Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012206.1 Corchorus capsularis cultivar CVL-1 contig12227, 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: 68926
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:527 original size:31 final size:31
Alignment explanation
Indices: 480--548 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
470 CCTGCTACAC
* *
480 GTAATA-CCCACGTGGTTACATATGTTAAAG
1 GTAATACCCCACGTGGTTACACACGTTAAAG
* *
510 GTAATACCCCACTTGGTTACACACGTTACAG
1 GTAATACCCCACGTGGTTACACACGTTAAAG
541 GTAATACC
1 GTAATACC
549 TTGTGACTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (31 bp):
GTAATACCCCACGTGGTTACACACGTTAAAG
Found at i:854 original size:25 final size:25
Alignment explanation
Indices: 820--871 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
810 ATAGTAGCCA
820 TGATAGCCAAAAATGTTTGATATCT
1 TGATAGCCAAAAATGTTTGATATCT
845 TGATAGCCAAAAATGTTTGATATCT
1 TGATAGCCAAAAATGTTTGATATCT
870 TG
1 TG
872 CATATTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (25 bp):
TGATAGCCAAAAATGTTTGATATCT
Found at i:1212 original size:46 final size:46
Alignment explanation
Indices: 1145--1232 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
1135 ACCGATGGGA
* * *
1145 GTGACGTGGCCTACCCTTACCTCTTCAGGAAAATATCACTGTTACC
1 GTGACGTGACCTACCCTTACCTCTTCAGAAAAATACCACTGTTACC
*
1191 GTGACGTGACTTACCCTTACCTCTTCAGAAAAATACCACTGT
1 GTGACGTGACCTACCCTTACCTCTTCAGAAAAATACCACTGT
1233 CACCATAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (46 bp):
GTGACGTGACCTACCCTTACCTCTTCAGAAAAATACCACTGTTACC
Found at i:5729 original size:12 final size:12
Alignment explanation
Indices: 5697--5721 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5687 TTGTGTTGTG
5697 AAAAAAAGAAAA
1 AAAAAAAGAAAA
5709 AAAAAAAGAAAA
1 AAAAAAAGAAAA
5721 A
1 A
5722 GGAAAAGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:12701 original size:13 final size:13
Alignment explanation
Indices: 12682--12719 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
12672 AACCAAGTAT
12682 ATACATTATGTAA
1 ATACATTATGTAA
*
12695 CTACATTATGTAA
1 ATACATTATGTAA
12708 ATACATTATGTA
1 ATACATTATGTA
12720 TGTTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (13 bp):
ATACATTATGTAA
Found at i:13698 original size:18 final size:18
Alignment explanation
Indices: 13675--13710 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13665 CTAAGCAAGG
13675 TTCTGGAAAACCTGGAAA
1 TTCTGGAAAACCTGGAAA
*
13693 TTCTGGTAAACCTGGAAA
1 TTCTGGAAAACCTGGAAA
13711 ATTCCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (18 bp):
TTCTGGAAAACCTGGAAA
Found at i:18108 original size:13 final size:13
Alignment explanation
Indices: 18090--18114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18080 AACCAAGTAG
18090 ATACATTATGTAA
1 ATACATTATGTAA
18103 ATACATTATGTA
1 ATACATTATGTA
18115 TGTTCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
ATACATTATGTAA
Found at i:18749 original size:26 final size:26
Alignment explanation
Indices: 18720--18803 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
18710 ATGATTTGAG
18720 CATCCATTATAATTATGTGAAATACT
1 CATCCATTATAATTATGTGAAATACT
* * *** * *
18746 CATCCAATCATAA-AACAAGATATAGAT
1 CATCC-ATTATAATTATGTGAAATA-CT
18773 -ATCCATTATAATTATGTGAAATACT
1 CATCCATTATAATTATGTGAAATACT
18798 CATCCA
1 CATCCA
18804 ATCATAAAAC
Statistics
Matches: 40, Mismatches: 14, Indels: 8
0.65 0.23 0.13
Matches are distributed among these distances:
25 7 0.17
26 26 0.65
27 7 0.17
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (26 bp):
CATCCATTATAATTATGTGAAATACT
Found at i:18778 original size:52 final size:52
Alignment explanation
Indices: 18721--18824 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
18711 TGATTTGAGC
18721 ATCCATTATAATTATGTGAAATACTCATCCAATCATAAAACAAGATATAGAT
1 ATCCATTATAATTATGTGAAATACTCATCCAATCATAAAACAAGATATAGAT
18773 ATCCATTATAATTATGTGAAATACTCATCCAATCATAAAACAAGATATAGAT
1 ATCCATTATAATTATGTGAAATACTCATCCAATCATAAAACAAGATATAGAT
18825 CTAAAAGAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (52 bp):
ATCCATTATAATTATGTGAAATACTCATCCAATCATAAAACAAGATATAGAT
Found at i:24650 original size:32 final size:32
Alignment explanation
Indices: 24507--24747 Score: 356
Period size: 32 Copynumber: 7.4 Consensus size: 32
24497 GCGGAGCCTT
* *
24507 CCCACTAGGACGGCTCTGCCACGGCGGAGCCTC
1 CCCACTAGGACGGCTCTGCCACGGC-TAGCCGC
* *
24540 CCCACTAGGACGGCTCTGCCACGGCGGAGCCTC
1 CCCACTAGGACGGCTCTGCCACGGC-TAGCCGC
* *
24573 CCCACTAGGACGGCTCTGCCACGGCGGAGCCTC
1 CCCACTAGGACGGCTCTGCCACGGC-TAGCCGC
*
24606 CCCACTATGACGGCTCTGCCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
*
24638 TCCACTAGGACGGCTCTGCCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
* *
24670 CCCACTAGGATGGCTCTGCCACGGCTAGCCGT
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
24702 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
*
24734 CCCACTAGGGCGGC
1 CCCACTAGGACGGC
24748 AAGGCTTTTT
Statistics
Matches: 197, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
32 107 0.54
33 90 0.46
ACGTcount: A:0.15, C:0.42, G:0.29, T:0.14
Consensus pattern (32 bp):
CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
Found at i:24979 original size:32 final size:32
Alignment explanation
Indices: 24938--25074 Score: 193
Period size: 32 Copynumber: 4.2 Consensus size: 32
24928 AAACTAGCCG
*
24938 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCACCGGGACGGCCTGCCGTGGCGA
24970 AGCCGCCCCACCGGGACGGCCTGCCGTGGCGA
1 AGCCGCCCCACCGGGACGGCCTGCCGTGGCGA
* *
25002 AGCCGCCCCACCGGGACGGCCTGCCCTGGCTA
1 AGCCGCCCCACCGGGACGGCCTGCCGTGGCGA
** * * *
25034 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCACCGGGACGGCCTG-CCGTGGCGA
25067 AGCCGCCC
1 AGCCGCCC
25075 TCTTGAGACG
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 81 0.85
33 14 0.15
ACGTcount: A:0.12, C:0.44, G:0.36, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCACCGGGACGGCCTGCCGTGGCGA
Found at i:30137 original size:2 final size:2
Alignment explanation
Indices: 30132--30172 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30122 TTTTTATGCT
30132 TA TA TA TA 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 TA TA TA TA T
30173 CATCATTCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31214 original size:24 final size:24
Alignment explanation
Indices: 31175--31235 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
31165 AAAAGAAATA
31175 CATTTTC-TTTTTTCCTATTCTTC
1 CATTTTCTTTTTTTCCTATTCTTC
31198 CATTTTCTTTTTTTCCTATTCTTC
1 CATTTTCTTTTTTTCCTATTCTTC
*
31222 C-TTTATCTTGTTTT
1 CATTT-TCTTTTTTT
31236 ATGGAGGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.08, C:0.23, G:0.02, T:0.67
Consensus pattern (24 bp):
CATTTTCTTTTTTTCCTATTCTTC
Found at i:33027 original size:21 final size:21
Alignment explanation
Indices: 33001--33043 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32991 GGTCTTAGGT
*
33001 TCAACTATCACGGAATGTGAG
1 TCAACTACCACGGAATGTGAG
* *
33022 TCAACTCCCACGGAGTGTGAG
1 TCAACTACCACGGAATGTGAG
33043 T
1 T
33044 TTATTTGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
TCAACTACCACGGAATGTGAG
Found at i:42899 original size:21 final size:20
Alignment explanation
Indices: 42862--42900 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42852 TTTAGAAGCA
*
42862 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
42882 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
42901 GGAAGGGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:44823 original size:5 final size:5
Alignment explanation
Indices: 44813--44862 Score: 66
Period size: 5 Copynumber: 10.0 Consensus size: 5
44803 TTTCCTCTTC
* *
44813 CTTTT CTTTT CTTTT CTTTT CTTTT -TCTT CTTTT CCTTTT ATTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT -CTTTT CTTTT CTTTT
44863 TCCTTCTCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 3 0.08
5 31 0.79
6 5 0.13
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:44851 original size:25 final size:25
Alignment explanation
Indices: 44816--44869 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
44806 CCTCTTCCTT
*
44816 TTCTTTTCTTTTCTTTTCTTTTT-C
1 TTCTTTTCTTTTATTTTCTTTTTCC
44840 TTCTTTTCCTTTTATTTTCTTTTTCC
1 TTCTTTT-CTTTTATTTTCTTTTTCC
44866 TTCT
1 TTCT
44870 CCTTCTTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.26
25 15 0.56
26 5 0.19
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (25 bp):
TTCTTTTCTTTTATTTTCTTTTTCC
Found at i:44876 original size:35 final size:35
Alignment explanation
Indices: 44810--44877 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
44800 TTTTTTCCTC
* * **
44810 TTCCTTTTCTTTTCTTTTCTTTTCTTTTTCTTCTT
1 TTCCTTTTATTTTCTTTTCTCTTCTCCTTCTTCTT
44845 TTCCTTTTATTTTCTTTT-TCCTTCTCCTTCTTC
1 TTCCTTTTATTTTCTTTTCT-CTTCTCCTTCTTC
44878 GTTCTGTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.04
35 27 0.96
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (35 bp):
TTCCTTTTATTTTCTTTTCTCTTCTCCTTCTTCTT
Found at i:46937 original size:31 final size:31
Alignment explanation
Indices: 46897--46965 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
46887 CAAATCTAAA
* *
46897 TTGATCCAATTTTGAAACATTTAGTACCTAT
1 TTGAGCCAATTTTAAAACATTTAGTACCTAT
* * *
46928 TTGAGCCAATTTTAAAACGTTTGGTACCTGT
1 TTGAGCCAATTTTAAAACATTTAGTACCTAT
46959 TTGAGCC
1 TTGAGCC
46966 GGTTTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (31 bp):
TTGAGCCAATTTTAAAACATTTAGTACCTAT
Found at i:46974 original size:30 final size:31
Alignment explanation
Indices: 46897--46974 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
46887 CAAATCTAAA
* * *
46897 TTGATCCAATTTTGAAACATTTAGTACCTAT
1 TTGAGCCAAGTTTAAAACATTTAGTACCTAT
* * * *
46928 TTGAGCCAATTTTAAAACGTTTGGTACCTGT
1 TTGAGCCAAGTTTAAAACATTTAGTACCTAT
*
46959 TTGAGCC-GGTTTAAAA
1 TTGAGCCAAGTTTAAAA
46975 TATAAAAGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 7 0.17
31 33 0.82
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (31 bp):
TTGAGCCAAGTTTAAAACATTTAGTACCTAT
Found at i:47025 original size:18 final size:19
Alignment explanation
Indices: 46990--47034 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
46980 AAGTAAAAAA
46990 AAAAATTAAAACAAATATTT
1 AAAAA-TAAAACAAATATTT
47010 AAAAATAAAA-AAATATTT
1 AAAAATAAAACAAATATTT
47028 AAAAATA
1 AAAAATA
47035 CCACGTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 15 0.60
19 5 0.20
20 5 0.20
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATAAAACAAATATTT
Found at i:61438 original size:12 final size:12
Alignment explanation
Indices: 61421--61453 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
61411 TATTACTTGA
61421 TATCTTTTGCCT
1 TATCTTTTGCCT
61433 TATC-TTTGCCT
1 TATCTTTTGCCT
61444 TATCTTTTGC
1 TATCTTTTGC
61454 TATTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.09, C:0.24, G:0.09, T:0.58
Consensus pattern (12 bp):
TATCTTTTGCCT
Done.