Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015592.1 Corchorus capsularis cultivar CVL-1 contig15613, 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: 22094
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:4839 original size:19 final size:18
Alignment explanation
Indices: 4791--4840 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
4781 GAAGAGAAAT
*
4791 TATGTGATGGTATCTAAG
1 TATGTGATGGTATATAAG
** *
4809 GGTGTGAAGGTATATGAAG
1 TATGTGATGGTATAT-AAG
4828 TATGTGATGGTAT
1 TATGTGATGGTAT
4841 GTGATTTGTG
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (18 bp):
TATGTGATGGTATATAAG
Found at i:5819 original size:6 final size:6
Alignment explanation
Indices: 5808--5837 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5798 CTGAGCAGAG
5808 TCTATC TCTATC TCTATC TCTATC TCTATC
1 TCTATC TCTATC TCTATC TCTATC TCTATC
5838 ACAAATGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTATC
Found at i:6828 original size:13 final size:14
Alignment explanation
Indices: 6812--6840 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6802 TAGGTCAAGG
6812 TTTTTCTTT-TTCT
1 TTTTTCTTTCTTCT
6825 TTTTTCTTTCTTCT
1 TTTTTCTTTCTTCT
6839 TT
1 TT
6841 GAGTTGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTCTTCT
Found at i:12121 original size:11 final size:11
Alignment explanation
Indices: 12105--12147 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
12095 AAGTTCGTGT
12105 TTGAAGATTTC
1 TTGAAGATTTC
12116 TTGAAGATTTC
1 TTGAAGATTTC
12127 TTGAAGATATT-
1 TTGAAGAT-TTC
12138 TTGAAGATTT
1 TTGAAGATTT
12148 GAAGACAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 2 0.06
11 27 0.87
12 2 0.06
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (11 bp):
TTGAAGATTTC
Found at i:21221 original size:21 final size:21
Alignment explanation
Indices: 21143--21423 Score: 117
Period size: 21 Copynumber: 13.5 Consensus size: 21
21133 CTGATCACCC
*
21143 TTTT-CTCTTTACTGATTACCA
1 TTTTACTC-TTACTGATTACTA
* *
21164 TTTGACTCTTACTAATTA-TCA
1 TTTTACTCTTACTGATTACT-A
* ** *
21185 TTTTGCTCTTGTTGGTTACTA
1 TTTTACTCTTACTGATTACTA
* *
21206 TTTTACTCTTACTGGTTA-TC
1 TTTTACTCTTACTGATTACTA
21226 TTTTA----T--TGATTACTA
1 TTTTACTCTTACTGATTACTA
*
21241 TTTTACT----CT--TTACGGA
1 TTTTACTCTTACTGATTAC-TA
21257 TTTTACTCTTTACTGATTACCT-
1 TTTTACTC-TTACTGATTA-CTA
* * *
21279 TCTTACTTTTTACTGATTACCA
1 TTTTAC-TCTTACTGATTACTA
*
21301 TTTTACTCTTTTACTGATTACCA
1 TTTTACTC--TTACTGATTACTA
*
21324 TTTTACTCTTTTTTACTGATTACTC
1 TTTTACTC----TTACTGATTACTA
21349 TTTTACTTCTTACTGATTACTA
1 TTTTAC-TCTTACTGATTACTA
* * *
21371 TTTGACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
* * * * * *
21392 CTTTGCTCTCACCGGTTACTG
1 TTTTACTCTTACTGATTACTA
21413 TTTTACTCTTA
1 TTTTACTCTTA
21424 ATGACTACCT
Statistics
Matches: 197, Mismatches: 40, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
14 5 0.03
15 10 0.05
16 9 0.05
17 1 0.01
20 6 0.03
21 78 0.40
22 41 0.21
23 25 0.13
24 1 0.01
25 19 0.10
26 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:21258 original size:22 final size:22
Alignment explanation
Indices: 21256--21389 Score: 130
Period size: 22 Copynumber: 6.0 Consensus size: 22
21246 CTCTTTACGG
21256 ATTTTACTCTTTACTGATTACCT
1 ATTTTACTCTTTACTGATTA-CT
* * *
21279 -TCTTACTTTTTACTGATTACC
1 ATTTTACTCTTTACTGATTACT
*
21300 ATTTTACTCTTTTACTGATTACC
1 ATTTTACTC-TTTACTGATTACT
21323 ATTTTACTCTTTTTTACTGATTACT
1 ATTTTACTC---TTTACTGATTACT
*
21348 CTTTTACT-TCTTACTGATTACT
1 ATTTTACTCT-TTACTGATTACT
* *
21370 ATTTGACTC-TTACTAATTAC
1 ATTTTACTCTTTACTGATTAC
21390 CACTTTGCTC
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
21 12 0.13
22 41 0.43
23 22 0.23
25 20 0.21
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTACTCTTTACTGATTACT
Found at i:21261 original size:16 final size:16
Alignment explanation
Indices: 21240--21274 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
21230 ATTGATTACT
21240 ATTTTACTCTTTACGG
1 ATTTTACTCTTTACGG
*
21256 ATTTTACTCTTTACTG
1 ATTTTACTCTTTACGG
21272 ATT
1 ATT
21275 ACCTTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTTTACTCTTTACGG
Found at i:21290 original size:45 final size:46
Alignment explanation
Indices: 21235--21373 Score: 135
Period size: 45 Copynumber: 3.0 Consensus size: 46
21225 CTTTTATTGA
* *
21235 TTACTATTTTACTCTTTACGGATTTTACTC-TTTACTGATTACC-TT
1 TTACTATTTTACTCATTAC-CATTTTACTCTTTTACTGATTACCATT
*
21280 CTTACT-TTTTACTGATTACCATTTTACTCTTTTACTGATTACCATT
1 -TTACTATTTTACTCATTACCATTTTACTCTTTTACTGATTACCATT
* * * *
21326 TTACTCTTTTTTACTGATTACTC-TTTTACT-TCTTACTGATTACTATT
1 TTA--CTATTTTACTCATTAC-CATTTTACTCTTTTACTGATTACCATT
21373 T
1 T
21374 GACTCTTACT
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
44 9 0.11
45 27 0.33
46 7 0.09
47 18 0.22
48 20 0.24
49 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (46 bp):
TTACTATTTTACTCATTACCATTTTACTCTTTTACTGATTACCATT
Found at i:21488 original size:35 final size:35
Alignment explanation
Indices: 21414--21492 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 35
21404 CGGTTACTGT
*
21414 TTTACTCTTAATGACTACCTTCTACTGATCACTAT
1 TTTACTCTTAATGACTACCTTCTACTGATCACTAA
* ** * * *
21449 TTTACTCTTAATGGCTGTCTTTTGCTGATTACTAA
1 TTTACTCTTAATGACTACCTTCTACTGATCACTAA
21484 TTTACTCTT
1 TTTACTCTT
21493 TACTGATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.48
Consensus pattern (35 bp):
TTTACTCTTAATGACTACCTTCTACTGATCACTAA
Found at i:21531 original size:21 final size:21
Alignment explanation
Indices: 21484--21527 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21474 TGATTACTAA
*
21484 TTTACTCTTTACTGATTATTC
1 TTTACTCTTTACTCATTATTC
*
21505 TTTACTCTTTAC-CATTTTTC
1 TTTACTCTTTACTCATTATTC
21525 TTT
1 TTT
21528 TACTAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTACTCTTTACTCATTATTC
Found at i:21703 original size:31 final size:31
Alignment explanation
Indices: 21649--21714 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
21639 AATTACTGAT
21649 TTACTGATTACTATTTTTACCTTGACTCTTAA
1 TTACTGATTAC-ATTTTTACCTTGACTCTTAA
21681 TTACTGATTA-ATTTCTTACCTTGACTCTTAA
1 TTACTGATTACATTT-TTACCTTGACTCTTAA
21712 TTA
1 TTA
21715 TCAATTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 4 0.12
31 19 0.58
32 10 0.30
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (31 bp):
TTACTGATTACATTTTTACCTTGACTCTTAA
Found at i:21784 original size:55 final size:53
Alignment explanation
Indices: 21724--21902 Score: 152
Period size: 47 Copynumber: 3.5 Consensus size: 53
21714 ATCAATTTAC
21724 TGATTATTATGTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
1 TGATTA-TAT-TTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
* *
21779 TGATTA-A---TCT-CTT-TTTACTGATTTACTGATTACCATCACTTTGACTT
1 TGATTATATTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
* * * *
21826 TGATTA-A---TCT-CTT-TTTACTGATTTACTGATTACCATCACCTTGACTC
1 TGATTATATTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
*
21873 TGTTTA-AGCTCTTTTTAC-TGATTACTGATT
1 TGATTATA--T-TTTTTACTTGATTACTGATT
21903 ACCCCTTTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
47 84 0.77
48 3 0.03
49 2 0.02
53 4 0.04
54 10 0.09
55 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (53 bp):
TGATTATATTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
Found at i:21809 original size:26 final size:26
Alignment explanation
Indices: 21779--21857 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
21769 ACTTTGACTT
21779 TGATTAATCTCTTTTTACTGATTTAC
1 TGATTAATCTCTTTTTACTGATTTAC
* *
21805 TGATTACCATCAC---TT--TGACTT--
1 TGATTA--ATCTCTTTTTACTGATTTAC
21826 TGATTAATCTCTTTTTACTGATTTAC
1 TGATTAATCTCTTTTTACTGATTTAC
21852 TGATTA
1 TGATTA
21858 CCATCACCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
19 4 0.10
21 6 0.15
22 2 0.05
23 5 0.12
24 5 0.12
25 2 0.05
26 12 0.30
28 4 0.10
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (26 bp):
TGATTAATCTCTTTTTACTGATTTAC
Found at i:21815 original size:47 final size:47
Alignment explanation
Indices: 21746--21905 Score: 277
Period size: 47 Copynumber: 3.4 Consensus size: 47
21736 TTTTACTTGA
21746 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
21793 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
* * * *
21840 TTACTGATTTACTGATTACCATCACCTTGACTCTGTTTAAGCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
21887 TTACTGA-TTACTGATTACC
1 TTACTGATTTACTGATTACC
21906 CCTTTTTACT
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
46 12 0.11
47 97 0.89
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
Done.