Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015495.1 Corchorus capsularis cultivar CVL-1 contig15516, 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: 23815
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:900 original size:18 final size:18
Alignment explanation
Indices: 877--912 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
867 ATACTTCTTA
877 ATCCACTTATGGAGTGTG
1 ATCCACTTATGGAGTGTG
895 ATCCACTTATGGAGTGTG
1 ATCCACTTATGGAGTGTG
913 GAGTGGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (18 bp):
ATCCACTTATGGAGTGTG
Found at i:1198 original size:2 final size:2
Alignment explanation
Indices: 1191--1219 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1181 TTTTCTAAAC
1191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1220 ATCCTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5252 original size:34 final size:34
Alignment explanation
Indices: 5209--5275 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
5199 AGTTTAGTTA
* * *
5209 TCACATAAAAATTTACGTTACAGCCTTAGACATT
1 TCACATAAAAACTCACCTTACAGCCTTAGACATT
5243 TCACATAAAAACTCACCTTACAGCCTTAGACAT
1 TCACATAAAAACTCACCTTACAGCCTTAGACAT
5276 CTTAAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.28
Consensus pattern (34 bp):
TCACATAAAAACTCACCTTACAGCCTTAGACATT
Found at i:5752 original size:1 final size:1
Alignment explanation
Indices: 5746--5783 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
5736 TCAAGCCTTT
5746 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5784 GGTGTGCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6302 original size:2 final size:2
Alignment explanation
Indices: 6295--6334 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
6285 ATTTATGTTT
6295 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6335 CTAGTTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6553 original size:22 final size:22
Alignment explanation
Indices: 6520--6598 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
6510 GAGAATCTTA
* *
6520 TTAT-AAATTTTTTTTAACCTTC
1 TTATGAAA-TTTTGTTAACCTCC
6542 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGTTAACCTCC
* * * *
6564 CTAAGAAATTTTG-AAGACCTCA
1 TTATGAAATTTTGTTA-ACCTCC
*
6586 ATATGAAATTTTG
1 TTATGAAATTTTG
6599 ATAAACAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 1 0.02
22 43 0.91
23 3 0.06
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATGAAATTTTGTTAACCTCC
Found at i:6714 original size:22 final size:22
Alignment explanation
Indices: 6689--6923 Score: 91
Period size: 22 Copynumber: 10.9 Consensus size: 22
6679 GAATTGTTAG
*
6689 TAATCATACTCTGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
* *
6711 TAATCACACTATGAAATTGTGA
1 TAATCATACTATGAAATTTTGA
* *
6733 TAA-CCTCGCTATGAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
* * *
6755 TAAATCTTCCTATAAAATTTTGA
1 T-AATCATACTATGAAATTTTGA
* * * *
6778 TAAACCTCCTTATAAAATTTTGA
1 TAATCATAC-TATGAAATTTTGA
* * * *
6801 TAA-CTTTCTTATTAAATCTTGA
1 TAATCATAC-TATGAAATTTTGA
6823 TAA-C-TAC----AAATTTTGA
1 TAATCATACTATGAAATTTTGA
* **
6839 TAACCA-ACCTATGATTTTTTGA
1 TAATCATA-CTATGAAATTTTGA
*
6861 TAACCTCAT--TATGAAATTTTGT
1 TAA--TCATACTATGAAATTTTGA
* *
6883 TAAT-GTCCCTATGAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
*
6905 T-CTACATACTATGAAATTT
1 TAAT-CATACTATGAAATTT
6924 GGCTAATTGC
Statistics
Matches: 165, Mismatches: 29, Indels: 38
0.71 0.12 0.16
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
19 1 0.01
20 1 0.01
21 4 0.02
22 108 0.65
23 33 0.20
24 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATCATACTATGAAATTTTGA
Found at i:6772 original size:23 final size:23
Alignment explanation
Indices: 6741--6825 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
6731 GATAACCTCG
*
6741 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
*
6764 CTATAAAATTTTGATAAA-CCTC
1 CTATAAAATTTTGATAAATCTTC
*
6786 CTTATAAAATTTTGATAACT-TTC
1 C-TATAAAATTTTGATAAATCTTC
* * *
6809 TTATTAAATCTTGATAA
1 CTATAAAATTTTGATAA
6826 CTACAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
22 18 0.34
23 35 0.66
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.44
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:6824 original size:45 final size:46
Alignment explanation
Indices: 6730--6825 Score: 117
Period size: 45 Copynumber: 2.1 Consensus size: 46
6720 TATGAAATTG
* *
6730 TGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTATAAAATTT
1 TGATAAACCTCGCTATAAAATTTTGATAAATCTTCCTATAAAATCT
* * *
6775 TGATAAACCTC-CTTATAAAATTTTGATAACT-TTCTTATTAAATCT
1 TGATAAACCTCGC-TATAAAATTTTGATAAATCTTCCTATAAAATCT
6820 TGATAA
1 TGATAA
6826 CTACAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
45 22 0.50
46 22 0.50
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (46 bp):
TGATAAACCTCGCTATAAAATTTTGATAAATCTTCCTATAAAATCT
Found at i:10577 original size:22 final size:22
Alignment explanation
Indices: 10527--10578 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
10517 TCACATTTTG
10527 AAAA-TTTGATAACATCTTTAT
1 AAAATTTTGATAACATCTTTAT
* *
10548 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACATCTTTAT
10570 AAAATTTTG
1 AAAATTTTG
10579 TTGACCCCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACATCTTTAT
Found at i:10645 original size:25 final size:22
Alignment explanation
Indices: 10594--10654 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
10584 CCCCTCGTTT
*
10594 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAATATTCCTA
10616 T-AAATTTTGATAATATGATCTCTA
1 TGAAATTTTGATAATAT--TC-CTA
*
10640 TGAAATTTGGATAAT
1 TGAAATTTTGATAAT
10655 CACTCTGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 14 0.42
22 1 0.03
23 2 0.06
24 4 0.12
25 12 0.36
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (22 bp):
TGAAATTTTGATAATATTCCTA
Found at i:10817 original size:22 final size:22
Alignment explanation
Indices: 10725--11071 Score: 138
Period size: 22 Copynumber: 16.0 Consensus size: 22
10715 ATAAGTTTCG
10725 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* * *
10747 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * * *
10769 CATCAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
* *
10790 AAATGAAATTTTGTTAACCACAC
1 -TATGAAATTTTGATAACCACAC
* *
10813 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAC
* * * **
10835 TATGACATTTTGATAATCTCTT
1 TATGAAATTTTGATAACCACAC
* *
10857 TGAT-AACCATTCT-ATAA--A-AT
1 T-ATGAA--ATTTTGATAACCACAC
* *
10877 TGTGATAA--TT-A--ACCACCC
1 TATGA-AATTTTGATAACCACAC
**
10895 TATGAAATTTCAATAACCA-ACC
1 TATGAAATTTTGATAACCACA-C
* *
10917 TAAGAAATTTTAATAACCTGATC-C
1 TATGAAATTTTGATAACC--A-CAC
* *
10941 TATGAAATTTTGGTAATCACAC
1 TATGAAATTTTGATAACCACAC
10963 TATGAAATTTTGATAACTTC-CA-
1 TATGAAATTTTGATAAC--CACAC
*
10985 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
11007 TATGGAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCACAC
* * *
11028 TCATGAAATTGTAATAACCATC-T
1 T-ATGAAATTTTGATAACCA-CAC
11051 TATGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
11072 TAGAGACAAG
Statistics
Matches: 244, Mismatches: 49, Indels: 64
0.68 0.14 0.18
Matches are distributed among these distances:
15 1 0.00
17 5 0.02
18 4 0.02
19 3 0.01
20 5 0.02
21 11 0.05
22 181 0.74
23 13 0.05
24 21 0.09
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:10970 original size:46 final size:45
Alignment explanation
Indices: 10920--11068 Score: 164
Period size: 44 Copynumber: 3.3 Consensus size: 45
10910 ACCAACCTAA
* *
10920 GAAATTTTAATAACCTGATCC-TATGAAATTTTGGTAATCACACTAT
1 GAAATTTTGATAACCT--TCCATATGAAATTTTGGTAACCACACTAT
10966 GAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCTTCCATATGAAATTTTGGTAACCACACTAT
* * ** *
11010 GGAATTTTGATAACC-TCC-TCATGAAATTGTAATAACCATC-TTAT
1 GAAATTTTGATAACCTTCCAT-ATGAAATTTTGGTAACCA-CACTAT
11054 GAAATTTTGATAACC
1 GAAATTTTGATAACC
11069 ACATAGAGAC
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
43 4 0.04
44 71 0.78
45 4 0.04
46 12 0.13
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (45 bp):
GAAATTTTGATAACCTTCCATATGAAATTTTGGTAACCACACTAT
Found at i:12854 original size:30 final size:29
Alignment explanation
Indices: 12818--12913 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 29
12808 CATCAGATTA
12818 GGGCTTATTTGGCCTTTTTTAAGAGTTCAG
1 GGGCTTATTTGGCCTTTTTT-AGAGTTCAG
***
12848 GGGCTTATTTGG-CTGAAATTAGAGTTCAG
1 GGGCTTATTTGGCCT-TTTTTAGAGTTCAG
12877 GGGCTTATTTGGCCGTTTTGTGTA-AGTTCAG
1 GGGCTTATTTGGCC-TTTT-T-TAGAGTTCAG
*
12908 AGGCTT
1 GGGCTT
12914 TTTCGAGCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 23 0.43
30 15 0.28
31 14 0.26
32 2 0.04
ACGTcount: A:0.18, C:0.12, G:0.30, T:0.40
Consensus pattern (29 bp):
GGGCTTATTTGGCCTTTTTTAGAGTTCAG
Found at i:13137 original size:37 final size:37
Alignment explanation
Indices: 13096--13193 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 37
13086 ATCTAAGCCC
*
13096 AAATAGGATGTTGGAGACAAAAACAAAAAGCAAAATT
1 AAATAGGATGTTGGAAACAAAAACAAAAAGCAAAATT
** * * *
13133 AAATATAATGATTGGAAACAAAGACAAAAGGTAAAATT
1 AAATAGGATG-TTGGAAACAAAAACAAAAAGCAAAATT
**
13171 AAATAGGACATTGGAAACAAAAA
1 AAATAGGATGTTGGAAACAAAAA
13194 GTCAAATTGA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
37 20 0.41
38 29 0.59
ACGTcount: A:0.58, C:0.07, G:0.17, T:0.17
Consensus pattern (37 bp):
AAATAGGATGTTGGAAACAAAAACAAAAAGCAAAATT
Found at i:15071 original size:31 final size:29
Alignment explanation
Indices: 15008--15071 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
14998 TGACAATTTA
**
15008 GAAATATGTTTTAAAAAAGAGTACAATTG
1 GAAATATGTTTTAAAAAAGAGTACAAGCG
*
15037 GAAATATGTTTTTAAAAAAAGGGTACAAGCG
1 GAAATATG-TTTT-AAAAAAGAGTACAAGCG
15068 GAAA
1 GAAA
15072 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 4 0.13
31 18 0.60
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (29 bp):
GAAATATGTTTTAAAAAAGAGTACAAGCG
Found at i:15342 original size:6 final size:6
Alignment explanation
Indices: 15310--15341 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
15300 TTTTTTCTTT
*
15310 ATATTA ATATTA ATATTA ATATTA ATTTTA AT
1 ATATTA ATATTA ATATTA ATATTA ATATTA AT
15342 TGATTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATATTA
Found at i:15596 original size:262 final size:270
Alignment explanation
Indices: 15131--15675 Score: 863
Period size: 262 Copynumber: 2.0 Consensus size: 270
15121 TATCTATACT
* *
15131 ATATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCTTTATTTGTCAGATA
1 ATATTAAAAAGTACGTTCACCTGCAAAACTTTTGAATCGCCCATTATACCCTTATTTGTCAGATA
*
15196 TATTTCAAAATTGTCATTTTACAATTAATATTATTATTTATTTATATAATATTTTATTCAACACA
66 TATTTCAAAATTGTCATTCTACAATTAATATTATTATTTATTTATATAATATTTTATTCAACACA
* * *
15261 AACTTTTGACCAATTTTAACCTCAACAAATCTCATCAACTTTTTTCTTTATATTAATATTAATAT
131 AACTCTTGACCAATTTTAACCTCAACAAATATCATCAACTTATTTCTTTATATTAATATTAATAT
15326 TAATATTAAT-T-TTAA-T-T-G-ATTAAT-TA-ATATATATATTCTTATGTTTTAGCTAAGATC
196 TAATATTAATATATTAATTATGGAATTAATATATATATATATATTCTTATGTTTTAGCTAAGATC
15383 CGTATAAGCC
261 CGTATAAGCC
*
15393 ATATTAAAAAGTACGTTCACCTGCAAAACTTTTGAATCTCCCATTATACCCTTATTTGTCAGATA
1 ATATTAAAAAGTACGTTCACCTGCAAAACTTTTGAATCGCCCATTATACCCTTATTTGTCAGATA
*
15458 TATTTCAAAATTTTCATTCTACAATTAATATTATTATTTATTTATATAATATTTTATTCAACACA
66 TATTTCAAAATTGTCATTCTACAATTAATATTATTATTTATTTATATAATATTTTATTCAACACA
* *
15523 AACTCTTGACCAATTTTAACTTCAACCAATATCATCAACTTATTTCTTTATATTAATATTAATAT
131 AACTCTTGACCAATTTTAACCTCAACAAATATCATCAACTTATTTCTTTATATTAATATTAATAT
15588 TAATATTAATATATTAATTTTAATGGATTAATTAATAGATATATATATATATTCTTATGTTTTAG
196 TAATATTAATATATTAA--TT-ATGG---AATTAAT--ATATATATATATATTCTTATGTTTTAG
*
15653 CTAAGATTCGTATAAGCC
253 CTAAGATCCGTATAAGCC
15671 ATATT
1 ATATT
15676 TTCTCAATTA
Statistics
Matches: 256, Mismatches: 11, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
262 195 0.76
263 1 0.00
264 4 0.02
267 1 0.00
269 1 0.00
270 1 0.00
274 6 0.02
277 2 0.01
278 45 0.18
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.44
Consensus pattern (270 bp):
ATATTAAAAAGTACGTTCACCTGCAAAACTTTTGAATCGCCCATTATACCCTTATTTGTCAGATA
TATTTCAAAATTGTCATTCTACAATTAATATTATTATTTATTTATATAATATTTTATTCAACACA
AACTCTTGACCAATTTTAACCTCAACAAATATCATCAACTTATTTCTTTATATTAATATTAATAT
TAATATTAATATATTAATTATGGAATTAATATATATATATATATTCTTATGTTTTAGCTAAGATC
CGTATAAGCC
Found at i:15611 original size:6 final size:6
Alignment explanation
Indices: 15572--15599 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
15562 TTATTTCTTT
15572 ATATTA ATATTA ATATTA ATATTA ATAT
1 ATATTA ATATTA ATATTA ATATTA ATAT
15600 ATTAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:18928 original size:2 final size:2
Alignment explanation
Indices: 18921--18958 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
18911 GTTTAAATTC
* *
18921 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18959 TGGTGGGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Done.