Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001256.1 Corchorus capsularis cultivar CVL-1 contig01256, 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: 2258
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:22 original size:6 final size:6
Alignment explanation
Indices: 1--62 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
* *
1 AAAAA- AAAAGAG AAAAAG AAAAAG AAGAAG AAGAAG AAAAA- AAAAGAG
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG
* *
49 AAAGAG AAAGAG AA
1 AAAAAG AAAAAG AA
63 GCTCTTGGGT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
5 8 0.16
6 35 0.70
7 7 0.14
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1083 original size:35 final size:33
Alignment explanation
Indices: 1043--1131 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 33
1033 TTGATTAACC
*
1043 CAGGGCGGTCTTCATTCAGTAAATTTCAATTGATT
1 CAGGGCGGTCTTC-TTCAGT-AATTTCAATTGACT
*
1078 CAGGGCGGTCTCTCTTCAATAATTTCAATTGACT
1 CAGGGCGGTCT-TCTTCAGTAATTTCAATTGACT
* *
1112 CAAGGCAGTCTTTCTTCAGT
1 CAGGGCGGTC-TTCTTCAGT
1132 TGCTTTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 28 0.60
35 17 0.36
36 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (33 bp):
CAGGGCGGTCTTCTTCAGTAATTTCAATTGACT
Found at i:1608 original size:71 final size:70
Alignment explanation
Indices: 1532--1883 Score: 330
Period size: 71 Copynumber: 4.9 Consensus size: 70
1522 GTTCAGTTCG
* * * *
1532 GAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTTAGTTGGCCCAGGGTGGTCTTTCTTTAGGTT
1 GAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCAGTTGACCCAGGGTGGTCTTTCTTCA-GTT
1597 GAGTCA
65 GAGTCA
* ** *
1603 GAATGATCGAGGGTGGTTGTTCTTCAGTTCATTTCAACTGACCCAGGGTGGTCTTTCTTCAATTT
1 GAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCAGTTGACCCAGGGTGGTCTTTCTTC-AGTT
*
1668 GTGTCA
65 GAGTCA
* * * * * * *
1674 GAATGATCGAGGGTGGTTGTTCTTCAGTTCAGTCCGGAATGATCGAGGGTGGT-TGTTCTTCAGT
1 GAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCAG-TTGACCCAGGGTGGTCT-TTCTTCAGT
* * *
1738 TCAATCCG
64 TGAGT-CA
* * * *
1746 GAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGTTAACCCAAGGTGGTCTTTCTTCAGTTT
1 GAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTG
*
1811 ACGTCG
66 A-GTCA
* * * * * *
1817 GAACGATCGAGGGTGGTCGCTTTTTCATTTCAAGTTT-GGAATGATCCAGGGTGGTCTTTCTTCA
1 GAATGATCGAGGGTGGTCG-TTCTTCAGTTC-A-TTTCAG-TTGACCCAGGGTGGTCTTTCTTCA
1881 GTT
62 GTT
1884 ACTTATTTTA
Statistics
Matches: 229, Mismatches: 42, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
71 139 0.61
72 62 0.27
73 2 0.01
74 26 0.11
ACGTcount: A:0.18, C:0.17, G:0.28, T:0.37
Consensus pattern (70 bp):
GAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTG
AGTCA
Found at i:1619 original size:36 final size:35
Alignment explanation
Indices: 1576--1774 Score: 197
Period size: 36 Copynumber: 5.6 Consensus size: 35
1566 TAGTTGGCCC
* *
1576 AGGGTGGTCT-TTCTTTAGGTTGAGTCAGAATGATCG
1 AGGGTGGT-TGTTCTTCA-GTTCAGTCAGAATGATCG
* * * *
1612 AGGGTGGTTGTTCTTCAGTTCATTTCA-ACTGACCC
1 AGGGTGGTTGTTCTTCAGTTCA-GTCAGAATGATCG
* **
1647 AGGGTGGTCT-TTCTTCAATTTGTGTCAGAATGATCG
1 AGGGTGGT-TGTTCTTC-AGTTCAGTCAGAATGATCG
*
1683 AGGGTGGTTGTTCTTCAGTTCAGTCCGGAATGATCG
1 AGGGTGGTTGTTCTTCAGTTCAGT-CAGAATGATCG
* *
1719 AGGGTGGTTGTTCTTCAGTTCAATCCGGAATGATCG
1 AGGGTGGTTGTTCTTCAGTTCAGT-CAGAATGATCG
*
1755 AGGGTGGTCGTTCTTCAGTT
1 AGGGTGGTTGTTCTTCAGTT
1775 TATTTCAGTT
Statistics
Matches: 137, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
35 33 0.24
36 104 0.76
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (35 bp):
AGGGTGGTTGTTCTTCAGTTCAGTCAGAATGATCG
Found at i:1761 original size:143 final size:145
Alignment explanation
Indices: 1574--1883 Score: 385
Period size: 143 Copynumber: 2.2 Consensus size: 145
1564 TTTAGTTGGC
* * * * *
1574 CCAGGGTGGTCTTTCTTTAGGTTGAGT-CAGAATGATCGAGGGTGGTTGTTCTTCAGTTCATTTC
1 CCAGGGTGGTCTTTCTTCA-GTTCAATCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTC
* * ** * *
1638 AACTGACCCAGGGTGGTCTTTCTTCAATTTGTGTCAGAATGATCGAGGGTGGTTG-TTCTTCAGT
65 AACTAACCCAAGGTGGTCTTTCTTCAATTTACGTCAGAACGATCGAGGGTGGTCGCTTCTTCAGT
1702 TC-AGTCCGGAATGAT
130 TCAAGTCCGGAATGAT
* *
1717 CGAGGGTGGT-TGTTCTTCAGTTCAATCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTC
1 CCAGGGTGGTCT-TTCTTCAGTTCAATCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTC
** * * * *
1781 AGTTAACCCAAGGTGGTCTTTCTTCAGTTTACGTCGGAACGATCGAGGGTGGTCGCTTTTTCATT
65 AACTAACCCAAGGTGGTCTTTCTTCAATTTACGTCAGAACGATCGAGGGTGGTCGCTTCTTCAGT
**
1846 TCAAGTTTGGAATGAT
130 TCAAGTCCGGAATGAT
1862 CCAGGGTGGTCTTTCTTCAGTT
1 CCAGGGTGGTCTTTCTTCAGTT
1884 ACTTATTTTA
Statistics
Matches: 140, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
142 6 0.04
143 94 0.67
144 9 0.06
145 30 0.21
146 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.28, T:0.37
Consensus pattern (145 bp):
CCAGGGTGGTCTTTCTTCAGTTCAATCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCA
ACTAACCCAAGGTGGTCTTTCTTCAATTTACGTCAGAACGATCGAGGGTGGTCGCTTCTTCAGTT
CAAGTCCGGAATGAT
Done.