Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018177.1 Corchorus olitorius cultivar O-4 contig18210, 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: 38269
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Found at i:3610 original size:6 final size:6
Alignment explanation
Indices: 3599--3626 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3589 AGACCGGATG
3599 GAAGTT GAAGTT GAAGTT GAAGTT GAAG
1 GAAGTT GAAGTT GAAGTT GAAGTT GAAG
3627 ATAAGGAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (6 bp):
GAAGTT
Found at i:6534 original size:121 final size:127
Alignment explanation
Indices: 6383--6632 Score: 386
Period size: 121 Copynumber: 2.0 Consensus size: 127
6373 CATTGTTTAA
*
6383 ACTTTTATAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
*
6445 A-ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATAT-T-AGAATTTTTTAAATAT
66 ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATAAGAATTTTTTAAATAT
* *
6504 ACTTTTACAGTTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-C
6569 TATTTTATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATAAGAATTTTTTAAAT
65 TA---TATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATAAGAATTTTTTAAAT
6633 TTATTTCTTA
Statistics
Matches: 115, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
121 53 0.46
122 3 0.03
123 2 0.02
125 2 0.02
129 40 0.35
130 1 0.01
131 14 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATAAGAATTTTTTAAATAT
Found at i:7352 original size:16 final size:16
Alignment explanation
Indices: 7331--7361 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7321 CTCAGGTCAC
*
7331 TCGGATTTTGGATTTT
1 TCGGATTTAGGATTTT
7347 TCGGATTTAGGATTT
1 TCGGATTTAGGATTT
7362 GGATCAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.26, T:0.52
Consensus pattern (16 bp):
TCGGATTTAGGATTTT
Found at i:20425 original size:92 final size:93
Alignment explanation
Indices: 20267--20539 Score: 376
Period size: 92 Copynumber: 2.9 Consensus size: 93
20257 GGGTCTTTAC
* * * *
20267 TAGTCTGGA-TCAAGTCACATTAGACCCATATATG-GG-AAGCTTTTTGTTATAAGATTGGATTT
1 TAGTCTGGAGTCAAGTCACATTAGACCCATAT-TGTGGAAAG--TTCTATTATAAGACTGGATTC
*
20329 CGAGACATTGCTCAAAGGGTATTGACTTGAT
63 CGAGACATTGCTTAAAGGGTATTGACTTGAT
*
20360 TAGTCTGGAGTCCAGTCACATTAGACCCATATTGTGGAAAGTTCT-TTATAAGACTGGATTCCGA
1 TAGTCTGGAGTCAAGTCACATTAGACCCATATTGTGGAAAGTTCTATTATAAGACTGGATTCCGA
*
20424 GACATTGCTTAAAGGGTATTGACTTTAT
66 GACATTGCTTAAAGGGTATTGACTTGAT
* *
20452 TAGTCCGGAGTCAAGTCATATTAGACCCATA-TGTGGAAAGTTCTACATTATAAGACTGGATTCC
1 TAGTCTGGAGTCAAGTCACATTAGACCCATATTGTGGAAAGTTCT--ATTATAAGACTGGATTCC
*
20516 GAGACATTACTTAAAGGGTATTGA
64 GAGACATTGCTTAAAGGGTATTGA
20540 ATTCCTTCCG
Statistics
Matches: 164, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
91 13 0.08
92 71 0.43
93 14 0.09
94 63 0.38
95 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (93 bp):
TAGTCTGGAGTCAAGTCACATTAGACCCATATTGTGGAAAGTTCTATTATAAGACTGGATTCCGA
GACATTGCTTAAAGGGTATTGACTTGAT
Found at i:37703 original size:2 final size:2
Alignment explanation
Indices: 37696--37821 Score: 144
Period size: 2 Copynumber: 57.0 Consensus size: 2
37686 ATACGCGGAA
37696 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37738 AG AG AG AG AG AG AG AG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 AG AG AG AG AG AG AG AG -AG -AG -AG -AG -AG -AG -AG -AG -AG -AG
37784 TAG TAG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 -AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37822 TGTGTGTGTG
Statistics
Matches: 123, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 88 0.72
3 35 0.28
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.10
Consensus pattern (2 bp):
AG
Found at i:37760 original size:3 final size:3
Alignment explanation
Indices: 37752--37789 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
37742 AGAGAGAGAG
37752 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AG
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AG
37790 AGAGAGAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
AGT
Done.