Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006568.1 Corchorus capsularis cultivar CVL-1 contig06589, 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: 111488
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4955 original size:2 final size:2
Alignment explanation
Indices: 4912--4941 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4902 ATAAATCAGA
4912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4942 GCTTGCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5868 original size:30 final size:30
Alignment explanation
Indices: 5834--5892 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
5824 ATTATATTTA
5834 TATTTTTAAAAATTCAAAAGAATCCTTTTC
1 TATTTTTAAAAATTCAAAAGAATCCTTTTC
5864 TATTTTTAAAAATTCAAAAGAATCCTTTT
1 TATTTTTAAAAATTCAAAAGAATCCTTTT
5893 GAACCAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (30 bp):
TATTTTTAAAAATTCAAAAGAATCCTTTTC
Found at i:7074 original size:23 final size:23
Alignment explanation
Indices: 7038--7084 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
7028 TCACAGTGGC
7038 TTTGGCCAGGAACTGAGTTTTGG
1 TTTGGCCAGGAACTGAGTTTTGG
7061 TTTGGCC-GGCAACTGAGTTTTGG
1 TTTGGCCAGG-AACTGAGTTTTGG
7084 T
1 T
7085 GTAATGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.15, C:0.15, G:0.34, T:0.36
Consensus pattern (23 bp):
TTTGGCCAGGAACTGAGTTTTGG
Found at i:9018 original size:1 final size:1
Alignment explanation
Indices: 9012--9037 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
9002 ACTTCATCTG
9012 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
9038 CGAGCTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9231 original size:23 final size:23
Alignment explanation
Indices: 9205--9252 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
9195 AAAGGCCTCA
9205 CGGATTTGCCCTTTCCCAAAAGG
1 CGGATTTGCCCTTTCCCAAAAGG
9228 CGGATTTGCCCTTTCCCAAAAGG
1 CGGATTTGCCCTTTCCCAAAAGG
9251 CG
1 CG
9253 CCTCACAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (23 bp):
CGGATTTGCCCTTTCCCAAAAGG
Found at i:12347 original size:16 final size:16
Alignment explanation
Indices: 12326--12360 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12316 TATCATTCTA
*
12326 AAAAAAATACTTAGCT
1 AAAAAAACACTTAGCT
12342 AAAAAAACACTTAGCT
1 AAAAAAACACTTAGCT
12358 AAA
1 AAA
12361 TATTGTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAAAAACACTTAGCT
Found at i:17466 original size:19 final size:19
Alignment explanation
Indices: 17439--17476 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17429 AGAGAGAAGG
17439 AATGAAAGTTTTTTGCAAC
1 AATGAAAGTTTTTTGCAAC
*
17458 AATGGAAGTTTTTTGCAAC
1 AATGAAAGTTTTTTGCAAC
17477 CGAGAAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (19 bp):
AATGAAAGTTTTTTGCAAC
Found at i:20910 original size:28 final size:28
Alignment explanation
Indices: 20878--20936 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
20868 ATATTAAGCT
**
20878 ACCAACTACACATGGAACATGGACAAGG
1 ACCAACTACACATAAAACATGGACAAGG
*
20906 ACCAACTACACATAAAACATGTACAAGG
1 ACCAACTACACATAAAACATGGACAAGG
20934 ACC
1 ACC
20937 CAAATATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.12
Consensus pattern (28 bp):
ACCAACTACACATAAAACATGGACAAGG
Found at i:25545 original size:3 final size:3
Alignment explanation
Indices: 25537--25571 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
25527 AAACCAAAAG
25537 GAA GAA GAAA GAA GAAA GAA GAA GAA GAA GAA GAA
1 GAA GAA G-AA GAA G-AA GAA GAA GAA GAA GAA GAA
25572 TCTGTGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:25548 original size:7 final size:7
Alignment explanation
Indices: 25538--25571 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
25528 AACCAAAAGG
25538 AAGAAGA
1 AAGAAGA
25545 AAGAAGA
1 AAGAAGA
25552 AAGAAG-
1 AAGAAGA
25558 AAGAAG-
1 AAGAAGA
25564 AAGAAGA
1 AAGAAGA
25571 A
1 A
25572 TCTGTGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:30949 original size:15 final size:16
Alignment explanation
Indices: 30929--30959 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
30919 GCTAAATTTC
30929 ATTATATGAA-AAATA
1 ATTATATGAATAAATA
30944 ATTATATGAATAAATA
1 ATTATATGAATAAATA
30960 CTAAATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTATATGAATAAATA
Found at i:32202 original size:92 final size:92
Alignment explanation
Indices: 32031--32214 Score: 341
Period size: 94 Copynumber: 2.0 Consensus size: 92
32021 ATTTTTTAAT
*
32031 AATGGCAATTTAGAAATATATTTGAAAAAAAGGTACAATCGGAAAACATAAAGTTTACCCTTATT
1 AATGGCAATTTAGAAATATATTTGAAAAAAAGATACAATCGGAAAACATAAAGTTTACCCTTATT
32096 CGTGCTTTTATATATAGTATAGATAAA
66 CGTGCTTTTATATATAGTATAGATAAA
32123 AATGGCAATTTAGAAATATATTTGAAAAAAAATGATACAATCGGAAAACATAAAGTTTACCCTTA
1 AATGGCAATTTAGAAATATATTTG-AAAAAAA-GATACAATCGGAAAACATAAAGTTTACCCTTA
32188 TTCGTGCTTTTATATATAGTATAGATA
64 TTCGTGCTTTTATATATAGTATAGATA
32215 TAGATAATAA
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
92 24 0.27
93 7 0.08
94 58 0.65
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (92 bp):
AATGGCAATTTAGAAATATATTTGAAAAAAAGATACAATCGGAAAACATAAAGTTTACCCTTATT
CGTGCTTTTATATATAGTATAGATAAA
Found at i:32595 original size:26 final size:26
Alignment explanation
Indices: 32565--32644 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
32555 TCCCAAATTA
32565 TAAAAGGATTGTTCCTAAAAAAATAT
1 TAAAAGGATTGTTCCTAAAAAAATAT
* **
32591 TAAAAGGATTG-TCCCAAATCTAATA-
1 TAAAAGGATTGTTCCTAAA-AAAATAT
32616 TAAAAGGATTGTTCCTAAAAAAATAT
1 TAAAAGGATTGTTCCTAAAAAAATAT
32642 TAA
1 TAA
32645 GATTGTGTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 21 0.47
26 24 0.53
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (26 bp):
TAAAAGGATTGTTCCTAAAAAAATAT
Found at i:32625 original size:25 final size:24
Alignment explanation
Indices: 32563--32641 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 24
32553 TGTCCCAAAT
*
32563 TATAAAAGGATTGTTCCTAAAAAAA
1 TATAAAAGGATTG-TCCCAAAAAAA
**
32588 TATTAAAAGGATTGTCCCAAATCTAA
1 TA-TAAAAGGATTGTCCCAAA-AAAA
*
32614 TATAAAAGGATTGTTCCTAAAAAAA
1 TATAAAAGGATTG-TCCCAAAAAAA
32639 TAT
1 TAT
32642 TAAGATTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 24 0.53
26 21 0.47
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.30
Consensus pattern (24 bp):
TATAAAAGGATTGTCCCAAAAAAA
Found at i:36658 original size:6 final size:6
Alignment explanation
Indices: 36649--36679 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
36639 AGTATAGATA
36649 ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
36680 TAAAAAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATCTAT
Found at i:37897 original size:65 final size:65
Alignment explanation
Indices: 37793--37922 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
37783 CAACTTGTTT
37793 ATATTAATTATCTTAATTTGCATTTCAATAAATCTATTTCACCTCATCACCGTAGATTTTTCTTC
1 ATATTAATTATCTTAATTTGCATTTCAATAAATCTATTTCACCTCATCACCGTAGATTTTTCTTC
*
37858 ATATTAATTATCTTAATTTGCATTTGAATAAATCTATTTCACCTCATCACCGTAGATTTTTCTTC
1 ATATTAATTATCTTAATTTGCATTTCAATAAATCTATTTCACCTCATCACCGTAGATTTTTCTTC
37923 CTAAAATTCT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.46
Consensus pattern (65 bp):
ATATTAATTATCTTAATTTGCATTTCAATAAATCTATTTCACCTCATCACCGTAGATTTTTCTTC
Found at i:58669 original size:75 final size:75
Alignment explanation
Indices: 58539--58702 Score: 265
Period size: 75 Copynumber: 2.2 Consensus size: 75
58529 TTTGAATACC
*
58539 CTCTGAAATTTACTAATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTCTCGCCCAGTTTTGG
1 CTCTGAAATTTACTAACAGCTCCCATCAACTTTTAACGTGGGAGAACCTTCTCGCCCAGTTTTGG
58604 TCTTTTCTCA
66 TCTTTTCTCA
* * * * *
58614 CTCTGAAATTTACTAACAGTTCCCATCAACTTTTAACGTGGGAGAACTTTTTCGCCCCGTTTTGT
1 CTCTGAAATTTACTAACAGCTCCCATCAACTTTTAACGTGGGAGAACCTTCTCGCCCAGTTTTGG
*
58679 TGTTTTCTCA
66 TCTTTTCTCA
58689 CTCTGAAATTTACT
1 CTCTGAAATTTACT
58703 TATAGGTCCC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 82 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (75 bp):
CTCTGAAATTTACTAACAGCTCCCATCAACTTTTAACGTGGGAGAACCTTCTCGCCCAGTTTTGG
TCTTTTCTCA
Found at i:58765 original size:4 final size:4
Alignment explanation
Indices: 58751--58782 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
58741 AGCTTCTTCC
*
58751 AATA GATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA
58783 TTAATATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:60573 original size:16 final size:16
Alignment explanation
Indices: 60552--60591 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
60542 ATTGGGCGGG
60552 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
60568 TTCGGGTTCTGGTATT
1 TTCGGGTTCGGGTATT
60584 TTCGGGTT
1 TTCGGGTT
60592 TTGTCGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.12, G:0.35, T:0.47
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:60598 original size:26 final size:25
Alignment explanation
Indices: 60558--60617 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 25
60548 CGGGTTCGGG
*
60558 TTCGGGTATTTTCGGGTTCTGGTATT
1 TTCGGGT-TTTTCGGGTTCAGGTATT
60584 TTCGGGTTTTGTCGGGTTCAGGTATT
1 TTCGGGTTTT-TCGGGTTCAGGTATT
60610 TTCGGGTT
1 TTCGGGTT
60618 CGGGCTCGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 3 0.09
26 29 0.91
ACGTcount: A:0.07, C:0.12, G:0.33, T:0.48
Consensus pattern (25 bp):
TTCGGGTTTTTCGGGTTCAGGTATT
Found at i:60616 original size:16 final size:15
Alignment explanation
Indices: 60552--60620 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
60542 ATTGGGCGGG
60552 TTCGGGTTCGGGTATT
1 TTCGGGTTC-GGTATT
60568 TTCGGGTTCTGGTATT
1 TTCGGGTTC-GGTATT
60584 TTCGGG-T---T-TT
1 TTCGGGTTCGGTATT
*
60594 GTCGGGTTCAGGTATT
1 TTCGGGTTC-GGTATT
60610 TTCGGGTTCGG
1 TTCGGGTTCGG
60621 GCTCGGATCG
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
10 7 0.16
11 2 0.05
15 4 0.09
16 31 0.70
ACGTcount: A:0.06, C:0.13, G:0.36, T:0.45
Consensus pattern (15 bp):
TTCGGGTTCGGTATT
Found at i:60633 original size:17 final size:17
Alignment explanation
Indices: 60611--60655 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
60601 TCAGGTATTT
*
60611 TCGGGTTCGGGCTCGGA
1 TCGGGTTCGGGCCCGGA
60628 TCGGGTTCGGGCCCGGA
1 TCGGGTTCGGGCCCGGA
60645 TCGGGTTCGGG
1 TCGGGTTCGGG
60656 TTCACTTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.04, C:0.24, G:0.49, T:0.22
Consensus pattern (17 bp):
TCGGGTTCGGGCCCGGA
Found at i:61454 original size:16 final size:16
Alignment explanation
Indices: 61433--61473 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
61423 GGGTTGTCTC
61433 GGTTCGGGTAATTTCG
1 GGTTCGGGTAATTTCG
*
61449 GGTTCGAGTAATTTCG
1 GGTTCGGGTAATTTCG
61465 GGTTCGGGT
1 GGTTCGGGT
61474 TCAGATGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.39, T:0.37
Consensus pattern (16 bp):
GGTTCGGGTAATTTCG
Found at i:69101 original size:13 final size:13
Alignment explanation
Indices: 69083--69112 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
69073 TAAATAGGAC
69083 ACAAATGGCATTA
1 ACAAATGGCATTA
69096 ACAAATGGCATTA
1 ACAAATGGCATTA
69109 ACAA
1 ACAA
69113 TATTGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (13 bp):
ACAAATGGCATTA
Found at i:70754 original size:15 final size:15
Alignment explanation
Indices: 70715--70764 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
70705 TAAGTTGTAA
* *
70715 AAACAATCAACGATAC
1 AAACAACCAAC-AAAC
70731 AATACAACCAACAAAC
1 AA-ACAACCAACAAAC
*
70747 AAACAACCAACAATC
1 AAACAACCAACAAAC
70762 AAA
1 AAA
70765 GAGTTAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 15 0.50
16 7 0.23
17 8 0.27
ACGTcount: A:0.62, C:0.28, G:0.02, T:0.08
Consensus pattern (15 bp):
AAACAACCAACAAAC
Found at i:70803 original size:64 final size:64
Alignment explanation
Indices: 70697--70817 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 64
70687 AAAACTAATA
*
70697 CAAAAAGTTAAGTTGTAAAAACAATCAACGATACAATACAACCAACAAACAAACAACCAACAAT
1 CAAAAAGTTAAGTTGCAAAAACAATCAACGATACAATACAACCAACAAACAAACAACCAACAAT
* *
70761 CAAAGAGTTAAGTTGCAAAAACAATCAACGATACAATACAACCAACAAACAACCAAC
1 CAAAAAGTTAAGTTGCAAAAACAATCAACGATACAATACAACCAACAAACAAACAAC
70818 AATCAGAACC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.56, C:0.23, G:0.07, T:0.13
Consensus pattern (64 bp):
CAAAAAGTTAAGTTGCAAAAACAATCAACGATACAATACAACCAACAAACAAACAACCAACAAT
Found at i:70814 original size:11 final size:12
Alignment explanation
Indices: 70780--70820 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
70770 AAGTTGCAAA
*
70780 AACAAT-CAACG
1 AACAATACAACC
70791 ATACAATACAACC
1 A-ACAATACAACC
70804 AACAA-ACAACC
1 AACAATACAACC
70815 AACAAT
1 AACAAT
70821 CAGAACCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 12 0.46
12 9 0.35
13 5 0.19
ACGTcount: A:0.59, C:0.29, G:0.02, T:0.10
Consensus pattern (12 bp):
AACAATACAACC
Found at i:73270 original size:20 final size:21
Alignment explanation
Indices: 73245--73289 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
73235 TACACTGCAC
73245 AACCAAAAACAAACAAA-CCA
1 AACCAAAAACAAACAAAGCCA
**
73265 AACCAAATTCAAACAAAGCCA
1 AACCAAAAACAAACAAAGCCA
73286 AACC
1 AACC
73290 GCGTCTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.62, C:0.31, G:0.02, T:0.04
Consensus pattern (21 bp):
AACCAAAAACAAACAAAGCCA
Found at i:74398 original size:45 final size:45
Alignment explanation
Indices: 74334--74422 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
74324 CTCGGTTGAT
* *
74334 GGCGGAATTTCAAAGCAACAAGGTGAAGTCTTCATCTGGGTCGAC
1 GGCGGAATTGCAAAGCAACAAGGTGAAGTCGTCATCTGGGTCGAC
74379 GGCGGAATTGCAAAGCAACAAGGTGAAGTCGTCATCTGGGTCGA
1 GGCGGAATTGCAAAGCAACAAGGTGAAGTCGTCATCTGGGTCGA
74423 ATTCGATGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.20
Consensus pattern (45 bp):
GGCGGAATTGCAAAGCAACAAGGTGAAGTCGTCATCTGGGTCGAC
Found at i:75814 original size:196 final size:197
Alignment explanation
Indices: 75468--75840 Score: 520
Period size: 196 Copynumber: 1.9 Consensus size: 197
75458 AGTGTTTATC
* * *
75468 ATAATGTAATGTACTTGCATATATTGCTAATTACAGATTGTAATGAGAATAGACTATTTATGCTT
1 ATAATGTAATGTACTTGCA-ATATTGCAAATGACAGATTGTAATGAGAATAAACTATTTATGCTT
* * *
75533 TACCTCTGTTCTTGAGTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACTAGAATTTTCA
65 GACCTCTGTTCTTGACTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACCAGAATTTTCA
* * *
75598 GTCTTTCATAGGGCACCAAGACTTTTGGTATGATTCTGGTTT-TTTTGTGATCACTTATTTCTCC
130 GTCTTTCATAGGGAACCAAGACTTTGGGTATGATTCTAGTTTCTTTTGTGATCACTTATTTCTCC
75662 TAT
195 TAT
75665 ATAATGTAATGTGA-TTGC-ATATTG-AAATGACAGATTGTAATGAGAATAAACTATTTATGCTT
1 ATAATGTAATGT-ACTTGCAATATTGCAAATGACAGATTGTAATGAGAATAAACTATTTATGCTT
* * * * * *
75727 AGACCCTCTGTTCTTGACTCTACTTTGAAATTAAAGGAGTTTCAGTGCATGTATACCGGAATTTT
65 -GA-CCTCTGTTCTTGACTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACCAGAATTTT
* * *
75792 CATTCTTTGATATGGAACCAAGACTTTGGGTATGATTCTAGTTTCTTTT
128 CAGTCTTTCATAGGGAACCAAGACTTTGGGTATGATTCTAGTTTCTTTT
75841 TCTTTTCCCA
Statistics
Matches: 154, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
194 35 0.23
195 7 0.05
196 91 0.59
197 20 0.13
198 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (197 bp):
ATAATGTAATGTACTTGCAATATTGCAAATGACAGATTGTAATGAGAATAAACTATTTATGCTTG
ACCTCTGTTCTTGACTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACCAGAATTTTCAG
TCTTTCATAGGGAACCAAGACTTTGGGTATGATTCTAGTTTCTTTTGTGATCACTTATTTCTCCT
AT
Found at i:79572 original size:30 final size:31
Alignment explanation
Indices: 79533--79592 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
79523 GCGACGTTTT
*
79533 ACCCCTGAACGT-CAAATCAGGACATTTTGC
1 ACCCCTGAACGTCCAAATCAAGACATTTTGC
* *
79563 ACCCTTGAACTTCCCAAATCAAGACATTTT
1 ACCCCTGAACGT-CCAAATCAAGACATTTT
79593 ACCCCCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
32 15 0.60
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.27
Consensus pattern (31 bp):
ACCCCTGAACGTCCAAATCAAGACATTTTGC
Found at i:81161 original size:11 final size:11
Alignment explanation
Indices: 81145--81188 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
81135 TATACTATAT
81145 CTAATTAATAA
1 CTAATTAATAA
*
81156 CTAATTAATAT
1 CTAATTAATAA
*
81167 CTAATTAATAG
1 CTAATTAATAA
*
81178 TTAATTAATAA
1 CTAATTAATAA
81189 TGAATTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:81169 original size:22 final size:22
Alignment explanation
Indices: 81141--81187 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
81131 CCATTATACT
81141 ATATCTAATTAATAACTAATTA
1 ATATCTAATTAATAACTAATTA
**
81163 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAACTAATTA
81185 ATA
1 ATA
81188 ATGAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAACTAATTA
Found at i:81194 original size:11 final size:11
Alignment explanation
Indices: 81146--81194 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
81136 ATACTATATC
*
81146 TAATTAATAAC
1 TAATTAATAAT
81157 TAATTAAT-AT
1 TAATTAATAAT
*
81167 CTAATTAATAGT
1 -TAATTAATAAT
81179 TAATTAATAAT
1 TAATTAATAAT
*
81190 GAATT
1 TAATT
81195 TATTCAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 1 0.03
11 30 0.94
12 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (11 bp):
TAATTAATAAT
Found at i:92082 original size:30 final size:31
Alignment explanation
Indices: 92033--92097 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
92023 AACTTTATGT
***
92033 TTTCCGATTATACCCCTTTTTCTTAAATATA
1 TTTCCGATTATACCCCTTTTTAAAAAATATA
92064 TTTCCGATTATA-CCCTTTTTAAAAAATATA
1 TTTCCGATTATACCCCTTTTTAAAAAATATA
92094 TTTC
1 TTTC
92098 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCGATTATACCCCTTTTTAAAAAATATA
Found at i:92955 original size:26 final size:27
Alignment explanation
Indices: 92916--92967 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
92906 CTGAGACTAA
* *
92916 ACTCGAAACTGACTAAAAAACAAACTG
1 ACTCGAAACCGACTAAAAAAAAAACTG
92943 ACTC-AAACCGACTAAAAAAAAAACT
1 ACTCGAAACCGACTAAAAAAAAAACT
92968 CAAATAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.56, C:0.23, G:0.08, T:0.13
Consensus pattern (27 bp):
ACTCGAAACCGACTAAAAAAAAAACTG
Found at i:93383 original size:22 final size:21
Alignment explanation
Indices: 93216--93799 Score: 153
Period size: 22 Copynumber: 27.1 Consensus size: 21
93206 AACTTCTATT
* *
93216 ATATGGAGTAATCAAAATTTC
1 ATATGAAGTTATCAAAATTTC
* * * *
93237 A-AGGAGGATATCAAATTTTC
1 ATATGAAGTTATCAAAATTTC
*
93257 ATATAAAGGTTATCAAAATTTC
1 ATATGAA-GTTATCAAAATTTC
* ** *
93279 ATCGTTTAGTTTTCAAAATTTC
1 AT-ATGAAGTTATCAAAATTTC
* *
93301 ACAAGAGAGTTATCAAAATTTC
1 ATATGA-AGTTATCAAAATTTC
* *
93323 ATA-GTATGTAGATCAAAATTTC
1 ATATG-AAGT-TATCAAAATTTC
* * *
93345 ATAGGGAGATTAACAAAATTTC
1 ATATGAAG-TTATCAAAATTTC
***
93367 ATTATGAAGTTATCAAAAAAAC
1 A-TATGAAGTTATCAAAATTTC
* *
93389 ATAGGGAGGTTATCAAAATTT-
1 ATA-TGAAGTTATCAAAATTTC
*
93410 -T-T--AGTTATCAAGATTTC
1 ATATGAAGTTATCAAAATTTC
* *
93427 ATAAGAAAGTTATCAAAATTTT
1 ATATG-AAGTTATCAAAATTTC
* * *
93449 ATAGGGAGGTTTATCAAAATTTT
1 ATA-TGAAG-TTATCAAAATTTC
*
93472 ATAGGAAGATTTATCAAAATTTC
1 ATATGAAG--TTATCAAAATTTC
* * *
93495 ATAGCGAGGTTATCACAATTTC
1 ATA-TGAAGTTATCAAAATTTC
*
93517 ATAGTG-TGATTATCAAAATTTC
1 ATA-TGAAG-TTATCAAAATTTC
* * * *
93539 AGA-G-TGTGATCACTAACAATTC
1 ATATGAAGTTATCA--AA-ATTTC
* * *
93561 ATATGAAGGTTTTTAAATTTTC
1 ATATGAA-GTTATCAAAATTTC
* ** * *
93583 ATAACGTGGTTATCAATATATC
1 AT-ATGAAGTTATCAAAATTTC
* *
93605 ATATGGAGATTATCAACA--TC
1 ATATGAAG-TTATCAAAATTTC
**
93625 GCATG--GTTATCAAAATTTC
1 ATATGAAGTTATCAAAATTTC
93644 AT-TGGGAAGTTATCAAAATTTC
1 ATAT--GAAGTTATCAAAATTTC
* *
93666 ATATTGAGGTCT-TCAAAATTCC
1 ATA-TGAAGT-TATCAAAATTTC
* * *
93688 TTA-GAGAGGTTAACCAAATTTC
1 ATATGA-A-GTTATCAAAATTTC
* ** *
93710 ATAAGAAGGTTAAAAAAAATT-
1 ATATGAA-GTTATCAAAATTTC
** * *
93731 ATAAAAAGGTTCTCGAAATTTC
1 ATATGAA-GTTATCAAAATTTC
*
93753 ATA-GTATAGTTATTAAAATTTC
1 ATATG-A-AGTTATCAAAATTTC
*
93775 ATAGGAAGGTTATCAAAATTTC
1 ATATGAA-GTTATCAAAATTTC
93797 ATA
1 ATA
93800 ATGGGATCAT
Statistics
Matches: 412, Mismatches: 104, Indels: 93
0.68 0.17 0.15
Matches are distributed among these distances:
16 12 0.03
17 8 0.02
18 3 0.01
19 7 0.02
20 26 0.06
21 31 0.08
22 265 0.64
23 52 0.13
24 4 0.01
25 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ATATGAAGTTATCAAAATTTC
Found at i:93445 original size:104 final size:105
Alignment explanation
Indices: 93308--93515 Score: 242
Period size: 104 Copynumber: 2.0 Consensus size: 105
93298 TTCACAAGAG
* * *
93308 AGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGA-GATTAACAAAATTTCATTAT
1 AGTTATCAAAATTTCATAGAAAGTAGATCAAAATTTCATAGGGAGGATTAACAAAATTTCA-TAG
*
93372 GAAG-TTATCAAAAAAACATAGGGAGGTTATCAAAATTTTT
65 GAAGATTATCAAAAAAACATAGCGAGGTTATCAAAATTTTT
* * * * * *
93412 AGTTATCAAGATTTCATAAGAAAGT-TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAG
1 AGTTATCAAAATTTCAT-AGAAAGTAGATCAAAATTTCATAGGGAGGATTAACAAAATTTCATAG
*** *
93476 GAAGATTTATCAAAATTTCATAGCGAGGTTATCACAATTT
65 GAAGA-TTATCAAAAAAACATAGCGAGGTTATCAAAATTT
93516 CATAGTGTGA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
104 39 0.45
105 18 0.21
106 29 0.34
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (105 bp):
AGTTATCAAAATTTCATAGAAAGTAGATCAAAATTTCATAGGGAGGATTAACAAAATTTCATAGG
AAGATTATCAAAAAAACATAGCGAGGTTATCAAAATTTTT
Found at i:93794 original size:44 final size:44
Alignment explanation
Indices: 93245--93799 Score: 189
Period size: 44 Copynumber: 12.8 Consensus size: 44
93235 TCAAGGAGGA
* ** * *
93245 TATCAAATTTTCATATAAAGGTTATCAAAATTTCATCGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATAGT
* * *
93289 TTTCAAAATTTCACAAG-AGAGTTATCAAAATTTCATAGTAT-GT
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAGTATAGT
* * * *
93332 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCAT--TATGAAGT
1 -TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTAT--AGT
*** *
93377 TATCAAAAAAACATAGGGAGGTTATCAAAA-TT--T--T-TAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATAGT
* * * * * *
93415 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGA-GGTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA-GTATAG-T
* * * *
93460 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA-GGT
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAG-TATAGT
* * * *
93505 TATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAG--T-GT
1 TATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGTATAGT
* * * * * * *** *
93546 GATCACTAACAATTCATATGAAGGTTTTTAAATTTTCATAACGTGGT
1 TATCA--AA-ATTTCATAGGAAGGTTATCAAAATTTCATAGTATAGT
* * * * * *
93593 TATCAATATATCATATGG-AGATTATC--AA---CATCGCATGGT
1 TATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGTATAGT
*
93632 TATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATA-T-TGAGGT
1 TATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGTAT-A-GT
* * * *
93676 CT-TCAAAATTCCTTA-GAGAGGTTAACCAAATTTCATAAG-A-AGGT
1 -TATCAAAATTTCATAGGA-AGGTTATCAAAATTTCAT-AGTATA-GT
** * ** * *
93720 TAAAAAAAATT-ATAAAAAGGTTCTCGAAATTTCATAGTATAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATAGT
*
93763 TATTAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
93800 ATGGGATCAT
Statistics
Matches: 375, Mismatches: 90, Indels: 92
0.67 0.16 0.17
Matches are distributed among these distances:
38 26 0.07
39 28 0.07
40 3 0.01
41 11 0.03
42 9 0.02
43 39 0.10
44 190 0.51
45 42 0.11
46 21 0.06
47 6 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATAGT
Found at i:97637 original size:3 final size:3
Alignment explanation
Indices: 97631--97664 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
97621 CTCCGATTTT
97631 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
97665 CATCTAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:105597 original size:30 final size:30
Alignment explanation
Indices: 105537--105627 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
105527 ACATGTCGCG
105537 TTTGGATATTTTGCCCCTTGAACT-TCAAT
1 TTTGGATATTTTGCCCCTTGAACTCTCAAT
* *
105566 TTTGGATATTTTGCCTCTTGAGCTCTCAAT
1 TTTGGATATTTTGCCCCTTGAACTCTCAAT
*
105596 TTTGGACATTTTGCCCCTTGAACTCTCAAT
1 TTTGGATATTTTGCCCCTTGAACTCTCAAT
105626 TT
1 TT
105628 GAGTCTCTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 22 0.39
30 34 0.61
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (30 bp):
TTTGGATATTTTGCCCCTTGAACTCTCAAT
Found at i:105761 original size:30 final size:30
Alignment explanation
Indices: 105707--105845 Score: 174
Period size: 30 Copynumber: 4.6 Consensus size: 30
105697 CATGGACGGA
* *
105707 GTTTTGGATGTTTTGTCTCCTGAAATTGTAC
1 GTTTTGGACGTTTTG-CCCCTGAAATTGTAC
*
105738 GTTTTGGACATTTTGCCCCTGAAATTGTAC
1 GTTTTGGACGTTTTGCCCCTGAAATTGTAC
* *
105768 GTTTTGGACATTTTGCCCCTGAACTTGTAC
1 GTTTTGGACGTTTTGCCCCTGAAATTGTAC
* *
105798 ATTTTGGACGTTTTGCCCCCTGAATTTGTA-
1 GTTTTGGACGTTTTG-CCCCTGAAATTGTAC
*
105828 G-TTTGGATGTTTTGCCCC
1 GTTTTGGACGTTTTGCCCC
105846 CTAAGAAACA
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
28 4 0.04
29 12 0.12
30 56 0.57
31 26 0.27
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (30 bp):
GTTTTGGACGTTTTGCCCCTGAAATTGTAC
Found at i:105955 original size:30 final size:31
Alignment explanation
Indices: 105912--105973 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
105902 ACGGAGGCTC
*
105912 AAATTGAAAGTTCAGGGAGAAAAATGTCCAA
1 AAATTGAAAGTTCAGGGAGAAAAACGTCCAA
* * *
105943 AAATTG-AAGTTCATGGTGCAAAACGTCCAA
1 AAATTGAAAGTTCAGGGAGAAAAACGTCCAA
105973 A
1 A
105974 CGCTACAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (31 bp):
AAATTGAAAGTTCAGGGAGAAAAACGTCCAA
Found at i:106505 original size:12 final size:12
Alignment explanation
Indices: 106488--106512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
106478 ATGTCACCGA
106488 ATATCCGTCAAT
1 ATATCCGTCAAT
106500 ATATCCGTCAAT
1 ATATCCGTCAAT
106512 A
1 A
106513 AAACTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (12 bp):
ATATCCGTCAAT
Found at i:111264 original size:16 final size:18
Alignment explanation
Indices: 111225--111264 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
111215 TTGGAACCAT
111225 ATGACCCAAAACCGAAAA
1 ATGACCCAAAACCGAAAA
*
111243 A-CACCC-AAACC-AAAA
1 ATGACCCAAAACCGAAAA
111258 ATGACCC
1 ATGACCC
111265 GACTTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 4 0.21
18 1 0.05
ACGTcount: A:0.53, C:0.35, G:0.07, T:0.05
Consensus pattern (18 bp):
ATGACCCAAAACCGAAAA
Done.