Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013403.1 Corchorus capsularis cultivar CVL-1 contig13424, 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: 29247
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2074 original size:20 final size:20
Alignment explanation
Indices: 2030--2070 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2020 TCCGTCCCTG
*
2030 GTCATTTTTCTTTTATTTTT
1 GTCAATTTTCTTTTATTTTT
*
2050 GTCAATTTTGTTTT-TTTTT
1 GTCAATTTTCTTTTATTTTT
2069 GT
1 GT
2071 TCAAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (20 bp):
GTCAATTTTCTTTTATTTTT
Found at i:2554 original size:15 final size:15
Alignment explanation
Indices: 2536--2570 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2526 GGGATTGACT
2536 TATATATATAAATAA
1 TATATATATAAATAA
* *
2551 TATATATATATATAT
1 TATATATATAAATAA
2566 TATAT
1 TATAT
2571 GTGTGTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATAAATAA
Found at i:7759 original size:14 final size:16
Alignment explanation
Indices: 7734--7767 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
7724 AACAACTAAG
7734 AAAGCAAACAGATTA-
1 AAAGCAAACAGATTAT
7749 AAAGC-AACAGATTAT
1 AAAGCAAACAGATTAT
7764 AAAG
1 AAAG
7768 AAAGTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (16 bp):
AAAGCAAACAGATTAT
Found at i:15801 original size:48 final size:48
Alignment explanation
Indices: 15727--15914 Score: 286
Period size: 48 Copynumber: 3.9 Consensus size: 48
15717 GCCTAGCGAC
* * * *
15727 CGACCACTTCCAAGTCTGGCGCTCTACCACTTAAAACCATGAGGCGCT
1 CGACCACTTCCATGCCCGGCGCTCTACCACTTATAACCATGAGGCGCT
* * *
15775 CGACCACTTCCATGCCCGGCGTTCTACCACTTATAACCATGGGGTGCT
1 CGACCACTTCCATGCCCGGCGCTCTACCACTTATAACCATGAGGCGCT
*
15823 CGACCACTTTCATGCCCGGCGCTCTACCACTTATAACCATGAGGCGCT
1 CGACCACTTCCATGCCCGGCGCTCTACCACTTATAACCATGAGGCGCT
* *
15871 CGACCACCTCCATGTCCGGCGCTCTACCACTTATAACCATGAGG
1 CGACCACTTCCATGCCCGGCGCTCTACCACTTATAACCATGAGG
15915 AGCCTGACCC
Statistics
Matches: 126, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 126 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (48 bp):
CGACCACTTCCATGCCCGGCGCTCTACCACTTATAACCATGAGGCGCT
Found at i:15846 original size:23 final size:22
Alignment explanation
Indices: 15769--15902 Score: 65
Period size: 23 Copynumber: 5.7 Consensus size: 22
15759 AAAACCATGA
*
15769 GGCGCTCGACCACTTCCATGCCC
1 GGCGCTCGACCACTTTCATG-CC
* * *
15792 GGCGTTCTACCACTTATAACCATG-G
1 GGCGCTCGACCACTT-T---CATGCC
*
15817 GGTGCTCGACCACTTTCATGCCC
1 GGCGCTCGACCACTTTCATG-CC
* *
15840 GGCGCTCTACCACTTATAACCATG-A
1 GGCGCTCGACCACTT-T---CATGCC
* *
15865 GGCGCTCGACCACCTCCATGTCC
1 GGCGCTCGACCACTTTCATG-CC
*
15888 GGCGCTCTACCACTT
1 GGCGCTCGACCACTT
15903 ATAACCATGA
Statistics
Matches: 82, Mismatches: 17, Indels: 24
0.67 0.14 0.20
Matches are distributed among these distances:
21 8 0.10
23 39 0.48
24 2 0.02
25 25 0.30
27 8 0.10
ACGTcount: A:0.18, C:0.39, G:0.20, T:0.23
Consensus pattern (22 bp):
GGCGCTCGACCACTTTCATGCC
Found at i:16037 original size:14 final size:13
Alignment explanation
Indices: 15996--16037 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
15986 TATCGTACGA
15996 CCACACGTGACCT
1 CCACACGTGACCT
*
16009 CCA-ACGGGCACCT
1 CCACACGTG-ACCT
16022 CCTACACGTGACCT
1 CC-ACACGTGACCT
16036 CC
1 CC
16038 GAAGTACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 4 0.17
13 9 0.38
14 7 0.29
15 4 0.17
ACGTcount: A:0.21, C:0.48, G:0.17, T:0.14
Consensus pattern (13 bp):
CCACACGTGACCT
Found at i:19395 original size:31 final size:31
Alignment explanation
Indices: 19326--19488 Score: 146
Period size: 31 Copynumber: 5.5 Consensus size: 31
19316 TCCTTTTGTG
* * * * **
19326 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCGTGTCACGTGTCACTTTTTGGTA
* *
19357 CATGTGGCATGTCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGTCACGTGTCACTTTTTGGTA
* *
19388 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGTCACGTGTCACTTTTTGGTA
*
19419 CA--T---GTGGCAC--G--ACTTTTTGGTA
1 CACGTGGCGTGTCACGTGTCACTTTTTGGTA
* *
19441 CATGTGGCGTGTCACATGTCACTTTTTGGTA
1 CACGTGGCGTGTCACGTGTCACTTTTTGGTA
19472 CACGTGGCGTGTCACGT
1 CACGTGGCGTGTCACGT
19489 CGGATACCGT
Statistics
Matches: 108, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
26 5 0.05
27 6 0.06
29 2 0.02
31 80 0.74
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.34
Consensus pattern (31 bp):
CACGTGGCGTGTCACGTGTCACTTTTTGGTA
Found at i:19435 original size:53 final size:53
Alignment explanation
Indices: 19377--19479 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
19367 GTCACGTGTC
** *
19377 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
19430 ACTTTTTGGTACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
19480 GTGTCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:20458 original size:83 final size:84
Alignment explanation
Indices: 20344--20516 Score: 296
Period size: 83 Copynumber: 2.1 Consensus size: 84
20334 TAAAAATATT
*
20344 GAAATCAATTAAATAAAAAAATAGTGTTTTCAGTTTCAAAAGTTTATTTAAAAAAAATTGTAAAA
1 GAAATCAATTAAAT-AAAAAATAGTGTTTTCAGTTGCAAAAGTTTATTTAAAAAAAATTGTAAAA
20409 GTTTAAACAATGTCATTCAA
65 GTTTAAACAATGTCATTCAA
*
20429 GAAATCAATTAAAT-AAAAATAGT-TATTTCAGTTGCAAAAGTTTATTTTAAAAAAATTGTAAAA
1 GAAATCAATTAAATAAAAAATAGTGT-TTTCAGTTGCAAAAGTTTATTTAAAAAAAATTGTAAAA
20492 GTTTAAACAATGTCATTCAA
65 GTTTAAACAATGTCATTCAA
20512 GAAAT
1 GAAAT
20517 ATATTTTTTA
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
82 1 0.01
83 70 0.82
85 14 0.16
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (84 bp):
GAAATCAATTAAATAAAAAATAGTGTTTTCAGTTGCAAAAGTTTATTTAAAAAAAATTGTAAAAG
TTTAAACAATGTCATTCAA
Found at i:20639 original size:73 final size:71
Alignment explanation
Indices: 20561--20719 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 71
20551 TAATTAAAAT
* * * * *
20561 AGTAAAATGGTAAAATACAATAGTTATAAGGATATTAGATTTAATTATATAAAAAAAAATGAGTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAAT-AAAAAAAA-GAGTT
20626 TTTAGTTG
64 TTTAGTTG
* *
20634 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAAATAGAGTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAAAAAGAGTTTT
20699 TAGTTG
66 TAGTTG
20705 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
20720 ACCTAAACAA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 25 0.32
72 9 0.12
73 44 0.56
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (71 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAAAAAGAGTTTT
TAGTTG
Found at i:20844 original size:147 final size:147
Alignment explanation
Indices: 20685--20972 Score: 549
Period size: 147 Copynumber: 2.0 Consensus size: 147
20675 TAATTAAATA
20685 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATT
1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATT
*
20750 TGACAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAGTA
66 TGACAAATAAGGGTATAATAGACGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAGTA
20815 TAGATATAGATATAGAT
131 TAGATATAGATATAGAT
*
20832 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGTAATTTAGAAATATATT
1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATT
*
20897 TGACAAATAAGGGTATAATAGACGATTTAAAAGTTTTACAGCTGAACGTACTTTTTAATATAGTA
66 TGACAAATAAGGGTATAATAGACGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAGTA
20962 TAGATATAGAT
131 TAGATATAGAT
20973 TAAACCAAGA
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
147 138 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (147 bp):
AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATT
TGACAAATAAGGGTATAATAGACGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAGTA
TAGATATAGATATAGAT
Found at i:21629 original size:27 final size:27
Alignment explanation
Indices: 21586--21640 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
21576 TTCAACAGAT
21586 ATGTAAACCGACATGTGTAAGTGTAAC
1 ATGTAAACCGACATGTGTAAGTGTAAC
**
21613 ATGTAAACCGATGTGTGTAAGTGTAAC
1 ATGTAAACCGACATGTGTAAGTGTAAC
21640 A
1 A
21641 GTTCATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (27 bp):
ATGTAAACCGACATGTGTAAGTGTAAC
Found at i:22376 original size:20 final size:19
Alignment explanation
Indices: 22329--22382 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
22319 TGTTTGCAAA
*
22329 AAAAACATAATCTTTATTTT
1 AAAAA-ATAATTTTTATTTT
22349 AAATAAATAATTTTATATTTT
1 AAA-AAATAATTTT-TATTTT
*
22370 TAAAAAT-ATTTTT
1 AAAAAATAATTTTT
22383 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 5 0.17
20 14 0.47
21 10 0.33
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAAAATAATTTTTATTTT
Found at i:23741 original size:25 final size:28
Alignment explanation
Indices: 23694--23751 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 28
23684 ATTAAATTTC
* *
23694 ATAATTTCAAAATTGTAACTAATAATTA
1 ATAATTACAAAATTGTAACTAATAATCA
23722 ATAATTACAAAA-T-TAA-TAATAATCA
1 ATAATTACAAAATTGTAACTAATAATCA
23747 ATAAT
1 ATAAT
23752 AAAAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 13 0.46
26 3 0.11
27 1 0.04
28 11 0.39
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (28 bp):
ATAATTACAAAATTGTAACTAATAATCA
Found at i:23752 original size:28 final size:28
Alignment explanation
Indices: 23694--23753 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
23684 ATTAAATTTC
* *
23694 ATAATTTCAAAATTGTAACTAATAATTA
1 ATAATTACAAAATTATAACTAATAATTA
23722 ATAATTACAAAATTAATAA-TAATCAA-TA
1 ATAATTACAAAATT-ATAACTAAT-AATTA
23750 ATAA
1 ATAA
23754 AAAAAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (28 bp):
ATAATTACAAAATTATAACTAATAATTA
Found at i:23909 original size:13 final size:13
Alignment explanation
Indices: 23893--23917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23883 TTCCAAAATT
23893 TTAGATCTACAAC
1 TTAGATCTACAAC
23906 TTAGATCTACAA
1 TTAGATCTACAA
23918 AATAACAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TTAGATCTACAAC
Found at i:24480 original size:15 final size:16
Alignment explanation
Indices: 24447--24485 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
24437 AATTTGTATG
*
24447 AATTTATTAATATATA
1 AATTAATTAATATATA
24463 AATTAATTAATA-ATA
1 AATTAATTAATATATA
24478 AATTAATT
1 AATTAATT
24486 GGAGATTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAATTAATATATA
Done.