Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019564.1 Corchorus olitorius cultivar O-4 contig19597, 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: 39931
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2987 original size:33 final size:33
Alignment explanation
Indices: 2950--3015 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2940 GCAACCAGCT
*
2950 GAAGATGCAAGTGGAAGCCTAAAACAGCTTGCC
1 GAAGATGCAAATGGAAGCCTAAAACAGCTTGCC
* *
2983 GAAGATGCAAATGGAAGCCTAGAGCAGCTTGCC
1 GAAGATGCAAATGGAAGCCTAAAACAGCTTGCC
3016 TTCAATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.15
Consensus pattern (33 bp):
GAAGATGCAAATGGAAGCCTAAAACAGCTTGCC
Found at i:3865 original size:15 final size:15
Alignment explanation
Indices: 3842--3883 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3832 CATGAATGAA
*
3842 GAGAAAATCGAATAC-
1 GAGACAATCGAAT-CT
3857 GAGACAATCGAATCT
1 GAGACAATCGAATCT
3872 GAGACAATCGAA
1 GAGACAATCGAA
3884 GAAGTTTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 1 0.04
15 24 0.96
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (15 bp):
GAGACAATCGAATCT
Found at i:4551 original size:70 final size:70
Alignment explanation
Indices: 4436--4576 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
4426 ATTACCTTAT
* * *
4436 ATCTTAATTATTACCTTGTCAAATCCACTTGTAATAATGAAACTTTTTCAATCTATATAATAAAA
1 ATCTTAATTATTACCTTATCAAATCCACTTGTAACAATGAAACTTTATCAATCTATATAATAAAA
4501 ATCAA
66 ATCAA
* *
4506 ATCTTAATTATTACCTTATCAAATCCACTTGTAACAATGACACTTTATCAATCTATATAATGAAA
1 ATCTTAATTATTACCTTATCAAATCCACTTGTAACAATGAAACTTTATCAATCTATATAATAAAA
4571 ATCAA
66 ATCAA
4576 A
1 A
4577 CCACTTGTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (70 bp):
ATCTTAATTATTACCTTATCAAATCCACTTGTAACAATGAAACTTTATCAATCTATATAATAAAA
ATCAA
Found at i:4582 original size:47 final size:48
Alignment explanation
Indices: 4523--4622 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 48
4513 TTATTACCTT
*
4523 ATCAAATCCACTTGTAACAATGACACTTTATCAATCTATATAATGAAA
1 ATCAAATCCACTTGTAACAATGACAATTTATCAATCTATATAATGAAA
4571 ATCAAA-CCACTTGTAACAATGACAATTTATCAATCTATATAATGAAA
1 ATCAAATCCACTTGTAACAATGACAATTTATCAATCTATATAATGAAA
4618 ATCAA
1 ATCAA
4623 CCAGCCTTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 45 0.88
48 6 0.12
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (48 bp):
ATCAAATCCACTTGTAACAATGACAATTTATCAATCTATATAATGAAA
Found at i:18421 original size:15 final size:15
Alignment explanation
Indices: 18403--18435 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18393 TTTGTAAAAA
18403 AAATGAGCGTTTTGT
1 AAATGAGCGTTTTGT
*
18418 AAATGAGTGTTTTGT
1 AAATGAGCGTTTTGT
18433 AAA
1 AAA
18436 GTTCTATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.39
Consensus pattern (15 bp):
AAATGAGCGTTTTGT
Found at i:20469 original size:16 final size:16
Alignment explanation
Indices: 20448--20478 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20438 ATAACCAATG
20448 CAATTCTTAAATTTGC
1 CAATTCTTAAATTTGC
20464 CAATTCTTAAATTTG
1 CAATTCTTAAATTTG
20479 GCCTGCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (16 bp):
CAATTCTTAAATTTGC
Found at i:24845 original size:33 final size:34
Alignment explanation
Indices: 24807--24876 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
24797 AAGTCTAAAC
* * *
24807 AAATAAAGAGTCTAC-AAAGAGGTTTACTAATAA
1 AAATAAAGAATCTACAAAAAAGGTTAACTAATAA
* *
24840 AAATAAAGAATCTCCAAAAAAGGTTAACTAATGA
1 AAATAAAGAATCTACAAAAAAGGTTAACTAATAA
24874 AAA
1 AAA
24877 CAATTACAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (34 bp):
AAATAAAGAATCTACAAAAAAGGTTAACTAATAA
Found at i:25197 original size:31 final size:30
Alignment explanation
Indices: 25126--25197 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
25116 GTCTATCAGC
25126 TTTTAATTTGTTTAATTTAAGGCTTTCATT
1 TTTTAATTTGTTTAATTTAAGGCTTTCATT
* * *
25156 TTAATGATTTGTTTAATTTAATGCTTT-AGTT
1 TT-TTAATTTGTTTAATTTAAGGCTTTCA-TT
25187 GTTTTAATTTG
1 -TTTTAATTTG
25198 CAATTAGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
30 3 0.09
31 29 0.85
32 2 0.06
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.60
Consensus pattern (30 bp):
TTTTAATTTGTTTAATTTAAGGCTTTCATT
Found at i:29861 original size:25 final size:26
Alignment explanation
Indices: 29833--29892 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
29823 CGTGTAATTT
* * *
29833 CATTTTTATGAA-TAAAAATTAAATA
1 CATTTTTATAAACAAAAAACTAAATA
29858 CATTTTCT-TAAACAAAAAACTAAATA
1 CATTTT-TATAAACAAAAAACTAAATA
29884 CATTTTTAT
1 CATTTTTAT
29893 TATGCAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (26 bp):
CATTTTTATAAACAAAAAACTAAATA
Found at i:36681 original size:92 final size:93
Alignment explanation
Indices: 36597--36780 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
36587 ACTTTTTTAT
* * *
36597 TAAATTAGTAATATCGTAAAAA-AAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
36661 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
*
36689 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAATGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
36754 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
36781 ATTTAAATAA
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
92 19 0.22
93 67 0.78
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:36698 original size:22 final size:22
Alignment explanation
Indices: 36673--36718 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
36663 TTTTTAGTTG
*
36673 AGTAAAACTA-TAAAAGTAAAAT
1 AGTAAAA-TAGTAAAAATAAAAT
36695 AGTAAAATAGTAAAAATAAAAT
1 AGTAAAATAGTAAAAATAAAAT
36717 AG
1 AG
36719 GTATAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (22 bp):
AGTAAAATAGTAAAAATAAAAT
Found at i:36712 original size:9 final size:8
Alignment explanation
Indices: 36687--36718 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
36677 AAACTATAAA
36687 AGTAAAAT
1 AGTAAAAT
36695 AGTAAAAT
1 AGTAAAAT
36703 AGTAAAA-
1 AGTAAAAT
36710 A-TAAAAT
1 AGTAAAAT
36717 AG
1 AG
36719 GTATAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.23
7 2 0.09
8 15 0.68
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (8 bp):
AGTAAAAT
Found at i:36857 original size:31 final size:31
Alignment explanation
Indices: 36816--36877 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
36806 ATATTCGAAA
*
36816 AATAATGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
36847 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
36878 TACTATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (31 bp):
AATAAGGGTATAATAGGCGATTCAAAAGTTT
Found at i:36903 original size:21 final size:21
Alignment explanation
Indices: 36874--36913 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36864 CGATTCAAAA
* *
36874 GTTTTACTATCAAATTTTGGG
1 GTTTAACTATCAAAATTTGGG
36895 GTTTAACTATCAAAATTTG
1 GTTTAACTATCAAAATTTG
36914 TCGTTTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (21 bp):
GTTTAACTATCAAAATTTGGG
Found at i:36919 original size:21 final size:21
Alignment explanation
Indices: 36874--36919 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
36864 CGATTCAAAA
* * *
36874 GTTTTACTATCAAATTTTGGG
1 GTTTAACTATCAAAATTTGGC
*
36895 GTTTAACTATCAAAATTTGTC
1 GTTTAACTATCAAAATTTGGC
36916 GTTT
1 GTTT
36920 GACCATTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (21 bp):
GTTTAACTATCAAAATTTGGC
Found at i:37123 original size:55 final size:55
Alignment explanation
Indices: 37052--37397 Score: 185
Period size: 55 Copynumber: 6.3 Consensus size: 55
37042 ACCATCATCC
* * * *
37052 TTTGGGGTTTGCCCATGCATGTACAA-T-GATGTTTTTGGAGGTTTGACTATTAAAA
1 TTTGGGGTTTGACCATGCATATACAATTAAATG-TTTT-GAGGTTTGACTATCAAAA
* * *
37107 TTTGGGGTTTGACCATGCATATACAATTAAATGTTTTGTGGTTTGACTATCGAAT
1 TTTGGGGTTTGACCATGCATATACAATTAAATGTTTTGAGGTTTGACTATCAAAA
* * * * ** * ***
37162 TTTGGGGTTTGACCAT---TAT-C-CTT--TTGGGTTTGACCATGCATGTACAATGC-TGT
1 TTTGGGGTTTGACCATGCATATACAATTAAAT-GTTTTG---AGGTTTG-ACTAT-CAAAA
* * * * * * *
37215 TTTGGGGTTTGATCATGCATATACAATGAAATGTTTTTTGTGATATGACTATCGAAC
1 TTTGGGGTTTGACCATGCATATACAATTAAATG--TTTTGAGGTTTGACTATCAAAA
* * * * * *
37272 TTTGGGGATTGATCATACATGTACAA-T-GATGTTTTTGGAGGTTTGACTATTAAAA
1 TTTGGGGTTTGACCATGCATATACAATTAAATG-TTTT-GAGGTTTGACTATCAAAA
* * * * *
37327 TTTGGGGTTTGACCATGCATAAACAATGAAATGTTTTGTGGTTTGACTATCGAAC
1 TTTGGGGTTTGACCATGCATATACAATTAAATGTTTTGAGGTTTGACTATCAAAA
37382 TTTGGGGTTTGACCAT
1 TTTGGGGTTTGACCAT
37398 CATCCTTTGG
Statistics
Matches: 218, Mismatches: 52, Indels: 42
0.70 0.17 0.13
Matches are distributed among these distances:
48 1 0.00
49 5 0.02
50 2 0.01
51 1 0.00
52 6 0.03
53 20 0.09
54 6 0.03
55 120 0.55
56 13 0.06
57 34 0.16
58 4 0.02
59 1 0.00
60 1 0.00
61 4 0.02
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.40
Consensus pattern (55 bp):
TTTGGGGTTTGACCATGCATATACAATTAAATGTTTTGAGGTTTGACTATCAAAA
Found at i:37218 original size:31 final size:32
Alignment explanation
Indices: 37183--37242 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
37173 ACCATTATCC
*
37183 TTTT-GGGTTTGACCATGCATGTACAATGCTG
1 TTTTGGGGTTTGACCATGCATATACAATGCTG
*
37214 TTTTGGGGTTTGATCATGCATATACAATG
1 TTTTGGGGTTTGACCATGCATATACAATG
37243 AAATGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (32 bp):
TTTTGGGGTTTGACCATGCATATACAATGCTG
Found at i:37390 original size:21 final size:21
Alignment explanation
Indices: 37361--37418 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
37351 AATGAAATGT
* *
37361 TTTGTGGTTTGACTATCGA-AC
1 TTTGGGGTTTGACCATC-ATAC
*
37382 TTTGGGGTTTGACCATCATCC
1 TTTGGGGTTTGACCATCATAC
37403 TTTGGGGTTTGACCAT
1 TTTGGGGTTTGACCAT
37419 GCATGTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (21 bp):
TTTGGGGTTTGACCATCATAC
Found at i:37464 original size:33 final size:34
Alignment explanation
Indices: 37403--37473 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
37393 ACCATCATCC
* * *
37403 TTTGGGGTTTGACCATGCATGTATAATG-ATGTT
1 TTTGGGGATTGACCATGCATATACAATGAATGTT
* *
37436 TTTGGGGATTGATCATTCATATACAATGAAATGTT
1 TTTGGGGATTGACCATGCATATACAATG-AATGTT
37471 TTT
1 TTT
37474 TGTGATATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 23 0.74
35 8 0.26
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (34 bp):
TTTGGGGATTGACCATGCATATACAATGAATGTT
Found at i:37540 original size:55 final size:55
Alignment explanation
Indices: 37436--37612 Score: 187
Period size: 55 Copynumber: 3.2 Consensus size: 55
37426 TAATGATGTT
* * * * *
37436 TTTGGGGATTGATCATTCATATACAATGAAATGTTTTTTGTGATATGACTATCGAAC
1 TTTGGGGTTTGACCATGCATATACAATG--ATGTTTTTTGTGGTTTGACTATCGAAC
* * * * *
37493 TTTGGGGTTTGACCATACATGTACAATGATGTTTTTTGAGGTTTGACTAAT-AAAG
1 TTTGGGGTTTGACCATGCATATACAATGATGTTTTTTGTGGTTTGACT-ATCGAAC
* *
37548 TTTGGGGTTTGACCATGCATATACAATGACATGTTTTTT-TGGTTTGACTATTGAAG
1 TTTGGGGTTTGACCATGCATATACAATG--ATGTTTTTTGTGGTTTGACTATCGAAC
37604 TTTGGGGTT
1 TTTGGGGTT
37613 AAATCATTAT
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
55 47 0.46
56 23 0.22
57 33 0.32
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (55 bp):
TTTGGGGTTTGACCATGCATATACAATGATGTTTTTTGTGGTTTGACTATCGAAC
Found at i:37567 original size:221 final size:221
Alignment explanation
Indices: 37051--37662 Score: 956
Period size: 220 Copynumber: 2.8 Consensus size: 221
37041 GACCATCATC
* *
37051 CTTTGGGGTTTGCCCATGCATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTTGGGGTT
1 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTTGGGGTT
* *
37116 TGACCATGCATATACAATTAAATGTTTTGTGGTTTGACTATCGAATTTTGGGGTTTGACCATTAT
66 TGACCATGCATATACAATGAAATGTTTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCATTAT
* * *
37181 CCTTTTGGGTTTGACCATGCATGTACAATGCTG-TTTTGGGGTTTGATCATGCATATACAATGAA
131 CCTTTAGGGTTTGACCATGCATGTACAATGATGTTTTTGGGGATTGATCATGCATATACAATGAA
37245 ATGTTTTTTGTGATATGACTATCGAA
196 ATGTTTTTTGTGATATGACTATCGAA
* *
37271 CTTTGGGGATTGATCATACATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTTGGGGTT
1 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTTGGGGTT
* *
37336 TGACCATGCATAAACAATGAAATGTTTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCATCAT
66 TGACCATGCATATACAATGAAATGTTTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCATTAT
* * *
37401 CCTTTGGGGTTTGACCATGCATGTATAATGATGTTTTTGGGGATTGATCATTCATATACAATGAA
131 CCTTTAGGGTTTGACCATGCATGTACAATGATGTTTTTGGGGATTGATCATGCATATACAATGAA
37466 ATGTTTTTTGTGATATGACTATCGAA
196 ATGTTTTTTGTGATATGACTATCGAA
* * *
37492 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTTTGAGGTTTGACTAATAAAGTTTGGGGTT
1 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTTGGGGTT
* * * * ** *
37557 TGACCATGCATATACAATGACATGTTTTTTTGGTTTGACTATTGAAGTTTGGGGTTAAATCATTA
66 TGACCATGCATATACAATGAAATG-TTTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCATTA
* * * *
37622 TCCTTTAGGATTTTACCATACATGTACAATGGTGTTTTTGG
130 TCCTTTAGGGTTTGACCATGCATGTACAATGATGTTTTTGG
37663 ATAACAATAC
Statistics
Matches: 357, Mismatches: 33, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
220 152 0.43
221 137 0.38
222 68 0.19
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.41
Consensus pattern (221 bp):
CTTTGGGGTTTGACCATACATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTTGGGGTT
TGACCATGCATATACAATGAAATGTTTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCATTAT
CCTTTAGGGTTTGACCATGCATGTACAATGATGTTTTTGGGGATTGATCATGCATATACAATGAA
ATGTTTTTTGTGATATGACTATCGAA
Done.