Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014483.1 Corchorus capsularis cultivar CVL-1 contig14504, 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: 68424
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:604 original size:2 final size:2
Alignment explanation
Indices: 567--595 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
557 TTATAGTTAA
567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
596 GACATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:693 original size:21 final size:21
Alignment explanation
Indices: 650--693 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
640 ATTTATGGGG
* *
650 TTGCTAAATACCGTCCTAGTT
1 TTGCTAAATACCGCCCCAGTT
*
671 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCAGTT
692 TT
1 TT
694 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCAGTT
Found at i:717 original size:14 final size:15
Alignment explanation
Indices: 692--738 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
682 CGCCCCATTT
*
692 TTTACACTTTTGCTC
1 TTTACACTTTTGCAC
707 TTTAC-CTTTTGCAC
1 TTTACACTTTTGCAC
*
721 TTTTTACACTTTTACAC
1 --TTTACACTTTTGCAC
738 T
1 T
739 GAGCCTCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.30
15 6 0.22
16 5 0.19
17 8 0.30
ACGTcount: A:0.17, C:0.26, G:0.04, T:0.53
Consensus pattern (15 bp):
TTTACACTTTTGCAC
Found at i:793 original size:33 final size:31
Alignment explanation
Indices: 739--835 Score: 86
Period size: 33 Copynumber: 3.0 Consensus size: 31
729 CTTTTACACT
* * *
739 GAGCCTCCCCATTAGGACGGCTCAACCACGGCG
1 GAGCCTCCCCACTGGGGCGGCTC-ACCACGG-G
*
772 GAGCCTCCCCACTGGGGCGGCTTCACCATGGG
1 GAGCCTCCCCACTGGGGCGGC-TCACCACGGG
* * *
804 CAGGCCGCCCCACTGGGGCGGCTTCGCCACGG
1 GA-GCCTCCCCACTGGGGCGGC-TCACCACGG
836 TAAGCCGCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.04
33 50 0.93
34 2 0.04
ACGTcount: A:0.14, C:0.40, G:0.33, T:0.12
Consensus pattern (31 bp):
GAGCCTCCCCACTGGGGCGGCTCACCACGGG
Found at i:6209 original size:29 final size:29
Alignment explanation
Indices: 6154--6210 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
6144 CTTTTAATTA
* ****
6154 TTCTTGTGAAGTTAAATTTTTTTTGCTAC
1 TTCTCGTGAAGTTAAATTTGAGATGCTAC
6183 TTCTCGTGAAGTTAAATTTGAGATGCTA
1 TTCTCGTGAAGTTAAATTTGAGATGCTA
6211 TAAATGGCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.47
Consensus pattern (29 bp):
TTCTCGTGAAGTTAAATTTGAGATGCTAC
Found at i:6587 original size:2 final size:2
Alignment explanation
Indices: 6580--6614 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6570 CCTTATTTGC
6580 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
6615 CACATTCAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:33044 original size:2 final size:2
Alignment explanation
Indices: 33037--33082 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
33027 ACATACATAC
* *
33037 AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33079 AT AT
1 AT AT
33083 GCCTCTTGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33054 original size:22 final size:22
Alignment explanation
Indices: 33029--33075 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
33019 ACATACATAC
33029 ATACATACATATATATATATAT
1 ATACATACATATATATATATAT
33051 ATACATACATATATATATATAT
1 ATACATACATATATATATATAT
33073 ATA
1 ATA
33076 TATATATGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
ATACATACATATATATATATAT
Found at i:38901 original size:19 final size:19
Alignment explanation
Indices: 38877--38918 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
38867 TGGTCCGGGT
38877 CGTGCGCGACCCATGATCG
1 CGTGCGCGACCCATGATCG
38896 CGT--GCGACCCATGATCG
1 CGTGCGCGACCCATGATCG
38913 CGTGCG
1 CGTGCG
38919 ACCCGGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 17 0.81
19 4 0.19
ACGTcount: A:0.14, C:0.36, G:0.33, T:0.17
Consensus pattern (19 bp):
CGTGCGCGACCCATGATCG
Found at i:38904 original size:17 final size:17
Alignment explanation
Indices: 38882--38922 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
38872 CGGGTCGTGC
38882 GCGACCCATGATCGCGT
1 GCGACCCATGATCGCGT
38899 GCGACCCATGATCGCGT
1 GCGACCCATGATCGCGT
38916 GCGACCC
1 GCGACCC
38923 GGACCATGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.17, C:0.39, G:0.29, T:0.15
Consensus pattern (17 bp):
GCGACCCATGATCGCGT
Found at i:54716 original size:3 final size:3
Alignment explanation
Indices: 54710--54746 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
54700 TTATTATATT
54710 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54747 AATGCAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55598 original size:20 final size:21
Alignment explanation
Indices: 55570--55612 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
55560 AAAATAAAAT
* *
55570 AAAAGTACCAATTTTA-GATA
1 AAAACTACCAATTATAGGATA
55590 AAAACTACCAATTATAGGATA
1 AAAACTACCAATTATAGGATA
55611 AA
1 AA
55613 TATAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (21 bp):
AAAACTACCAATTATAGGATA
Found at i:56196 original size:23 final size:23
Alignment explanation
Indices: 56147--56190 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56137 ATTTCTTCTT
* *
56147 TTTTCTTTCTGTTTTCCTTTTAA
1 TTTTCGTTCTGTCTTCCTTTTAA
*
56170 TTTTCGTTCTGTCTTCGTTTT
1 TTTTCGTTCTGTCTTCCTTTT
56191 TGTTTTTGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.05, C:0.18, G:0.09, T:0.68
Consensus pattern (23 bp):
TTTTCGTTCTGTCTTCCTTTTAA
Found at i:67324 original size:2 final size:2
Alignment explanation
Indices: 67317--67347 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
67307 TTCCACGATG
67317 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67348 TGAAGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67337 original size:13 final size:13
Alignment explanation
Indices: 67319--67344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67309 CCACGATGAT
67319 ATATATATATATA
1 ATATATATATATA
67332 ATATATATATATA
1 ATATATATATATA
67345 TATTGAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:67337 original size:15 final size:15
Alignment explanation
Indices: 67317--67346 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
67307 TTCCACGATG
67317 ATATATATATATATA
1 ATATATATATATATA
67332 ATATATATATATATA
1 ATATATATATATATA
67347 TTGAAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Done.