Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015364.1 Corchorus capsularis cultivar CVL-1 contig15385, 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: 7306
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1981 original size:31 final size:30
Alignment explanation
Indices: 1883--1989 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 30
1873 TTTGACAAGG
* * * *
1883 AAGACGCCGCTATTTTGCGGTGTTTGAAAAAG
1 AAGACGCCGCTATTTTGCGGCGTCT--AGAAC
* * ***
1915 AAGACGCCGCTAATTCGCGGCGTCTTAGTGT
1 AAGACGCCGCTATTTTGCGGCGTC-TAGAAC
*
1946 AAGACGCCGCTATTTTGCGGCGTCTAGCACC
1 AAGACGCCGCTATTTTGCGGCGTCTAG-AAC
1977 AAGACGCCGCTAT
1 AAGACGCCGCTAT
1990 ATTTTATAGC
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
30 3 0.05
31 36 0.60
32 20 0.33
33 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (30 bp):
AAGACGCCGCTATTTTGCGGCGTCTAGAAC
Found at i:2148 original size:226 final size:226
Alignment explanation
Indices: 1751--2165 Score: 620
Period size: 226 Copynumber: 1.8 Consensus size: 226
1741 GCATACAGAA
*
1751 AAGACGCCGCTATATATTATATGCGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAATTT
1 AAGACGCCGCTATATATTATATGCGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAAATT
1816 TTCCCTCCAACAAAAAGGAAAAAAAAATCCCTCCCTCCATATATTAAAATAGCGGCGTTTGACAA
66 TTCCCTCCAACAAAAAGGAAAAAAAAATCCCTCCCTCCATATATTAAAATAGCGGCGTTTGACAA
* * *
1881 GGAAGACGCCGCTATTTTGCGGTGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCTTAGTGT
131 AGAAGACGCCGCTATTTCGCGGCGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCTTAGTGT
1946 AAGACGCCGCTATTTTGCGGCGTCTAGCACC
196 AAGACGCCGCTATTTTGCGGCGTCTAGCACC
* * * * * * * *
1977 AAGACGCCGCTATATTTTATA-GCCGTGTAGTTGTAAATTTTTCTTTGTTTTAGGGGTGGGAAAT
1 AAGACGCCGCTATATATTATATG-CGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAAAT
* *
2041 TTTCCTTCCAACAAAAAGGAAAAAAAAAATCTCTCCCTCCATATATTAAAACT-GCGGCGTTTGA
65 TTTCCCTCCAACAAAAAGG-AAAAAAAAATCCCTCCCTCCATATATTAAAA-TAGCGGCGTTTGA
* * * *
2105 CAAAGAAGACGCCGCTATTTCGCGGCGTTTG-TAAAGTAGACGCCGGTATTTCGCGGCGTCT
128 CAAAGAAGACGCCGCTATTTCGCGGCGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCT
2166 AGCACCAAGA
Statistics
Matches: 168, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
225 1 0.01
226 97 0.58
227 69 0.41
228 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (226 bp):
AAGACGCCGCTATATATTATATGCGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAAATT
TTCCCTCCAACAAAAAGGAAAAAAAAATCCCTCCCTCCATATATTAAAATAGCGGCGTTTGACAA
AGAAGACGCCGCTATTTCGCGGCGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCTTAGTGT
AAGACGCCGCTATTTTGCGGCGTCTAGCACC
Found at i:2149 original size:31 final size:32
Alignment explanation
Indices: 2094--2163 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
2084 TATTAAAACT
2094 GCGGCGTTTGACAAAGAAGACGCCGCTATTTC
1 GCGGCGTTTGACAAAGAAGACGCCGCTATTTC
* * *
2126 GCGGCGTTTG-TAAAGTAGACGCCGGTATTTC
1 GCGGCGTTTGACAAAGAAGACGCCGCTATTTC
2157 GCGGCGT
1 GCGGCGT
2164 CTAGCACCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 25 0.71
32 10 0.29
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (32 bp):
GCGGCGTTTGACAAAGAAGACGCCGCTATTTC
Found at i:2178 original size:226 final size:226
Alignment explanation
Indices: 1690--2184 Score: 617
Period size: 226 Copynumber: 2.2 Consensus size: 226
1680 CTTACAAAAC
* * * * * * **
1690 AGACGCCGCTAAATAGTGGCGTCTTA-ACAAAAGACGCCACTATTTAGCGGCG-CATA-CAGAAA
1 AGACGCCGCTAATTCGCGGCGTCTTAGAC-CAAGACGCCGCTATTTTGCGGCGTC-TAGCA-CCA
*
1752 AGACGCCGCTATATATTATATGCGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAATTTT
63 AGACGCCGCTATATATTATATGCGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAAATTT
*
1817 TCCCTCCAACAAAAAGGAAAAAAAAATCCCTCCCTCCATATATTAAAATAGCGGCGTTTGACAAG
128 TCCCTCCAACAAAAAGGAAAAAAAAATCCCTCCCTCCATATATTAAAATAGCGGCGTTTGACAAA
* *
1882 GAAGACGCCGCTATTTTGCGGTGTTTGAAAAAGA
193 GAAGACGCCGCTATTTCGCGGCGTTTGAAAAAGA
***
1916 AGACGCCGCTAATTCGCGGCGTCTTAGTGTAAGACGCCGCTATTTTGCGGCGTCTAGCACCAAGA
1 AGACGCCGCTAATTCGCGGCGTCTTAGACCAAGACGCCGCTATTTTGCGGCGTCTAGCACCAAGA
* * * * * * * *
1981 CGCCGCTATATTTTATA-GCCGTGTAGTTGTAAATTTTTCTTTGTTTTAGGGGTGGGAAATTTTC
66 CGCCGCTATATATTATATG-CGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAAATTTTC
* *
2045 CTTCCAACAAAAAGGAAAAAAAAAATCTCTCCCTCCATATATTAAAACT-GCGGCGTTTGACAAA
130 CCTCCAACAAAAAGG-AAAAAAAAATCCCTCCCTCCATATATTAAAA-TAGCGGCGTTTGACAAA
* *
2109 GAAGACGCCGCTATTTCGCGGCGTTTG-TAAAGT
193 GAAGACGCCGCTATTTCGCGGCGTTTGAAAAAGA
* *
2142 AGACGCCGGTATTTCGCGGCGTC-TAGCACCAAGACGCCGCTAT
1 AGACGCCGCTAATTCGCGGCGTCTTAG-ACCAAGACGCCGCTAT
2185 ATTTTATAAC
Statistics
Matches: 231, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
225 4 0.02
226 154 0.67
227 72 0.31
228 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (226 bp):
AGACGCCGCTAATTCGCGGCGTCTTAGACCAAGACGCCGCTATTTTGCGGCGTCTAGCACCAAGA
CGCCGCTATATATTATATGCGTGTAATTGCAAAATTTACTTTGTTTCAGAGGAGGGAAATTTTCC
CTCCAACAAAAAGGAAAAAAAAATCCCTCCCTCCATATATTAAAATAGCGGCGTTTGACAAAGAA
GACGCCGCTATTTCGCGGCGTTTGAAAAAGA
Found at i:2261 original size:195 final size:194
Alignment explanation
Indices: 1898--2282 Score: 603
Period size: 195 Copynumber: 2.0 Consensus size: 194
1888 GCCGCTATTT
* ** *
1898 TGCGGTGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCTTAGTGTAAGACGCCGCTATTTTG
1 TGCGGCGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCTTAAAGTAAGACGCCGCTATTTCG
*
1963 CGGCGTCTAGCACCAAGACGCCGCTATATTTTATAGCCGTGTAGTTGTAAATTTTTCTTTGTTTT
66 CGGCGTCTAGCACCAAGACGCCGCTATATTTTATAACCGTGTAGTTGTAAATTTTTCTTTGTTTT
* * *
2028 AGGGGTGGGAAATTTTCCTTCCAACAAAAAGGAAAAAAAAAATCTCTCCCTCCATATATTAAAAC
131 AGGGGAGGGAAATTTTCCCTCCAACAAAAAGG-AAAAAAAAATCTCTCCCTCCACATATTAAAAC
* * * *
2093 TGCGGCGTTTGACAAAGAAGACGCCGCTATTTCGCGGCGTTTGTAAAGT-AGACGCCGGTATTTC
1 TGCGGCGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCT-TAAAGTAAGACGCCGCTATTTC
*
2157 GCGGCGTCTAGCACCAAGACGCCGCTATATTTTATAACCGTGTAGTTGTATATTTTTCTTTGTTT
65 GCGGCGTCTAGCACCAAGACGCCGCTATATTTTATAACCGTGTAGTTGTAAATTTTTCTTTGTTT
* *
2222 TAGGGGAGGGAATTTTTCCCTCCAA-AAAAAGGAAAAAAAAATCTCTCCCTGCACATATTAA
130 TAGGGGAGGGAAATTTTCCCTCCAACAAAAAGGAAAAAAAAATCTCTCCCTCCACATATTAA
2283 TATGGCGGCG
Statistics
Matches: 174, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
193 27 0.16
194 7 0.04
195 136 0.78
196 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (194 bp):
TGCGGCGTTTGAAAAAGAAGACGCCGCTAATTCGCGGCGTCTTAAAGTAAGACGCCGCTATTTCG
CGGCGTCTAGCACCAAGACGCCGCTATATTTTATAACCGTGTAGTTGTAAATTTTTCTTTGTTTT
AGGGGAGGGAAATTTTCCCTCCAACAAAAAGGAAAAAAAAATCTCTCCCTCCACATATTAAAAC
Found at i:5253 original size:19 final size:18
Alignment explanation
Indices: 5219--5256 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5209 CTTGAATTAT
5219 TTCTTCAATGATCTTCAA
1 TTCTTCAATGATCTTCAA
*
5237 TTCTTCAAATTATCTTCAA
1 TTCTTC-AATGATCTTCAA
5256 T
1 T
5257 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (18 bp):
TTCTTCAATGATCTTCAA
Done.