Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012207.1 Corchorus capsularis cultivar CVL-1 contig12228, 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: 22524
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1086 original size:2 final size:2
Alignment explanation
Indices: 1079--1103 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1069 TGCTAGGTCC
1079 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1104 ATACACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:10800 original size:2 final size:2
Alignment explanation
Indices: 10793--10819 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10783 GCATGCCTAA
10793 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
10820 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17535 original size:67 final size:67
Alignment explanation
Indices: 17425--17555 Score: 201
Period size: 67 Copynumber: 2.0 Consensus size: 67
17415 GATTACTGAC
* * *
17425 TTTTTGTTAGTACTAGTTTTTGCTTTCACTTGCACGTAACCGAATGTGTTTAAATTAAGAAAGTG
1 TTTTTGTTAGTACTAGTTTTAGCTTTCACGTGCACGTAACCGAATGCGTTTAAATTAAGAAAGTG
17490 AA
66 AA
* *
17492 TTTTTGTTAGTACTAGTTTTAGGTTTCACGTGCATG-AAGCCGAATGCGTTTAAATTAAGAAAGT
1 TTTTTGTTAGTACTAGTTTTAGCTTTCACGTGCACGTAA-CCGAATGCGTTTAAATTAAGAAAGT
17556 ACTTATAGCC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 2 0.03
67 56 0.97
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.40
Consensus pattern (67 bp):
TTTTTGTTAGTACTAGTTTTAGCTTTCACGTGCACGTAACCGAATGCGTTTAAATTAAGAAAGTG
AA
Found at i:18044 original size:149 final size:148
Alignment explanation
Indices: 17770--18085 Score: 544
Period size: 149 Copynumber: 2.1 Consensus size: 148
17760 GAAATATTCA
*
17770 TATGAAATTATGATAATCCCTATATTAAATTATGATAATTACACTTTTTTTATGATCCCATTATG
1 TATGAAATTATGATAACCCCTATATTAAATTATGATAATTACACTTTTTTTATGATCCCATTATG
*
17835 AAATTTTGATAATATTCCAATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTAT
66 AAATTTTGATAACATTCCAATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTAT
17900 AA-ATTTTTTAACCTTCT
131 AATATTTTTTAACCTTCT
17917 TATGATAATTATGATAACCCCTATATTAAATTATGATAATTACACTATTTTTTATGATCCCATTA
1 TATGA-AATTATGATAACCCCTATATTAAATTATGATAATTACACT-TTTTTTATGATCCCATTA
* *
17982 TGAAATTTTGATAACATTCCTATGAAATTTTAGTAATGATACTATGGAATTTCGAGAACCTTTTT
64 TGAAATTTTGATAACATTCCAATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTT
*
18047 ATAATTTTTTTTAACCTTCT
129 ATAATATTTTTTAACCTTCT
* *
18067 TATGAAATTTTGTTAACCC
1 TATGAAATTATGATAACCC
18086 TAAGGAATTT
Statistics
Matches: 159, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
147 5 0.03
148 39 0.25
149 96 0.60
150 19 0.12
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (148 bp):
TATGAAATTATGATAACCCCTATATTAAATTATGATAATTACACTTTTTTTATGATCCCATTATG
AAATTTTGATAACATTCCAATGAAATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTAT
AATATTTTTTAACCTTCT
Found at i:18063 original size:21 final size:22
Alignment explanation
Indices: 18038--18084 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
18028 GAATTTCGAG
* * *
18038 AACCTTTTTAT-AATTTTTTTT
1 AACCTTCTTATGAAATTTTGTT
18059 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
18081 AACC
1 AACC
18085 CTAAGGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:18316 original size:45 final size:43
Alignment explanation
Indices: 18267--18369 Score: 107
Period size: 46 Copynumber: 2.3 Consensus size: 43
18257 TCACACTATG
* * *
18267 AAATTGTGATAACATCGCTATGAATTTTTGATAAATCTTCTTATA
1 AAATT-TGATAACATCCCTATAAAATTTTGATAAAT-TTCTTATA
* * *
18312 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATG
1 AAA-TTTGAT-AACATCCCTATAAAATTTTGATAAATTTCTTATA
18357 AAATCTTGATAAC
1 AAAT-TTGATAAC
18370 TACAAATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
44 4 0.08
45 22 0.45
46 23 0.47
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (43 bp):
AAATTTGATAACATCCCTATAAAATTTTGATAAATTTCTTATA
Found at i:18320 original size:23 final size:23
Alignment explanation
Indices: 18292--18368 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 23
18282 CGCTATGAAT
18292 TTTTGATAAATCTTCTTATAAAA
1 TTTTGATAAATCTTCTTATAAAA
* * *
18315 TTTTGATAAACCTCCCTATAAAA
1 TTTTGATAAATCTTCTTATAAAA
* *
18338 TTTTGATAACT-TTCTTATGAAA
1 TTTTGATAAATCTTCTTATAAAA
*
18360 TCTTGATAA
1 TTTTGATAA
18369 CTACAAATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.36
23 29 0.64
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.44
Consensus pattern (23 bp):
TTTTGATAAATCTTCTTATAAAA
Found at i:18423 original size:22 final size:22
Alignment explanation
Indices: 18103--18486 Score: 152
Period size: 22 Copynumber: 17.6 Consensus size: 22
18093 TTTTCAAGAG
*
18103 CTCAATATGAAATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
* * * *
18125 TTCCCAAAGAAATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
* * * *
18147 CAACACTGTGAGATGTTGATAAC
1 C-TCACTATGAAATTTTGATAAC
* *
18170 CTC-CATATGATATATTGATAAC
1 CTCAC-TATGAAATTTTGATAAC
* ** * * *
18192 CACGTTATGAAAATTTAAAAAC
1 CTCACTATGAAATTTTGATAAC
*
18214 CTC-CATATG-AATTGTT-AGTAAT
1 CTCAC-TATGAAATT-TTGA-TAAC
* * *
18236 CACACTCTGAAATTTTGATAAT
1 CTCACTATGAAATTTTGATAAC
* *
18258 CACACTATGAAATTGTGATAAC
1 CTCACTATGAAATTTTGATAAC
* * *
18280 ATCGCTATGAATTTTTGATAAATC
1 CTCACTATGAAATTTTGAT-AA-C
* * *
18304 TTC-TTATAAAATTTTGATAAAC
1 CTCACTATGAAATTTTGAT-AAC
* *
18326 CTCCCTATAAAATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
* * *
18348 TTTC-TTATGAAATCTTGATAA-
1 -CTCACTATGAAATTTTGATAAC
18369 CT-AC----AAATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
* **
18386 CTCCCTATGATTTTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
* *
18408 CTCATTATGAAATTTTGTTAATC
1 CTCACTATGAAATTTTGATAA-C
* * *
18431 TTCA-TATGAAATTTTAATCTAC
1 CTCACTATGAAATTTTGAT-AAC
*
18453 AT-A-TATGAAATTTTGATAACC
1 CTCACTATGAAATTTTGATAA-C
*
18474 CTC-TTATGAAATT
1 CTCACTATGAAATT
18487 AAACTATGAA
Statistics
Matches: 269, Mismatches: 68, Indels: 50
0.70 0.18 0.13
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 2 0.01
21 21 0.08
22 170 0.63
23 59 0.22
24 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
CTCACTATGAAATTTTGATAAC
Found at i:18449 original size:19 final size:20
Alignment explanation
Indices: 18425--18466 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
18415 TGAAATTTTG
*
18425 TTAATCTTC-ATATGAAATT
1 TTAATCTACAATATGAAATT
18444 TTAATCTACATATATGAAATT
1 TTAATCTACA-ATATGAAATT
18465 TT
1 TT
18467 GATAACCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (20 bp):
TTAATCTACAATATGAAATT
Found at i:18657 original size:21 final size:21
Alignment explanation
Indices: 18628--18681 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
18618 GTAATCACAT
18628 TTTA-AAAATTTGATAACCTC
1 TTTATAAAATTTGATAACCTC
*
18648 TTTATGAAATTTTGATAACCTC
1 TTTAT-AAAATTTGATAACCTC
18670 TTTATAAAATTT
1 TTTATAAAATTT
18682 TGTTGACCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (21 bp):
TTTATAAAATTTGATAACCTC
Found at i:18663 original size:22 final size:22
Alignment explanation
Indices: 18636--19000 Score: 108
Period size: 22 Copynumber: 16.4 Consensus size: 22
18626 ATTTTAAAAA
*
18636 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCATTATGAAAT
* *
18658 TTTGATAACCTCTTTATAAAAT
1 TTTGATAACCTCATTATGAAAT
* * * **
18680 TTTGTTGACCCCCCTATGAAAT
1 TTTGATAACCTCATTATGAAAT
* * * *
18702 TCTGATAATCACATTATGTAAT
1 TTTGATAACCTCATTATGAAAT
** *
18724 TTTGATAATATCGCTT-TGAAAT
1 TTTGATAACCTC-ATTATGAAAT
** *
18746 TTTGATAACAACACTATGAAAT
1 TTTGATAACCTCATTATGAAAT
* *
18768 TTTGATAATCTGATCTCTATGAAAT
1 TTTGATAACCTCA--T-TATGAAAT
*
18793 TTCGATAA--TCATTAT-ATCAGA-
1 TTTGATAACCTCATTATGA--A-AT
* *
18814 TTTGATAA-CT-TTCTATCAAAT
1 TTTGATAACCTCAT-TATGAAAT
* *
18835 TTTGGT-A-CTCCTTATGAAATT
1 TTTGATAACCTCATTATGAAA-T
*
18856 GAGACTTTTATAACCTTCA-TATGAAAT
1 -----TTTGATAACC-TCATTATGAAAT
* * *
18883 TTTGATAACCACACTATAAAAT
1 TTTGATAACCTCATTATGAAAT
***
18905 TTTGATAACCTCCCCATGAAAT
1 TTTGATAACCTCATTATGAAAT
* * *
18927 ATT-AGTAACCTCCTAATGAAAT
1 TTTGA-TAACCTCATTATGAAAT
* *
18949 TTTGTTAA-CTACACTATGAAAT
1 TTTGATAACCT-CATTATGAAAT
** * *
18971 TCTT-ATAACCTCGCTATCATAT
1 T-TTGATAACCTCATTATGAAAT
18993 TTTGATAA
1 TTTGATAA
19001 TCTCTTTGGT
Statistics
Matches: 256, Mismatches: 58, Indels: 58
0.69 0.16 0.16
Matches are distributed among these distances:
19 1 0.00
20 13 0.05
21 26 0.10
22 176 0.69
23 9 0.04
25 15 0.06
26 4 0.02
27 2 0.01
28 8 0.03
29 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTGATAACCTCATTATGAAAT
Found at i:18836 original size:20 final size:22
Alignment explanation
Indices: 18759--18836 Score: 61
Period size: 25 Copynumber: 3.5 Consensus size: 22
18749 GATAACAACA
* *
18759 CTATGAAATTTTGATAATCTGATCT
1 CTATCAAATTTCGATAATC--AT-T
*
18784 CTATGAAATTTCGATAATCATT
1 CTATCAAATTTCGATAATCATT
* * *
18806 ATATCAGATTT-GATAA-CTTT
1 CTATCAAATTTCGATAATCATT
18826 CTATCAAATTT
1 CTATCAAATTT
18837 TGGTACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.26
21 5 0.11
22 9 0.20
23 2 0.04
25 18 0.39
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (22 bp):
CTATCAAATTTCGATAATCATT
Found at i:19182 original size:19 final size:20
Alignment explanation
Indices: 19151--19188 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
19141 TATTGACATT
19151 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
19170 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
19189 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:20564 original size:15 final size:15
Alignment explanation
Indices: 20546--20596 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
20536 TATATAATCT
20546 AATAATTAATAATGG
1 AATAATTAATAATGG
* *
20561 AATAATTTATAAT-T
1 AATAATTAATAATGG
*
20575 AA-AA-AAATAATGG
1 AATAATTAATAATGG
20588 AATAATTAA
1 AATAATTAA
20597 AATATTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 4 0.15
15 14 0.52
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
AATAATTAATAATGG
Done.