Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006392.1 Corchorus capsularis cultivar CVL-1 contig06413, 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: 4383
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Found at i:1644 original size:6 final size:6
Alignment explanation
Indices: 1621--1685 Score: 64
Period size: 6 Copynumber: 10.8 Consensus size: 6
1611 ACAAAACAAA
* *
1621 AAAAAG AAGAAG AGAAAAG AAAAAC AAAACA- AACAAA- AAAAAG -AAAAG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAA-AG AA-AAAG AAAAAG AAAAAG
1669 AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAA
1686 AAGAAAGGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
5 8 0.16
6 35 0.69
7 8 0.16
ACGTcount: A:0.82, C:0.05, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1686 original size:42 final size:42
Alignment explanation
Indices: 1604--1685 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1594 AAGGTTCCAA
*
1604 AAAAAAAACAAAACAAAAAAAAGAAGAAGAGAAAAGAAAAAC
1 AAAAAAAACAAAACAAAAAAAAGAAAAAGAGAAAAGAAAAAC
*
1646 AAAACAAACAAAA-AAAAGAAAAGAAAAAGA-AAAAGAAAAA
1 AAAAAAAACAAAACAAAA-AAAAGAAAAAGAGAAAAGAAAAA
1686 AAGAAAGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 14 0.38
42 23 0.62
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (42 bp):
AAAAAAAACAAAACAAAAAAAAGAAAAAGAGAAAAGAAAAAC
Found at i:1687 original size:29 final size:29
Alignment explanation
Indices: 1602--1692 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 29
1592 TAAAGGTTCC
*
1602 AAAAAAAAAACAAAACAAAAAAAAGAAGAAGAG
1 AAAAGAAAAACAAAAC-AAAAAAA-AA-AA-AG
*
1635 AAAAGAAAAACAAAACAAACAAAAAAAAG
1 AAAAGAAAAACAAAACAAAAAAAAAAAAG
* *
1664 AAAAGAAAAAGAAAA-AGAAAAAAAGAAAG
1 AAAAGAAAAACAAAACA-AAAAAAAAAAAG
1693 GAATAAAAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 26 0.50
30 2 0.04
31 2 0.04
32 6 0.12
33 15 0.29
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (29 bp):
AAAAGAAAAACAAAACAAAAAAAAAAAAG
Found at i:2631 original size:35 final size:35
Alignment explanation
Indices: 2585--2738 Score: 220
Period size: 35 Copynumber: 4.4 Consensus size: 35
2575 TTTCGAAGAG
* *
2585 CAGAGTTGATCTCATTCTAAGAGGTTTCCAACGAT
1 CAGAGTTGATCTCATTCCAAGAAGTTTCCAACGAT
*
2620 CAGAGTTGATCTCATTCCAAGAAGTTTTCGAA-GAT
1 CAGAGTTGATCTCATTCCAAGAAG-TTTCCAACGAT
*
2655 CAGAGTTGATCTCATTCCAAGAAGTTTTCAACGAT
1 CAGAGTTGATCTCATTCCAAGAAGTTTCCAACGAT
* ** *
2690 CAGAGTTGATCTCATTTCAAGAAGTTTTTAATGAT
1 CAGAGTTGATCTCATTCCAAGAAGTTTCCAACGAT
2725 CAGAGTTGATCTCA
1 CAGAGTTGATCTCA
2739 AATTGATCCG
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
34 5 0.05
35 98 0.90
36 6 0.06
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (35 bp):
CAGAGTTGATCTCATTCCAAGAAGTTTCCAACGAT
Found at i:2648 original size:70 final size:70
Alignment explanation
Indices: 2571--2738 Score: 266
Period size: 70 Copynumber: 2.4 Consensus size: 70
2561 TGATCTTTCA
* * *
2571 AAGTTTTCGAAGAGCAGAGTTGATCTCATTCTAAGAGGTTTCCAACGATCAGAGTTGATCTCATT
1 AAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCTCATT
2636 CCAAG
66 CCAAG
*
2641 AAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTCATT
1 AAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCTCATT
*
2706 TCAAG
66 CCAAG
*
2711 AAGTTTT-TAATGATCAGAGTTGATCTCA
1 AAGTTTTCGAA-GATCAGAGTTGATCTCA
2739 AATTGATCCG
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
69 2 0.02
70 89 0.98
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (70 bp):
AAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCTCATT
CCAAG
Found at i:2783 original size:54 final size:54
Alignment explanation
Indices: 2701--2973 Score: 300
Period size: 54 Copynumber: 5.1 Consensus size: 54
2691 AGAGTTGATC
* * * * *
2701 TCATTTCAAGAAGTTTTTAATGATCAGAGTTGATCTCAAATTGATCCGGTGCGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
* * * * * *
2755 TCATTCCAAGGAGTTTTCGGTGGTCAGAGTTGACCCCTAATTGATCCGGTGTGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
* * * * * *
2809 TC-GTCTAAAAAATTTTCAGTGGTCAGAGTTGATCTCGAATGGA-CCGTTGCGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
* * * *
2861 TCATTTCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCCAATTGATACGGTGTGG
1 TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
* * *
2915 TC-GTCTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCAG
1 TCATTC-CAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
2969 TCATT
1 TCATT
2974 TCAGAAAGAT
Statistics
Matches: 175, Mismatches: 40, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
52 9 0.05
53 66 0.38
54 99 0.57
55 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
Found at i:2911 original size:106 final size:108
Alignment explanation
Indices: 2724--2989 Score: 369
Period size: 106 Copynumber: 2.5 Consensus size: 108
2714 TTTTTAATGA
* * * *
2724 TCAGAGTTGATCTCAAATTGATCCGGTGCGGTCATTCCAAGGAGTTTTCGGTGGTCAGAGTTGAC
1 TCAGAGTTGATCTCGAATTGATCCGGTGCGGTCATTTCAAGAAGTTTTCAGTGGTCAGAGTTGAC
*
2789 CCCTAATTGATCCGGTGTGGTCGTCT-AAAAAATTTTCAGTGG
66 CCCTAATTGATACGGTGTGGTCGTCTCAAAAAATTTTCAGTGG
* *
2831 TCAGAGTTGATCTCGAATGGA-CCGTTGCGGTCATTTCAAGAAGTTTTCAGTGGTCAGAGTTGAT
1 TCAGAGTTGATCTCGAATTGATCCGGTGCGGTCATTTCAAGAAGTTTTCAGTGGTCAGAGTTGA-
* * * *
2895 CTCC-AATTGATACGGTGTGGTCGTCTCAAGAAGTTTTCGGTGG
65 CCCCTAATTGATACGGTGTGGTCGTCTCAAAAAATTTTCAGTGG
* *
2938 TCAGAGTTGATCTCGAATTGATCCGGTGCAGTCATTTC-AGAAAGATTTCAGT
1 TCAGAGTTGATCTCGAATTGATCCGGTGCGGTCATTTCAAG-AAGTTTTCAGT
2990 AATAAAGGTT
Statistics
Matches: 140, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
106 59 0.42
107 57 0.41
108 24 0.17
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (108 bp):
TCAGAGTTGATCTCGAATTGATCCGGTGCGGTCATTTCAAGAAGTTTTCAGTGGTCAGAGTTGAC
CCCTAATTGATACGGTGTGGTCGTCTCAAAAAATTTTCAGTGG
Done.