Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012942.1 Corchorus olitorius cultivar O-4 contig12975, 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: 5326
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:476 original size:218 final size:221
Alignment explanation
Indices: 88--528 Score: 798
Period size: 218 Copynumber: 2.0 Consensus size: 221
78 GACATTGTTT
*
88 AAATTTTATCAGTTTTTTGTTAGAAATAAACTTTTTACAGTTATTCTGCTAAAAACTCTATTTTT
1 AAATCTTATCAGTTTTTTGTTAGAAATAAACTTTTTACAGTTATTCTGCTAAAAACTCTATTTTT
* *
153 ATTTAATTAAATTCAATATTTTTATAAATATTTTATTTTTACCATTTTAATTTTAAAAAATTGGA
66 ATTTAATTAAATTCAATATTTTTACAAAAATTTTATTTTTACCATTTTAATTTTAAAAAATTGGA
*
218 GACTTTTTGATAGTTCTGGACCAATTTCAATTTTATAATATAAATTAAT-AAAGTATTATTATCA
131 GACTTTTTGATAGTTCTGGACCAATTTCAATTTTATAATATAAACTAATAAAAGTATTATTATCA
282 AGTTTAAAAGTTAAAATAAATTGCCC
196 AGTTTAAAAGTTAAAATAAATTGCCC
*
308 AAATCTTA-CAGTTTTTTGTTAGAAATAAAC-TTTTACAGTTATTCTGCTAAAAACTTTATTTTT
1 AAATCTTATCAGTTTTTTGTTAGAAATAAACTTTTTACAGTTATTCTGCTAAAAACTCTATTTTT
371 ATTTAATTAAATTCAATATTTTTACAAAAATTTTATTTTTACCATTTTAATTTTAAAAAATTGGA
66 ATTTAATTAAATTCAATATTTTTACAAAAATTTTATTTTTACCATTTTAATTTTAAAAAATTGGA
*
436 GACTTTTTGATAGTTCTGGACCCATTTCAATTTTATAATATAAACTAATAAAAGTATTATTATCA
131 GACTTTTTGATAGTTCTGGACCAATTTCAATTTTATAATATAAACTAATAAAAGTATTATTATCA
*
501 AGTTTAAAAGTTAAAATAAGTTGCCC
196 AGTTTAAAAGTTAAAATAAATTGCCC
527 AA
1 AA
529 TCATTAATTA
Statistics
Matches: 213, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
218 142 0.67
219 64 0.30
220 7 0.03
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (221 bp):
AAATCTTATCAGTTTTTTGTTAGAAATAAACTTTTTACAGTTATTCTGCTAAAAACTCTATTTTT
ATTTAATTAAATTCAATATTTTTACAAAAATTTTATTTTTACCATTTTAATTTTAAAAAATTGGA
GACTTTTTGATAGTTCTGGACCAATTTCAATTTTATAATATAAACTAATAAAAGTATTATTATCA
AGTTTAAAAGTTAAAATAAATTGCCC
Found at i:2861 original size:18 final size:18
Alignment explanation
Indices: 2838--2909 Score: 99
Period size: 18 Copynumber: 4.0 Consensus size: 18
2828 GTCAATCCTA
2838 GGGAACTAACTTTGAATG
1 GGGAACTAACTTTGAATG
**
2856 GGGAACTGCCTTTGAATG
1 GGGAACTAACTTTGAATG
2874 GGGAACTAACTTTGAATG
1 GGGAACTAACTTTGAATG
* * *
2892 GAGAACTGACTTGGAATG
1 GGGAACTAACTTTGAATG
2910 AGAGATTGAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (18 bp):
GGGAACTAACTTTGAATG
Found at i:2885 original size:36 final size:36
Alignment explanation
Indices: 2838--2909 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
2828 GTCAATCCTA
* * *
2838 GGGAACTAACTTTGAATGGGGAACTGCCTTTGAATG
1 GGGAACTAACTTTGAATGGAGAACTGACTTGGAATG
2874 GGGAACTAACTTTGAATGGAGAACTGACTTGGAATG
1 GGGAACTAACTTTGAATGGAGAACTGACTTGGAATG
2910 AGAGATTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (36 bp):
GGGAACTAACTTTGAATGGAGAACTGACTTGGAATG
Found at i:2922 original size:36 final size:36
Alignment explanation
Indices: 2840--2927 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
2830 CAATCCTAGG
* * * *
2840 GAACTAACTTTGAATGGGGAACTGCCTTTGAATGGG
1 GAACTAACTTTGAATGGAGAACTGACTTGGAATGGA
2876 GAACTAACTTTGAATGGAGAACTGACTTGGAAT-GA
1 GAACTAACTTTGAATGGAGAACTGACTTGGAATGGA
* *
2911 GAGATTGACTTTGAATG
1 GA-ACTAACTTTGAATG
2928 ACCCTTAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 3 0.07
36 42 0.93
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (36 bp):
GAACTAACTTTGAATGGAGAACTGACTTGGAATGGA
Found at i:3111 original size:18 final size:18
Alignment explanation
Indices: 3088--3176 Score: 94
Period size: 18 Copynumber: 4.9 Consensus size: 18
3078 AGCAACCTTA
3088 TCAAAGGCAGTTCCCTAT
1 TCAAAGGCAGTTCCCTAT
3106 TCAAAGGCAGTTCTCC-AT
1 TCAAAGGCAGTTC-CCTAT
*
3124 TCAAA-ACTAGTT-CCTCAT
1 TCAAAGGC-AGTTCCCT-AT
*
3142 TCAAAGGCAGTTCCCCAT
1 TCAAAGGCAGTTCCCTAT
**
3160 TCAAAGTTAGTTCCCTA
1 TCAAAGGCAGTTCCCTA
3177 GGATTGACTC
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
16 2 0.03
17 1 0.02
18 51 0.86
19 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (18 bp):
TCAAAGGCAGTTCCCTAT
Found at i:3136 original size:36 final size:36
Alignment explanation
Indices: 3096--3176 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
3086 TATCAAAGGC
*
3096 AGTTCCCTATTCAAAGGCAGTTCTCCATTCAAAACT
1 AGTTCCCTATTCAAAGGCAGTTCCCCATTCAAAACT
**
3132 AGTT-CCTCATTCAAAGGCAGTTCCCCATTCAAAGTT
1 AGTTCCCT-ATTCAAAGGCAGTTCCCCATTCAAAACT
3168 AGTTCCCTA
1 AGTTCCCTA
3177 GGATTGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
35 3 0.08
36 34 0.85
37 3 0.08
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (36 bp):
AGTTCCCTATTCAAAGGCAGTTCCCCATTCAAAACT
Done.