Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008555.1 Corchorus capsularis cultivar CVL-1 contig08576, 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: 62927
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:736 original size:18 final size:18
Alignment explanation
Indices: 722--776 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
712 GCATTCTCTG
722 CTTGCTCACCATTCTCAC
1 CTTGCTCACCATTCTCAC
*
740 CTTGCTCAACATTCTCAC
1 CTTGCTCACCATTCTCAC
758 CTTGCTCACCATTCTCAC
1 CTTGCTCACCATTCTCAC
776 C
1 C
777 ATCATTCGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.44, G:0.05, T:0.33
Consensus pattern (18 bp):
CTTGCTCACCATTCTCAC
Found at i:740 original size:9 final size:9
Alignment explanation
Indices: 726--778 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
716 TCTCTGCTTG
726 CTCACCATT
1 CTCACCATT
735 CTCACC-TT
1 CTCACCATT
*
743 GCTCAACATT
1 -CTCACCATT
753 CTCACC-TT
1 CTCACCATT
761 GCTCACCATT
1 -CTCACCATT
771 CTCACCAT
1 CTCACCAT
779 CATTCGCAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 4 0.11
9 30 0.79
10 4 0.11
ACGTcount: A:0.21, C:0.43, G:0.04, T:0.32
Consensus pattern (9 bp):
CTCACCATT
Found at i:2669 original size:105 final size:106
Alignment explanation
Indices: 2516--2759 Score: 368
Period size: 107 Copynumber: 2.3 Consensus size: 106
2506 TATAAATTTT
*
2516 AATTCTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTTCTAAAACCCTATAACA
* *
2579 AT-ATTATTAATTATGGAATTTACCCTTAAAATGAAAATAA
66 ATAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* * * ** *
2619 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAATTCTATAGCA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTTCTAAAACCCTATAACA
*
2684 ATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAA
66 AT-AATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
2726 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
2760 GGCTAAACTT
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
103 10 0.08
104 15 0.12
105 33 0.26
107 68 0.54
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (106 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTTCTAAAACCCTATAACA
ATAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
Found at i:10583 original size:41 final size:41
Alignment explanation
Indices: 10538--10615 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
10528 TCCCTTCTAA
* *
10538 ATAATTAAGGA-AACAAATTAAATTCAGGTTTAGCCCCCCTG
1 ATAATTAA-GATAACAAATTAAATCCAGATTTAGCCCCCCTG
*
10579 ATAATTAAGATAAGAAATTAAATCCAGATTTAGCCCC
1 ATAATTAAGATAACAAATTAAATCCAGATTTAGCCCC
10616 TAGTTATAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (41 bp):
ATAATTAAGATAACAAATTAAATCCAGATTTAGCCCCCCTG
Found at i:10896 original size:41 final size:42
Alignment explanation
Indices: 10837--10915 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
10827 TTTATAACTA
*
10837 GGGCTTAAACCTGGATTTAATTTCTTACCTTAATTATTATGG
1 GGGCTTAAACCTGAATTTAATTTCTTACCTTAATTATTATGG
* * *
10879 GGGC-TAAACTTGAATTTAATTTGTTTCCTTAATTATT
1 GGGCTTAAACCTGAATTTAATTTCTTACCTTAATTATT
10916 TAGAAGGGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 29 0.88
42 4 0.12
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (42 bp):
GGGCTTAAACCTGAATTTAATTTCTTACCTTAATTATTATGG
Found at i:19903 original size:25 final size:24
Alignment explanation
Indices: 19870--19917 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19860 ATGATGCACT
19870 GTTTTCCCCCAGCAATGCAGGAAA
1 GTTTTCCCCCAGCAATGCAGGAAA
*
19894 GTTTTCCCCCAGTAATGCAGGAAA
1 GTTTTCCCCCAGCAATGCAGGAAA
19918 CTTAGAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (24 bp):
GTTTTCCCCCAGCAATGCAGGAAA
Found at i:20445 original size:3 final size:3
Alignment explanation
Indices: 20437--20471 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
20427 TGAAATGGAA
*
20437 CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT -TT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
20472 TTTGACATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
CTT
Found at i:22799 original size:27 final size:28
Alignment explanation
Indices: 22743--22799 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
22733 TAACTATCCA
* *
22743 TTTTGGGACAAATTGGCCCCTTAGCTTT
1 TTTTGGAACAAATTGGCCCCTTAACTTT
22771 TTTTGGAACAAATTGGCCCCTTAACTTT
1 TTTTGGAACAAATTGGCCCCTTAACTTT
22799 T
1 T
22800 AAAAACAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (28 bp):
TTTTGGAACAAATTGGCCCCTTAACTTT
Found at i:22806 original size:26 final size:27
Alignment explanation
Indices: 22750--22807 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
22740 CCATTTTGGG
* ***
22750 ACAAATTGGCCCCTTAGCTTTTTTTGGA
1 ACAAATTGGCCCCTTAAC-TTTTTAAAA
22778 ACAAATTGGCCCCTTAAC-TTTTAAAA
1 ACAAATTGGCCCCTTAACTTTTTAAAA
22804 ACAA
1 ACAA
22808 GACAAATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 9 0.35
28 17 0.65
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (27 bp):
ACAAATTGGCCCCTTAACTTTTTAAAA
Found at i:23546 original size:28 final size:28
Alignment explanation
Indices: 23490--23546 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
23480 TCTCGTTTTT
* *
23490 AAAAGTTAAGGGGCCAATTTGTGCAAAA
1 AAAAGTTAAGAGGCCAATTTGTCCAAAA
*
23518 AAAAGTTAAGAGGCCAATTTGTCCCAAA
1 AAAAGTTAAGAGGCCAATTTGTCCAAAA
23546 A
1 A
23547 TGGATAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (28 bp):
AAAAGTTAAGAGGCCAATTTGTCCAAAA
Found at i:27763 original size:31 final size:30
Alignment explanation
Indices: 27706--27835 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 30
27696 ACGACATACG
* * * *
27706 ACGTGGCATGCCACGTGGACAAAAAGTGAC
1 ACGTGTCACGCCACATGTACAAAAAGTGAC
* *
27736 ATGTGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGTCACGCCACATGTA-CAAAAAGTGAC
* *
27767 ACGTGTCATGCCACATGTACACAAAGTGAC
1 ACGTGTCACGCCACATGTACAAAAAGTGAC
* * * *
27797 ACGTGGCATGCCACATGCACAAAAA-AGAC
1 ACGTGTCACGCCACATGTACAAAAAGTGAC
*
27826 ATGTGTCACG
1 ACGTGTCACG
27836 TGTCACTTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
29 10 0.12
30 47 0.56
31 27 0.32
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (30 bp):
ACGTGTCACGCCACATGTACAAAAAGTGAC
Found at i:27822 original size:61 final size:61
Alignment explanation
Indices: 27706--27823 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
27696 ACGACATACG
* * * * * *
27706 ACGTGGCATGCCACGTGGACAAAAAGTGACATGTGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGGACAAAAAGTGACACGTGGCACGCCACATGCACAAAAAAGTGAC
* * * *
27767 ACGTGTCATGCCACATGTACACAAAGTGACACGTGGCATGCCACATGCACAAAAAAG
1 ACGTGGCATGCCACATGGACAAAAAGTGACACGTGGCACGCCACATGCACAAAAAAG
27824 ACATGTGTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (61 bp):
ACGTGGCATGCCACATGGACAAAAAGTGACACGTGGCACGCCACATGCACAAAAAAGTGAC
Found at i:29672 original size:1 final size:1
Alignment explanation
Indices: 29661--29701 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
29651 CACACACATC
*
29661 AAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29702 CAGTAAAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.98, C:0.02, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:34815 original size:16 final size:16
Alignment explanation
Indices: 34785--34829 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
34775 AACTCGCCCA
*
34785 ACCCGAGACCTGAATG
1 ACCCGAGACCCGAATG
34801 ACCC-AGAACCCGAATG
1 ACCCGAG-ACCCGAATG
34817 ACCCGAGACCCGA
1 ACCCGAGACCCGA
34830 GATCCAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.33, C:0.38, G:0.22, T:0.07
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:37351 original size:22 final size:22
Alignment explanation
Indices: 37329--37369 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37319 AGTTGATTTA
*
37329 AAAAAT-ATTAATTTAATTATT
1 AAAAATAATTAATTAAATTATT
*
37350 AAACATAATTAATTAAATTA
1 AAAAATAATTAATTAAATTA
37370 CAAGGGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATAATTAATTAAATTATT
Found at i:37531 original size:39 final size:39
Alignment explanation
Indices: 37456--37532 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
37446 TCTAATTTAC
* ** *
37456 AATTTTGAGTAAACTAGTAAATATGGTTGTAGGATTAGT
1 AATTTTGAGTAAACTAATAAATATGGTCATAAGATTAGT
* * *
37495 AATTTTGGGTAAATTAATAAATGTGGTCATAAGATTAG
1 AATTTTGAGTAAACTAATAAATATGGTCATAAGATTAG
37533 ATGAAGGATC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (39 bp):
AATTTTGAGTAAACTAATAAATATGGTCATAAGATTAGT
Found at i:38530 original size:74 final size:74
Alignment explanation
Indices: 38439--38586 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
38429 AAAGGTTGTT
* *
38439 CAAACCCGTCTGTTTGGTTTTAACAAGTTGTCCAAACTCGTCTAATATGCTTTAAAATGTTATTT
1 CAAACCCGTCTGCTTGGTTTTAACAAGTTGTCCAAACTCGTCTAATATGCTTTAAAATGTTATCT
38504 AAGTCCGTC
66 AAGTCCGTC
38513 CAAACCCGTCTGCTTGGTTTTAACAAGTTGTCCAAACTCGTCTAATATGCTTTAAAATGTTATCT
1 CAAACCCGTCTGCTTGGTTTTAACAAGTTGTCCAAACTCGTCTAATATGCTTTAAAATGTTATCT
38578 AAGTCCGTC
66 AAGTCCGTC
38587 TAACGGGCTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (74 bp):
CAAACCCGTCTGCTTGGTTTTAACAAGTTGTCCAAACTCGTCTAATATGCTTTAAAATGTTATCT
AAGTCCGTC
Found at i:38656 original size:33 final size:32
Alignment explanation
Indices: 38584--38661 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
38574 ATCTAAGTCC
* *
38584 GTCTAACGGGCTTTAAAAAGTTGTCCAAACCT
1 GTCTAACGGGTTTTAAAAAGTTATCCAAACCT
* * * * *
38616 ATTTAACGGGTTTTCAAAAAGTTATTCAAGCTT
1 GTCTAACGGGTTTT-AAAAAGTTATCCAAACCT
38649 GTCTAACGGGTTT
1 GTCTAACGGGTTT
38662 AAAGTTTTGT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 11 0.31
33 25 0.69
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
GTCTAACGGGTTTTAAAAAGTTATCCAAACCT
Found at i:41784 original size:16 final size:16
Alignment explanation
Indices: 41763--41796 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41753 CATCATAAAT
41763 TTAAATTTGAAAATTA
1 TTAAATTTGAAAATTA
41779 TTAAATTTGAAAATTA
1 TTAAATTTGAAAATTA
41795 TT
1 TT
41797 CAATACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TTAAATTTGAAAATTA
Found at i:45422 original size:46 final size:46
Alignment explanation
Indices: 45355--45446 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
45345 TGGTGTCCAA
45355 GAAAGACAATATTTCATGAAGGAGTTCATCCGTCAAACTGCTGATT
1 GAAAGACAATATTTCATGAAGGAGTTCATCCGTCAAACTGCTGATT
*
45401 GAAAGACAATATTTCATGAAGGAGTTCATCCGTCGAACTGCTGATT
1 GAAAGACAATATTTCATGAAGGAGTTCATCCGTCAAACTGCTGATT
45447 CTGTCTATCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (46 bp):
GAAAGACAATATTTCATGAAGGAGTTCATCCGTCAAACTGCTGATT
Found at i:52990 original size:54 final size:54
Alignment explanation
Indices: 52897--53007 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
52887 TCAACACTCT
* *
52897 CCTCATCCTTGGTAACTTTATCAATTATCTCGGAGTCATCTTTCCTCTGAGTGA
1 CCTCATCCTTGGCAACTGTATCAATTATCTCGGAGTCATCTTTCCTCTGAGTGA
* *
52951 CCTCATCCTTGGCAACTGTATCACA-TGTCAT-GGATTCATCTTTCCTCTGAGTGA
1 CCTCATCCTTGGCAACTGTATCA-ATTATC-TCGGAGTCATCTTTCCTCTGAGTGA
53005 CCT
1 CCT
53008 GTATCTCTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 49 0.96
55 2 0.04
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (54 bp):
CCTCATCCTTGGCAACTGTATCAATTATCTCGGAGTCATCTTTCCTCTGAGTGA
Found at i:54828 original size:27 final size:29
Alignment explanation
Indices: 54798--54872 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 29
54788 ATTTGTAGCG
*
54798 TTTGGACGTTTTGCCCCTTGAATTTC-A-
1 TTTGGACGTTTTGCCCCTTAAATTTCAAT
* * *
54825 TTTGGACATTCTGCCCCCTAAATTTCAAT
1 TTTGGACGTTTTGCCCCTTAAATTTCAAT
54854 TTTGGGACGTTTTGCCCCT
1 TTT-GGACGTTTTGCCCCT
54873 CAGACTAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 22 0.58
28 1 0.03
29 3 0.08
30 12 0.32
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCTTAAATTTCAAT
Done.