Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022941.1 Corchorus olitorius cultivar O-4 contig22974, 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: 25032
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:3232 original size:13 final size:13
Alignment explanation
Indices: 3186--3237 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
3176 AAGTCCATTC
3186 CAGTTAAAGTACT
1 CAGTTAAAGTACT
* *
3199 CATTTATATATTA-T
1 CAGTTA-A-AGTACT
3213 CCAGTTAAAGTACT
1 -CAGTTAAAGTACT
3227 CAGTTAAAGTA
1 CAGTTAAAGTA
3238 ATTCTGAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 19 0.61
14 4 0.13
15 8 0.26
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (13 bp):
CAGTTAAAGTACT
Found at i:5475 original size:17 final size:16
Alignment explanation
Indices: 5453--5487 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5443 TCAAGGTATA
5453 TTTTCTTTACTTTTTCT
1 TTTTCTTTAC-TTTTCT
*
5470 TTTTCTTTTCTTTTCT
1 TTTTCTTTACTTTTCT
5486 TT
1 TT
5488 CTAAGTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTTACTTTTCT
Found at i:19987 original size:38 final size:38
Alignment explanation
Indices: 19942--20046 Score: 158
Period size: 39 Copynumber: 2.7 Consensus size: 38
19932 GTTTTTAATT
19942 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTG
1 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTG
* *
19980 AGGTAATTCCAAAAGAAGATTTTGGAAAAATAAAAGTTT
1 AAGTAATTCCAAAAGAAGATTTTGG-AAAATAAAAGTTG
*
20019 AAG-ATATCCCAAAAGAAGATTTTGGAAA
1 AAGTA-ATTCCAAAAGAAGATTTTGGAAA
20047 TTAATTAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 28 0.46
39 33 0.54
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.26
Consensus pattern (38 bp):
AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTG
Found at i:22020 original size:5 final size:5
Alignment explanation
Indices: 22012--22053 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
22002 TAAAAATATA
* *
22012 ATAAT ATAAT ATAAT ATAAC ATAAT AT-TT ATAAT AT-AT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
22054 GATAGAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 7 0.23
5 24 0.77
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:22035 original size:23 final size:23
Alignment explanation
Indices: 22009--22053 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21999 ATTTAAAAAT
22009 ATAATA-ATATAATATAATATAAC
1 ATAATATATATAATAT-ATATAAC
*
22032 ATAATATTTATAATATATATAA
1 ATAATATATATAATATATATAA
22054 GATAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATATATATAATATATATAAC
Found at i:22046 original size:9 final size:9
Alignment explanation
Indices: 22006--22053 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 9
21996 TAGATTTAAA
22006 AATATA-AT
1 AATATATAT
22014 AATATAATAT
1 AATAT-ATAT
*
22024 AATATAACAT
1 AATAT-ATAT
*
22034 AATATTTAT
1 AATATATAT
22043 AATATATAT
1 AATATATAT
22052 AA
1 AA
22054 GATAGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 5 0.15
9 13 0.38
10 16 0.47
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
AATATATAT
Found at i:22760 original size:22 final size:22
Alignment explanation
Indices: 22547--23179 Score: 272
Period size: 22 Copynumber: 28.4 Consensus size: 22
22537 AATATAATCT
* * *
22547 CCTATAAAATTTTGAGAACCAC
1 CCTATGAAATTTTGATAACCTC
* * * *
22569 ACAACGAAATTTTGATAACCTA
1 CCTATGAAATTTTGATAACCTC
*
22591 CCTAT-ATAATTTTGATAACTTC
1 CCTATGA-AATTTTGATAACCTC
** * *
22613 ATTATGAAATTTTAATAACCAAACC
1 CCTATGAAATTTTGATAACC---TC
* *
22638 GCACTATGAAATTTCGATAAACTC
1 -C-CTATGAAATTTTGATAACCTC
*
22662 ACTATGTAAATTTTGATAACCTC
1 CCTATG-AAATTTTGATAACCTC
*
22685 CCTATGAAATTTTGATAACCTT
1 CCTATGAAATTTTGATAACCTC
*
22707 CCTATAAAATTTTGATAACCAT-
1 CCTATGAAATTTTGATAACC-TC
* * *
22729 ACTATAAAATTTTGATAATCTC
1 CCTATGAAATTTTGATAACCTC
* * * *
22751 CCTATGAAATGTCGGTAACCAC
1 CCTATGAAATTTTGATAACCTC
* * * *
22773 ACTATAAAATTTTGAT-GCTTAC
1 CCTATGAAATTTTGATAACCT-C
** * *
22795 ATTATG-AGTTGTGATAA-CTC
1 CCTATGAAATTTTGATAACCTC
* * *
22815 TCTTATGAAATTTTCATAACCTT
1 -CCTATGAAATTTTGATAACCTC
* * *
22838 ACTATGAAATTTTGGATAAATCTT
1 CCTATGAAATTTT-GAT-AACCTC
*
22862 CCTATAAAATTTTGATAACCTC
1 CCTATGAAATTTTGATAACCTC
**
22884 TTTATGAAATTTT-ACTAA-CTAC
1 CCTATGAAATTTTGA-TAACCT-C
* *
22906 ACTATGAAATTTTGATAATCTC
1 CCTATGAAATTTTGATAACCTC
* *
22928 CCTAT-AAAATTTCAGTAACCTC
1 CCTATGAAATTTTGA-TAACCTC
* *
22950 CGTATGAAATTTTGATAACTTC
1 CCTATGAAATTTTGATAACCTC
* ** * ** *
22972 CTTATGATTTTTTTTTTTTTATAATTTT
1 CCTATGA------AATTTTGATAACCTC
23000 CCTATGAAATTTTGATAA---C
1 CCTATGAAATTTTGATAACCTC
* * * * *
23019 ACAATGAAATTTTGATAGCTTG
1 CCTATGAAATTTTGATAACCTC
* * *
23041 CTTATGAAATTTTGATAAGCAC
1 CCTATGAAATTTTGATAACCTC
* *
23063 ACTATAAAATTTTGAT-ACCT-
1 CCTATGAAATTTTGATAACCTC
23083 CCTAATGAAATTTTGATAACCAT-
1 CCT-ATGAAATTTTGATAACC-TC
* * * * *
23106 ACTATGAAAATTTGATAGCTTT
1 CCTATGAAATTTTGATAACCTC
* *
23128 ACTATGAAATTTTGATAACGTC
1 CCTATGAAATTTTGATAACCTC
* * *
23150 CTTA-GAAAATATCGATAACCTC
1 CCTATG-AAATTTTGATAACCTC
23172 CC-ATGAAA
1 CCTATGAAA
23180 ATTCAATAAC
Statistics
Matches: 451, Mismatches: 122, Indels: 77
0.69 0.19 0.12
Matches are distributed among these distances:
19 15 0.03
20 3 0.01
21 46 0.10
22 297 0.66
23 41 0.09
24 17 0.04
25 1 0.00
27 15 0.03
28 16 0.04
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTC
Found at i:23112 original size:65 final size:65
Alignment explanation
Indices: 23021--23144 Score: 153
Period size: 65 Copynumber: 1.9 Consensus size: 65
23011 TTGATAACAC
* * * *
23021 AATGAAATTTTGATAGCTTGCTTATGAAATTTTGATAAGC-ACACTATAAAATTTTGATACCTCC
1 AATGAAATTTTGATACCATACTTATGAAAATTTGAT-AGCTACACTATAAAATTTTGATACCTCC
23085 T
65 T
** *
23086 AATGAAATTTTGATAACCATAC-TATGAAAATTTGATAGCTTTACTATGAAATTTTGATA
1 AATGAAATTTTGAT-ACCATACTTATGAAAATTTGATAGCTACACTATAAAATTTTGATA
23145 ACGTCCTTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
64 3 0.06
65 43 0.86
66 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (65 bp):
AATGAAATTTTGATACCATACTTATGAAAATTTGATAGCTACACTATAAAATTTTGATACCTCCT
Found at i:23116 original size:44 final size:43
Alignment explanation
Indices: 22999--23146 Score: 139
Period size: 43 Copynumber: 3.5 Consensus size: 43
22989 TTTATAATTT
* *
22999 TCCT-ATGAAATTTTGATAA-C-ACAATG-AAATTTTGATAGCT
1 TCCTAATGAAATTTTGATAACCAACTATGAAAATTTTGATA-CC
* * *
23039 TGCTTATGAAATTTTGATAAGCACACTAT-AAAATTTTGATACC
1 TCCTAATGAAATTTTGATAACCA-ACTATGAAAATTTTGATACC
*
23082 TCCTAATGAAATTTTGATAACCATACTATGAAAA-TTTGATAGC
1 TCCTAATGAAATTTTGATAACCA-ACTATGAAAATTTTGATACC
*
23125 T-TTACTATGAAATTTTGATAAC
1 TCCTA--ATGAAATTTTGATAAC
23147 GTCCTTAGAA
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
40 3 0.03
41 15 0.16
42 3 0.03
43 35 0.38
44 35 0.38
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (43 bp):
TCCTAATGAAATTTTGATAACCAACTATGAAAATTTTGATACC
Found at i:23179 original size:87 final size:87
Alignment explanation
Indices: 22999--23172 Score: 200
Period size: 87 Copynumber: 2.0 Consensus size: 87
22989 TTTATAATTT
* *
22999 TCCT-ATGAAATTTTGATAA-C--ACAATGAAATTTTGATAGCTTGCTTATGAAATTTTGATAAG
1 TCCTAATGAAATTTTGATAACCATACAATGAAAATTTGATAGCTTACTTATGAAATTTTGATAAG
* * *
23060 CACACTATAAAATTTTGATACC
66 CACACTAGAAAATATCGATACC
*
23082 TCCTAATGAAATTTTGATAACCATACTATGAAAATTTGATAGCTTTAC-TATGAAATTTTGATAA
1 TCCTAATGAAATTTTGATAACCATACAATGAAAATTTGATAGC-TTACTTATGAAATTTTGATAA
*
23146 CGTC-C-TTAGAAAATATCGATAACC
65 -G-CACACTAGAAAATATCGAT-ACC
23170 TCC
1 TCC
23173 CATGAAAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
83 4 0.05
84 15 0.20
85 1 0.01
87 44 0.58
88 11 0.14
89 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (87 bp):
TCCTAATGAAATTTTGATAACCATACAATGAAAATTTGATAGCTTACTTATGAAATTTTGATAAG
CACACTAGAAAATATCGATACC
Found at i:23301 original size:22 final size:22
Alignment explanation
Indices: 23276--23327 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
23266 TGAGAACCTC
* *
23276 TTTGATAACCTCTTTATGAAAA
1 TTTGATAACCACATTATGAAAA
23298 TTTGATAACCACATTATGAAAA
1 TTTGATAACCACATTATGAAAA
23320 TTTGATAA
1 TTTGATAA
23328 TATTCCTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTGATAACCACATTATGAAAA
Found at i:23360 original size:22 final size:21
Alignment explanation
Indices: 23313--23415 Score: 73
Period size: 22 Copynumber: 4.8 Consensus size: 21
23303 TAACCACATT
* * *
23313 ATGAAAATTTGATAATATTCCT
1 ATGAAATTTTGATAAT-TCCCA
23335 ATGAAATTTTGATAAGTTCCCA
1 ATGAAATTTTGATAA-TTCCCA
** *
23357 ATGAAATTTTG-TTTTTACACA
1 ATGAAATTTTGATAATT-CCCA
* * *
23378 ATGAAATTTTGGTAACCTCCCT
1 ATGAAATTTTGATAA-TTCCCA
*
23400 ATGAAATTTTGGTAAT
1 ATGAAATTTTGATAAT
23416 CACCAAGGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.03
21 15 0.23
22 46 0.71
23 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (21 bp):
ATGAAATTTTGATAATTCCCA
Found at i:23720 original size:22 final size:22
Alignment explanation
Indices: 23651--23722 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
23641 ATAACCACGT
* * *
23651 TATGAAATTGTGATAAACACAC
1 TATGAAATTATGATAACCTCAC
* * *
23673 TATAAAATTACGATAACCTCAA
1 TATGAAATTATGATAACCTCAC
* *
23695 TATGAAATTTTGATAACCTCCC
1 TATGAAATTATGATAACCTCAC
23717 TATGAA
1 TATGAA
23723 TTAATGCCTA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (22 bp):
TATGAAATTATGATAACCTCAC
Found at i:24647 original size:21 final size:23
Alignment explanation
Indices: 24601--24649 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
24591 GATAAGCTAA
*
24601 CTATGAAATTTTAATAAACTTTC
1 CTATGAAATTTTAATAAACCTTC
*
24624 CTATGAAATTTT-GT-AACCTTC
1 CTATGAAATTTTAATAAACCTTC
24645 CTATG
1 CTATG
24650 CTTTTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 1 0.04
23 12 0.50
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Done.