Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014445.1 Corchorus capsularis cultivar CVL-1 contig14466, 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: 88099
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:109 original size:32 final size:30
Alignment explanation
Indices: 24--118 Score: 93
Period size: 32 Copynumber: 3.1 Consensus size: 30
14 CGCCCCACCG
*
24 GGGCGGCCTGCCTTGCACGAAGCCGCCCCAT
1 GGGCGGCCTGCCTTG-GCGAAGCCGCCCCAT
* ** * *
55 GGGCAGTTTGCCGTGGCGAAGCCGCCCCTT
1 GGGCGGCCTGCCTTGGCGAAGCCGCCCCAT
85 GAGGGCGGCCTGCCTTGGCGAAGCCTG-CCCAT
1 --GGGCGGCCTGCCTTGGCGAAGCC-GCCCCAT
117 GG
1 GG
119 TGAAGCCGTC
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
30 15 0.30
31 11 0.22
32 23 0.46
33 1 0.02
ACGTcount: A:0.12, C:0.36, G:0.37, T:0.16
Consensus pattern (30 bp):
GGGCGGCCTGCCTTGGCGAAGCCGCCCCAT
Found at i:202 original size:17 final size:16
Alignment explanation
Indices: 179--218 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
169 GGAGGCTCAG
* *
179 TGTAAAAGTGTAAAAA
1 TGTAAAAGGGCAAAAA
195 TGGTAAAAGGGCAAAAA
1 T-GTAAAAGGGCAAAAA
212 TGTAAAA
1 TGTAAAA
219 AGTGAGGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.20
Consensus pattern (16 bp):
TGTAAAAGGGCAAAAA
Found at i:5658 original size:12 final size:11
Alignment explanation
Indices: 5636--5674 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
5626 TTTAGTACTA
5636 TCTTTTTTCTT
1 TCTTTTTTCTT
5647 TCTTTCTTTCTT
1 TCTTT-TTTCTT
5659 TCTTTTTT-TT
1 TCTTTTTTCTT
5669 T-TTTTT
1 TCTTTTT
5675 CATTTGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.11
11 8 0.30
12 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:5672 original size:8 final size:8
Alignment explanation
Indices: 5638--5675 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
5628 TAGTACTATC
5638 TTTTTTCT
1 TTTTTTCT
*
5646 TTCTTTCT
1 TTTTTTCT
*
5654 TTCTTTCT
1 TTTTTTCT
5662 TTTTTT-T
1 TTTTTTCT
5669 TTTTTTC
1 TTTTTTC
5676 ATTTGGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTCT
Found at i:27538 original size:100 final size:106
Alignment explanation
Indices: 27347--27603 Score: 334
Period size: 100 Copynumber: 2.5 Consensus size: 106
27337 AGTTTAGCCT
* * *
27347 TAATTTCACTAAGTTTAGCCCCAAATTAATTTTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAATTTATTATTTTTATTTTAAGGGTAAATTCCAAAACT
27412 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
27454 TAATTTCACT-AGTTTAGCCCC-AATT-A-TTATT-TTTTTATTTTAAGGGTAAATTCCATAACT
1 TAATTTCACTAAGTTTAGCCCCAAATTAATTTATTATTTTTATTTTAAGGGTAAATTCCAAAACT
* * *
27514 AATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAT
66 AATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * * *
27554 TAA-TTCACTAAGTTTAG-CTCAAATTAAAATTA-AAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATT-AATTTATTATTTTTATTTTAAGGGT
27604 GAGAAAAATA
Statistics
Matches: 134, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
99 8 0.06
100 46 0.34
102 32 0.24
103 22 0.16
104 1 0.01
105 4 0.03
106 11 0.08
107 10 0.07
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (106 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAATTTATTATTTTTATTTTAAGGGTAAATTCCAAAACT
AATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:28384 original size:2 final size:2
Alignment explanation
Indices: 28373--28404 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28363 GCATATACCC
28373 AT AT -T 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 AT AT A
28405 ATTTCCCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33292 original size:19 final size:20
Alignment explanation
Indices: 33246--33293 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
33236 TGTGGCACGC
*
33246 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
33268 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
33287 CACATGT
1 CACATGT
33294 CACGCCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:33298 original size:53 final size:53
Alignment explanation
Indices: 33213--33315 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
33203 GACGTAGCAC
* **
33213 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* **
33266 GCCACATGTACCAAAAAGTGACACATGTCACGCCATGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
33316 GACACGTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:64334 original size:30 final size:29
Alignment explanation
Indices: 64265--64336 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 29
64255 GTAGCGTTTA
64265 GACGTTTTGCCCCCCGAACTTCAATCTTG
1 GACGTTTTGCCCCCCGAACTTCAATCTTG
* * *
64294 GACATTTTGCCCCCTGAACTTCAATTTTGG
1 GACGTTTTGCCCCCCGAACTTCAATCTT-G
64324 GACGTTTTGCCCC
1 GACGTTTTGCCCC
64337 ATCAACTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (29 bp):
GACGTTTTGCCCCCCGAACTTCAATCTTG
Found at i:64559 original size:29 final size:29
Alignment explanation
Indices: 64505--64611 Score: 126
Period size: 29 Copynumber: 3.6 Consensus size: 29
64495 CGGGGCTGTT
*
64505 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGT-CCAAAATTG
*
64535 AAGTTCAGGGGGCAAAATGTCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCAAAATTG
* **
64564 AAGTTC-GGGGAGCAAAACGTCTAAACACTAC
1 AAGTTCAGGGG-GCAAAACGTCCAAA-A-TTG
64595 AAGTTCAGGGGGCAAAA
1 AAGTTCAGGGGGCAAAA
64612 TGGTTGATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
28 4 0.06
29 27 0.40
30 19 0.28
31 13 0.19
32 4 0.06
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (29 bp):
AAGTTCAGGGGGCAAAACGTCCAAAATTG
Found at i:64695 original size:27 final size:28
Alignment explanation
Indices: 64650--64702 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
64640 TTAATTAACA
*
64650 AAAAGATATCTTCTAAGAAACTATATAC
1 AAAAGATACCTTCTAAGAAACTATATAC
*
64678 AAAA-ATACCTTCTTAGAAACTATAT
1 AAAAGATACCTTCTAAGAAACTATAT
64703 TCACAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAAGATACCTTCTAAGAAACTATATAC
Found at i:72260 original size:21 final size:21
Alignment explanation
Indices: 72234--72284 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
72224 AGCACCTGAA
* *
72234 CTTCCTCATCATCTTCAACTT
1 CTTCCTCATCATCTGCAACAT
* * *
72255 CTTCCTCCTCTTCTGCATCAT
1 CTTCCTCATCATCTGCAACAT
72276 CTTCCTCAT
1 CTTCCTCAT
72285 TACCTGGTTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.14, C:0.41, G:0.02, T:0.43
Consensus pattern (21 bp):
CTTCCTCATCATCTGCAACAT
Found at i:73536 original size:13 final size:13
Alignment explanation
Indices: 73518--73546 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
73508 CAAAAGCTTG
73518 AAATTAGAACTAA
1 AAATTAGAACTAA
73531 AAATTAGAACTAA
1 AAATTAGAACTAA
73544 AAA
1 AAA
73547 CTACCATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATTAGAACTAA
Found at i:74267 original size:12 final size:12
Alignment explanation
Indices: 74252--74289 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
74242 CTCTTCCTCT
*
74252 TCATCATCCTCG
1 TCATCATCATCG
74264 TCATCATCATCG
1 TCATCATCATCG
*
74276 TCGTCATCATCG
1 TCATCATCATCG
74288 TC
1 TC
74290 CTCCACCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.18, C:0.37, G:0.11, T:0.34
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:74272 original size:15 final size:15
Alignment explanation
Indices: 74252--74292 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
74242 CTCTTCCTCT
74252 TCATCATCCTCGTCA
1 TCATCATCCTCGTCA
*
74267 TCATCATCGTCGTCA
1 TCATCATCCTCGTCA
*
74282 TCATCGTCCTC
1 TCATCATCCTC
74293 CACCCCATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.39, G:0.10, T:0.34
Consensus pattern (15 bp):
TCATCATCCTCGTCA
Found at i:74644 original size:15 final size:15
Alignment explanation
Indices: 74624--74661 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
74614 CCCAGGATCA
74624 TCTTCATCATCCTCC
1 TCTTCATCATCCTCC
*
74639 TCTTCATCTTCCTCC
1 TCTTCATCATCCTCC
*
74654 TCCTCATC
1 TCTTCATC
74662 TGACTCCGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.47, G:0.00, T:0.42
Consensus pattern (15 bp):
TCTTCATCATCCTCC
Found at i:80438 original size:168 final size:165
Alignment explanation
Indices: 80069--80491 Score: 553
Period size: 168 Copynumber: 2.5 Consensus size: 165
80059 TGAGTCATTT
* * * *
80069 GTCAATTGAGAAATGACCAAAAATTTTAGCTATTTAATCCCCTCAAGAATCAAAAGATAGGACAT
1 GTCAATTGAGAAATGACCAAAAA-GTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTATGACAT
* * * * * ** *
80134 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAATTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACAAAAAAAAATAATTCTCTAACTCAAAAGCAATCCTTG
* * * *
80199 ATGGGGATCTTTTATTAATTCCACTACTTTATTCAA
130 ATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
80235 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTATGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTATGACAT
*
80300 TTAAGTAATCTACCAAGTAGGAAAAGACAAAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGT-C
65 TTAAGTAATCTGCCAAGTAGGAAAAGACAAAAAAAAATAA-TTCTCTAACT-CAAAAGCAA-TCC
*
80364 TTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
127 TTGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
80403 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAATAATCAAAAGTTATGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTATGACAT
* *
80468 TTTAGTAATCGGCCAAGT-GGAAAA
65 TTAAGTAATCTGCCAAGTAGGAAAA
80492 ATACGGAAAT
Statistics
Matches: 224, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
166 93 0.42
167 16 0.07
168 114 0.51
169 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTATGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACAAAAAAAAATAATTCTCTAACTCAAAAGCAATCCTTGA
TAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:80742 original size:145 final size:145
Alignment explanation
Indices: 80366--80784 Score: 702
Period size: 143 Copynumber: 2.9 Consensus size: 145
80356 AGCAAGTCTT
80366 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGTCTA
1 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGTCTA
* * *
80431 GTTATTTAATCACCTCAATAATCAAAAGTTATGGCATTTTAGTAATCGGCCAAGTGGAAAAATAC
66 GTTATTTAATCACCTCAAGAATCAAAAGTTA-GGCATTTAAGTAATCGGCCAAGTGGAAAAAGAC
80496 GGAAATATTAATTCGG
130 GGAAATATTAATTCGG
80512 GGTAGGGA---TTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGTCTA
1 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGTCTA
80574 GTTATTTAATCACCTCAAGAATCAAAAGTTAGAGCATTTAAGTAATCGGCCAAGTGGAAAAAGAC
66 GTTATTTAATCACCTCAAGAATCAAAAGTTAG-GCATTTAAGTAATCGGCCAAGTGGAAAAAGAC
80639 GGAAATATTAATTCGG
130 GGAAATATTAATTCGG
* * *
80655 GGTAAGGATCTTTTAGTAATTCC-CTACTCTATTAAAATCAATTGATAAATGACCAAAAAGTCTA
1 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGTCTA
* * *
80719 GTTATTTAATCACCTTAAGAATCAAAAGTTAGGGCATTTAAGTAATTGGCCAAGTGGGAAAAGAC
66 GTTATTTAATCACCTCAAGAATCAAAAGTTA-GGCATTTAAGTAATCGGCCAAGTGGAAAAAGAC
80784 G
130 G
80785 AAAAAAATTA
Statistics
Matches: 259, Mismatches: 9, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
142 1 0.00
143 137 0.53
145 100 0.39
146 21 0.08
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (145 bp):
GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGTCTA
GTTATTTAATCACCTCAAGAATCAAAAGTTAGGCATTTAAGTAATCGGCCAAGTGGAAAAAGACG
GAAATATTAATTCGG
Found at i:82153 original size:42 final size:41
Alignment explanation
Indices: 82107--82221 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 41
82097 CTCTCTCCCC
* *
82107 AAAGTCCCCAAACACATATAACACAGGGGCAATTCTCCTTCT
1 AAAGTCCCCAAACACATATAACACAGGGGCAATTCT-ATACT
* * *
82149 AAAGTCCTCAAACACATATAACACAGAGAC-A-TCTATACT
1 AAAGTCCCCAAACACATATAACACAGGGGCAATTCTATACT
* ** *
82188 AAAGTCCCTAAACACATGCAACACAAGGGCAATT
1 AAAGTCCCCAAACACATATAACACAGGGGCAATT
82222 TTCTCTACAT
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
39 26 0.44
40 4 0.07
41 2 0.03
42 27 0.46
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATAACACAGGGGCAATTCTATACT
Found at i:83590 original size:13 final size:13
Alignment explanation
Indices: 83569--83598 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
83559 AATTATTAGA
*
83569 AGGGTCAAATTGG
1 AGGGACAAATTGG
83582 AGGGACAAATTGG
1 AGGGACAAATTGG
83595 AGGG
1 AGGG
83599 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.43, T:0.17
Consensus pattern (13 bp):
AGGGACAAATTGG
Done.