Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013531.1 Corchorus capsularis cultivar CVL-1 contig13552, 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: 5818
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:990 original size:22 final size:22
Alignment explanation
Indices: 965--1027 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
955 GTCCCAAGCT
*
965 ATAACTACACTATGAAATTGTG
1 ATAACTACACTATGAAATTATG
*
987 ATAACCT-CTCTATGAAATTATG
1 ATAA-CTACACTATGAAATTATG
1009 ATAA-TCACACTATGAAATT
1 ATAACT-ACACTATGAAATT
1028 TCAGTAACCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (22 bp):
ATAACTACACTATGAAATTATG
Found at i:1403 original size:22 final size:22
Alignment explanation
Indices: 1378--1845 Score: 168
Period size: 22 Copynumber: 21.6 Consensus size: 22
1368 ATGATCCCAT
1378 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
1400 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
1422 TATGGAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAACCTTCC
**
1444 TAT-AAATTTTTTTTAACCTT-C
1 TATGAAA-TTTTGATAACCTTCC
* *
1465 TCATAAAATTTTGTTAACC-TCC
1 T-ATGAAATTTTGATAACCTTCC
* * *
1487 TTAAGGAATTTTGA-AGACC-TCAA
1 -TATGAAATTTTGATA-ACCTTC-C
*
1510 TATGAAAATTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
1532 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
1555 TATGAGATGTTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
1577 TATGAAATTTAGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
1600 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
1623 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
1645 TATGAAATCTTGATAA---T--
1 TATGAAATTTTGATAACCTTCC
* *
1662 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
1683 TATGATTTTTTGATAA-CATCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
1705 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*** * *
1727 TATG-AATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
* *
1748 TATAAAATTTTGATAA-CTCTCT
1 TATGAAATTTTGATAACCT-TCC
* **
1770 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
1792 TATGAAATTTTTATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
1813 -CTGAAATTTTGATATCCTACC
1 TATGAAATTTTGATAACCTTCC
1834 --TGAAATTTTGAT
1 TATGAAATTTTGAT
1846 TACTCCATAA
Statistics
Matches: 326, Mismatches: 93, Indels: 56
0.69 0.20 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
19 1 0.00
20 27 0.08
21 29 0.09
22 190 0.58
23 64 0.20
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:1607 original size:23 final size:23
Alignment explanation
Indices: 1467--1638 Score: 99
Period size: 23 Copynumber: 7.7 Consensus size: 23
1457 TAACCTTCTC
*
1467 ATAAAATTTTG-TTAACCT-CCT
1 ATAAAATTTTGATAAACCTCCCT
* **
1488 -TAAGGAATTTTGA-AGACCTCAAT
1 ATAA--AATTTTGATAAACCTCCCT
* *
1511 ATGAAAA-TTTGAT-AACTTCCCA
1 AT-AAAATTTTGATAAACCTCCCT
* * *
1533 ATGAAATTTTGAT-AACCAACACT
1 ATAAAATTTTGATAAACC-TCCCT
* * * *
1556 ATGAGATGTTGAT-AACCTCGCT
1 ATAAAATTTTGATAAACCTCCCT
* * * *
1578 ATGAAATTTAGATAAATCTTCCT
1 ATAAAATTTTGATAAACCTCCCT
1601 ATAAAATTTTGATAAACCTCCCT
1 ATAAAATTTTGATAAACCTCCCT
1624 ATAAAATTTTGATAA
1 ATAAAATTTTGATAA
1639 CTTTCTTATG
Statistics
Matches: 113, Mismatches: 28, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
20 3 0.03
21 3 0.03
22 44 0.39
23 60 0.53
24 1 0.01
25 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (23 bp):
ATAAAATTTTGATAAACCTCCCT
Found at i:1613 original size:45 final size:44
Alignment explanation
Indices: 1564--1660 Score: 113
Period size: 46 Copynumber: 2.2 Consensus size: 44
1554 CTATGAGATG
* * *
1564 TTGATAACCTCGCTATGAAATTTAGATAAATCTTCCTATAAAATT
1 TTGATAACCTCCCTATAAAATTTAGATAAAT-TTCCTATAAAATC
* * * *
1609 TTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATC
1 TTGAT-AACCTCCCTATAAAATTTAGATAAATTTCCTATAAAATC
1654 TTGATAA
1 TTGATAA
1661 TTACAAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 2 0.05
45 20 0.45
46 22 0.50
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (44 bp):
TTGATAACCTCCCTATAAAATTTAGATAAATTTCCTATAAAATC
Found at i:1694 original size:60 final size:61
Alignment explanation
Indices: 1604--1721 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 61
1594 TCTTCCTATA
*
1604 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTC-TTATGAAATCTTGATAATTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAC-ATCATTATGAAATCTTGATAATTAC
* ** * *
1665 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACATCATTATGAAATTTTGTTAAT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATCATTATGAAATCTTGATAAT
1722 CTCCCTATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.04
60 38 0.76
61 10 0.20
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.43
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATCATTATGAAATCTTGATAATTAC
Found at i:1819 original size:20 final size:20
Alignment explanation
Indices: 1794--1845 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1784 AACTAAACTA
* *
1794 TGAAATTTTTATATCCTCCC
1 TGAAATTTTGATATCCTACC
1814 TGAAATTTTGATATCCTACC
1 TGAAATTTTGATATCCTACC
1834 TGAAATTTTGAT
1 TGAAATTTTGAT
1846 TACTCCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (20 bp):
TGAAATTTTGATATCCTACC
Found at i:2152 original size:22 final size:22
Alignment explanation
Indices: 1926--2197 Score: 143
Period size: 22 Copynumber: 12.5 Consensus size: 22
1916 AGAAATACCA
1926 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
1949 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * *
1970 TTATGAAATTTTGGTAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * *
1992 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
**
2014 CTATGAAATTCCGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
2037 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
2058 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
*
2080 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
2101 CCTAT-AAATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAATC--A-CT
2126 CTATGAAATTTTGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
2148 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
* * *
2168 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCACT
2189 -TATGAAATT
1 CTATGAAATT
2198 GAGACTTTTA
Statistics
Matches: 195, Mismatches: 39, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.01
20 16 0.08
21 35 0.18
22 121 0.62
23 3 0.02
24 4 0.02
25 15 0.08
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:2232 original size:22 final size:21
Alignment explanation
Indices: 2203--2342 Score: 79
Period size: 22 Copynumber: 6.4 Consensus size: 21
2193 AAATTGAGAC
2203 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
2224 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
2246 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
2268 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* ** *
2290 TTTTGTTAACCAGACTGTGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
2312 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
2334 TTTTGATAA
1 TTTTGATAA
2343 TCTCTTTGAT
Statistics
Matches: 89, Mismatches: 20, Indels: 19
0.70 0.16 0.15
Matches are distributed among these distances:
21 11 0.12
22 74 0.83
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:2459 original size:22 final size:22
Alignment explanation
Indices: 2378--2560 Score: 135
Period size: 22 Copynumber: 8.3 Consensus size: 22
2368 TTGTGAAAAT
**
2378 TAACCAC-CTATGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
2399 TAACCA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
* *
2421 TAACCTGATC-CTATGAAAATTTGG
1 TAACC--A-CACTATGAAATTTTGA
2445 TAACCACACTATGAAATTTTGA
1 TAACCACACTATGAAATTTTGA
** *
2467 TAACTTCTA-TATGAAATTTTGG
1 TAACCAC-ACTATGAAATTTTGA
*
2489 TAACCACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
2511 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
2533 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
2555 TAACCA
1 TAACCA
2561 AATAGAGACA
Statistics
Matches: 128, Mismatches: 23, Indels: 21
0.74 0.13 0.12
Matches are distributed among these distances:
21 10 0.08
22 99 0.77
23 3 0.02
24 16 0.12
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:2757 original size:19 final size:20
Alignment explanation
Indices: 2726--2763 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2716 TATTGACATT
2726 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
2745 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
2764 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:3890 original size:6 final size:6
Alignment explanation
Indices: 3879--3905 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3869 AAAGCAAAGC
3879 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
3906 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:3920 original size:13 final size:13
Alignment explanation
Indices: 3902--3936 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3892 AATCTAAATC
*
3902 TAAAGCAGATTAA
1 TAAAGCAAATTAA
3915 TAAAGCAAATTAA
1 TAAAGCAAATTAA
*
3928 TAAAACAAA
1 TAAAGCAAA
3937 CAATAATTAT
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:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:4861 original size:10 final size:10
Alignment explanation
Indices: 4846--4870 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4836 GAGGAATCTA
4846 GAATTTTCTG
1 GAATTTTCTG
4856 GAATTTTCTG
1 GAATTTTCTG
4866 GAATT
1 GAATT
4871 GTGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:5463 original size:20 final size:20
Alignment explanation
Indices: 5440--5478 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5430 AAAATAGGGT
5440 AAAAACACATAAAAATAGCA
1 AAAAACACATAAAAATAGCA
** *
5460 AAAAGTATATAAAAATAGC
1 AAAAACACATAAAAATAGC
5479 TATAAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAACACATAAAAATAGCA
Done.