Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013968.1 Corchorus capsularis cultivar CVL-1 contig13989, 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: 40625
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:6349 original size:24 final size:24
Alignment explanation
Indices: 6304--6350 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
6294 AATCATTCTT
* *
6304 AAAAATTCCAAGCAATCATCAATC
1 AAAAATTCAAAGCAATAATCAATC
6328 AAAAA-TCAAAGCAATAACTCAAT
1 AAAAATTCAAAGCAATAA-TCAAT
6351 ATGTACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.55, C:0.21, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAAATTCAAAGCAATAATCAATC
Found at i:13827 original size:12 final size:12
Alignment explanation
Indices: 13810--13841 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
13800 GCTGCGCAAC
13810 ACCGGCCAAATG
1 ACCGGCCAAATG
*
13822 ACCGGCCACATG
1 ACCGGCCAAATG
13834 ACCGGCCA
1 ACCGGCCA
13842 TCGCATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.41, G:0.25, T:0.06
Consensus pattern (12 bp):
ACCGGCCAAATG
Found at i:17996 original size:35 final size:35
Alignment explanation
Indices: 17938--18017 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
17928 TTTTTTTATC
*
17938 ACAAAAATCTCTTTTTTTTTAGAAAAATCGGAAAAA
1 ACAAAAA-CTCTTTTTTTTTAGAAAAAACGGAAAAA
**
17974 GGAAAAACT-TTTTTTTTATAGAAAAAACGGAAAAA
1 ACAAAAACTCTTTTTTTT-TAGAAAAAACGGAAAAA
18009 ACAAAAACT
1 ACAAAAACT
18018 AATTCTTGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
34 8 0.21
35 25 0.66
36 5 0.13
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (35 bp):
ACAAAAACTCTTTTTTTTTAGAAAAAACGGAAAAA
Found at i:18312 original size:6 final size:6
Alignment explanation
Indices: 18297--18328 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
18287 AAAACAAAGC
18297 AAAT-T AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
18329 GCAAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:31597 original size:43 final size:43
Alignment explanation
Indices: 31550--31635 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
31540 GCCAAGTCAT
* * *
31550 GTGGCCGGTTGTGGCCGGGCATGGCCTAGTCATGTGGCCGGTG
1 GTGGCCGGTGGTGGCCGGGCATCGCCAAGTCATGTGGCCGGTG
*
31593 GTGGCCGGTGGTGGCCGGGCATCTCCAAGTCATGTGGCCGGTG
1 GTGGCCGGTGGTGGCCGGGCATCGCCAAGTCATGTGGCCGGTG
31636 TTGCACGGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.08, C:0.24, G:0.45, T:0.22
Consensus pattern (43 bp):
GTGGCCGGTGGTGGCCGGGCATCGCCAAGTCATGTGGCCGGTG
Found at i:31608 original size:33 final size:33
Alignment explanation
Indices: 31516--31600 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
31506 TTAAGGATCT
31516 TGTGGCCGGTTGTGGCCGGGCATGGCCAAGTCA
1 TGTGGCCGGTTGTGGCCGGGCATGGCCAAGTCA
*
31549 TGTGGCCGGTTGTGGCCGGGCATGGCCTAGTCA
1 TGTGGCCGGTTGTGGCCGGGCATGGCCAAGTCA
*
31582 TGTGGCCGGTGGTGGCCGG
1 TGTGGCCGGTTGTGGCCGG
31601 TGGTGGCCGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.08, C:0.24, G:0.46, T:0.22
Consensus pattern (33 bp):
TGTGGCCGGTTGTGGCCGGGCATGGCCAAGTCA
Found at i:32100 original size:158 final size:159
Alignment explanation
Indices: 31775--32662 Score: 1424
Period size: 158 Copynumber: 5.6 Consensus size: 159
31765 GGCGCATTAA
* *
31775 GAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCTTGTGCAAAAACAAAG
1 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCTGTGCAAAAACAAAG
* * * * * *
31840 CTATCCTTGAAGCCCAAAACCTCAACAACGCGTGTTTGTGTGCAAAACATCATTCTTAGT-GTAA
66 CTCTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTA-TCGAAA
*
31904 GGCTCATTCCAGAAGCATTTTTTACGCAAC
130 GGCTCATTCCAGAAGCATTTTTTGCGCAAC
* * *
31934 GAGTGCTCAAAAGGCTTGTGTCGGAGTGAGATGAGCCTGTTCGACAACCCTGTGCAAAAACAAAG
1 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCTGTGCAAAAACAAAG
** *
31999 CTCTCCTTGAAG-CCAAAGCCTCAACATTGCGCGTTTGTTTGCAAAACGTCGTTCTTATCGAAAG
66 CTCTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAG
32063 GCTCATTCCAGAAGCATTTTTTGCGCAAC
131 GCTCATTCCAGAAGCATTTTTTGCGCAAC
* *
32092 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAAATGAGCTTGTTGGACAGCCCTGTGCAAAAACAAAG
1 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCTGTGCAAAAACAAAG
** *
32157 CTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAAAACGTCATTCTTATCGAAAG
66 CTCTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAG
* *
32222 GCTCATTCCAGAAGCATTTTTTGCACAAA
131 GCTCATTCCAGAAGCATTTTTTGCGCAAC
* * * *
32251 GGGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCTTGTGCAAAAAAAAAA
1 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCTGTGC--AAAAACAA
* *
32316 AGCTACTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACATCGTTCTTAGCGA
64 AGCT-CTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGA
* *
32381 AAGGCTCATTCTAGAAGCATTTTTTGCGTAAC
128 AAGGCTCATTCCAGAAGCATTTTTTGCGCAAC
32413 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCTGTGCAAAAA-AAAG
1 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCTGTGCAAAAACAAAG
32477 CTCTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAG
66 CTCTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAG
32542 GCTCATTCCAGAAGCATTTTTTGCGCAAC
131 GCTCATTCCAGAAGCATTTTTTGCGCAAC
32571 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAG-CCTGGTGCAAAAACAAA
1 GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCT-GTGCAAAAACAAA
*
32635 GCTCTCCTTGAAGCCCAAAGCCTTAACA
65 GCTCTCCTTGAAGCCCAAAGCCTCAACA
32663 TTGAAACCGA
Statistics
Matches: 676, Mismatches: 46, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
157 4 0.01
158 286 0.42
159 235 0.35
160 5 0.01
161 11 0.02
162 135 0.20
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (159 bp):
GAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTGGACAGCCCTGTGCAAAAACAAAG
CTCTCCTTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAG
GCTCATTCCAGAAGCATTTTTTGCGCAAC
Found at i:32675 original size:21 final size:21
Alignment explanation
Indices: 32642--32686 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32632 AAAGCTCTCC
* *
32642 TTGAAGCCCAAAGCCTTAACA
1 TTGAAACCCAAAGCCTCAACA
*
32663 TTGAAACCGAAAGCCTCAACA
1 TTGAAACCCAAAGCCTCAACA
32684 TTG
1 TTG
32687 CGGGTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.20
Consensus pattern (21 bp):
TTGAAACCCAAAGCCTCAACA
Found at i:32794 original size:180 final size:180
Alignment explanation
Indices: 32483--32842 Score: 605
Period size: 180 Copynumber: 2.0 Consensus size: 180
32473 AAAGCTCTCC
*
32483 TTGAAGCCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAGGCTCAT
1 TTGAAACCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAGGCTCAT
* *
32548 TCCAGAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCCTGTTG
66 TCCAGAAGCATTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCAGAGTGAGATGAGCCTGTTG
*
32613 GACAG-CCTGGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTTAACA
131 GACAGCCCT-GTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACA
* ** *
32663 TTGAAACCGAAAGCCTCAACATTGCGGGTTTGTGTGCAAAACGTCGTTCTTATCGAAAGGCTCAT
1 TTGAAACCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAGGCTCAT
*
32728 TCCATAAGCATTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCAGAGTGAGATGAGCCTGTTG
66 TCCAGAAGCATTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCAGAGTGAGATGAGCCTGTTG
* *
32793 GATAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCGAAAGCCTCAACA
131 GACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACA
32843 ACGCGCGTTT
Statistics
Matches: 168, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
180 165 0.98
181 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (180 bp):
TTGAAACCCAAAGCCTCAACAACGCGCGTTTGTGTGCAAAACGTCGTTCTTATCGAAAGGCTCAT
TCCAGAAGCATTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCAGAGTGAGATGAGCCTGTTG
GACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACA
Found at i:33756 original size:12 final size:12
Alignment explanation
Indices: 33724--33760 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
33714 GTTGTGGCCG
*
33724 GATGGCCCATGC
1 GATGGCCCGTGC
*
33736 AATGGCCCGTGC
1 GATGGCCCGTGC
33748 GATGGCCCGTGC
1 GATGGCCCGTGC
33760 G
1 G
33761 GCGTCCCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.38, T:0.16
Consensus pattern (12 bp):
GATGGCCCGTGC
Found at i:35477 original size:33 final size:33
Alignment explanation
Indices: 35406--35480 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
35396 AAAGGATCGT
* * *
35406 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCGT
1 GTGGCCGGTTGTAGCCGGACATGGCCGAGTCGC
* *
35439 TTGGCCGGTTGTAGCCGGACATGTCC-ATGTCGC
1 GTGGCCGGTTGTAGCCGGACATGGCCGA-GTCGC
35472 GTGGCCGGT
1 GTGGCCGGT
35481 CTTGTGGCCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.08, C:0.25, G:0.43, T:0.24
Consensus pattern (33 bp):
GTGGCCGGTTGTAGCCGGACATGGCCGAGTCGC
Done.