Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014261.1 Corchorus capsularis cultivar CVL-1 contig14282, 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: 27101
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:8056 original size:21 final size:21
Alignment explanation
Indices: 8032--8087 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
8022 TGCTAAACAC
* *
8032 CGTTATGAAACGGTGATGCAG
1 CGTTATCAAACGGTGACGCAG
* *
8053 CGTTATCTAACGGTGACGCGG
1 CGTTATCAAACGGTGACGCAG
*
8074 CGTTATCTAACGGT
1 CGTTATCAAACGGT
8088 TTCGAAACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (21 bp):
CGTTATCAAACGGTGACGCAG
Found at i:12926 original size:145 final size:147
Alignment explanation
Indices: 12724--13017 Score: 502
Period size: 145 Copynumber: 2.0 Consensus size: 147
12714 GATATACAGT
* *
12724 TTCAAAATAAGAAAAAAAATTAGTAATTGCTAAAAACCCTCTTCAAAACAAAAACGAAAAGACTG
1 TTCAAAATAAG-AAAAAAATTAGTAATTGCTAAAAACCCTCTTCAAAAAAAAAACGAAAAGACTA
*
12789 CCATTCAAGTTTCAAACCAAACCGCCATTAACTTTTGTCGACTAAAAATTTGTCCTTAGAAAACT
65 CCATTCAAGTTTCAAACCAAACCACCATTAACTTTTGTCGACTAAAAATTTGTCCTTAGAAAACT
12854 CTGCAAACCTTAATCGTA
130 CTGCAAACCTTAATCGTA
12872 TTCAAAATAAG-AAAAAATTAGTAATTGCTAAAAA-CCTCTTCAAAAAAAAAACGAAAAGACTAC
1 TTCAAAATAAGAAAAAAATTAGTAATTGCTAAAAACCCTCTTCAAAAAAAAAACGAAAAGACTAC
* * * *
12935 CATTCAAGTTTTAAACCAAACCACCGTTAACTTTTTTCGACTAAAAATTTGTCCTTAGAAGACTC
66 CATTCAAGTTTCAAACCAAACCACCATTAACTTTTGTCGACTAAAAATTTGTCCTTAGAAAACTC
13000 TGCAAACCTTAATCGTA
131 TGCAAACCTTAATCGTA
13017 T
1 T
13018 GGTAAAATTC
Statistics
Matches: 139, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
145 105 0.76
146 23 0.17
148 11 0.08
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (147 bp):
TTCAAAATAAGAAAAAAATTAGTAATTGCTAAAAACCCTCTTCAAAAAAAAAACGAAAAGACTAC
CATTCAAGTTTCAAACCAAACCACCATTAACTTTTGTCGACTAAAAATTTGTCCTTAGAAAACTC
TGCAAACCTTAATCGTA
Found at i:20103 original size:13 final size:13
Alignment explanation
Indices: 20085--20125 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
20075 CTTTTTTTAT
20085 TATAATAATAATA
1 TATAATAATAATA
*
20098 TATAATTATAATA
1 TATAATAATAATA
20111 TATATTATAATAATA
1 TATA--ATAATAATA
20126 ATCGTAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.67
15 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAATAATAATA
Found at i:26764 original size:167 final size:165
Alignment explanation
Indices: 26378--26817 Score: 578
Period size: 167 Copynumber: 2.6 Consensus size: 165
26368 TGAGTCATTT
* *
26378 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACAAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** * *
26443 TTAAGTAATCTGCCAAGTA-GATAAAGACGAAAAAGATTAGTTTTCTAGCTCATCATCAATCCTT
65 TTAAGTAATCTGTCAAGTAGGA-AAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTT
* *
26507 GATGAGGATCTTTTATTAATTCCACTACTCTATTCAA
129 GATGAGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * * * * *
26544 GTCCATTAAGAAATGACCAAAAAAATTACTTATTTAATCCACTCAATAATCAAAAGTTAGGACAC
1 GTCAATTGAGAAATGA-CAAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
26609 TTAAGTAATATGTCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCTAAAAGCAAGCCTT
65 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTC-AAAAGCAAGCCTT
* *
26674 GGT-AGAGATCTTTTAGTAATTTCACTACTCTATTAAA
129 GATGAG-GATCTTTTAGTAATTCCACTACTCTATTAAA
*
26711 GTCAATTGAGAAATGACTAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACAAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
26776 TTAGGTAATCTGTCAAGTCGGAAAAGACGAAAAAAATTAGTT
65 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTT
26818 TTCTCGCTCC
Statistics
Matches: 234, Mismatches: 35, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
166 100 0.43
167 134 0.57
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACAAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGA
TGAGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:26957 original size:19 final size:17
Alignment explanation
Indices: 26916--26956 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
26906 TATAATAATA
26916 ATATATACTAATTCTTC
1 ATATATACTAATTCTTC
26933 ATATATACTAATTCTTC
1 ATATATACTAATTCTTC
*
26950 ATTTATA
1 ATATATA
26957 TTATATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATACTAATTCTTC
Done.