Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006098.1 Corchorus capsularis cultivar CVL-1 contig06116, 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: 16811
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:1428 original size:156 final size:155
Alignment explanation
Indices: 887--1432 Score: 500
Period size: 156 Copynumber: 3.5 Consensus size: 155
877 CCATTTTAAA
* *
887 CAGACTTAAG-ATGAAAAACTTATGCAAGTTTTTTTATTTAAGGACAGTTTGGGGTGTGAAACCA
1 CAGAC-TAAGAATGAAAAACTTATGCAAG-TTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCA
* * * * *
951 ACTTCACTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTCCATAGTTTTATGG-GAATAATCT
64 ACTTCACCATGATAGGGAGTTCGGTTTTACTTGGATTTTTTCCATAATCTTATGGAG-ATAATCT
* * *
1015 AATTAGTCTCTTGGCCAAGTTTCATCTTCAT
128 -A--AGTCCCTTGGCAAAGTTTCAACTTCAT
** * * *
1046 TGGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCAAC
1 CAGACTAAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCAAC
* * * *
1111 TTCACTATGATAGGGAGTTCAGTTTTACTTAGAATTTTTTCCA-AAACTTTATGGAGATAATCTA
66 TTCACCATGATAGGGAGTTCGGTTTTACTT-GGATTTTTTCCATAATC-TTATGGAGATAATCTA
* *
1175 AG-CCTACTTGTGGAAA--ATCAACTTCAT
129 AGTCC--CTTG-GCAAAGTTTCAACTTCAT
** * * * * * * *
1202 TGGACTTAGAATAAAAAACTTATGTAAGTTTTTCATTTAAGCACAGTTT-AGGGAGAGAAACCAG
1 CAGACTAAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGA-GGTGTGAAACCAA
** * * * * *
1266 GATCACCATCA-AGGGGAGCTGGGTTTTACTTGGGATTTTTTCCATAATCTTGTGGAGAGAATCT
65 CTTCACCATGATA-GGGAGTTCGGTTTTACTT-GGATTTTTTCCATAATCTTATGGAGATAATCT
*
1330 AAGTCCCTTGGCAAAGTTTCAGC-TCAAT
128 AAGTCCCTTGGCAAAGTTTCAACTTC-AT
* * *
1358 CAGACATAAG-GTGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCTA
1 CAGAC-TAAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCAA
*
1422 GTTCACCATGA
65 CTTCACCATGA
1433 AGGAGGGCTC
Statistics
Matches: 317, Mismatches: 54, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
154 4 0.01
155 8 0.03
156 176 0.56
157 13 0.04
158 72 0.23
159 43 0.14
160 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (155 bp):
CAGACTAAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCAAC
TTCACCATGATAGGGAGTTCGGTTTTACTTGGATTTTTTCCATAATCTTATGGAGATAATCTAAG
TCCCTTGGCAAAGTTTCAACTTCAT
Found at i:1767 original size:17 final size:17
Alignment explanation
Indices: 1745--1827 Score: 139
Period size: 17 Copynumber: 4.9 Consensus size: 17
1735 GATACAGCAG
*
1745 ATGCTACCTGGTACTTC
1 ATGCTACCTGGTACCTC
1762 ATGCTACCTGGTACCTC
1 ATGCTACCTGGTACCTC
*
1779 ATGCTACCTAGTACCTC
1 ATGCTACCTGGTACCTC
*
1796 ATGCTACCTAGTACCTC
1 ATGCTACCTGGTACCTC
1813 ATGCTACCTGGTACC
1 ATGCTACCTGGTACC
1828 ATGAGGGGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 63 1.00
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (17 bp):
ATGCTACCTGGTACCTC
Found at i:1803 original size:10 final size:10
Alignment explanation
Indices: 1773--1821 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
1763 TGCTACCTGG
1773 TACCTCATGC
1 TACCTCATGC
1783 TACCT-A-G-
1 TACCTCATGC
1790 TACCTCATGC
1 TACCTCATGC
1800 TACCT-A-G-
1 TACCTCATGC
1807 TACCTCATGC
1 TACCTCATGC
1817 TACCT
1 TACCT
1822 GGTACCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
7 10 0.30
8 4 0.12
9 4 0.12
10 15 0.45
ACGTcount: A:0.22, C:0.37, G:0.10, T:0.31
Consensus pattern (10 bp):
TACCTCATGC
Found at i:3329 original size:4 final size:4
Alignment explanation
Indices: 3320--3344 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3310 GTTTTAAAAT
3320 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
3345 AACCCTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:15068 original size:11 final size:11
Alignment explanation
Indices: 15048--15132 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
15038 ACTTTTATCA
15048 TTTT-TTACTC
1 TTTTCTTACTC
15058 TTTTCTTACTC
1 TTTTCTTACTC
*
15069 TTTTTACCAATA-TC
1 -TTTT--C-TTACTC
15083 ATTTT-TTACTC
1 -TTTTCTTACTC
15094 TTTTCTTACTC
1 TTTTCTTACTC
15105 TTTTTACCAATTACTC
1 -TTTT--C--TTACTC
15121 TTTTCTTACTC
1 TTTTCTTACTC
15132 T
1 T
15133 CTTTTATTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 23
0.70 0.03 0.27
Matches are distributed among these distances:
10 10 0.17
11 21 0.35
12 8 0.13
13 1 0.02
14 8 0.13
15 6 0.10
16 6 0.10
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTCTTACTC
Found at i:15084 original size:36 final size:37
Alignment explanation
Indices: 15042--15132 Score: 150
Period size: 36 Copynumber: 2.5 Consensus size: 37
15032 TTTGCTACTT
15042 TTATCATTTTTTACTCTTTTCTTACTCTTTTTACCAA
1 TTATCATTTTTTACTCTTTTCTTACTCTTTTTACCAA
15079 -TATCATTTTTTACTCTTTTCTTACTCTTTTTACCAA
1 TTATCATTTTTTACTCTTTTCTTACTCTTTTTACCAA
15115 TTACTC-TTTTCTTACTCT
1 TTA-TCATTTT-TTACTCT
15133 CTTTTATTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
36 36 0.71
37 6 0.12
38 9 0.18
ACGTcount: A:0.18, C:0.23, G:0.00, T:0.59
Consensus pattern (37 bp):
TTATCATTTTTTACTCTTTTCTTACTCTTTTTACCAA
Found at i:15289 original size:21 final size:21
Alignment explanation
Indices: 15211--15286 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
15201 CTGATCACCC
15211 TTTACTCTTACTGATTACTAT
1 TTTACTCTTACTGATTACTAT
* * *
15232 TTGACTCTTACTAATTA-TCAC
1 TTTACTCTTACTGATTACT-AT
* *
15253 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTGATTACTAT
15274 TTTACTCTTACTG
1 TTTACTCTTACTG
15287 GTTTTCTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.50
Consensus pattern (21 bp):
TTTACTCTTACTGATTACTAT
Found at i:15387 original size:15 final size:15
Alignment explanation
Indices: 15332--15388 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
15322 GATTACCTTC
15332 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
15347 TTAC-CATTTT-CTGC
1 TTACTC-TTTTACTGA
** *
15361 TCCCTTTTTTACTGA
1 TTACTCTTTTACTGA
15376 TTACTCTTTTACT
1 TTACTCTTTTACT
15389 TTTTACTGAT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.16, C:0.25, G:0.05, T:0.54
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:15387 original size:74 final size:72
Alignment explanation
Indices: 15293--15485 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 72
15283 ACTGGTTTTC
**
15293 TTTTACTGATTACTATTTTACTCTTTGTTGATTACCTTCTTACTCTTTTACTGATTACCATTTTC
1 TTTTACTGATTACTATTTTACTCTTTACTGATTACCTT-TTACT-TTTTACTGATTACCATTTTC
15358 TGCTCCCTT
64 TGCTCCCTT
* * ** *
15367 TTTTACTGATTACTCTTTTACTTTTTACTGATTGTCTTTTGCTTTTTACTGATTACC--TTT-T-
1 TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTTTACTTTTTACTGATTACCATTTTCTG
*
15428 -T--ATT
66 CTCCCTT
* * *
15432 TCTTACTGATTAGCT-TTTTACTCTTTACTGATCACCTTTT-CATTCTTACTGATT
1 TTTTACTGATTA-CTATTTTACTCTTTACTGATTACCTTTTAC-TTTTTACTGATT
15486 TCCTTTTACT
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
64 1 0.01
65 45 0.44
66 2 0.02
67 1 0.01
69 1 0.01
70 3 0.03
72 14 0.14
73 4 0.04
74 32 0.31
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (72 bp):
TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTTTACTTTTTACTGATTACCATTTTCTG
CTCCCTT
Found at i:15391 original size:21 final size:21
Alignment explanation
Indices: 15366--15502 Score: 134
Period size: 21 Copynumber: 6.4 Consensus size: 21
15356 TCTGCTCCCT
15366 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTAC-CTTTTAC
** *
15388 TTTTTACTGATTGTCTTTTGC
1 TTTTTACTGATTACCTTTTAC
15409 TTTTTACTGATTACCTTTTTA-
1 TTTTTACTGATTACC-TTTTAC
*
15430 TTTCTTACTGATTAGCTTTTTAC
1 TTT-TTACTGATTA-CCTTTTAC
* *
15453 TCTTTACTGATCACCTTTT-C
1 TTTTTACTGATTACCTTTTAC
* *
15473 ATTCTTACTGATTTCCTTTTAC
1 -TTTTTACTGATTACCTTTTAC
*
15495 TTCTTACT
1 TTTTTACT
15503 TGTTACTTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.01
21 50 0.53
22 41 0.43
23 3 0.03
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTTACTGATTACCTTTTAC
Found at i:15391 original size:22 final size:22
Alignment explanation
Indices: 15366--15523 Score: 127
Period size: 21 Copynumber: 7.4 Consensus size: 22
15356 TCTGCTCCCT
15366 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTACTCTTTTAC
* *
15388 TTTTTACTGATT-GTCTTTTGC
1 TTTTTACTGATTACTCTTTTAC
15409 TTTTTACTGATTAC-CTTTTTA-
1 TTTTTACTGATTACTC-TTTTAC
15430 TTTCTTACTGATTAGCT-TTTTAC
1 TTT-TTACTGATTA-CTCTTTTAC
* *
15453 TCTTTACTGATCAC-CTTTT-C
1 TTTTTACTGATTACTCTTTTAC
* *
15473 ATTCTTACTGATTTC-CTTTTAC
1 -TTTTTACTGATTACTCTTTTAC
* **
15495 TTCTTACTTG-TTACT-TTTTTT
1 TTTTTAC-TGATTACTCTTTTAC
15516 TTTTTACT
1 TTTTTACT
15524 CTTACTGATT
Statistics
Matches: 111, Mismatches: 14, Indels: 24
0.74 0.09 0.16
Matches are distributed among these distances:
20 2 0.02
21 63 0.57
22 43 0.39
23 3 0.03
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.60
Consensus pattern (22 bp):
TTTTTACTGATTACTCTTTTAC
Found at i:15429 original size:43 final size:41
Alignment explanation
Indices: 15366--15519 Score: 143
Period size: 43 Copynumber: 3.6 Consensus size: 41
15356 TCTGCTCCCT
*
15366 TTTTTACTGATTACTCTTTTACTTTTTACTGATTGTCTTTTGC
1 TTTTTACTGATTACT-TTTTA-TTTTTACTGATTGTCTTTTAC
15409 TTTTTACTGATTACCTTTTTATTTCTTACTGATTAG-CTTTTTAC
1 TTTTTACTGATTA-CTTTTTATTT-TTACTGATT-GTC-TTTTAC
* * * *
15453 TCTTTACTGATCACCTTTTCATTCTTACTGATT-TCCTTTTAC
1 TTTTTACTGATTA-CTTTTTATTTTTACTGATTGT-CTTTTAC
* *
15495 TTCTTACTTG-TTACTTTTTTTTTTT
1 TTTTTAC-TGATTACTTTTTATTTTT
15520 TACTCTTACT
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
41 9 0.10
42 16 0.17
43 40 0.43
44 28 0.30
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.60
Consensus pattern (41 bp):
TTTTTACTGATTACTTTTTATTTTTACTGATTGTCTTTTAC
Found at i:15438 original size:65 final size:63
Alignment explanation
Indices: 15369--15523 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 63
15359 GCTCCCTTTT
*** * *
15369 TTACTGATTACTCTTTTACTTTTTACTGATTGTCTTTTGC-TTTTTACTGATTACCTTTTTATTT
1 TTACTGATTACT-TTTTACTTTTTACTGATCACCTTTT-CATTCTTACTGATTACC-TTTTACTT
15433 C
63 C
* *
15434 TTACTGATTAGCTTTTTACTCTTTACTGATCACCTTTTCATTCTTACTGATTTCCTTTTACTTC
1 TTACTGATTA-CTTTTTACTTTTTACTGATCACCTTTTCATTCTTACTGATTACCTTTTACTTC
**
15498 TTACTTG-TTACTTTTTTTTTTTTACT
1 TTAC-TGATTACTTTTTACTTTTTACT
15524 CTTACTGATT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 13 0.17
64 16 0.21
65 46 0.60
66 2 0.03
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.59
Consensus pattern (63 bp):
TTACTGATTACTTTTTACTTTTTACTGATCACCTTTTCATTCTTACTGATTACCTTTTACTTC
Found at i:15542 original size:27 final size:28
Alignment explanation
Indices: 15489--15542 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
15479 ACTGATTTCC
* *
15489 TTTTACTTCTTACTTGTTACTTTTTTTT
1 TTTTACTTCTTACTTGTTAATTATTTTT
15517 TTTTAC-TCTTAC-TGATTAATTATTTT
1 TTTTACTTCTTACTTG-TTAATTATTTT
15543 ACTTTTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 15 0.65
28 6 0.26
ACGTcount: A:0.17, C:0.13, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTTACTTCTTACTTGTTAATTATTTTT
Found at i:15846 original size:22 final size:24
Alignment explanation
Indices: 15819--15862 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
15809 TTAACCACTC
15819 AACTCTTAATTAT-GA-TCACTTT
1 AACTCTTAATTATCGATTCACTTT
15841 AACTCTTAATTATCGATTCACT
1 AACTCTTAATTATCGATTCACT
15863 GATTACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (24 bp):
AACTCTTAATTATCGATTCACTTT
Found at i:16009 original size:55 final size:56
Alignment explanation
Indices: 15945--16060 Score: 173
Period size: 56 Copynumber: 2.1 Consensus size: 56
15935 TATCTTTTAC
*
15945 CTGA-TTACTGATTACTATTACCTTAACTC-TAATTAATCTCTTTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACTCATAATTAATCTCTTTTTACTTAATTA
* * * *
15999 CTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACTCATAATTAATCTCTTTTTACTTAATTA
16055 CTGATT
1 CTGATT
16061 GCCCCCTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 4 0.07
55 21 0.38
56 30 0.55
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (56 bp):
CTGATTTACTGATTACTACTACCTTAACTCATAATTAATCTCTTTTTACTTAATTA
Done.