Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011680.1 Corchorus capsularis cultivar CVL-1 contig11701, 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: 69044
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:469 original size:10 final size:10
Alignment explanation
Indices: 454--478 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
444 GAGGACTCTA
454 GAATTTTCTG
1 GAATTTTCTG
464 GAATTTTCTG
1 GAATTTTCTG
474 GAATT
1 GAATT
479 GAGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:6229 original size:40 final size:41
Alignment explanation
Indices: 6185--6269 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
6175 CCCTAATTTT
*
6185 AAAAAC-GAAAAAATAAA-TTTTTTTTTATAGAAAAAACGGA
1 AAAAACGGAAAAAAAAAACTTTTTTTTT-TAGAAAAAACGGA
*
6225 AAAAACGGAAAAAAAAAACTTTTTTTTTTAGAAAAACCGGA
1 AAAAACGGAAAAAAAAAACTTTTTTTTTTAGAAAAAACGGA
6266 AAAA
1 AAAA
6270 CCAAAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 6 0.15
41 26 0.63
42 9 0.22
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.25
Consensus pattern (41 bp):
AAAAACGGAAAAAAAAAACTTTTTTTTTTAGAAAAAACGGA
Found at i:6239 original size:10 final size:9
Alignment explanation
Indices: 6214--6238 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6204 TTTTTTTATA
6214 GAAAAAACG
1 GAAAAAACG
6223 GAAAAAACG
1 GAAAAAACG
6232 GAAAAAA
1 GAAAAAA
6239 AAAACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (9 bp):
GAAAAAACG
Found at i:6578 original size:11 final size:11
Alignment explanation
Indices: 6558--6587 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6548 AAAGCAAAGG
*
6558 AAATCAAATCT
1 AAATCTAATCT
6569 AAATCTAATCT
1 AAATCTAATCT
6580 AAATCTAA
1 AAATCTAA
6588 AGCAGATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATCTAATCT
Found at i:6621 original size:13 final size:13
Alignment explanation
Indices: 6585--6629 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
6575 AATCTAAATC
6585 TAAAGCAGATT-A
1 TAAAGCAGATTAA
* *
6597 TAAAACAAATTAA
1 TAAAGCAGATTAA
6610 TAAAGCAGATTAA
1 TAAAGCAGATTAA
6623 TAAAGCA
1 TAAAGCA
6630 AACAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:6636 original size:25 final size:25
Alignment explanation
Indices: 6585--6637 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
6575 AATCTAAATC
*
6585 TAAAGCAGATTATAAAACAAATTAA
1 TAAAGCAGATTATAAAACAAATCAA
*
6610 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAACAAATCAA
6635 TAA
1 TAA
6638 TTAAAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAACAAATCAA
Found at i:7560 original size:10 final size:10
Alignment explanation
Indices: 7545--7569 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7535 GAGGACTCTA
7545 GAATTTTCTG
1 GAATTTTCTG
7555 GAATTTTCTG
1 GAATTTTCTG
7565 GAATT
1 GAATT
7570 GAGCAGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:8329 original size:49 final size:49
Alignment explanation
Indices: 8235--8331 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
8225 AATGAATTTG
* * * * *
8235 CCTTTCGTCCGGAAAAGGCATTTTGGGAAAGGGCAGGTAAGAATAAATA
1 CCTTCCGTCCGGAAAAGGCATTTTGGGAAAGAGCAAGCAAAAATAAATA
* * * *
8284 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGCAAAAATAAAT
1 CCTTCCGTCCGGAAAAGGCATTTTGGGAAAGAGCAAGCAAAAATAAAT
8332 GGTTATCATC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (49 bp):
CCTTCCGTCCGGAAAAGGCATTTTGGGAAAGAGCAAGCAAAAATAAATA
Found at i:23929 original size:8 final size:8
Alignment explanation
Indices: 23913--23950 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
23903 TTAATAAGCC
23913 TTGCCTAA
1 TTGCCTAA
*
23921 TTCCCTAA
1 TTGCCTAA
23929 TTGCCTAA
1 TTGCCTAA
23937 TTGCCTAA
1 TTGCCTAA
23945 TTGCCT
1 TTGCCT
23951 TTACCTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (8 bp):
TTGCCTAA
Found at i:30651 original size:46 final size:46
Alignment explanation
Indices: 30584--30722 Score: 278
Period size: 46 Copynumber: 3.0 Consensus size: 46
30574 GACTTGAGAC
30584 AAAAACTATCTTGTGGTAACAGAATAATTAGTCCTTACTGTTTGCT
1 AAAAACTATCTTGTGGTAACAGAATAATTAGTCCTTACTGTTTGCT
30630 AAAAACTATCTTGTGGTAACAGAATAATTAGTCCTTACTGTTTGCT
1 AAAAACTATCTTGTGGTAACAGAATAATTAGTCCTTACTGTTTGCT
30676 AAAAACTATCTTGTGGTAACAGAATAATTAGTCCTTACTGTTTGCT
1 AAAAACTATCTTGTGGTAACAGAATAATTAGTCCTTACTGTTTGCT
30722 A
1 A
30723 CTGTGAGATA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 93 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (46 bp):
AAAAACTATCTTGTGGTAACAGAATAATTAGTCCTTACTGTTTGCT
Found at i:41332 original size:3 final size:3
Alignment explanation
Indices: 41326--41369 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
41316 AATAAGAAAG
*
41326 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA CAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
41370 CTGTCAGCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43714 original size:43 final size:43
Alignment explanation
Indices: 43653--43739 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
43643 AGACAACACC
43653 AGCAAAATGCAGAAGTATTATACTCAGCATACATACCATTTCA
1 AGCAAAATGCAGAAGTATTATACTCAGCATACATACCATTTCA
43696 AGCAAAATGCAGAAGTATTATACTCAGCATACATACCATTTCA
1 AGCAAAATGCAGAAGTATTATACTCAGCATACATACCATTTCA
43739 A
1 A
43740 ATCAAGCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (43 bp):
AGCAAAATGCAGAAGTATTATACTCAGCATACATACCATTTCA
Found at i:46026 original size:31 final size:32
Alignment explanation
Indices: 45985--46049 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
45975 CTCTCTAGTG
45985 TTTTTATTTTTCT-C-CCTTCTAAACATACTT
1 TTTTTATTTTTCTCCACCTTCTAAACATACTT
* *
46015 TTTTTAATTTTTTTCCATCCTTCTACACATACTT
1 TTTTT-ATTTTTCTCCA-CCTTCTAAACATACTT
46049 T
1 T
46050 AATAAACTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 7 0.24
32 1 0.03
34 16 0.55
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTTTATTTTTCTCCACCTTCTAAACATACTT
Found at i:47957 original size:30 final size:30
Alignment explanation
Indices: 47922--47980 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
47912 TATGATAATA
*
47922 ATTATTATTATATTTTGTTCGTCATTTCTG
1 ATTATTATTATATTTTGTTCATCATTTCTG
47952 ATTATTATTATATTTTGTTCATCATTTCT
1 ATTATTATTATATTTTGTTCATCATTTCT
47981 AATTTGGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.10, G:0.07, T:0.61
Consensus pattern (30 bp):
ATTATTATTATATTTTGTTCATCATTTCTG
Found at i:49668 original size:25 final size:25
Alignment explanation
Indices: 49637--49685 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
49627 TAAAATAATT
49637 ATAAAATATTGAATTT-TTTGAAATA
1 ATAAAATATTGAATTTATTT-AAATA
49662 ATAAAATATTGAATTTATTTAAAT
1 ATAAAATATTGAATTTATTTAAAT
49686 GAAAATAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (25 bp):
ATAAAATATTGAATTTATTTAAATA
Found at i:59483 original size:22 final size:22
Alignment explanation
Indices: 59455--59531 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
59445 TGTAATTATG
* *
59455 AAATTTTCATAACTACCCTATT
1 AAATTTTGATAACTACCCTATA
* * *
59477 AAATTTTGATAACCACCATATG
1 AAATTTTGATAACTACCCTATA
*
59499 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAACTACCCTATA
*
59520 AAATTGTGATAA
1 AAATTTTGATAA
59532 ACCCATAAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 15 0.33
22 31 0.67
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATA
Found at i:59551 original size:42 final size:43
Alignment explanation
Indices: 59471--59552 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
59461 TCATAACTAC
* * * * *
59471 CCTATTAAATTTTGATAACCACCATATGAAATTTTGATAATTA
1 CCTATAAAATTGTGATAAACACCATAAGAAACTTTGATAATTA
59514 CCTATAAAATTGTGATAAAC-CCATAAGAAACTTTGATAA
1 CCTATAAAATTGTGATAAACACCATAAGAAACTTTGATAA
59553 CGTAACTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 17 0.50
43 17 0.50
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (43 bp):
CCTATAAAATTGTGATAAACACCATAAGAAACTTTGATAATTA
Found at i:59567 original size:43 final size:43
Alignment explanation
Indices: 59472--59576 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
59462 CATAACTACC
* * * * * *
59472 CTATTAAATTTTGATAACCACCATATGAAATTTTGATAATTAC
1 CTATAAAATTTTGATAAACACCATAAGAAACTTTGATAAGTAA
*
59515 CTATAAAATTGTGATAAAC-CCATAAGAAACTTTGATAACGTAA
1 CTATAAAATTTTGATAAACACCATAAGAAACTTTGATAA-GTAA
* *
59558 CTATGAAATTTTAATAAAC
1 CTATAAAATTTTGATAAAC
59577 TTTCCTATGA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 17 0.33
43 34 0.67
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (43 bp):
CTATAAAATTTTGATAAACACCATAAGAAACTTTGATAAGTAA
Found at i:59612 original size:20 final size:21
Alignment explanation
Indices: 59558--59617 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
59548 GATAACGTAA
* *
59558 CTATGAAATTTTAATAAACTTTC
1 CTATGAAA-TTTGAT-AATTTTC
59581 CTATGAAATTTG-TAATTTTC
1 CTATGAAATTTGATAATTTTC
**
59601 CTATGATTTTTGATAAT
1 CTATGAAATTTGATAAT
59618 CTCTCTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.50
21 5 0.16
22 3 0.09
23 8 0.25
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (21 bp):
CTATGAAATTTGATAATTTTC
Found at i:61659 original size:2 final size:2
Alignment explanation
Indices: 61652--61681 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61642 GACAATAATA
61652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61682 TAAACCTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62982 original size:178 final size:177
Alignment explanation
Indices: 62683--63023 Score: 558
Period size: 178 Copynumber: 1.9 Consensus size: 177
62673 GTTTAGAAAA
** * *
62683 ATGCAAATAAGGTATTGTTGGAAAGAGGATTCCAAGATCTGCAATTTTTATGTACCTCGAGACCT
1 ATGCAAATAAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTACCTCGAGACCT
*
62748 AATTCTGCGATTCCGATGGACAATTTTGCCCTTCAAATTTCTGGACAAAATTGATCTTCTCCTAA
66 AATTCTGCCATTCCGATGGA-AATTTTGCCCTTCAAATTTCTGGACAAAATTGATCTTCTCCTAA
62813 ACCGACTTGGAGAATGTTTTGGACGAAAATTCATTTTTAATCTAAGCT
130 ACCGACTTGGAGAATGTTTTGGACGAAAATTCATTTTTAATCTAAGCT
*
62861 ATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTTACCTCGAGAC
1 ATGCAAATAAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATG--TACCTCGAGAC
* * *
62926 CTAATTCTGCCATTCTGGTGG-AATTTTGCCCTTCAAATTTCTGGACAGAATTGATCTTCTCCTA
64 CTAATTCTGCCATTCCGATGGAAATTTTGCCCTTCAAATTTCTGGACAAAATTGATCTTCTCCTA
*
62990 AACCGACTTGGAGAATGTTTTGGATGAAAATTCA
129 AACCGACTTGGAGAATGTTTTGGACGAAAATTCA
63024 GATGCTAAAG
Statistics
Matches: 151, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
178 122 0.81
180 29 0.19
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (177 bp):
ATGCAAATAAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTACCTCGAGACCT
AATTCTGCCATTCCGATGGAAATTTTGCCCTTCAAATTTCTGGACAAAATTGATCTTCTCCTAAA
CCGACTTGGAGAATGTTTTGGACGAAAATTCATTTTTAATCTAAGCT
Found at i:64083 original size:12 final size:12
Alignment explanation
Indices: 64066--64091 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64056 AACCACGAAC
64066 TATTTGTGAAGT
1 TATTTGTGAAGT
64078 TATTTGTGAAGT
1 TATTTGTGAAGT
64090 TA
1 TA
64092 AAAAGACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (12 bp):
TATTTGTGAAGT
Found at i:66885 original size:14 final size:14
Alignment explanation
Indices: 66865--66901 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
66855 CCCGAATGAT
66865 CGGGAATTGTCTGG
1 CGGGAATTGTCTGG
*
66879 TGGGAATTGTCTGG
1 CGGGAATTGTCTGG
66893 CGGGAATTG
1 CGGGAATTG
66902 ACTCGCTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.43, T:0.30
Consensus pattern (14 bp):
CGGGAATTGTCTGG
Found at i:68227 original size:21 final size:21
Alignment explanation
Indices: 68201--68242 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68191 TTATATAAAT
68201 TTTATTT-TATTATTTTAATTA
1 TTTATTTAT-TTATTTTAATTA
*
68222 TTTATTTATTTATTTTTATTA
1 TTTATTTATTTATTTTAATTA
68243 CTATTACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTTATTTATTTTAATTA
Found at i:68640 original size:33 final size:33
Alignment explanation
Indices: 68593--68699 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 33
68583 AGCACAAGTG
*
68593 ACCGGCCACACGACTTGGAGATGACCGACCATC
1 ACCGGCCACGCGACTTGGAGATGACCGACCATC
* * * *
68626 ACCGGCTACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGACCGACCATC
* * * *
68659 ACCGGCCACGCGACATGGACATGTCCGGCCA-C
1 ACCGGCCACGCGACTTGGAGATGACCGACCATC
68691 AACCGGCCA
1 -ACCGGCCA
68700 TCGCTTGGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 1 0.02
33 62 0.98
ACGTcount: A:0.23, C:0.39, G:0.27, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGACCGACCATC
Done.