Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013170.1 Corchorus capsularis cultivar CVL-1 contig13191, 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: 35361
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:152 original size:49 final size:49
Alignment explanation
Indices: 1--410 Score: 355
Period size: 49 Copynumber: 8.4 Consensus size: 49
* * ** *
1 GCCCTTCCCGGACAGAAGGCACTGATTACTACCTG-TTTTTCCCAAAAC
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAAT
* * * *
49 GCCCTTCCCAGACGGAAGGCAATAATCTTTACCTG-TTTTTCCCAAAAT
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAAT
* * *
97 GCCCTTCCTGGACGGAAGGCACTTA-TTTTACTTGCTATTTTCCAAAAAT
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCT-TTTTCCCAAAAT
* * * * **
146 GCCCTTCCCAGATGGAAGACGCTTATTTTTACCCACTTTTTCCCAAAAT
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAAT
** * * *
195 GCCCTTCCAAGACGGAAGGCACTTA-TTTTACTTGATATTTTCCAAAAAT
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCT-TTTTCCCAAAAT
* * * ** * *
244 GCCCTTCCCGGATGGAAGACGCTTATTTTTACCCACTTTTCCCCAAAGT
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAAT
* * * * * *
293 GCCCTTCCCCGACGGAAGGCACTAACTTTTACTTGCTTTTTCCTAAAAC
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAAT
* * * **
342 GCCCTTCCCGGACAGAAGGC-GTTAGTTTTA-CTCGCTTTTTCTTAAAAT
1 GCCCTTCCCGGACGGAAGGCACTTATTTTTACCT-GCTTTTTCCCAAAAT
* * *
390 ACCCTTTCCGGACGAAAGGCA
1 GCCCTTCCCGGACGGAAGGCA
411 AGTTCGCTAT
Statistics
Matches: 285, Mismatches: 70, Indels: 13
0.77 0.19 0.04
Matches are distributed among these distances:
47 8 0.03
48 105 0.37
49 157 0.55
50 15 0.05
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (49 bp):
GCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAAT
Found at i:351 original size:98 final size:98
Alignment explanation
Indices: 1--410 Score: 434
Period size: 98 Copynumber: 4.2 Consensus size: 98
* * * * * *
1 GCCCTTCCCGGACAGAAGGCACTGATTACTACCTG-T-TTTTCCCAAAACGCCCTTCCCAGACGG
1 GCCCTTCCCGGACGGAAGGCACTTATT-TTACTTGCTATTTTCCAAAAACGCCCTTCCCAGATGG
* ** * * **
64 AAGGCAATAATCTTTA-CCTGTTTTTCCCAAAAT
65 AAGACGCTTATTTTTACCCACTTTTTCCCAAAAT
* *
97 GCCCTTCCTGGACGGAAGGCACTTATTTTACTTGCTATTTTCCAAAAATGCCCTTCCCAGATGGA
1 GCCCTTCCCGGACGGAAGGCACTTATTTTACTTGCTATTTTCCAAAAACGCCCTTCCCAGATGGA
162 AGACGCTTATTTTTACCCACTTTTTCCCAAAAT
66 AGACGCTTATTTTTACCCACTTTTTCCCAAAAT
** * * *
195 GCCCTTCCAAGACGGAAGGCACTTATTTTACTTGATATTTTCCAAAAATGCCCTTCCCGGATGGA
1 GCCCTTCCCGGACGGAAGGCACTTATTTTACTTGCTATTTTCCAAAAACGCCCTTCCCAGATGGA
* *
260 AGACGCTTATTTTTACCCACTTTTCCCCAAAGT
66 AGACGCTTATTTTTACCCACTTTTTCCCAAAAT
* * * * **
293 GCCCTTCCCCGACGGAAGGCACTAACTTTTACTTGCT-TTTTCCTAAAACGCCCTTCCCGGACAG
1 GCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCTATTTTCCAAAAACGCCCTTCCCAGATGG
* * * * **
357 AAGGCG-TTAGTTTTACTCGCTTTTTCTTAAAAT
65 AAGACGCTTATTTTTACCCACTTTTTCCCAAAAT
* * *
390 ACCCTTTCCGGACGAAAGGCA
1 GCCCTTCCCGGACGGAAGGCA
411 AGTTCGCTAT
Statistics
Matches: 269, Mismatches: 41, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
95 5 0.02
96 25 0.09
97 72 0.27
98 157 0.58
99 10 0.04
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (98 bp):
GCCCTTCCCGGACGGAAGGCACTTATTTTACTTGCTATTTTCCAAAAACGCCCTTCCCAGATGGA
AGACGCTTATTTTTACCCACTTTTTCCCAAAAT
Found at i:2588 original size:25 final size:25
Alignment explanation
Indices: 2557--2607 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2547 GTTGATGTAA
2557 TGAAACCAAACATTGGCTGTAATGC
1 TGAAACCAAACATTGGCTGTAATGC
* *
2582 TGAAACCAAACTTTGGTTGTAATGC
1 TGAAACCAAACATTGGCTGTAATGC
2607 T
1 T
2608 TTAGATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (25 bp):
TGAAACCAAACATTGGCTGTAATGC
Found at i:6029 original size:27 final size:29
Alignment explanation
Indices: 5999--6078 Score: 119
Period size: 27 Copynumber: 2.8 Consensus size: 29
5989 TTGTAATCGG
*
5999 GACCTAAAGATTAAGTTTTTTTT-GCTA-
1 GACCTAAAGATTAAGTTTTTTTTGGCGAT
6026 GACCTAAAGATTAAGTTTTTTTTTGGCGAT
1 GACCTAAAGATTAAG-TTTTTTTTGGCGAT
*
6056 GACCTAAAGAATAAGTTTTTTTT
1 GACCTAAAGATTAAGTTTTTTTT
6079 TTGGCATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 15 0.31
28 8 0.17
29 11 0.23
30 14 0.29
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (29 bp):
GACCTAAAGATTAAGTTTTTTTTGGCGAT
Found at i:6060 original size:30 final size:28
Alignment explanation
Indices: 5999--6079 Score: 119
Period size: 30 Copynumber: 2.9 Consensus size: 28
5989 TTGTAATCGG
*
5999 GACCTAAAGATTAAG-TTTTTTTTGCTA
1 GACCTAAAGATTAAGTTTTTTTTTGCGA
6026 GACCTAAAGATTAAGTTTTTTTTTGGCGA
1 GACCTAAAGATTAAGTTTTTTTTT-GCGA
*
6055 TGACCTAAAGAATAAGTTTTTTTTT
1 -GACCTAAAGATTAAGTTTTTTTTT
6080 TGGCATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
27 15 0.31
28 8 0.16
29 3 0.06
30 23 0.47
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (28 bp):
GACCTAAAGATTAAGTTTTTTTTTGCGA
Found at i:6404 original size:1 final size:1
Alignment explanation
Indices: 6400--6424 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6390 AATTTTTAGG
6400 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
6425 ACTTTTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13516 original size:6 final size:7
Alignment explanation
Indices: 13484--13514 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
13474 TAATTTTAGA
13484 TTTTCTT
1 TTTTCTT
13491 TTTTCTT
1 TTTTCTT
13498 TTTTCTT
1 TTTTCTT
13505 TTTTCTT
1 TTTTCTT
13512 TTT
1 TTT
13515 CTGTGGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:13930 original size:45 final size:46
Alignment explanation
Indices: 13861--13953 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 46
13851 CCAGAACATT
*
13861 GAACCAGCCCCCAAGGCTTTGTTAAAAAAA-AAGATAAGCTTAATA
1 GAACCAGCCCCCAAGGATTTGTTAAAAAAATAAGATAAGCTTAATA
** *
13906 GAACCAG-CCCCAAGGATTTGGTTAAAAAAATACTATATGCTTAATA
1 GAACCAGCCCCCAAGGATTT-GTTAAAAAAATAAGATAAGCTTAATA
13952 GA
1 GA
13954 TATTTTCGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 11 0.26
45 17 0.40
46 14 0.33
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (46 bp):
GAACCAGCCCCCAAGGATTTGTTAAAAAAATAAGATAAGCTTAATA
Found at i:13933 original size:44 final size:47
Alignment explanation
Indices: 13861--13953 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 47
13851 CCAGAACATT
*
13861 GAACCAGCCCCCAAGGCTTTGTTAAAAAAAA-A-GATAAGCTTAATA
1 GAACCAGCCCCCAAGGATTTGTTAAAAAAAATACGATAAGCTTAATA
* *
13906 GAACCAG-CCCCAAGGATTTGGTT-AAAAAAATACTATATGCTTAATA
1 GAACCAGCCCCCAAGGATTT-GTTAAAAAAAATACGATAAGCTTAATA
13952 GA
1 GA
13954 TATTTTCGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 18 0.43
45 11 0.26
46 13 0.31
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (47 bp):
GAACCAGCCCCCAAGGATTTGTTAAAAAAAATACGATAAGCTTAATA
Found at i:15509 original size:15 final size:15
Alignment explanation
Indices: 15489--15522 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
15479 AAAACAACTT
15489 ATAAAACAAGTTA-TA
1 ATAAAACAA-TTAGTA
15504 ATAAAACAATTAGTA
1 ATAAAACAATTAGTA
15519 ATAA
1 ATAA
15523 TAAATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
ATAAAACAATTAGTA
Found at i:19619 original size:20 final size:19
Alignment explanation
Indices: 19580--19619 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
19570 ATGAGATGTC
* *
19580 TTAAAACCCACTTAACATA
1 TTAAAACCCACTCAAAATA
19599 TTAAAACCCCACTCAAAATA
1 TTAAAA-CCCACTCAAAATA
19619 T
1 T
19620 CAATAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (19 bp):
TTAAAACCCACTCAAAATA
Found at i:27454 original size:21 final size:21
Alignment explanation
Indices: 27430--27471 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27420 AAAGTTCTTG
*
27430 CAAAATTGAACTTGTCACCAA
1 CAAAATTGAACCTGTCACCAA
27451 CAAAATTGAACCTGTCACCAA
1 CAAAATTGAACCTGTCACCAA
27472 TATACATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (21 bp):
CAAAATTGAACCTGTCACCAA
Found at i:27844 original size:19 final size:19
Alignment explanation
Indices: 27820--27858 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
27810 CATTCATCAC
27820 ACAAGCATTTCACATTAGT
1 ACAAGCATTTCACATTAGT
*
27839 ACAAGCATTTTACATTAGT
1 ACAAGCATTTCACATTAGT
27858 A
1 A
27859 TTAGGTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (19 bp):
ACAAGCATTTCACATTAGT
Found at i:30039 original size:49 final size:49
Alignment explanation
Indices: 29986--30079 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
29976 GTCTTTACCT
* * *
29986 ACTTTTTCCCAAAACGCCCTTTCCGGATGGAAGGCGTTTATTTTTATTA
1 ACTTTTTCCCAAAACGCCCTTCCCAGATGGAAGGCATTTATTTTTATTA
30035 ACTTTTTCCCAAAACGCCCTTCCCAGATGGAAGGCATTTATTTTT
1 ACTTTTTCCCAAAACGCCCTTCCCAGATGGAAGGCATTTATTTTT
30080 CCCAAAATGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (49 bp):
ACTTTTTCCCAAAACGCCCTTCCCAGATGGAAGGCATTTATTTTTATTA
Found at i:30115 original size:38 final size:38
Alignment explanation
Indices: 30037--30117 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
30027 TTTTATTAAC
* **
30037 TTTTTCCCAAAACGCCCTTCCCAGATGGAAGGCATTTA
1 TTTTTCCCAAAACGCCCTTCCCAGATGAAAGGCACCTA
* * * * *
30075 TTTTTCCCAAAATGCCCTTTCCGGTTGAAAGGCGCCTA
1 TTTTTCCCAAAACGCCCTTCCCAGATGAAAGGCACCTA
30113 TTTTT
1 TTTTT
30118 ACTTGCTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (38 bp):
TTTTTCCCAAAACGCCCTTCCCAGATGAAAGGCACCTA
Done.