Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000129.1 Corchorus capsularis cultivar CVL-1 contig00129, 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: 6170
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:1536 original size:53 final size:52
Alignment explanation
Indices: 1438--1590 Score: 220
Period size: 53 Copynumber: 2.9 Consensus size: 52
1428 CATTTATAAG
*
1438 TCCCTAAACACAGAGGCAATTCTATATCAAAGTCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGC-A-TCTACATCAAAGTCCTCAAACACAAGGGTATTCA
*
1492 TCCTTAAACACAGAGGCACCTCT-C-TCAAAAGTCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGCA--TCTACATC-AAAGTCCTCAAACACAAGGGTATTCA
*
1545 TCCCTAAACACAGAGGCATTTACATCAAAGTCCTCAAACACAAGGG
1 TCCCTAAACACAGAGGCATCTACATCAAAGTCCTCAAACACAAGGG
1591 CATCTATATT
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
51 2 0.02
52 23 0.26
53 46 0.51
54 19 0.21
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (52 bp):
TCCCTAAACACAGAGGCATCTACATCAAAGTCCTCAAACACAAGGGTATTCA
Found at i:1586 original size:30 final size:28
Alignment explanation
Indices: 1545--1646 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 28
1535 AGGGTATTCA
1545 TCCCTAAACACAGAGGCATTTACATCAAAG
1 TCCC-AAACACAGAGGCATTTACAT-AAAG
* *
1575 TCCTCAAACACA-AGGGCATCTATATTAAAG
1 TCC-CAAACACAGA-GGCATTTACA-TAAAG
1605 TCCCTAAACACAGAGGCATCTATAC-TAAAG
1 TCCC-AAACACAGAGGCAT-T-TACATAAAG
1635 TCCCCAAACACA
1 T-CCCAAACACA
1647 TGTAACACAG
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
29 2 0.03
30 50 0.83
31 6 0.10
32 2 0.03
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (28 bp):
TCCCAAACACAGAGGCATTTACATAAAG
Found at i:1748 original size:31 final size:30
Alignment explanation
Indices: 1710--1814 Score: 140
Period size: 31 Copynumber: 3.5 Consensus size: 30
1700 ATGGGCGGCT
* *
1710 AAATGCTCAATTTGGTACTAAACCTTTGACG
1 AAATGCTCAATTTGATACTAAACCTTTCA-G
*
1741 AAATGCTCAATTTGATACTAAACC-TTCAA
1 AAATGCTCAATTTGATACTAAACCTTTCAG
1770 AAATGCTCAATTTGATACTAAACCTTTCAGG
1 AAATGCTCAATTTGATACTAAACCTTTCA-G
**
1801 ATCTGCTCAATTTG
1 AAATGCTCAATTTG
1815 GTACGATTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
29 24 0.36
30 7 0.11
31 35 0.53
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (30 bp):
AAATGCTCAATTTGATACTAAACCTTTCAG
Found at i:1783 original size:29 final size:30
Alignment explanation
Indices: 1710--1795 Score: 129
Period size: 29 Copynumber: 2.9 Consensus size: 30
1700 ATGGGCGGCT
* * *
1710 AAATGCTCAATTTGGTACTAAACCTTTGACG
1 AAATGCTCAATTTGATACTAAACC-TTCACA
1741 AAATGCTCAATTTGATACTAAACCTTCA-A
1 AAATGCTCAATTTGATACTAAACCTTCACA
1770 AAATGCTCAATTTGATACTAAACCTT
1 AAATGCTCAATTTGATACTAAACCTT
1796 TCAGGATCTG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 26 0.50
30 3 0.06
31 23 0.44
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (30 bp):
AAATGCTCAATTTGATACTAAACCTTCACA
Found at i:2063 original size:27 final size:27
Alignment explanation
Indices: 2033--2100 Score: 73
Period size: 32 Copynumber: 2.3 Consensus size: 27
2023 CTCTTTCAAC
*
2033 TTGAAAAATAATTTTTCTTCTCTTTGA
1 TTGAAAAATAATTTTCCTTCTCTTTGA
2060 TTGAAAAATCTGATAATTTTCCTTCTCTTTGA
1 TTG-AAAA----ATAATTTTCCTTCTCTTTGA
*
2092 TTAAAAAAT
1 TTGAAAAAT
2101 CTGTGGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
27 5 0.15
28 4 0.12
31 4 0.12
32 21 0.62
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (27 bp):
TTGAAAAATAATTTTCCTTCTCTTTGA
Found at i:2098 original size:31 final size:32
Alignment explanation
Indices: 2040--2103 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2030 AACTTGAAAA
* *
2040 ATAATTTTTCTTCTCTTTGATTGAAAAATCTG
1 ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
2072 ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
1 ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
2104 TGGGGGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (32 bp):
ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
Found at i:2912 original size:78 final size:78
Alignment explanation
Indices: 2779--2933 Score: 247
Period size: 78 Copynumber: 2.0 Consensus size: 78
2769 ATGTTGAAAT
* * *
2779 CATTAGTTAAGTATTGCTGTTATAAATAAAAGTTGAATTTTAATGACATCGTGTGTCTCCCTTCT
1 CATTAGTTAAGTATTGCTGTTATAAATAAAAGCTGAATTTTAATGACAACGTGTGTCTCCATTCT
2844 GCTAATTTTAAAG
66 GCTAATTTTAAAG
* * * *
2857 CATTAGTTAAGTATTGTTGTTATAAGTAAAAGCTGAATTTTAATGACAACTTGTGTCTTCATTCT
1 CATTAGTTAAGTATTGCTGTTATAAATAAAAGCTGAATTTTAATGACAACGTGTGTCTCCATTCT
2922 GCTAATTTTAAA
66 GCTAATTTTAAA
2934 CAGATTAAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (78 bp):
CATTAGTTAAGTATTGCTGTTATAAATAAAAGCTGAATTTTAATGACAACGTGTGTCTCCATTCT
GCTAATTTTAAAG
Found at i:4035 original size:24 final size:24
Alignment explanation
Indices: 4003--4049 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3993 CAGCAGCTCC
**
4003 TAAATCTTCATTATGGTGACCTCT
1 TAAATCTTCATTATCCTGACCTCT
4027 TAAATCTTCATTATCCTGACCTC
1 TAAATCTTCATTATCCTGACCTC
4050 CACCTTGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (24 bp):
TAAATCTTCATTATCCTGACCTCT
Found at i:5523 original size:29 final size:30
Alignment explanation
Indices: 5465--5569 Score: 122
Period size: 31 Copynumber: 3.5 Consensus size: 30
5455 GAAATCGTAC
* * *
5465 CAAATTGAGCAGATCCTGAAAGGTTTAGTAT
1 CAAATTGAGCA-TTTCTCAAAGGTTTAGTAT
**
5496 CAAATTGAGCATTT-TTGAAGGTTTAGTAT
1 CAAATTGAGCATTTCTCAAAGGTTTAGTAT
* *
5525 CAAATTGAGCATTTCGTCAAAGGTTTGGTAC
1 CAAATTGAGCATTTC-TCAAAGGTTTAGTAT
5556 CAAATTGAGCATTT
1 CAAATTGAGCATTT
5570 AGCCTTTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.42
30 1 0.02
31 36 0.56
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34
Consensus pattern (30 bp):
CAAATTGAGCATTTCTCAAAGGTTTAGTAT
Done.