Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020440.1 Corchorus olitorius cultivar O-4 contig20473, 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: 18189
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:408 original size:212 final size:212
Alignment explanation
Indices: 1--486 Score: 796
Period size: 212 Copynumber: 2.3 Consensus size: 212
1 GGGATGATGAGAAATAATTTGGGTATAAAGTATATTACTTTTGGGATACTGAATTTTGCATTTTG
1 GGGATGATGAGAAATAATTTGGGTATAAAGTATATTAC-TTTGGGATACTGAATTTTGCATTTTG
* * *
66 TTTAATTATTAGATGGCACTAAAATCATATAGACGAGGTTTATTCAATTAATATATGGATTAAAA
65 TTTAATCATTAGATGACACTAAAATCATATAGACGAGGTATATTCAATTAATATATGGATTAAAA
*
131 CACCTTCTAAAGACAATTTTGGGGTATGCGAGAAAAAAATGTCCATCTCTAAAGAATTTGGGGAT
130 CACCTTCTAAAGACAATTTTGGGGTATACGAGAAAAAAATGTCCATCTCTAAAGAATTTGGGGAT
196 GCTGCATACGATTATTTG
195 GCTGCATACGATTATTTG
*
214 GGGATGATGAGAAACAATTTGGGTATAAAGTATATTACTTTGGGATACTGAATTTTGCATTTTGT
1 GGGATGATGAGAAATAATTTGGGTATAAAGTATATTACTTTGGGATACTGAATTTTGCATTTTGT
*
279 TTAATCATTAGATGACACTAAAATCATATAGACGGGGATATATTCAATTAATATATGGATTAAAA
66 TTAATCATTAGATGACACTAAAATCATATAGACGAGG-TATATTCAATTAATATATGGATTAAAA
* * * *
344 CACCTTTTAAAGTCAATTTT-GGGTATATGAG-AACAAATGTCCATCTCTAAAGAATTTGGGGGA
130 CACCTTCTAAAGACAATTTTGGGGTATACGAGAAAAAAATGTCCATCTCTAAAGAATTT-GGGGA
* *
407 TGGTGCATATGATTATTTG
194 TGCTGCATACGATTATTTG
* *
426 GGGATGATGAGATATAATTTGGGTATAAAGTATATTACTTTGTAGATACTGAATTTTGCAT
1 GGGATGATGAGAAATAATTTGGGTATAAAGTATATTACTTTG-GGATACTGAATTTTGCAT
487 ATCAATAATC
Statistics
Matches: 255, Mismatches: 15, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
211 25 0.10
212 132 0.52
213 98 0.38
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (212 bp):
GGGATGATGAGAAATAATTTGGGTATAAAGTATATTACTTTGGGATACTGAATTTTGCATTTTGT
TTAATCATTAGATGACACTAAAATCATATAGACGAGGTATATTCAATTAATATATGGATTAAAAC
ACCTTCTAAAGACAATTTTGGGGTATACGAGAAAAAAATGTCCATCTCTAAAGAATTTGGGGATG
CTGCATACGATTATTTG
Found at i:5268 original size:26 final size:25
Alignment explanation
Indices: 5239--5287 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5229 TTGTATTATT
*
5239 TATTTAATAATATTTTTAATTAATGG
1 TATTTAATAATATTATT-ATTAATGG
* *
5265 TATTTAGTTATATTATTATTAAT
1 TATTTAATAATATTATTATTAAT
5288 TTGTTTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (25 bp):
TATTTAATAATATTATTATTAATGG
Found at i:10276 original size:33 final size:33
Alignment explanation
Indices: 10239--10434 Score: 157
Period size: 33 Copynumber: 5.9 Consensus size: 33
10229 ATTAGCATCC
*
10239 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
10272 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * *
10304 CAAATTAGTTTTAGTATCATCACTAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
* *
10338 AGAACAGATTTAGTGTCATCGCAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * *
10370 CAAATTAGGTTTAGTATCGTCACTAACAACA-CT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
* * **
10403 CAAAACAAATTTCGTGTCATTGCAAACAACAC
1 -AAAACAGATTTAGTGTCATCACAAACAACAC
10435 TCAAATTAGG
Statistics
Matches: 127, Mismatches: 31, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
32 8 0.06
33 117 0.92
34 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:10440 original size:66 final size:67
Alignment explanation
Indices: 10254--10446 Score: 293
Period size: 66 Copynumber: 2.9 Consensus size: 67
10244 AGAATTTGTT
* * *
10254 TCATCACAAACAACAC-CTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAG
1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
10318 TA
66 TA
*
10320 TCATCACTAACAACA-TCTAGAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
10384 TA
66 TA
* * * *
10386 TCGTCACTAACAACACTC-AAAACAAATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT
10447 CAGAATTACT
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
66 114 0.98
67 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (67 bp):
TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
TA
Found at i:18038 original size:21 final size:21
Alignment explanation
Indices: 18003--18043 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
17993 CGTTTAAAAG
18003 CAAAAGCCAGAAATTGGAATTT
1 CAAAAGCCAGAAATT-GAATTT
*
18025 CAAAATCCA-AAATTGAATT
1 CAAAAGCCAGAAATTGAATT
18044 CCGTCCTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (21 bp):
CAAAAGCCAGAAATTGAATTT
Done.