Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012133.1 Corchorus capsularis cultivar CVL-1 contig12154, 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: 35708
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:151 original size:35 final size:35
Alignment explanation
Indices: 112--251 Score: 178
Period size: 35 Copynumber: 4.0 Consensus size: 35
102 TTACTGATTG
*
112 CCATTTCTT-TTTACTGATTAATATTTTACTCTTTA
1 CCATTTCTTCTTTACTGATTACT-TTTTACTCTTTA
* * *
147 CCATTTTTTCTTTACCGATTACTCTTTACTCTTTA
1 CCATTTCTTCTTTACTGATTACTTTTTACTCTTTA
* * *
182 CCATTT-TTCTTTACTGATTTCTCTATAACTCTTTA
1 CCATTTCTTCTTTACTGATTACT-TTTTACTCTTTA
217 CCATTTC-TCTTTACTGATTACTTTTTACTCTTTA
1 CCATTTCTTCTTTACTGATTACTTTTTACTCTTTA
251 C
1 C
252 TGATTACCAT
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
34 25 0.28
35 54 0.60
36 11 0.12
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (35 bp):
CCATTTCTTCTTTACTGATTACTTTTTACTCTTTA
Found at i:175 original size:7 final size:7
Alignment explanation
Indices: 165--287 Score: 53
Period size: 7 Copynumber: 17.7 Consensus size: 7
155 TCTTTACCGA
165 TTACTCT
1 TTACTCT
172 TTACTCT
1 TTACTCT
179 TTAC-CAT
1 TTACTC-T
*
186 TT-TTCT
1 TTACTCT
*
192 TTACTGAT
1 TTACT-CT
200 TT-CTCT
1 TTACTCT
*
206 ATAACTCT
1 -TTACTCT
214 TTAC-CAT
1 TTACTC-T
221 TT-CTCT
1 TTACTCT
**
227 TTACTGA
1 TTACTCT
*
234 TTACTTT
1 TTACTCT
241 TTACTCT
1 TTACTCT
**
248 TTACTGA
1 TTACTCT
*
255 TTAC-CA
1 TTACTCT
*
261 TTACTTT
1 TTACTCT
268 TTAC-CATT
1 TTACTC--T
276 TTACTCT
1 TTACTCT
283 TTACT
1 TTACT
288 GATTGCCTTT
Statistics
Matches: 86, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
6 15 0.17
7 58 0.67
8 12 0.14
9 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:194 original size:20 final size:21
Alignment explanation
Indices: 155--196 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
145 TACCATTTTT
155 TCTTTACCGATTACTCTTTAC
1 TCTTTACCGATTACTCTTTAC
**
176 TCTTTACC-ATTTTTCTTTAC
1 TCTTTACCGATTACTCTTTAC
196 T
1 T
197 GATTTCTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.55
Consensus pattern (21 bp):
TCTTTACCGATTACTCTTTAC
Found at i:419 original size:15 final size:14
Alignment explanation
Indices: 398--437 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 14
388 TATTGTTTCT
398 TACTCTTTTACTGA
1 TACTCTTTTACTGA
412 TGACTCTTTT-CT--
1 T-ACTCTTTTACTGA
424 TACTCTTTTACTGA
1 TACTCTTTTACTGA
438 ATATTGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
11 8 0.36
12 3 0.14
14 3 0.14
15 8 0.36
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (14 bp):
TACTCTTTTACTGA
Found at i:425 original size:51 final size:52
Alignment explanation
Indices: 366--562 Score: 335
Period size: 51 Copynumber: 3.8 Consensus size: 52
356 TACTATTACG
366 CTTTTCTTACTC-TTTTACTGAATATTGTTTCTTACTCTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTACTGATGACT
* *
417 CTTTTCTTACTC-TTTTACTGAATATTGCTTCTTACTCTTTTACTGATGGCT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTACTGATGACT
*
468 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTATTTACTGATGACC
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCT-TTTACTGATGACT
*
521 CTTTTCTTACTCTTTTTACTGAATATTGTTTTTTACTCTTTT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTT
563 TTACTGATTA
Statistics
Matches: 138, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
51 61 0.44
52 28 0.20
53 49 0.36
ACGTcount: A:0.17, C:0.20, G:0.08, T:0.56
Consensus pattern (52 bp):
CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTACTGATGACT
Found at i:563 original size:26 final size:26
Alignment explanation
Indices: 367--562 Score: 208
Period size: 26 Copynumber: 7.6 Consensus size: 26
357 ACTATTACGC
367 TTTTCTTACTCTTTTACTGAATATTG
1 TTTTCTTACTCTTTTACTGAATATTG
* *
393 -TTTCTTACTCTTTTACTG-ATGACTC
1 TTTTCTTACTCTTTTACTGAAT-ATTG
418 TTTTCTTACTCTTTTACTGAATATTG
1 TTTTCTTACTCTTTTACTGAATATTG
* ** *
444 -CTTCTTACTCTTTTACTG-ATGGCTC
1 TTTTCTTACTCTTTTACTGAAT-ATTG
469 TTTTCTTACTCTTTTTACTGAATATTG
1 TTTTCTTACTC-TTTTACTGAATATTG
***
496 -TTTCTTACTCTATTTACTG-ATGACCC
1 TTTTCTTACTCT-TTTACTGAAT-ATTG
522 TTTTCTTACTCTTTTTACTGAATATTG
1 TTTTCTTACTC-TTTTACTGAATATTG
549 TTTT-TTACTCTTTT
1 TTTTCTTACTCTTTT
563 TTACTGATTA
Statistics
Matches: 140, Mismatches: 18, Indels: 25
0.77 0.10 0.14
Matches are distributed among these distances:
24 4 0.03
25 45 0.32
26 53 0.38
27 33 0.24
28 5 0.04
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (26 bp):
TTTTCTTACTCTTTTACTGAATATTG
Found at i:651 original size:21 final size:20
Alignment explanation
Indices: 627--757 Score: 61
Period size: 21 Copynumber: 7.0 Consensus size: 20
617 TACTGATTTA
627 CTGATTACTGCTACTTTGACC
1 CTGATTACTGCTACTTTGA-C
* * *
648 CTGATTAAT-CTCCTTTTTAC
1 CTGATTACTGCTAC-TTTGAC
* *
668 TTAATTACTG--A-TTT-A-
1 CTGATTACTGCTACTTTGAC
683 CTGATTACTGCTACTTTGACC
1 CTGATTACTGCTACTTTGA-C
* * *
704 CTGATTAAT-CTCCTTTTAC
1 CTGATTACTGCTACTTTGAC
* *
723 TTAATTACTG--A-TTT-A-
1 CTGATTACTGCTACTTTGAC
738 CTGATTACTGCTACTTTGAC
1 CTGATTACTGCTACTTTGAC
758 TCATGATTAA
Statistics
Matches: 78, Mismatches: 18, Indels: 29
0.62 0.14 0.23
Matches are distributed among these distances:
15 16 0.21
16 2 0.03
17 8 0.10
18 6 0.08
19 9 0.12
20 17 0.22
21 20 0.26
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (20 bp):
CTGATTACTGCTACTTTGAC
Found at i:731 original size:111 final size:110
Alignment explanation
Indices: 563--791 Score: 372
Period size: 111 Copynumber: 2.1 Consensus size: 110
553 TTACTCTTTT
* *
563 TTACTGA-TTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTACTTAATTACTGATTTA
1 TTACTGATTTACTGATTACTACTACCTTAACCCTGATTAATCTCTTTTACTTAATTACTGATTTA
*
627 CTGATTACTGCTACTTTGAC-CCTGATTAATCTCCTTTTTACTTAA
66 CTGATTACTGCTACTTTGACTCATGATTAATCT-CTTTTTACTTAA
* * *
672 TTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCTCCTTTTACTTAATTACTGATTT
1 TTACTGATTTACTGATTACTACTACCTTAACCCTGATTAATCT-CTTTTACTTAATTACTGATTT
737 ACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
65 ACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
783 TTACTGATT
1 TTACTGATT
792 GCCCCCTTTC
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
109 7 0.06
110 30 0.27
111 63 0.57
112 11 0.10
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (110 bp):
TTACTGATTTACTGATTACTACTACCTTAACCCTGATTAATCTCTTTTACTTAATTACTGATTTA
CTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
Found at i:809 original size:55 final size:55
Alignment explanation
Indices: 563--791 Score: 363
Period size: 56 Copynumber: 4.2 Consensus size: 55
553 TTACTCTTTT
** * * *
563 TTACTGA-TTACTGATTACTATTACCTTAACTCTGATTAATCTC-TTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCTCTTTTTACTTAA
616 TTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCTCCTTTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCT-CTTTTTACTTAA
*
672 TTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCTCCTTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCTCTTTTTACTTAA
*
727 TTACTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACTGCTACTTTGAC-CCTGATTAATCTCTTTTTACTTAA
783 TTACTGATT
1 TTACTGATT
792 GCCCCCTTTC
Statistics
Matches: 164, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
53 7 0.04
54 30 0.18
55 43 0.26
56 84 0.51
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (55 bp):
TTACTGATTTACTGATTACTGCTACTTTGACCCTGATTAATCTCTTTTTACTTAA
Found at i:1475 original size:51 final size:51
Alignment explanation
Indices: 1333--1733 Score: 465
Period size: 51 Copynumber: 7.9 Consensus size: 51
1323 AAAACAATCA
* * * *
1333 TTTTATTTACTAATGAC-CTAAAAGTTCACA-CTTCTAATTCCAAA-ATGACA-
1 TTTTATTTACTAATTACTCTAAAAATTCA-ATCTT-TTA-CCCAAAGATGACAT
* * *
1383 TTTTATTTACTAATTACT-TAAAAATTCAATCTTTTATCCAAAGATTAGAT
1 TTTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
* *
1433 CTTTATTTACTAATTACTCTAAAGATTCAATCTTTTACCCAAAG-TCGACAT
1 TTTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCAAAGAT-GACAT
* * ** * * *
1484 TTTTATTTACCAATTACTC-AAAAATCCAAATCTTTTATTCAAAGGTTAAAT
1 TTTTATTTACTAATTACTCTAAAAATTC-AATCTTTTACCCAAAGATGACAT
* * * *
1535 CTTTACTTACTAATTACTTTAAAGATTCAATCTTTTACCCAAAGATGACAT
1 TTTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
* * *
1586 TTTCATTTACTAATTATTCTAAAAATTCAATCTTTTACCCAAGGATGACAT
1 TTTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
*
1637 TTTTATTTACTAATTACTCTTAAAAATTCCATCTTTTACCCAAAGATGACAT
1 TTTTATTTACTAATTACTC-TAAAAATTCAATCTTTTACCCAAAGATGACAT
*
1689 TTTTATTTACTAATTACTCTTAAAAATTCCATCTTTTACCCAAAG
1 TTTTATTTACTAATTACTC-TAAAAATTCAATCTTTTACCCAAAG
1734 GTTATACCTT
Statistics
Matches: 301, Mismatches: 40, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
48 6 0.02
49 7 0.02
50 52 0.17
51 154 0.51
52 82 0.27
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (51 bp):
TTTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
Found at i:4255 original size:29 final size:29
Alignment explanation
Indices: 4222--4297 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 29
4212 GGTGATCTAA
*
4222 AAAAATGACTAAAATGCCCTCCTGAGTGC
1 AAAAATGACCAAAATGCCCTCCTGAGTGC
* *
4251 AAAAATGACCGAAATG-CC-CCTGGGTGC
1 AAAAATGACCAAAATGCCCTCCTGAGTGC
*
4278 AAAAATGACCAAAATACCCT
1 AAAAATGACCAAAATGCCCT
4298 TGGGCGGCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 22 0.55
28 4 0.10
29 14 0.35
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (29 bp):
AAAAATGACCAAAATGCCCTCCTGAGTGC
Found at i:8758 original size:31 final size:32
Alignment explanation
Indices: 8708--8769 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
8698 CAAGGGAGAG
8708 TGTTATGGAAATTGGACTTCACATGGGCCAAA
1 TGTTATGGAAATTGGACTTCACATGGGCCAAA
*
8740 TGTTATGGAGA-TGGACTTCACATGGGCCAA
1 TGTTATGGAAATTGGACTTCACATGGGCCAA
8770 CTGGAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (32 bp):
TGTTATGGAAATTGGACTTCACATGGGCCAAA
Found at i:10754 original size:17 final size:17
Alignment explanation
Indices: 10734--10766 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10724 TTTACTTTGA
10734 TTTTTTTTATTGGTACT
1 TTTTTTTTATTGGTACT
10751 TTTTTTTTATTGGTAC
1 TTTTTTTTATTGGTAC
10767 CGAGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.70
Consensus pattern (17 bp):
TTTTTTTTATTGGTACT
Found at i:31740 original size:9 final size:9
Alignment explanation
Indices: 31726--31782 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
31716 AACTATCTCC
31726 TCACCTACA
1 TCACCTACA
*
31735 TCACCTTCA
1 TCACCTACA
**
31744 TCATTTACA
1 TCACCTACA
** *
31753 TCATTTATA
1 TCACCTACA
31762 TCACCTACA
1 TCACCTACA
*
31771 TCACCTTCA
1 TCACCTACA
31780 TCA
1 TCA
31783 TCAACTCCTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
TCACCTACA
Found at i:31754 original size:18 final size:18
Alignment explanation
Indices: 31730--31784 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
31720 ATCTCCTCAC
31730 CTACATCACCTTCATCAT
1 CTACATCACCTTCATCAT
* * * *
31748 TTACATCA-TTTATATCAC
1 CTACATCACCTT-CATCAT
31766 CTACATCACCTTCATCAT
1 CTACATCACCTTCATCAT
31784 C
1 C
31785 AACTCCTGAA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.36
Consensus pattern (18 bp):
CTACATCACCTTCATCAT
Done.