Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013461.1 Corchorus capsularis cultivar CVL-1 contig13482, 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: 23727
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Found at i:894 original size:25 final size:26
Alignment explanation
Indices: 866--916 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
856 TTTAACTTGC
866 ACGTGTGTTGCACA-TCACCTAACAT
1 ACGTGTGTTGCACAGTCACCTAACAT
891 ACGTGTGTTGCACAGTCACCTAACAT
1 ACGTGTGTTGCACAGTCACCTAACAT
917 GTTGCGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (26 bp):
ACGTGTGTTGCACAGTCACCTAACAT
Found at i:967 original size:22 final size:22
Alignment explanation
Indices: 935--1121 Score: 129
Period size: 22 Copynumber: 8.5 Consensus size: 22
925 TGAATAGTTT
935 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* * *
957 TATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACTACCC
979 TATGAAATTTTGATATA-TA-CC
1 TATGAAATTTTGATA-ACTACCC
* *
1000 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCC
**
1022 TATGAAATTTTGATAACCTA-AA
1 TATGAAATTTTGATAA-CTACCC
* *
1044 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTACCC
** *
1067 TATGAAATTTTG-TAACCTTTCT
1 TATGAAATTTTGATAA-CTACCC
*
1089 TAT-AATTTTTGATAACCT-CCC
1 TATGAAATTTTGATAA-CTACCC
*
1110 TATGAGATTTTG
1 TATGAAATTTTG
1122 TTAAACTCCT
Statistics
Matches: 134, Mismatches: 20, Indels: 22
0.76 0.11 0.12
Matches are distributed among these distances:
21 33 0.25
22 84 0.63
23 17 0.13
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:1014 original size:43 final size:44
Alignment explanation
Indices: 935--1038 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
925 TGAATAGTTT
* * *
935 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAACCACGC-
1 TATGAAATTTTGATAACTACCCTATGAAATTGTGATAAACAC-CA
*
979 TATGAAATTTTGATATA-TA-CCTATGAAATTGTGATAAACTCCA
1 TATGAAATTTTGATA-ACTACCCTATGAAATTGTGATAAACACCA
1022 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
1039 CTAAATATGA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
42 2 0.04
43 33 0.62
44 17 0.32
45 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCCTATGAAATTGTGATAAACACCA
Found at i:1061 original size:44 final size:42
Alignment explanation
Indices: 935--1082 Score: 156
Period size: 44 Copynumber: 3.4 Consensus size: 42
925 TGAATAGTTT
* * *
935 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACTA-CCTATGAAATTTTGATAAACTC-C
*
979 TATGAAATTTTGATATA-TACCTATGAAATTGTGATAAACTCC
1 TATGAAATTTTGATA-ACTACCTATGAAATTTTGATAAACTCC
** *
1021 ATATGAAATTTTGATAACCTAAATATGAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATAA-CTACCTATGAAATTTTGATAAA-C-TCC
1067 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
1083 CTTTCTTATA
Statistics
Matches: 90, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
42 2 0.02
43 34 0.38
44 37 0.41
45 14 0.16
46 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (42 bp):
TATGAAATTTTGATAACTACCTATGAAATTTTGATAAACTCC
Found at i:1112 original size:43 final size:43
Alignment explanation
Indices: 935--1122 Score: 132
Period size: 43 Copynumber: 4.3 Consensus size: 43
925 TGAATAGTTT
** * * *
935 TATGAAATTTTGATAA-CTACCCTATTAAATTTTGATAACCACGC
1 TATGAAATTTTG-TAACCTA-AATATGAAATTTTGATAACCTCCC
** * * *
979 TATGAAATTTTGATATA--TACCTATGAAATTGTGATAAACTCCA
1 TATGAAATTTTG-TA-ACCTAAATATGAAATTTTGATAACCTCCC
* *
1022 TATGAAATTTTGATAACCTAAATATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTG-TAACCTAAATATGAAATTTTGAT-AACCTCCC
*** *
1067 TATGAAATTTTGTAACCTTTCTTAT-AATTTTTGATAACCTCCC
1 TATGAAATTTTGTAACC-TAAATATGAAATTTTGATAACCTCCC
*
1110 TATGAGATTTTGT
1 TATGAAATTTTGT
1123 TAAACTCCTT
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
42 1 0.01
43 52 0.44
44 44 0.37
45 22 0.18
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (43 bp):
TATGAAATTTTGTAACCTAAATATGAAATTTTGATAACCTCCC
Found at i:1134 original size:43 final size:44
Alignment explanation
Indices: 1059--1146 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 44
1049 AATTTTAATA
* * *
1059 AACCTTCCTATGAAATTTTGTAACCTTTCTTATAATTTT-TGAT
1 AACCTCCCTATGAAATTTTGTAAACTTCCTTATAATTTTCTGAT
* *
1102 AACCTCCCTATGAGATTTTGTTAAAC-TCCTTATCATTTTCTGAT
1 AACCTCCCTATGAAATTTTG-TAAACTTCCTTATAATTTTCTGAT
1146 A
1 A
1147 TTATAGTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
43 29 0.76
44 9 0.24
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (44 bp):
AACCTCCCTATGAAATTTTGTAAACTTCCTTATAATTTTCTGAT
Found at i:1797 original size:18 final size:16
Alignment explanation
Indices: 1766--1810 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
1756 AGTGAACAAT
1766 AAAATAAATAAGCAAG
1 AAAATAAATAAGCAAG
*
1782 AAAATAAAATTAAGCAAC
1 AAAAT-AAA-TAAGCAAG
*
1800 AAGATAAATAA
1 AAAATAAATAA
1811 ATACTCCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 11 0.44
ACGTcount: A:0.69, C:0.07, G:0.09, T:0.16
Consensus pattern (16 bp):
AAAATAAATAAGCAAG
Found at i:13129 original size:19 final size:18
Alignment explanation
Indices: 13096--13132 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
13086 TTGAAATAAT
13096 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
13114 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
13133 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:16127 original size:18 final size:18
Alignment explanation
Indices: 16104--16140 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16094 GGCATGACTC
16104 TAGCCAGGACGCGATATT
1 TAGCCAGGACGCGATATT
16122 TAGCCAGGACGCGATATT
1 TAGCCAGGACGCGATATT
16140 T
1 T
16141 GGCACGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (18 bp):
TAGCCAGGACGCGATATT
Found at i:20036 original size:55 final size:55
Alignment explanation
Indices: 19975--20271 Score: 497
Period size: 55 Copynumber: 5.4 Consensus size: 55
19965 AAAAAGGGGC
** *
19975 AATCAGTAATTAAGTAAAATTAGATTAGTCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
20030 AATCAGTAATTAAGTAAAAAGAGATTAA-CAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
20084 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
20139 AATCAGTAATTAAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATT-AAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
20195 AATCAGTAATTAAGTAAAAAGAGATTAAGCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
**
20250 AATCAGTAACCAAGTAAAAAGA
1 AATCAGTAATTAAGTAAAAAGA
20272 TGGTAATCAG
Statistics
Matches: 230, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
54 53 0.23
55 122 0.53
56 55 0.24
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:20217 original size:111 final size:109
Alignment explanation
Indices: 19975--20271 Score: 495
Period size: 111 Copynumber: 2.7 Consensus size: 109
19965 AAAAAGGGGC
** *
19975 AATCAGTAATTAAGTAAAATTAGATTAGTCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
* *
20040 TAAGTAAAAAGAGATTAACAGAGTTAAGGTAATAGTAATCAGTA
66 TAAGTAAAAAGAGATTAACAGAGTCAAAGTAATAGTAATCAGTA
*
20084 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
20149 TAAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
66 T-AAGTAAAAAGAGATTAA-CAGAGTCAAAGTAATAGTAATCAGTA
* *
20195 AATCAGTAATTAAGTAAAAAGAGATTAAGCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAC
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
*
20260 CAAGTAAAAAGA
66 TAAGTAAAAAGA
20272 TGGTAATCAG
Statistics
Matches: 176, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
109 62 0.35
110 28 0.16
111 86 0.49
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (109 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
TAAGTAAAAAGAGATTAACAGAGTCAAAGTAATAGTAATCAGTA
Found at i:20530 original size:24 final size:24
Alignment explanation
Indices: 20502--20548 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20492 GAGATTGGTA
20502 ATTAAAGTAGTAATTAAGATTCAT
1 ATTAAAGTAGTAATTAAGATTCAT
* *
20526 ATTAAAGTGGTAATTGAGATTCA
1 ATTAAAGTAGTAATTAAGATTCA
20549 AAGTAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (24 bp):
ATTAAAGTAGTAATTAAGATTCAT
Found at i:20778 original size:26 final size:26
Alignment explanation
Indices: 20730--20959 Score: 131
Period size: 26 Copynumber: 8.7 Consensus size: 26
20720 GAGAGTAATT
* *
20730 AGTAAATAAGAGTAAGAACTGGTGA-TC
1 AGTAAA-AAGAGTAAAAAGTGGT-ATTC
20757 AGTAAAAAGAGTAAAAAGTGGTATTC
1 AGTAAAAAGAGTAAAAAGTGGTATTC
* *
20783 AGTAAAAAGGGATATAAA-TGG---T-
1 AGTAAAAAGAG-TAAAAAGTGGTATTC
*
20805 A--AAAAAGAGTAAAAA-TGGTATTA
1 AGTAAAAAGAGTAAAAAGTGGTATTC
* *
20828 AGTGAAAAAAGGAGAGTAAAAAAATGGTAATTA
1 AGT---AAAA--AGAGT-AAAAAGTGGT-ATTC
*
20861 AGTAAAAAGAGTAAGAAGTGGTATTC
1 AGTAAAAAGAGTAAAAAGTGGTATTC
* * *
20887 AGTCAAAATAGA-AAGAAAAGGGGTAATC
1 AGT-AAAA-AGAGTA-AAAAGTGGTATTC
*
20915 AGTAAAAAGAGTAAAATA-TGGTAATC
1 AGTAAAAAGAGTAAAA-AGTGGTATTC
*
20941 AGTACAAAGAGTAGAAAAG
1 AGTAAAAAGAGTA-AAAAG
20960 AATGGTAGTT
Statistics
Matches: 164, Mismatches: 16, Indels: 46
0.73 0.07 0.20
Matches are distributed among these distances:
19 8 0.05
20 7 0.04
22 2 0.01
23 2 0.01
25 1 0.01
26 61 0.37
27 33 0.20
28 25 0.15
30 9 0.05
31 5 0.03
32 4 0.02
33 7 0.04
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.20
Consensus pattern (26 bp):
AGTAAAAAGAGTAAAAAGTGGTATTC
Found at i:20836 original size:28 final size:27
Alignment explanation
Indices: 20805--20894 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 27
20795 TATAAATGGT
20805 AAAAAAGAGTAAAAATGGTATTAAGTGA
1 AAAAAAGAGTAAAAATGGTATTAAGT-A
20833 AAAAAGGAGAGTAAAAAAATGGTAATTAAGT-
1 AAAAA--AGAGT--AAAAATGGT-ATTAAGTA
* * *
20864 -AAAAAGAGTAAGAAGTGGTATTCAGTC
1 AAAAAAGAGTAA-AAATGGTATTAAGTA
20891 AAAA
1 AAAA
20895 TAGAAAGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
26 8 0.15
27 6 0.12
28 13 0.25
30 9 0.17
32 9 0.17
33 7 0.13
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (27 bp):
AAAAAAGAGTAAAAATGGTATTAAGTA
Found at i:20846 original size:30 final size:31
Alignment explanation
Indices: 20810--20868 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
20800 ATGGTAAAAA
20810 AGAGT-AAAAATGGT-ATTAAGTGAAAAAAGG
1 AGAGTAAAAAATGGTAATTAAGT-AAAAAAGG
20840 AGAGTAAAAAAATGGTAATTAAGTAAAAA
1 AGAGT-AAAAAATGGTAATTAAGTAAAAA
20869 GAGTAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.19
32 14 0.54
33 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.20
Consensus pattern (31 bp):
AGAGTAAAAAATGGTAATTAAGTAAAAAAGG
Done.