Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016907.1 Corchorus olitorius cultivar O-4 contig16940, 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: 52026
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:17463 original size:2 final size:2
Alignment explanation
Indices: 17456--17484 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17446 AAACCCAAAC
17456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17485 GTGTAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23004 original size:30 final size:30
Alignment explanation
Indices: 22789--23476 Score: 897
Period size: 30 Copynumber: 23.2 Consensus size: 30
22779 AATTTGAAAG
* *
22789 GTAAAATCATGACAACTTCTGGTGTCAAAT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* *
22819 G--A-ATTATGACAACTTATGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* * ** *
22846 G--A-ATTATGACATCTTCAAGTGTCTATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* * *
22873 GGAAATTTATCATGACAACTTTTGGTGTCAATT
1 -GTAA--GATCATGACAACTTCTGGTGTCAATT
*
22906 G--A-ATTATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
22933 -T-A-ATCATGACAACTTCT-G-GTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
22958 GTAAGACCATTGACAACTTCTGGTGTCAATT
1 GTAAGATCA-TGACAACTTCTGGTGTCAATT
*
22989 GTAAGATCATGACAACTGCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
23019 GTAAGATCATGACAACTGCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
23049 GTAAGATCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
23079 GTAAGACCAATGACAACTTCTGGTGTCAATT
1 GTAAGATC-ATGACAACTTCTGGTGTCAATT
*
23110 GTAAGACCATTGACAACTTCTGGTGTCAATT
1 GTAAGATCA-TGACAACTTCTGGTGTCAATT
*
23141 GTAAGATCTTGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
23171 GTAAGATCTTGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
23201 GTAAGATCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
23231 GCAAGATCATGACAAC-TCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
23260 GTAAGAGCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* *
23290 GCAAGTTCATTGACAAC-TCTGGTGTCAATT
1 GTAAGATCA-TGACAACTTCTGGTGTCAATT
* *
23320 GCAAGAGCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* * *
23350 GCAAGAGCATGACAACTTCTGGTATCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
23380 GCAAGATCATTGACAACTTCTGGTGTCAATT
1 GTAAGATCA-TGACAACTTCTGGTGTCAATT
* *
23411 GCAAGACCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
23441 GTAAGATCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
23471 G-AAGAT
1 GTAAGAT
23477 TAAAATAAAT
Statistics
Matches: 600, Mismatches: 39, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.01
26 2 0.00
27 83 0.14
28 5 0.01
29 50 0.08
30 325 0.54
31 108 0.18
32 1 0.00
33 19 0.03
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (30 bp):
GTAAGATCATGACAACTTCTGGTGTCAATT
Found at i:23315 original size:301 final size:293
Alignment explanation
Indices: 22885--23476 Score: 911
Period size: 301 Copynumber: 2.0 Consensus size: 293
22875 AAATTTATCA
* * *
22885 TGACAACTTTTGGTGTCAATTGAATTATGACAACTTCTGGTGTCAATTTAATCATGACAACTTCT
1 TGACAACTTCTGGTGTCAATTGAATCATGACAACTTCTGGTGTCAATTAAATCATGACAACTTCT
*
22950 GGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGATCATGACAACTGCTGGTGTC
66 GGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTGCTGGTGTC
* * * * *
23015 AATTGTAAGATCATGACAACTGCTGGTGTCAATTGTAAGATCATGACAACTTCTGGTGTCAATTG
131 AATTGCAAGAGCATGACAACTGCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTATCAATTG
* *
23080 TAAGACCAATGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAA
196 CAAGACCAATGACAACTTCTGGTGTCAATTGCAAGACCA-TGACAACTTCTGGTGTCAATTGTAA
*
23145 GATCTTGACAACTTCTGGTGTCAATTGTAAGATCT
260 GATCATGACAACTTCTGGTGTCAATTG-AAGATCT
23180 TGACAACTTCTGGTGTCAATTGTAAGATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACA
1 TGACAACTTCTGGTGTCAATTG--A-ATCATGACAACTTCTGGTGTCAATT--AA-ATCATGACA
* *
23245 AC-TCTGGTGTCAATTGTAAGAGCA-TGACAACTTCTGGTGTCAATTGCAAGTTCATTGACAACT
60 ACTTCT-G-GTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGCAAGATCA-TGACAACT
*
23308 -CTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGG
122 GCTGGTGTCAATTGCAAGAGCATGACAACTGCTGGTGTCAATTGCAAGAGCATGACAACTTCTGG
* *
23372 TATCAATTGCAAGATCATTGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTC
187 TATCAATTGCAAGACCAATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTC
23437 AATTGTAAGATCATGACAACTTCTGGTGTCAATTGAAGAT
252 AATTGTAAGATCATGACAACTTCTGGTGTCAATTGAAGAT
23477 TAAAATAAAT
Statistics
Matches: 271, Mismatches: 17, Indels: 14
0.90 0.06 0.05
Matches are distributed among these distances:
295 21 0.08
297 1 0.00
298 24 0.09
299 5 0.02
300 55 0.20
301 142 0.52
302 23 0.08
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (293 bp):
TGACAACTTCTGGTGTCAATTGAATCATGACAACTTCTGGTGTCAATTAAATCATGACAACTTCT
GGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTGCTGGTGTC
AATTGCAAGAGCATGACAACTGCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTATCAATTG
CAAGACCAATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAG
ATCATGACAACTTCTGGTGTCAATTGAAGATCT
Found at i:27176 original size:17 final size:17
Alignment explanation
Indices: 27154--27189 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27144 ATACAAAGAG
27154 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
27171 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
27188 CT
1 CT
27190 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:32624 original size:106 final size:104
Alignment explanation
Indices: 32401--32661 Score: 371
Period size: 106 Copynumber: 2.5 Consensus size: 104
32391 AATTTTTCTA
* ** * *
32401 ACCCTTAAAATAAAATTTTAATTTTAATTTGGACTAAACTTAGTG-AATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTACTTATATATTTTAT
* *
32465 TTCCAAAACCCTATAAAAATATTATTAATTATGGAATTT
66 TTCCAAAACCCTATAAAAAAATTATTAATTATGAAATTT
* * * *
32504 ACACTTAAAATAAAAATAAAATTATAATTTGGGCTAAACTTAGTGAAATTACTTTTGTATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTACTTATATATTTTAT
* *
32569 TTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTCCAAAACCCTATAA-AA-AAATTATTAATTATGAAATTT
32610 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTA
32662 AGACTAAACT
Statistics
Matches: 139, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
103 39 0.28
104 31 0.22
105 2 0.01
106 46 0.33
107 21 0.15
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTACTTATATATTTTAT
TTCCAAAACCCTATAAAAAAATTATTAATTATGAAATTT
Found at i:33450 original size:30 final size:31
Alignment explanation
Indices: 33414--33473 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
33404 TTGGGCCGCA
33414 CGGGGGAGA-GATGAGGACTCACATGTGAAT
1 CGGGGGAGATGATGAGGACTCACATGTGAAT
* *
33444 CGGGGGAGATTGTTGAGGATTCACATGTGA
1 CGGGGGAGA-TGATGAGGACTCACATGTGA
33474 GGAAATATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
32 17 0.65
ACGTcount: A:0.27, C:0.12, G:0.40, T:0.22
Consensus pattern (31 bp):
CGGGGGAGATGATGAGGACTCACATGTGAAT
Found at i:34724 original size:4 final size:4
Alignment explanation
Indices: 34717--34762 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
34707 TTTTTTTTTT
34717 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TT
34763 GTTGTTGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:38230 original size:34 final size:34
Alignment explanation
Indices: 38192--38260 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
38182 GGGTTTGGAG
38192 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
1 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
*
38226 TCAAACCCCAAACATTTGAAAGTTAAACCACGTT
1 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
38260 T
1 T
38261 TGACCCCACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.23
Consensus pattern (34 bp):
TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
Found at i:38724 original size:21 final size:21
Alignment explanation
Indices: 38700--38744 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38690 AACTTTGGGT
*
38700 TCAAACTATGGGGTTTGAATA
1 TCAAAATATGGGGTTTGAATA
* *
38721 TCAAAATTTGGGGTTTGACTA
1 TCAAAATATGGGGTTTGAATA
38742 TCA
1 TCA
38745 TCCTTTGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (21 bp):
TCAAAATATGGGGTTTGAATA
Found at i:40682 original size:21 final size:21
Alignment explanation
Indices: 40657--40739 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
40647 TATCTTAGAT
40657 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
40678 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
**
40699 ATAAATAATA-AGTTCAAAATAA
1 AT-AATAATATA-TTTTAAATAA
40721 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
40740 TTACTAAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.02
21 18 0.35
22 21 0.41
23 11 0.22
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:40690 original size:25 final size:25
Alignment explanation
Indices: 40659--40709 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
40649 TCTTAGATAT
*
40659 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
40684 AATATATTTTAAATAATAAATAATA
1 AATATATATTAAATAATAAATAATA
40709 A
1 A
40710 GTTCAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Done.