Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019793.1 Corchorus olitorius cultivar O-4 contig19826, 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: 58299
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:16123 original size:2 final size:2
Alignment explanation
Indices: 16118--16162 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16108 AAGATTTTTT
16118 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16160 TG T
1 TG T
16163 AAATGATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:31688 original size:114 final size:114
Alignment explanation
Indices: 31504--31733 Score: 460
Period size: 114 Copynumber: 2.0 Consensus size: 114
31494 GATATCCATA
31504 TTGCATATTTTTATTCTTCTAATATTATTTTTTATAATTAAATATATTATTTCATTAAAAAAATA
1 TTGCATATTTTTATTCTTCTAATATTATTTTTTATAATTAAATATATTATTTCATTAAAAAAATA
31569 TGAATACCTCATAATCTACTCCTAAAAATCTTTATCCAAACTAAGATTT
66 TGAATACCTCATAATCTACTCCTAAAAATCTTTATCCAAACTAAGATTT
31618 TTGCATATTTTTATTCTTCTAATATTATTTTTTATAATTAAATATATTATTTCATTAAAAAAATA
1 TTGCATATTTTTATTCTTCTAATATTATTTTTTATAATTAAATATATTATTTCATTAAAAAAATA
31683 TGAATACCTCATAATCTACTCCTAAAAATCTTTATCCAAACTAAGATTT
66 TGAATACCTCATAATCTACTCCTAAAAATCTTTATCCAAACTAAGATTT
31732 TT
1 TT
31734 TAAAAGCTAG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (114 bp):
TTGCATATTTTTATTCTTCTAATATTATTTTTTATAATTAAATATATTATTTCATTAAAAAAATA
TGAATACCTCATAATCTACTCCTAAAAATCTTTATCCAAACTAAGATTT
Found at i:33224 original size:24 final size:24
Alignment explanation
Indices: 33187--33236 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
33177 GCCATCGATG
*
33187 ATAATATTGGTGCTCCTGATGCTA
1 ATAATATTGCTGCTCCTGATGCTA
* *
33211 ATAATGTTGCTGCTCCTGATGTTA
1 ATAATATTGCTGCTCCTGATGCTA
33235 AT
1 AT
33237 GGAGGAGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
ATAATATTGCTGCTCCTGATGCTA
Found at i:44794 original size:19 final size:20
Alignment explanation
Indices: 44772--44814 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
44762 TTAGGCAGAC
* *
44772 TATTGTTTCTTAT-GTTTAT
1 TATTGTTTCCTATAATTTAT
*
44791 TATTTTTTCCTATAATTTAT
1 TATTGTTTCCTATAATTTAT
44811 TATT
1 TATT
44815 TTCCTGCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (20 bp):
TATTGTTTCCTATAATTTAT
Found at i:53746 original size:19 final size:18
Alignment explanation
Indices: 53717--53752 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53707 ATCTAACTTA
53717 TTTTTATTTTTATTTTAG
1 TTTTTATTTTTATTTTAG
*
53735 TTTTTATGTTTTCTTTTA
1 TTTTTAT-TTTTATTTTA
53753 ATTTAATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTTATTTTAG
Found at i:54057 original size:26 final size:26
Alignment explanation
Indices: 54021--54078 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
54011 GAAAAAAAAA
54021 TTGCAT-TTTTTCATTTT-TGTTTATGT
1 TTGCATATTTTTCATTTTCT-TTT-TGT
54047 TTGCATATTTTTCATTTTCTTTTTGT
1 TTGCATATTTTTCATTTTCTTTTTGT
54073 TTGCAT
1 TTGCAT
54079 GCATTGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 15 0.50
27 14 0.47
28 1 0.03
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.67
Consensus pattern (26 bp):
TTGCATATTTTTCATTTTCTTTTTGT
Found at i:58050 original size:29 final size:30
Alignment explanation
Indices: 57990--58069 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
57980 GCTAAATACC
* * *
57990 CAAAAAAATCCTTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
58021 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* *
58050 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
58070 CAAAAATGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.57
31 19 0.43
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:58232 original size:31 final size:31
Alignment explanation
Indices: 58183--58278 Score: 147
Period size: 31 Copynumber: 3.1 Consensus size: 31
58173 CCACATCAGC
* *
58183 AAGGGACTGATTTGTCCCAAAAGAAAAACAT
1 AAGGGATTGTTTTGTCCCAAAAGAAAAACAT
*
58214 AAGGGATTGTTTTATCCCAAAAGAAAAACAT
1 AAGGGATTGTTTTGTCCCAAAAGAAAAACAT
* *
58245 AAGGGATTTTTTTGTCCCAAAAGAAAAATAT
1 AAGGGATTGTTTTGTCCCAAAAGAAAAACAT
58276 AAG
1 AAG
58279 AGAAGTTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGGGATTGTTTTGTCCCAAAAGAAAAACAT
Found at i:58288 original size:31 final size:30
Alignment explanation
Indices: 58193--58288 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 30
58183 AAGGGACTGA
*
58193 TTTGTCCCAAAAGAAAAACATAAGGGATTGT
1 TTTGTCCCAAAAGAAAAACATAAGGAATT-T
* *
58224 TTTATCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAA-GGAATTT
* *
58255 TTTGTCCCAAAAGAAAAATATAAGAGAAGTT
1 TTTGTCCCAAAAGAAAAACATAAG-GAATTT
58286 TTT
1 TTT
58289 AGTATTTAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.02
31 51 0.91
32 4 0.07
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAACATAAGGAATTT
Done.