Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007251.1 Corchorus capsularis cultivar CVL-1 contig07272, 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: 24758
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1778 original size:2 final size:2
Alignment explanation
Indices: 1771--1799 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1761 CAATCTTATT
1771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1800 TGAAAAAAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2971 original size:31 final size:30
Alignment explanation
Indices: 2944--3043 Score: 121
Period size: 31 Copynumber: 3.3 Consensus size: 30
2934 AATAGGACTG
2944 AATTGAGCAGAAACTGGAAGGTTTAGGACCA
1 AATTGAGCAG-AACTGGAAGGTTTAGGACCA
* **
2975 AATTGAGCCGGTCT-GAAGGTTTAGGACCA
1 AATTGAGCAGAACTGGAAGGTTTAGGACCA
* * *
3004 AATCGAGCAGACCGTGAAAGGTTTAGGACCA
1 AATTGAGCAGAAC-TGGAAGGTTTAGGACCA
3035 AATTGAGCA
1 AATTGAGCA
3044 TTTAGCCTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
29 24 0.41
30 3 0.05
31 31 0.53
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (30 bp):
AATTGAGCAGAACTGGAAGGTTTAGGACCA
Found at i:3002 original size:29 final size:30
Alignment explanation
Indices: 2960--3043 Score: 116
Period size: 29 Copynumber: 2.8 Consensus size: 30
2950 GCAGAAACTG
* **
2960 GAAGGTTTAGGACCAAATTGAGCCGGTC-T
1 GAAGGTTTAGGACCAAATTGAGCAGACCGT
*
2989 GAAGGTTTAGGACCAAATCGAGCAGACCGT
1 GAAGGTTTAGGACCAAATTGAGCAGACCGT
3019 GAAAGGTTTAGGACCAAATTGAGCA
1 G-AAGGTTTAGGACCAAATTGAGCA
3044 TTTAGCCTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.50
30 2 0.04
31 22 0.46
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (30 bp):
GAAGGTTTAGGACCAAATTGAGCAGACCGT
Found at i:5243 original size:15 final size:16
Alignment explanation
Indices: 5211--5267 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
5201 CGAACCCGTC
5211 TGACCCGAGACCCGAA
1 TGACCCGAGACCCGAA
*
5227 TGACCCGA-ACCCTAA
1 TGACCCGAGACCCGAA
** * *
5242 TGAGTCAAAACCCGAA
1 TGACCCGAGACCCGAA
*
5258 TGACCAGAGA
1 TGACCCGAGA
5268 AAACTACCTA
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.37, C:0.32, G:0.21, T:0.11
Consensus pattern (16 bp):
TGACCCGAGACCCGAA
Found at i:5777 original size:78 final size:78
Alignment explanation
Indices: 5694--5862 Score: 248
Period size: 78 Copynumber: 2.2 Consensus size: 78
5684 TTTTTTTAAT
* * * *
5694 TAAAATTGTAAAATGGTAAACTAAAATAGTTATAAGGATATTATATTTAATTAAATAAAAATAGA
1 TAAAATTGTAAAATGGTAAAATAAAAGAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
5759 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * *
5772 TAAAATAGTAAAATGGTAAAATAAAAGCGTTATAAAGATATTAGATTTAATTAAATAAATATAGA
1 TAAAATTGTAAAATGGTAAAATAAAAGAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
*
5837 TTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* *
5850 TAAGATTATAAAA
1 TAAAATTGTAAAA
5863 GTTTAAACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.49, C:0.01, G:0.14, T:0.36
Consensus pattern (78 bp):
TAAAATTGTAAAATGGTAAAATAAAAGAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
GTTTTTAGTTGAG
Found at i:6199 original size:37 final size:37
Alignment explanation
Indices: 6151--6221 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
6141 CTTGATCAAC
* **
6151 ATACATATCTTTTCGTATAGACATAACTTTATGATCA
1 ATACATATCTTTCCAAATAGACATAACTTTATGATCA
*
6188 ATACATCTCTTTCCAAATAGACATAACTTTATGA
1 ATACATATCTTTCCAAATAGACATAACTTTATGA
6222 ATAATTATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (37 bp):
ATACATATCTTTCCAAATAGACATAACTTTATGATCA
Found at i:7421 original size:29 final size:28
Alignment explanation
Indices: 7389--7459 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 28
7379 TTTGCTTCTC
7389 TAAGAAACAAACATATCTCTTTGTTCCTT
1 TAAGAAAC-AACATATCTCTTTGTTCCTT
* *
7418 TAAGAAAGCAGCATATCTCTTTGTTTCTT
1 TAAGAAA-CAACATATCTCTTTGTTCCTT
7447 TAAGAAACCAACA
1 TAAGAAA-CAACA
7460 CACCTTCACT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (28 bp):
TAAGAAACAACATATCTCTTTGTTCCTT
Found at i:8514 original size:37 final size:37
Alignment explanation
Indices: 8470--8540 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
8460 CTTGATCAAC
* **
8470 ATACATGTCTTTTCGTATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
8507 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
8541 ATAATTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:9762 original size:2 final size:2
Alignment explanation
Indices: 9755--9783 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9745 TCAAAGAAAC
9755 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
9784 ACATGGGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9836 original size:15 final size:16
Alignment explanation
Indices: 9818--9851 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9808 ATTGAGTTCT
9818 GGTTAATTC-AATTCG
1 GGTTAATTCGAATTCG
*
9833 GGTTAATTCGGATTCG
1 GGTTAATTCGAATTCG
9849 GGT
1 GGT
9852 CACTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (16 bp):
GGTTAATTCGAATTCG
Found at i:11157 original size:19 final size:20
Alignment explanation
Indices: 11128--11167 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
11118 AAATAAGTTA
11128 AAAAGAACTCAAAGTCAACT
1 AAAAGAACTCAAAGTCAACT
*
11148 AAAA-AACTCAAAGTCCACT
1 AAAAGAACTCAAAGTCAACT
11167 A
1 A
11168 TCAAAGCCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAAGAACTCAAAGTCAACT
Found at i:13505 original size:19 final size:19
Alignment explanation
Indices: 13481--13520 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
13471 TTTTTCTTCT
*
13481 TTCAATCGTGAATATTCGA
1 TTCAATCATGAATATTCGA
13500 TTCAATCATGAATATTCGA
1 TTCAATCATGAATATTCGA
13519 TT
1 TT
13521 TGTTGTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (19 bp):
TTCAATCATGAATATTCGA
Found at i:19352 original size:31 final size:31
Alignment explanation
Indices: 19316--19488 Score: 175
Period size: 31 Copynumber: 5.4 Consensus size: 31
19306 TTTGTGCATA
** *
19316 TGGCATGCCACGTGTCACTTTTTGAAACATG
1 TGGCATGCCACGTGTCACTTTTTGGTACACG
* *
19347 TGGCATGCCACGTATCACTTTTTGGTGCACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACG
* *
19378 TGGCGTGCGACGTGTCACTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACG
* *
19409 TGGCATGACATGTGTCACTTTTTTGGTACACG
1 TGGCATGCCACGTGTCAC-TTTTTGGTACACG
* * * *
19441 TAGTATGTCACATGCATGTTACTTTTTGGTACACG
1 TGGCATG-C-CA--CGTGTCACTTTTTGGTACACG
*
19476 TGGCATGCGACGT
1 TGGCATGCCACGT
19489 CAGACACCGT
Statistics
Matches: 114, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
31 69 0.61
32 18 0.16
33 1 0.01
34 3 0.03
35 18 0.16
36 5 0.04
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACACG
Found at i:19391 original size:62 final size:62
Alignment explanation
Indices: 19296--19441 Score: 163
Period size: 62 Copynumber: 2.4 Consensus size: 62
19286 TGACACGTGG
** * *
19296 CACGTATC-C-TTTT-GTGCATATGGCATGCCACGTGTCACTTTTTGAAACATGTGGCATGC
1 CACGTATCACTTTTTGGTGCACGTGGCATGCCACGTGTCACTTTTTGAAACACGTGGCATGA
* * **
19355 CACGTATCACTTTTTGGTGCACGTGGCGTGCGACGTGTCACTTTTTGGTACACGTGGCATGA
1 CACGTATCACTTTTTGGTGCACGTGGCATGCCACGTGTCACTTTTTGAAACACGTGGCATGA
* * *
19417 CATGTGTCACTTTTTTGGTACACGT
1 CACGTATCAC-TTTTTGGTGCACGT
19442 AGTATGTCAC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
59 8 0.11
60 1 0.01
61 4 0.06
62 46 0.64
63 13 0.18
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (62 bp):
CACGTATCACTTTTTGGTGCACGTGGCATGCCACGTGTCACTTTTTGAAACACGTGGCATGA
Found at i:20253 original size:11 final size:11
Alignment explanation
Indices: 20234--20269 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
20224 CGTTTTTCTG
20234 GTTTTGTTTTT
1 GTTTTGTTTTT
* *
20245 GTTTCGTTTTC
1 GTTTTGTTTTT
20256 GTTTTGTTTTT
1 GTTTTGTTTTT
20267 GTT
1 GTT
20270 GCGCTGTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.06, G:0.19, T:0.75
Consensus pattern (11 bp):
GTTTTGTTTTT
Found at i:20260 original size:16 final size:16
Alignment explanation
Indices: 20217--20264 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
20207 ATATTTGGTA
*
20217 TCGTTTTCGTTTT-TC
1 TCGTTTTCGTTTTGTT
*
20232 TGGTTTT-GTTTTTGTT
1 TCGTTTTCG-TTTTGTT
20248 TCGTTTTCGTTTTGTT
1 TCGTTTTCGTTTTGTT
20264 T
1 T
20265 TTGTTGCGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 1 0.04
15 10 0.37
16 15 0.56
17 1 0.04
ACGTcount: A:0.00, C:0.10, G:0.19, T:0.71
Consensus pattern (16 bp):
TCGTTTTCGTTTTGTT
Done.