Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014002.1 Corchorus capsularis cultivar CVL-1 contig14023, 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: 8234
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2066 original size:17 final size:17
Alignment explanation
Indices: 2044--2077 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2034 AGCATCAGTA
2044 CTTTAGATTTGACTTAT
1 CTTTAGATTTGACTTAT
*
2061 CTTTAGATTTGATTTAT
1 CTTTAGATTTGACTTAT
2078 TCAGATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (17 bp):
CTTTAGATTTGACTTAT
Found at i:5582 original size:92 final size:92
Alignment explanation
Indices: 5471--5660 Score: 344
Period size: 92 Copynumber: 2.1 Consensus size: 92
5461 TTGGGCCTTA
5471 GTCTTACTTAAATTGGTTACTTTATTGCATTTGGGATGTCAATTTATGCATATGGGCTTTCAGTT
1 GTCTTACTTAAATTGGTTACTTTATTGCATTTGGGATGTCAATTTATGCATATGGGCTTTCAGTT
* *
5536 TTCTTCTATGCATTTGTGTCTTATTAG
66 TTATTCTATCCATTTGTGTCTTATTAG
*
5563 GTCTTACTTAAATTGGTTACTTTATTGCATTTGGGATGTCAATTTATGCATATGGGCTTTTAGTT
1 GTCTTACTTAAATTGGTTACTTTATTGCATTTGGGATGTCAATTTATGCATATGGGCTTTCAGTT
5628 TTATTCTATCCATTTGTGTCTTATTAG
66 TTATTCTATCCATTTGTGTCTTATTAG
*
5655 GGCTTA
1 GTCTTA
5661 GTCCAATTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (92 bp):
GTCTTACTTAAATTGGTTACTTTATTGCATTTGGGATGTCAATTTATGCATATGGGCTTTCAGTT
TTATTCTATCCATTTGTGTCTTATTAG
Found at i:8020 original size:198 final size:198
Alignment explanation
Indices: 7575--8232 Score: 830
Period size: 199 Copynumber: 3.3 Consensus size: 198
7565 AATCATTTTA
* *
7575 TATAATTTTTCTTATAGGATTATTATACAATACACTTTTCAGTGTAAATTTTACACTCCATAAGC
1 TATAATTTTTCTTATAGGATTATTATAC-A-ACACTTGTCAGTGTAAATTTTAGACTCCATAAGC
* * *
7640 GGGTTAAGAATTTGACACATACCCCATTTCATAATCAATTAAATATTGAATATTAATACATATTC
64 GGGTTAAGAAGTTGACACATACCACATTTCATAATCAATTAAATATTTAATATTAATACATATTC
* * * * * **
7705 CATAAGGGGACACATGTTAACCCTTAAACCCTGCACGTGCAATCTGCTAAATTCGGTTGACGGTG
129 CCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTTTGCTAAAATCCATTGACGGTG
7770 TATAG
194 TATAG
*
7775 TATAATTTTTCTTATAGGATTATTATACAATCCAC-TGTCAGTGTAAATTTTGGACTCCATAAGC
1 TATAATTTTTCTTATAGGATTATTATACAA--CACTTGTCAGTGTAAATTTTAGACTCCATAAGC
* * * *
7839 GAGTTGAGAAGTTGACATATACCACATTTCATAATTAATTAAATATTTAATATTAATACATATTC
64 GGGTTAAGAAGTTGACACATACCACATTTCATAATCAATTAAATATTTAATATTAATACATATTC
* * * * *
7904 CCTAA-GGGACATATGTCAACCCCTAAACCCCGCACGTGCAGTTTGCTAAAATCCACTGACGGTT
129 CCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTTTGCTAAAATCCATTGACGGTG
7968 TATTA-
194 TA-TAG
* * *
7973 TATAATTTTTTTTATAAGATTATTATACAACACGTTGTCAGTGTAAA-TTTAGACTCTATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAACAC-TTGTCAGTGTAAATTTTAGACTCCATAAGCG
* * * *
8037 GGTTAAGAAGTTGACACATACCTCATTTCATCATCAA-TAAATCTATAATAATAATAATACATAT
65 GGTTAAGAAGTTGACACATACCACATTTCATAATCAATTAAA--TAT-TTAATATTAATACATAT
* *
8101 TCCCTAAGGGGACACATGTCAA-CCTTAAACCCTGCACGTGCAGTTTGCTAAACTCCATTTACGG
127 TCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTTTGCTAAAATCCATTGACGG
*
8165 CGTATAG
192 TGTATAG
* * *
8172 TATAA-TTTTCTTATAGGATTATCATACAATAAAC-TGTCCGTGTAAATTTT-GAACTCCATAA
1 TATAATTTTTCTTATAGGATTATTATAC-A-ACACTTGTCAGTGTAAATTTTAG-ACTCCATAA
8233 AC
Statistics
Matches: 396, Mismatches: 48, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
196 7 0.02
197 46 0.12
198 127 0.32
199 169 0.43
200 47 0.12
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (198 bp):
TATAATTTTTCTTATAGGATTATTATACAACACTTGTCAGTGTAAATTTTAGACTCCATAAGCGG
GTTAAGAAGTTGACACATACCACATTTCATAATCAATTAAATATTTAATATTAATACATATTCCC
TAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTTTGCTAAAATCCATTGACGGTGTA
TAG
Done.