Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017869.1 Corchorus olitorius cultivar O-4 contig17902, 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: 38949
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1062 original size:22 final size:22
Alignment explanation
Indices: 1023--1064 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1013 TTTTTTTATC
**
1023 TATCTAAGCATTTTTTTTGAAT
1 TATCTAAGCATTAATTTTGAAT
1045 TATCTAAGCATTAATTTTGA
1 TATCTAAGCATTAATTTTGA
1065 TTCATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (22 bp):
TATCTAAGCATTAATTTTGAAT
Found at i:7881 original size:18 final size:18
Alignment explanation
Indices: 7858--7893 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7848 CCTTTTCCTG
*
7858 TTTCCCTTTGTTCAACTC
1 TTTCCCTCTGTTCAACTC
*
7876 TTTCCCTCTGTTGAACTC
1 TTTCCCTCTGTTCAACTC
7894 CATTAGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.33, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTCCCTCTGTTCAACTC
Found at i:9535 original size:102 final size:102
Alignment explanation
Indices: 9368--9753 Score: 524
Period size: 103 Copynumber: 3.7 Consensus size: 102
9358 ATATAATTCG
*
9368 ACTAAAATTCTAAAATTCTCTAAAAATAAATATTTTAAATTC-AGACATACCCTTACAATATTTT
1 ACTAAAATTCTAAAA--CTCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTT
9432 TTATTTAATTTGGGGCTAAACCTAAATGATTTGGAATTA
64 TTATTTAATTTGGGGCTAAACCTAAATGATTTGGAATTA
*
9471 GACTAAAATTCTAAAACCCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTT
1 -ACTAAAATTCTAAAACTCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTT
*
9536 TATTTAATTTGGGGCTAAACCTAAGTGATTTGGAATTCA
65 TATTTAATTTGGGGCTAAACCTAAATGATTTGGAATT-A
* * * * *
9575 ACTAAAATTATAAAACTCTAGAAATAAATATTTTAAATTCAAGATATATCCTTGAAATATTTTTT
1 ACTAAAATTCTAAAACTCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTT
* * * * * *
9640 ATATAATTTGGAGTTAAACCTAAATGATTGGGACTCA
66 ATTTAATTTGGGGCTAAACCTAAATGATTTGGAATTA
* ** * *
9677 ATTAAAATTCTAAAACAATAAAAATAAATATTTTAAATTCAATACATA-CTTATAAAATATTTTT
1 ACTAAAATTCTAAAACTCTAAAAATAAATATTTTAAATTCAAGACATACCCT-TAAAATATTTTT
9741 TATATATAATTTG
65 TAT-T-TAATTTG
9754 AGTTAAACCA
Statistics
Matches: 251, Mismatches: 26, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
101 2 0.01
102 80 0.32
103 146 0.58
104 23 0.09
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38
Consensus pattern (102 bp):
ACTAAAATTCTAAAACTCTAAAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTT
ATTTAATTTGGGGCTAAACCTAAATGATTTGGAATTA
Found at i:9743 original size:205 final size:207
Alignment explanation
Indices: 9362--9773 Score: 566
Period size: 205 Copynumber: 2.0 Consensus size: 207
9352 TAATGAATAT
* *
9362 AATTCGACTAAAATTCTAAAATTCTCTAAAAATAAATATTTTAAATTCAGACATACCCTTACAAT
1 AATTCAACTAAAATTATAAAA-TCTCTAAAAATAAATATTTTAAATTCAGACATACCCTTACAAT
* * * * **
9427 ATTTTTTATTTAATTTGGGGCTAAACCTAAATGATTTGGAATTAGACTAAAATTCTAAAACCCTA
65 ATTTTTTATATAATTTGGAGCTAAACCTAAATGATTGGGAATCAGACTAAAATTCTAAAACAATA
*
9492 AAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTAT-T-TAATTTGGGGCTAAA
130 AAAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTATATATAATTT-GAGCTAAA
*
9555 CCTAAGTGATTTGG
194 CCAAAGTGATTTGG
* * *
9569 AATTCAACTAAAATTATAAAA-CTCTAGAAATAAATATTTTAAATTCAAGATATATCCTTGA-AA
1 AATTCAACTAAAATTATAAAATCTCTAAAAATAAATATTTTAAATTC-AGACATACCCTT-ACAA
* * *
9632 TATTTTTTATATAATTTGGAGTTAAACCTAAATGATTGGGACTCA-ATTAAAATTCTAAAACAAT
64 TATTTTTTATATAATTTGGAGCTAAACCTAAATGATTGGGAATCAGACTAAAATTCTAAAACAAT
* * *
9696 AAAAATAAATATTTTAAATTCAATACATA-CTTATAAAATATTTTTTATATATAATTTGAGTTAA
129 AAAAATAAATATTTTAAATTCAAGACATACCCT-TAAAATATTTTTTATATATAATTTGAGCTAA
9760 ACCAAAGTGATTTG
193 ACCAAAGTGATTTG
9774 TACCTCAAAG
Statistics
Matches: 181, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
204 2 0.01
205 83 0.46
206 70 0.39
207 26 0.14
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (207 bp):
AATTCAACTAAAATTATAAAATCTCTAAAAATAAATATTTTAAATTCAGACATACCCTTACAATA
TTTTTTATATAATTTGGAGCTAAACCTAAATGATTGGGAATCAGACTAAAATTCTAAAACAATAA
AAATAAATATTTTAAATTCAAGACATACCCTTAAAATATTTTTTATATATAATTTGAGCTAAACC
AAAGTGATTTGG
Found at i:27444 original size:11 final size:11
Alignment explanation
Indices: 27428--27454 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27418 AGTCACAGAT
27428 GCCCATCTAAG
1 GCCCATCTAAG
27439 GCCCATCTAAG
1 GCCCATCTAAG
27450 GCCCA
1 GCCCA
27455 AACCTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.41, G:0.19, T:0.15
Consensus pattern (11 bp):
GCCCATCTAAG
Done.