Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008905.1 Corchorus capsularis cultivar CVL-1 contig08926, 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: 21035
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Found at i:5521 original size:2 final size:2
Alignment explanation
Indices: 5514--5544 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
5504 TGTGTAAATA
5514 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
5545 TTACATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9947 original size:2 final size:2
Alignment explanation
Indices: 9940--9964 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9930 GATGTACTAG
9940 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9965 TAACCGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10477 original size:31 final size:32
Alignment explanation
Indices: 10442--10502 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
10432 TGAAAATTGA
10442 GGTCG-TTGCCCTTATATAGATTACATTATCT
1 GGTCGATTGCCCTTATATAGATTACATTATCT
* * * *
10473 GGTCGATTGCCTTTGTATTGATTATATTAT
1 GGTCGATTGCCCTTATATAGATTACATTAT
10503 TTTGGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (32 bp):
GGTCGATTGCCCTTATATAGATTACATTATCT
Found at i:15351 original size:2 final size:2
Alignment explanation
Indices: 15344--15376 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15334 TCTCTTTTCC
15344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15377 CTCAATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16554 original size:17 final size:15
Alignment explanation
Indices: 16519--16549 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16509 AAAGTTAATA
16519 AAATAAAATAATAAG
1 AAATAAAATAATAAG
*
16534 AAATAAAATATTAAG
1 AAATAAAATAATAAG
16549 A
1 A
16550 GAAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAATAAAATAATAAG
Found at i:17414 original size:11 final size:11
Alignment explanation
Indices: 17398--17440 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
17388 TTTATCATTT
17398 TTACTCTTTTC
1 TTACTCTTTTC
*
17409 TTACTCTTTACTAA
1 TTACTCTTT--T-C
17423 TTACTCTTTTC
1 TTACTCTTTTC
17434 TTACTCT
1 TTACTCT
17441 CTTTTATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 16 0.59
12 1 0.04
13 1 0.04
14 9 0.33
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (11 bp):
TTACTCTTTTC
Found at i:17529 original size:21 final size:21
Alignment explanation
Indices: 17505--17820 Score: 186
Period size: 21 Copynumber: 14.8 Consensus size: 21
17495 ACTCTTTGAA
*
17505 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
17526 TTACTGATTA-CTATTCTACTC-
1 TTACTGATTACCT-TT-TACTCT
* * *
17547 TTACTAATTACCACTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
17568 TTACTGATTACCGTTTTACTC-
1 TTACTGATTACC-TTTTACTCT
* * **
17589 TTAATGAGTACCTTTTACTGA
1 TTACTGATTACCTTTTACTCT
*
17610 TTACT-ATTTTA-CTCTTTACTTT
1 TTACTGA--TTACCT-TTTACTCT
*
17632 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* *
17653 TTACTGATTACCTTCTTGCTTT
1 TTACTGATTACCTT-TTACTCT
*
17675 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* * *
17696 TTATTGATTACCTTCTTGCTTT
1 TTACTGATTACCTT-TTACTCT
*
17718 TTACTGATTACTATTTTACTCT
1 TTACTGATTAC-CTTTTACTCT
*
17740 TTACTGATTACCATTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
* *
17761 TCATTGATTACCATTTTAC-CTT
1 TTACTGATTACC-TTTTACTC-T
* * * *
17783 TTACTGGTTATC-ATTACTTTT
1 TTACTGATTACCTTTTAC-TCT
*
17804 TTATTGATTACCTTTTA
1 TTACTGATTACCTTTTA
17821 TTATTTCATT
Statistics
Matches: 226, Mismatches: 46, Indels: 45
0.71 0.15 0.14
Matches are distributed among these distances:
20 19 0.08
21 115 0.51
22 86 0.38
23 6 0.03
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.52
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:17621 original size:15 final size:15
Alignment explanation
Indices: 17601--17694 Score: 81
Period size: 15 Copynumber: 6.5 Consensus size: 15
17591 AATGAGTACC
17601 TTTTACTGATTACTA
1 TTTTACTGATTACTA
**
17616 TTTTACTCTTTACT-
1 TTTTACTGATTACTA
17630 TTTTACTGATTACTA
1 TTTTACTGATTACTA
*
17645 TTTTACT-CTTACTGA
1 TTTTACTGATTACT-A
** *
17660 --TTACCTTCTTGCT-
1 TTTTA-CTGATTACTA
17673 TTTTACTGATTACTA
1 TTTTACTGATTACTA
17688 TTTTACT
1 TTTTACT
17695 CTTATTGATT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
13 3 0.05
14 25 0.40
15 35 0.56
ACGTcount: A:0.20, C:0.18, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTTACTGATTACTA
Found at i:17634 original size:29 final size:29
Alignment explanation
Indices: 17601--17744 Score: 111
Period size: 29 Copynumber: 5.0 Consensus size: 29
17591 AATGAGTACC
17601 TTTTACTGATTACTATTTTACTCTTTACT
1 TTTTACTGATTACTATTTTACTCTTTACT
17630 TTTTACTGATTACTATTTTACTC-TTACT
1 TTTTACTGATTACTATTTTACTCTTTACT
** ** * **
17658 GATTACCTTCTTGCT-TTTTACTGATTACT
1 TTTTA-CTGATTACTATTTTACTCTTTACT
* * *
17687 ATTTTACT-CTTA-T-TGATTAC-CTTCTTGCT
1 -TTTTACTGATTACTAT-TTTACTC-T-TTACT
17716 TTTTACTGATTACTATTTTACTCTTTACT
1 TTTTACTGATTACTATTTTACTCTTTACT
17745 GATTACCATT
Statistics
Matches: 89, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
27 2 0.02
28 29 0.33
29 47 0.53
30 9 0.10
31 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (29 bp):
TTTTACTGATTACTATTTTACTCTTTACT
Found at i:17788 original size:43 final size:43
Alignment explanation
Indices: 17628--17759 Score: 230
Period size: 43 Copynumber: 3.0 Consensus size: 43
17618 TTACTCTTTA
17628 CTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTCTTG
1 CTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTCTTG
*
17671 CTTTTTACTGATTACTATTTTACTCTTATTGATTACCTTCTTG
1 CTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTCTTG
17714 CTTTTTACTGATTACTATTTTACTCTTTACTGATTACCATT-TTG
1 CTTTTTACTGATTACTATTTTACTC-TTACTGATTACC-TTCTTG
17758 CT
1 CT
17760 CTCATTGATT
Statistics
Matches: 85, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
43 67 0.79
44 16 0.19
45 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.55
Consensus pattern (43 bp):
CTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTCTTG
Found at i:17895 original size:35 final size:35
Alignment explanation
Indices: 17854--17976 Score: 158
Period size: 35 Copynumber: 3.5 Consensus size: 35
17844 CTTTTTACTT
*
17854 TTTACTGATTACCCTTTACTCTTTACCATTCTTCC
1 TTTACTGATTACCCTTTACTTTTTACCATTCTTCC
* *
17889 TTTACTGATTACTCTTTACTTTTTACCATTCTTCT
1 TTTACTGATTACCCTTTACTTTTTACCATTCTTCC
* *
17924 TTTACTGATTACTCTTTACTTTTTATCATT-TTACTC
1 TTTACTGATTACCCTTTACTTTTTACCATTCTT-C-C
*
17960 TTTACTAATTACTCCTT
1 TTTACTGATTAC-CCTT
17977 ACTGATTATT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
34 2 0.03
35 62 0.79
36 11 0.14
37 3 0.04
ACGTcount: A:0.19, C:0.24, G:0.02, T:0.54
Consensus pattern (35 bp):
TTTACTGATTACCCTTTACTTTTTACCATTCTTCC
Found at i:17928 original size:28 final size:29
Alignment explanation
Indices: 17897--17965 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
17887 CCTTTACTGA
*
17897 TTACTCTTTACTTTTTACCATTCT-TC-TT
1 TTACTCTTTACTCTTTA-CATTCTATCATT
** * *
17925 TTACTGATTACTCTTTACTTTTTATCATT
1 TTACTCTTTACTCTTTACATTCTATCATT
17954 TTACTCTTTACT
1 TTACTCTTTACT
17966 AATTACTCCT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 4 0.12
28 16 0.50
29 12 0.38
ACGTcount: A:0.17, C:0.22, G:0.01, T:0.59
Consensus pattern (29 bp):
TTACTCTTTACTCTTTACATTCTATCATT
Found at i:18177 original size:37 final size:37
Alignment explanation
Indices: 18122--18326 Score: 176
Period size: 37 Copynumber: 5.9 Consensus size: 37
18112 ATTAATCCCT
* *
18122 TTACTTTGACTCTTAATTACTGATTTACTGATCACTA
1 TTACCTTGACTCTTAATTACTGATTTACTGATTACTA
18159 TTACCTTGACTCTTAATTA-TGAATTTACTGATTA--A
1 TTACCTTGACTCTTAATTACTG-ATTTACTGATTACTA
* * *
18194 TCT-CTTTTA--CTTAATTACTGATTTACTGATTACTG
1 T-TACCTTGACTCTTAATTACTGATTTACTGATTACTA
*
18229 TTACCTTGACTCTTAATTA-TCAATTTACTGATTA--A
1 TTACCTTGACTCTTAATTACT-GATTTACTGATTACTA
18264 -T--C-T--CT-TT--TTACTGATTTACTGATTACTGA
1 TTACCTTGACTCTTAATTACTGATTTACTGATTACT-A
**
18293 TTACCTTGACTCTTAATTACCAATTTACTGATTA
1 TTACCTTGACTCTTAATTACTGATTTACTGATTA
18327 ATCTCTTTTT
Statistics
Matches: 134, Mismatches: 12, Indels: 43
0.71 0.06 0.23
Matches are distributed among these distances:
26 15 0.11
27 1 0.01
28 2 0.01
29 3 0.02
30 1 0.01
31 1 0.01
32 2 0.01
33 21 0.16
34 4 0.03
35 13 0.10
36 6 0.04
37 49 0.37
38 16 0.12
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (37 bp):
TTACCTTGACTCTTAATTACTGATTTACTGATTACTA
Found at i:18187 original size:77 final size:73
Alignment explanation
Indices: 18093--18352 Score: 282
Period size: 70 Copynumber: 3.7 Consensus size: 73
18083 TACTTTCTCC
*
18093 CTTAAGTATCAATTTACTGATTAATCCCTTTACTTTGACTCTTAATTACTGATTTACTGATCACT
1 CTTAATTATCAATTTACTGATTAAT-CCTTT-CTTTGA--CTTAATTACTGATTTACTGATCACT
18158 ATTACCTTGACT
62 ATTACCTTGACT
* * * *
18170 CTTAATTATGAATTTACTGATTAAT-C--TCTTTTACTTAATTACTGATTTACTGATTACTGTTA
1 CTTAATTATCAATTTACTGATTAATCCTTTCTTTGACTTAATTACTGATTTACTGATCACTATTA
18232 CCTTGACT
66 CCTTGACT
*
18240 CTTAATTATCAATTTACTGATTAAT-C--TC--T---TT--TTACTGATTTACTGATTACTGATT
1 CTTAATTATCAATTTACTGATTAATCCTTTCTTTGACTTAATTACTGATTTACTGATCACT-ATT
18295 ACCTTGACT
65 ACCTTGACT
* *
18304 CTTAATTACCAATTTACTGATTAAT-CTCTT-TTT-ACTGAATTACTGATTT
1 CTTAATTATCAATTTACTGATTAATCCT-TTCTTTGACTTAATTACTGATTT
18353 CTACTTTTAC
Statistics
Matches: 164, Mismatches: 9, Indels: 25
0.83 0.05 0.13
Matches are distributed among these distances:
63 20 0.12
64 36 0.22
65 2 0.01
67 1 0.01
68 2 0.01
70 63 0.38
72 15 0.09
73 1 0.01
75 1 0.01
77 23 0.14
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (73 bp):
CTTAATTATCAATTTACTGATTAATCCTTTCTTTGACTTAATTACTGATTTACTGATCACTATTA
CCTTGACT
Found at i:18238 original size:70 final size:70
Alignment explanation
Indices: 18133--18352 Score: 328
Period size: 70 Copynumber: 3.2 Consensus size: 70
18123 TACTTTGACT
* * *
18133 CTTAATTACTGATTTACTGATCACTATTACCTTGACTCTTAATTATGAATTTACTGATTAATCTC
1 CTTAATTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTATCAATTTACTGATTAATCTC
18198 TTTTA
66 TTTTA
18203 CTTAATTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTATCAATTTACTGATTAATCTC
1 CTTAATTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTATCAATTTACTGATTAATCTC
18268 ---T-
66 TTTTA
*
18269 -TT--TTACTGATTTACTGATTACTGATTACCTTGACTCTTAATTACCAATTTACTGATTAATCT
1 CTTAATTACTGATTTACTGATTACTG-TTACCTTGACTCTTAATTATCAATTTACTGATTAATCT
18331 CTTTTTA
65 C-TTTTA
*
18338 CTGAATTACTGATTT
1 CTTAATTACTGATTT
18353 CTACTTTTAC
Statistics
Matches: 136, Mismatches: 5, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
63 21 0.15
64 38 0.28
65 2 0.01
67 1 0.01
68 1 0.01
70 63 0.46
72 10 0.07
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (70 bp):
CTTAATTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTATCAATTTACTGATTAATCTC
TTTTA
Found at i:18317 original size:64 final size:63
Alignment explanation
Indices: 18208--18385 Score: 263
Period size: 64 Copynumber: 2.8 Consensus size: 63
18198 TTTTACTTAA
*
18208 TTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTT
1 TTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTACCAATTTACTGATTAATCTCTTT
18271 TTACTGATTTACTGATTACTGATTACCTTGACTCTTAATTACCAATTTACTGATTAATCTCTTT
1 TTACTGATTTACTGATTACTG-TTACCTTGACTCTTAATTACCAATTTACTGATTAATCTCTTT
* * * * *
18335 TTACTGAATTACTGATT--T-CTACTTTTACTCTTAATTATCAATTTTACTGAT
1 TTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTACCAA-TTTACTGAT
18386 CATTATTACT
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
60 19 0.18
61 9 0.08
62 1 0.01
63 21 0.20
64 57 0.53
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.49
Consensus pattern (63 bp):
TTACTGATTTACTGATTACTGTTACCTTGACTCTTAATTACCAATTTACTGATTAATCTCTTT
Found at i:18381 original size:19 final size:19
Alignment explanation
Indices: 18357--18420 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
18347 TGATTTCTAC
18357 TTTTACTCTTAATTATCAA
1 TTTTACTCTTAATTATCAA
** * * *
18376 TTTTACTGATCATTATTAC
1 TTTTACTCTTAATTATCAA
* * *
18395 TTTGATTCTCAATTATCAA
1 TTTTACTCTTAATTATCAA
18414 TTTTACT
1 TTTTACT
18421 GGTTACTATT
Statistics
Matches: 30, Mismatches: 15, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTACTCTTAATTATCAA
Found at i:18437 original size:38 final size:38
Alignment explanation
Indices: 18367--18446 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
18357 TTTTACTCTT
*
18367 AATTATCAATTTTACTGATCATTATTACTTTGATTCTC
1 AATTATCAATTTTACTGATCACTATTACTTTGATTCTC
* * ** *
18405 AATTATCAATTTTACTGGTTACTATTGTTTTGATTCTT
1 AATTATCAATTTTACTGATCACTATTACTTTGATTCTC
18443 AATT
1 AATT
18447 TTATTGGGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (38 bp):
AATTATCAATTTTACTGATCACTATTACTTTGATTCTC
Done.