Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016075.1 Corchorus capsularis cultivar CVL-1 contig16096, 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: 16864
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Found at i:9842 original size:63 final size:62
Alignment explanation
Indices: 9735--9970 Score: 204
Period size: 63 Copynumber: 3.7 Consensus size: 62
9725 TGACATCCAT
* * * * * * * *
9735 AATTAAATACATAGTCTGGACACATCATACACTACTAAATAATACCATAAATTCCGAGTACA
1 AATTAAACACATAGTCTGAAAATACCATCCACTACTGAATAATACCATAAACTCCGAGTACA
* * * * * *
9797 CAATTAAACACACAGTCTGAAAATAGCATCCACTGCTGAATAATACCATGAACTCCAAATACA
1 -AATTAAACACATAGTCTGAAAATACCATCCACTACTGAATAATACCATAAACTCCGAGTACA
* * * *
9860 AGCATTGAATAATAACATAGTCTGGAAACACCATCCCCTACTGAATAATACCATAAACTCCGAGT
1 A--ATT--A-AA-CACATAGTCTGAAAATACCATCCACTACTGAATAATACCATAAACTCCGAGT
9925 ACA
60 ACA
* *
9928 TAATTAAACATATAGTTTGAAAATACCA-CCAACTACTGAATAA
1 -AATTAAACACATAGTCTGAAAATACCATCC-ACTACTGAATAA
9971 CACATTGTCT
Statistics
Matches: 136, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
62 3 0.02
63 75 0.55
64 5 0.04
65 1 0.01
66 1 0.01
67 5 0.04
68 45 0.33
69 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.24
Consensus pattern (62 bp):
AATTAAACACATAGTCTGAAAATACCATCCACTACTGAATAATACCATAAACTCCGAGTACA
Found at i:13636 original size:22 final size:22
Alignment explanation
Indices: 13611--13873 Score: 195
Period size: 21 Copynumber: 11.9 Consensus size: 22
13601 ACTGATCACC
*
13611 TTTTACTCTTTACAGATTACTA
1 TTTTACTCTTTACTGATTACTA
* * *
13633 TTTTACTC-TTACTAATAACCA
1 TTTTACTCTTTACTGATTACTA
* *
13654 TTTTGCTC-TTACTAATTACTA
1 TTTTACTCTTTACTGATTACTA
* *
13675 TTTTAC-CTTTTATTGATTACTT
1 TTTTACTC-TTTACTGATTACTA
13697 TTTTACTATTTTACTCTTTACTGATTACCT-
1 TTTTAC-----T-C--TTTACTGATTA-CTA
* *
13727 TCTTACTTTTTACTGATTACTA
1 TTTTACTCTTTACTGATTACTA
*
13749 TTTTACTCTTTACTGATTACCA
1 TTTTACTCTTTACTGATTACTA
*
13771 TTTTACTC-TTACTGATTAC-C
1 TTTTACTCTTTACTGATTACTA
*
13791 TTTTACTCTTTACTGATTACCA
1 TTTTACTCTTTACTGATTACTA
* * *
13813 TTTTGCTCTCGT--TGATTACCA
1 TTTTACTCT-TTACTGATTACTA
*
13834 TTTTGCTC-TTACTGATTACTA
1 TTTTACTCTTTACTGATTACTA
13855 TTTTAC-CTTTTACTGATTA
1 TTTTACTC-TTTACTGATTA
13874 TCATTACTTT
Statistics
Matches: 197, Mismatches: 25, Indels: 38
0.76 0.10 0.15
Matches are distributed among these distances:
19 1 0.01
20 10 0.05
21 86 0.44
22 80 0.41
23 1 0.01
25 1 0.01
29 1 0.01
30 15 0.08
31 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTACTCTTTACTGATTACTA
Found at i:13703 original size:30 final size:31
Alignment explanation
Indices: 13669--13739 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
13659 CTCTTACTAA
* * *
13669 TTACTATTTTACCT-TTTATTGATTACTTTT
1 TTACTATTTTACCTCTTTACTGATTACCTTC
13699 TTACTATTTTA-CTCTTTACTGATTACCTTC
1 TTACTATTTTACCTCTTTACTGATTACCTTC
13729 TTACT-TTTTAC
1 TTACTATTTTAC
13740 TGATTACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 7 0.19
30 29 0.81
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.59
Consensus pattern (31 bp):
TTACTATTTTACCTCTTTACTGATTACCTTC
Found at i:13724 original size:52 final size:51
Alignment explanation
Indices: 13653--13755 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 51
13643 ACTAATAACC
* * * *
13653 ATTTTGCTCTTACTAATTA-CTATTTTACCTTTTATTGATTACTTTTTTACT
1 ATTTTACTCTTACTAATTACCT-TCTTACCTTTTACTGATTACTATTTTACT
* *
13704 ATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACTATTTTACT
1 ATTTTACTC-TTACTAATTACCTTCTTACCTTTTACTGATTACTATTTTACT
13756 CTTTACTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 8 0.18
52 34 0.77
53 2 0.05
ACGTcount: A:0.21, C:0.17, G:0.04, T:0.57
Consensus pattern (51 bp):
ATTTTACTCTTACTAATTACCTTCTTACCTTTTACTGATTACTATTTTACT
Found at i:13784 original size:21 final size:21
Alignment explanation
Indices: 13699--13902 Score: 193
Period size: 22 Copynumber: 9.6 Consensus size: 21
13689 GATTACTTTT
*
13699 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTC-TTACTGA
*
13721 TTACC-TTCTTACTTTTTACTGA
1 TTACCATT-TTAC-TCTTACTGA
*
13743 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTC-TTACTGA
13765 TTACCATTTTACTCTTACTGA
1 TTACCATTTTACTCTTACTGA
13786 TTACC-TTTTACTCTTTACTGA
1 TTACCATTTTACTC-TTACTGA
* ***
13807 TTACCATTTTGCTCTCGTTGA
1 TTACCATTTTACTCTTACTGA
*
13828 TTACCATTTTGCTCTTACTGA
1 TTACCATTTTACTCTTACTGA
* *
13849 TTACTATTTTACCTTTTACTGA
1 TTACCATTTTA-CTCTTACTGA
* * *
13871 TTATCA--TTACTTTTTATTGA
1 TTACCATTTTAC-TCTTACTGA
13891 TTACC-TTTTACT
1 TTACCATTTTACT
13903 ATTTCATTCT
Statistics
Matches: 153, Mismatches: 19, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
19 1 0.01
20 24 0.16
21 62 0.41
22 63 0.41
23 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (21 bp):
TTACCATTTTACTCTTACTGA
Found at i:13808 original size:42 final size:42
Alignment explanation
Indices: 13705--13902 Score: 206
Period size: 42 Copynumber: 4.7 Consensus size: 42
13695 TTTTTTACTA
* *
13705 TTTTACTCTTTACTGATTACC-TTCTTACTTTTTACTGATTACTA
1 TTTTACTCTTTACTGATTACCATT-TTAC-TCTTACTGATTAC-C
13749 TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACC
1 TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACC
* ***
13791 TTTTACTCTTTACTGATTACCATTTTGCTCTCGTTGATTACC
1 TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACC
* * * *
13833 ATTTTGCTC-TTACTGATTACTATTTTACCTTTTACTGATTATC
1 -TTTTACTCTTTACTGATTACCATTTTA-CTCTTACTGATTACC
* * *
13876 -ATTACTTTTTATTGATTACC-TTTTACT
1 TTTTACTCTTTACTGATTACCATTTTACT
13903 ATTTCATTCT
Statistics
Matches: 131, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.02
41 9 0.07
42 64 0.49
43 29 0.22
44 25 0.19
45 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (42 bp):
TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACC
Found at i:13902 original size:49 final size:51
Alignment explanation
Indices: 13849--13953 Score: 135
Period size: 49 Copynumber: 2.1 Consensus size: 51
13839 CTCTTACTGA
* * *
13849 TTACTATTTTAC-CTTTTACTGATTATC-ATT-ACTTTTTATTGATTACCTT
1 TTACTATTTCACTC-TTTACTGATTATCTATTCACTTTTTACTGATTACCCT
* *
13898 TTACTATTTCATTCTTTACTGATTATCTTTTCACTTTTTACTGATTACCCT
1 TTACTATTTCACTCTTTACTGATTATCTATTCACTTTTTACTGATTACCCT
13949 TTACT
1 TTACT
13954 CTTTACCATT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 23 0.48
50 3 0.06
51 22 0.46
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (51 bp):
TTACTATTTCACTCTTTACTGATTATCTATTCACTTTTTACTGATTACCCT
Found at i:13975 original size:35 final size:35
Alignment explanation
Indices: 13934--14026 Score: 152
Period size: 35 Copynumber: 2.7 Consensus size: 35
13924 CTTTTCACTT
*
13934 TTTACTGATTACCCTTTACTCTTT-ACCATTCTTCC
1 TTTACTGATTACTCTTTACT-TTTGACCATTCTTCC
*
13969 TTTACTGATTACTCTTTACTTTTGACCATTCTTCT
1 TTTACTGATTACTCTTTACTTTTGACCATTCTTCC
14004 TTTACTGATTACTCTTTACTTTT
1 TTTACTGATTACTCTTTACTTTT
14027 TTATCATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
34 3 0.05
35 52 0.95
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.54
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTTTTGACCATTCTTCC
Found at i:14060 original size:86 final size:86
Alignment explanation
Indices: 13948--14105 Score: 232
Period size: 86 Copynumber: 1.8 Consensus size: 86
13938 CTGATTACCC
* *
13948 TTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACT-TTTGACCATTCTTCT-TTTACTG
1 TTTACTCTTTACAATTATTCCTTTACTGATTACTCTTTACTGTTT-ACCATT-TTCTCTTTACTG
14011 ATTACTCTTTACTTTTTTATCAT
64 ATTACTCTTTACTTTTTTATCAT
* *
14034 TTTACTCTTTACTAATTATTCC-TTACTGATTATTCTTTACTGTTTACCATTTTTTCTTTACTGA
1 TTTACTCTTTAC-AATTATTCCTTTACTGATTACTCTTTACTGTTTACCATTTTCTCTTTACTGA
14098 TTACTCTT
65 TTACTCTT
14106 GTCTGAATAC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
85 3 0.05
86 52 0.80
87 10 0.15
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (86 bp):
TTTACTCTTTACAATTATTCCTTTACTGATTACTCTTTACTGTTTACCATTTTCTCTTTACTGAT
TACTCTTTACTTTTTTATCAT
Found at i:14065 original size:14 final size:14
Alignment explanation
Indices: 14042--14075 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
14032 ATTTTACTCT
*
14042 TTACTAATTATTCC
1 TTACTGATTATTCC
*
14056 TTACTGATTATTCT
1 TTACTGATTATTCC
14070 TTACTG
1 TTACTG
14076 TTTACCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (14 bp):
TTACTGATTATTCC
Found at i:14080 original size:21 final size:22
Alignment explanation
Indices: 14063--14103 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
14053 TCCTTACTGA
*
14063 TTATTCTTTACTGTTTAC-CAT
1 TTATTCTTTACTGATTACTCAT
*
14084 TTTTTCTTTACTGATTACTC
1 TTATTCTTTACTGATTACTC
14104 TTGTCTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.59
Consensus pattern (22 bp):
TTATTCTTTACTGATTACTCAT
Found at i:14080 original size:35 final size:35
Alignment explanation
Indices: 14034--14105 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
14024 TTTTTATCAT
* *
14034 TTTACTCTTTACTAATTATTCCTTACTGATTATTC
1 TTTACTCTTTACCAATTATTCCTTACTGATTACTC
* * * *
14069 TTTACTGTTTACCATTTTTTCTTTACTGATTACTC
1 TTTACTCTTTACCAATTATTCCTTACTGATTACTC
14104 TT
1 TT
14106 GTCTGAATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.57
Consensus pattern (35 bp):
TTTACTCTTTACCAATTATTCCTTACTGATTACTC
Found at i:14331 original size:71 final size:71
Alignment explanation
Indices: 14186--14341 Score: 158
Period size: 71 Copynumber: 2.2 Consensus size: 71
14176 GACTAATCCA
* * * *
14186 TTGACTTTTAATTA-CTGATTTACTGATTACTATTTTTATCTTGACTCTTAATTACTGATTAATC
1 TTGACTCTTAATTATC-AATTTACCGATTACTATTTTTATCTTGACTCTGAATTACTGATTAATC
* *
14250 TCTTATC
65 TATTACC
* * *
14257 TTGATTCTTAATTATCAATTTACCGATTACTATCTTTT-TACTTGATTACTGATTTACTGATT-A
1 TTGACTCTTAATTATCAATTTACCGATTACTAT-TTTTAT-CTTGACT-CTGAATTACTGATTAA
14320 -CTATTACC
63 TCTATTACC
*
14328 TTGACTCTTGATTA
1 TTGACTCTTAATTA
14342 ATCTCTTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
71 46 0.66
72 12 0.17
73 12 0.17
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.51
Consensus pattern (71 bp):
TTGACTCTTAATTATCAATTTACCGATTACTATTTTTATCTTGACTCTGAATTACTGATTAATCT
ATTACC
Found at i:14420 original size:55 final size:55
Alignment explanation
Indices: 14289--14474 Score: 300
Period size: 55 Copynumber: 3.4 Consensus size: 55
14279 CCGATTACTA
* *
14289 TCTTTTTACTTGATTACTGATTTACTGATTACTATTACCTTGACTCTTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTC-TGATTAATC
*
14345 TCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
* * *
14400 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGAGTCTGATTACTA
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
*
14455 TCTTTTTACTTGATTACTGA
1 TCTTTTTACTTAATTACTGA
14475 CTGCCCCTTT
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 79 0.65
56 43 0.35
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.51
Consensus pattern (55 bp):
TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
Found at i:15436 original size:50 final size:50
Alignment explanation
Indices: 15361--15529 Score: 196
Period size: 50 Copynumber: 3.4 Consensus size: 50
15351 ATTACTTTTT
* * * * * * *
15361 TTAAAACTTTAATCTTTTATTCAAAGGTTACATCTCTATTTACTAATTAC
1 TTAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
* *
15411 TCTAAAAA-TCAATCTTTTGCTCAAAGGTGACATTTTTACTTATTAATTAC
1 T-TAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
* * * * *
15461 TAAAAAATTCAATTTTTTACCCAAAGATGACATTTTTACTTACTAATTAT
1 TTAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
15511 TTAAAAATTCAATCTTTTA
1 TTAAAAATTCAATCTTTTA
15530 TTTACAAATT
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 5 0.05
50 89 0.90
51 5 0.05
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (50 bp):
TTAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
Done.