Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009389.1 Corchorus capsularis cultivar CVL-1 contig09410, 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: 77942
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:625 original size:19 final size:18
Alignment explanation
Indices: 603--654 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
593 TAATTAGGAG
*
603 TAATTTTTAAATAAGAATA
1 TAATATTTAAATAA-AATA
*
622 TAATATATAAATGAAAATA
1 TAATATTTAAAT-AAAATA
*
641 TAATATTAAAATAA
1 TAATATTTAAATAA
655 TTAATTAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.07
19 24 0.86
20 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
TAATATTTAAATAAAATA
Found at i:10755 original size:30 final size:30
Alignment explanation
Indices: 10678--10756 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
10668 ATTAAAATTT
*
10678 AATATTTTATTTAG-TTTCAAATAAAAGTA
1 AATATTTTATTTAGTTTTAAAATAAAAGTA
* * *
10707 AATCTTTTATTAAATTTTAAAAT-AAAGATA
1 AATATTTTATTTAGTTTTAAAATAAAAG-TA
*
10737 AATATTGTATTTAGTTTTAA
1 AATATTTTATTTAGTTTTAA
10757 TTTTATGCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (30 bp):
AATATTTTATTTAGTTTTAAAATAAAAGTA
Found at i:10792 original size:23 final size:22
Alignment explanation
Indices: 10766--10808 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
10756 ATTTTATGCC
10766 AAATA-AAAAGAATTATAAAACGA
1 AAATATAAAA-AATTA-AAAACGA
10789 AAATATAAAAAATTAAAAAC
1 AAATATAAAAAATTAAAAAC
10809 AAGATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (22 bp):
AAATATAAAAAATTAAAAACGA
Found at i:18675 original size:109 final size:109
Alignment explanation
Indices: 18468--18850 Score: 646
Period size: 109 Copynumber: 3.5 Consensus size: 109
18458 AAAAAAATTA
18468 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
18531 -AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
18575 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
18640 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
18684 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
18749 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* * * *
18793 TATAAAGATATTAAATTTAATTTAATTGAATAAAAATAGAGTTTCTAATAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
18851 CTATAATAGT
Statistics
Matches: 263, Mismatches: 5, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
107 6 0.02
108 55 0.21
109 172 0.65
110 2 0.01
111 1 0.00
114 27 0.10
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:24946 original size:14 final size:16
Alignment explanation
Indices: 24921--24954 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
24911 AACAACTAAG
24921 AAAGCAAACAGATTA-
1 AAAGCAAACAGATTAT
24936 AAAGC-AACAGATTAT
1 AAAGCAAACAGATTAT
24951 AAAG
1 AAAG
24955 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:28164 original size:30 final size:30
Alignment explanation
Indices: 28123--28205 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
28113 ACAAACAAAC
* *
28123 ATTCTATCAATCAATTAACAA-ATAATTGCA
1 ATTCAATCAATCAATTAACAAGAT-ATGGCA
*
28153 ATTCAATCAATCAA-TAGCAAGATATGGCA
1 ATTCAATCAATCAATTAACAAGATATGGCA
*
28182 ATTCAAATCAA-CAATTGA-AAGATA
1 ATTC-AATCAATCAATTAACAAGATA
28206 GAATAAGCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 23 0.51
30 22 0.49
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (30 bp):
ATTCAATCAATCAATTAACAAGATATGGCA
Found at i:38522 original size:82 final size:82
Alignment explanation
Indices: 38385--38552 Score: 318
Period size: 82 Copynumber: 2.0 Consensus size: 82
38375 AAGTTCTCTC
38385 TTTGTCTGTATATAGGATATTTCTTCGTTTTTAAAAAAGAAAAGCTTTAATTTTAAGTTGCAGCA
1 TTTGTCTGTATATAGGATATTTCTTCGTTTTTAAAAAAGAAAAGCTTTAATTTTAAGTTGCAGCA
38450 AGTTAATTTCTGTTAAA
66 AGTTAATTTCTGTTAAA
* *
38467 TTTGTCTGTATATATGATATTTCTTCGTTTTTGAAAAAGAAAAGCTTTAATTTTAAGTTGCAGCA
1 TTTGTCTGTATATAGGATATTTCTTCGTTTTTAAAAAAGAAAAGCTTTAATTTTAAGTTGCAGCA
38532 AGTTAATTTCTGTTAAA
66 AGTTAATTTCTGTTAAA
38549 TTTG
1 TTTG
38553 ACATATTTCA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (82 bp):
TTTGTCTGTATATAGGATATTTCTTCGTTTTTAAAAAAGAAAAGCTTTAATTTTAAGTTGCAGCA
AGTTAATTTCTGTTAAA
Found at i:47878 original size:109 final size:109
Alignment explanation
Indices: 47717--47940 Score: 448
Period size: 109 Copynumber: 2.1 Consensus size: 109
47707 TTGTCTATAG
47717 AATTTAGAGTTTTAACTACTTTTCTTAATCTTTGTAATATAGTTGAAATAGACTTATAATATGAG
1 AATTTAGAGTTTTAACTACTTTTCTTAATCTTTGTAATATAGTTGAAATAGACTTATAATATGAG
47782 ACAGATGGAGTAATAAATTTTAAGTATTATTTTAATATTTATTT
66 ACAGATGGAGTAATAAATTTTAAGTATTATTTTAATATTTATTT
47826 AATTTAGAGTTTTAACTACTTTTCTTAATCTTTGTAATATAGTTGAAATAGACTTATAATATGAG
1 AATTTAGAGTTTTAACTACTTTTCTTAATCTTTGTAATATAGTTGAAATAGACTTATAATATGAG
47891 ACAGATGGAGTAATAAATTTTAAGTATTATTTTAATATTTATTT
66 ACAGATGGAGTAATAAATTTTAAGTATTATTTTAATATTTATTT
47935 AATTTA
1 AATTTA
47941 AACACAATGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 115 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (109 bp):
AATTTAGAGTTTTAACTACTTTTCTTAATCTTTGTAATATAGTTGAAATAGACTTATAATATGAG
ACAGATGGAGTAATAAATTTTAAGTATTATTTTAATATTTATTT
Found at i:48686 original size:29 final size:29
Alignment explanation
Indices: 48624--48702 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
48614 GATATATGAC
* * *
48624 CTTTCAAAATTTTTTCATTTTGTCCTTTAAA
1 CTTTCAAAATTTTGTCA--TTGCCCCTTAAA
*
48655 CTTTCAAAATTTTGTCATTGCCCCTTGAA
1 CTTTCAAAATTTTGTCATTGCCCCTTAAA
*
48684 CTTTTAAAATTTTGTCATT
1 CTTTCAAAATTTTGTCATT
48703 AACCCATACT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 27 0.63
31 16 0.37
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (29 bp):
CTTTCAAAATTTTGTCATTGCCCCTTAAA
Found at i:49815 original size:16 final size:16
Alignment explanation
Indices: 49794--49828 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
49784 TATATATATA
49794 TATATATTATATAAACCC
1 TATATA-TATAT-AACCC
49812 TATATATATATAACCC
1 TATATATATATAACCC
49828 T
1 T
49829 GGTAATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATATATAACCC
Found at i:49823 original size:2 final size:2
Alignment explanation
Indices: 49771--49806 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
49761 CCTTACCAAA
49771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49807 AACCCTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53268 original size:15 final size:15
Alignment explanation
Indices: 53248--53281 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
53238 TAGAAGCATT
*
53248 TATATTTTTATACTA
1 TATATTTATATACTA
*
53263 TATATTTATATATTA
1 TATATTTATATACTA
53278 TATA
1 TATA
53282 GATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTTATATACTA
Found at i:54718 original size:33 final size:32
Alignment explanation
Indices: 54643--54718 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
54633 AAGTAAACAA
* *
54643 GTAAATATTCACATATAATAAAAAATTAGCAT
1 GTAAAAATACACATATAATAAAAAATTAGCAT
* *
54675 GTGAACATACACATATCAATAAAAAA-TAGCAT
1 GTAAAAATACACATAT-AATAAAAAATTAGCAT
54707 GTTAAAAATACA
1 G-TAAAAATACA
54719 TAAATATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 20 0.54
33 17 0.46
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (32 bp):
GTAAAAATACACATATAATAAAAAATTAGCAT
Found at i:55392 original size:2 final size:2
Alignment explanation
Indices: 55381--55411 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
55371 ATTCTCTTAC
55381 AT AT -T 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 AT
55412 GTTGGTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:64645 original size:78 final size:78
Alignment explanation
Indices: 64555--64801 Score: 415
Period size: 78 Copynumber: 3.2 Consensus size: 78
64545 TTGTTTAGCT
* * * *
64555 TTTTA-TAGTTTTACTCAACTAAAAACTTTATTTTTATTTAATTAAATATAATATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
64619 ATTTTATTTTACCA
65 ATTATATTTTACCA
64633 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
64698 TTATATTTTGCCA
66 TTATATTTTACCA
*
64711 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTAAAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
64776 TTATATTTTACCA
66 TTATATTTTACCA
64789 TTTTACTATTTTA
1 TTTTACTATTTTA
64802 ATTAAAAAAC
Statistics
Matches: 160, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
78 158 0.99
79 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACCA
Found at i:67754 original size:2 final size:2
Alignment explanation
Indices: 67747--67773 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67737 TTCAATGTAA
67747 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
67774 ATCTAAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68697 original size:30 final size:31
Alignment explanation
Indices: 68628--68707 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
68618 TAAATACAAA
* * *
68628 AAAAAAATCGCTTATGTTTTCTTTTTGAGAT
1 AAAATAATCCCTTATGTTTTCTTTTTGAGAC
*
68659 AAAATAATCCCTTATGTTTT-TTTTTGTGAC
1 AAAATAATCCCTTATGTTTTCTTTTTGAGAC
* *
68689 AAATTAATCCCTTACGTTT
1 AAAATAATCCCTTATGTTT
68708 CAAAAGTGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 25 0.58
31 18 0.42
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (31 bp):
AAAATAATCCCTTATGTTTTCTTTTTGAGAC
Found at i:69510 original size:10 final size:11
Alignment explanation
Indices: 69491--69522 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
69481 AAATTTTGTA
69491 ATTATTTTTAG
1 ATTATTTTTAG
69502 ATT-TTTTTA-
1 ATTATTTTTAG
69511 ATTATTTTTAG
1 ATTATTTTTAG
69522 A
1 A
69523 CCCGTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.16
10 12 0.63
11 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (11 bp):
ATTATTTTTAG
Found at i:69512 original size:20 final size:20
Alignment explanation
Indices: 69484--69522 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
69474 AAAAATTAAA
69484 TTTTGTAATTATTTTTAGAT
1 TTTTGTAATTATTTTTAGAT
*
69504 TTTTTTAATTATTTTTAGA
1 TTTTGTAATTATTTTTAGA
69523 CCCGTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTGTAATTATTTTTAGAT
Done.