAAAGG
17749 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17780 CTGTTGATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19134 original size:77 final size:78
Alignment explanation
Indices: 19039--19192 Score: 215
Period size: 77 Copynumber: 2.0 Consensus size: 78
19029 AAAGATAATA
* *
19039 CCAGGCCCAATCGCAAACTTTCTTGACCCAAAACAGAAT-TCCAAAGCCCAATCGGACAT-AAAG
1 CCAGGCCCAATCGCAAACTTTCCTGACCCAAAACA-AATGCCCAAAGCCCAATCGGAC-TCAAAG
*
19102 GGGAAAAGGAAGGGG
64 GGAAAAAGGAAGGGG
* * *
19117 CCAGGCCCAA-CGGAAACTTTCCTGACCCAAAACACATGCCCAAAGCCCAATTGGACTCAAAGGG
1 CCAGGCCCAATCGCAAACTTTCCTGACCCAAAACAAATGCCCAAAGCCCAATCGGACTCAAAGGG
19181 AAAAAGGAAGGG
66 AAAAAGGAAGGG
19193 ACCAAACGCA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
76 3 0.04
77 55 0.81
78 10 0.15
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.12
Consensus pattern (78 bp):
CCAGGCCCAATCGCAAACTTTCCTGACCCAAAACAAATGCCCAAAGCCCAATCGGACTCAAAGGG
AAAAAGGAAGGGG
Found at i:19632 original size:26 final size:27
Alignment explanation
Indices: 19593--19664 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
19583 GACCAGTTTG
19593 GAAACTAAGAAAGACCTGTCTGAGGTCT
1 GAAACT-AGAAAGACCTGTCTGAGGTCT
19621 GAAACTGAAAGAAAATGACCTGTCTGAGGTCT
1 GAAACT---AG-AAA-GACCTGTCTGAGGTCT
19653 GAAACT-GAAAGA
1 GAAACTAGAAAGA
19665 AAATGACCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
26 2 0.05
27 3 0.08
28 7 0.17
30 3 0.08
31 3 0.08
32 22 0.55
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (27 bp):
GAAACTAGAAAGACCTGTCTGAGGTCT
Found at i:19644 original size:32 final size:32
Alignment explanation
Indices: 19605--19687 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
19595 AACTAAGAAA
19605 GACCTGTCTGAGGTCTGAAACTGAAAGAAAAT
1 GACCTGTCTGAGGTCTGAAACTGAAAGAAAAT
19637 GACCTGTCTGAGGTCTGAAACTGAAAGAAAAT
1 GACCTGTCTGAGGTCTGAAACTGAAAGAAAAT
* *
19669 GACCTATCCGAGGTC-GAAA
1 GACCTGTCTGAGGTCTGAAA
19688 ATAAAAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 4 0.08
32 45 0.92
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (32 bp):
GACCTGTCTGAGGTCTGAAACTGAAAGAAAAT
Found at i:19770 original size:22 final size:18
Alignment explanation
Indices: 19736--19785 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
19726 GGTCTGGAAC
* *
19736 TAAAAGAAAATAAATTAA
1 TAAAAAAAAATAAAATAA
*
19754 -AAAAACAAATAAAATAA
1 TAAAAAAAAATAAAATAA
19771 TAAAAAAAAATAAAA
1 TAAAAAAAAATAAAA
19786 CTGAGAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (18 bp):
TAAAAAAAAATAAAATAA
Found at i:19872 original size:33 final size:32
Alignment explanation
Indices: 19788--19906 Score: 107
Period size: 33 Copynumber: 3.7 Consensus size: 32
19778 AAATAAAACT
* **
19788 GAGAAAGACCTGTCTGAGGTCTGGAGCT-AAAA
1 GAGAAAGACCTGTCTGAGGTC-GAAATTAAAAA
*
19820 GA-AAATGACATGTCTGAGGTCGAAATTAAAACA
1 GAGAAA-GACCTGTCTGAGGTCGAAATTAAAA-A
* **
19853 GAGAAAGACCTGTCTGAGGTCTAGAATTTGAAA
1 GAGAAAGACCTGTCTGAGGTCGA-AATTAAAAA
* *
19886 GATAAAGACCTTTCTGAGGTC
1 GAGAAAGACCTGTCTGAGGTC
19907 TGGAATAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
31 6 0.08
32 19 0.26
33 38 0.53
34 9 0.12
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (32 bp):
GAGAAAGACCTGTCTGAGGTCGAAATTAAAAA
Found at i:20034 original size:39 final size:39
Alignment explanation
Indices: 19973--20405 Score: 771
Period size: 39 Copynumber: 11.1 Consensus size: 39
19963 TTAGTAATCA
* *
19973 CTGAAAAGATAACCTGTCTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
20012 CTGAAAAGATGATCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
20051 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
20090 CTGAAAATATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
20129 CTGAAAATG-TGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAA-GATGACCTGTTTCCAGTCAACTTTGATAAATG
*
20168 CTGAAAATATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
20207 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
20246 CTGAAAATG-TGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAA-GATGACCTGTTTCCAGTCAACTTTGATAAATG
*
20285 CTGAAAATATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
20324 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
20363 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAGTG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
20402 CTGA
1 CTGA
20406 CCTGTTTGAG
Statistics
Matches: 379, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
39 378 1.00
40 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (39 bp):
CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
Done.