Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015611.1 Corchorus capsularis cultivar CVL-1 contig15632, 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: 22771
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:291 original size:121 final size:120
Alignment explanation
Indices: 150--584 Score: 463
Period size: 121 Copynumber: 3.6 Consensus size: 120
140 ACTATTATAG
* *
150 TTTTATTTTATTAAAAACTCTATTTTTA-TTAATTAAA-TCTAATATCTTTATAATTTCTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTC-AATAT-TTTATAATTT-TTTATT
*
213 TTTACCATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAACATACAA
63 TTTACCATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAATATACAA
* *
271 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATAAGTATTTTATTTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAA-TTTTTTATTTT
* * *
336 TACCATTTTA--A---TT-AA-AAAGATTATTGTGAT-TGATCT---ATTTCT-ATTTGA-TA
65 TACCATTTTACTATTTTTCAATAAA-A--ATTG-GATAT-AT-TAAAATTTTTAATAT-ACAA
* *
386 GTTTAGTGTACTACTAAAAACTCTATTTTTATTCAATTAAA-TCTAATATCTTTATAATTTCTTT
1 TTTTA-T-T-CTACTAAAAACTCTATTTTTATTTAATTAAATTC-AATAT-TTTATAATTT-TTT
* * *
450 ATTTTTACCATTTTACTATTTTTCAATAAAAACTGGATATATTAAAATTTTTAATGTACAG
60 ATTTTTACCATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAATATACAA
*
511 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAA-TTATTATTTTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAATTTTTTA-TTTT
575 TACCATTTTA
65 TACCATTTTA
585 ATTTAAAAGG
Statistics
Matches: 263, Mismatches: 20, Indels: 63
0.76 0.06 0.18
Matches are distributed among these distances:
114 3 0.01
115 10 0.04
116 9 0.03
117 8 0.03
118 41 0.16
119 30 0.11
120 16 0.06
121 59 0.22
122 56 0.21
123 9 0.03
124 9 0.03
125 10 0.04
126 3 0.01
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (120 bp):
TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAATTTTTTATTTTT
ACCATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTAATATACAA
Found at i:425 original size:118 final size:115
Alignment explanation
Indices: 271--624 Score: 350
Period size: 122 Copynumber: 3.0 Consensus size: 115
261 TAACATACAA
*
271 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATAAGTATTTTATTTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAA-TATTTTATTTT
336 TACCATTTTAATTAAAAAGATTATTGTGATTGATCTATTTCTATTTGATAG
65 TACCATTTTAATTAAAAAGATTATTGTGATTGATCTATTTCTATTTGATAG
* *
387 -TTTAGTGTACTACTAAAAACTCTATTTTTATTCAATTAAA-TCTAATATCTTTATAATTTCTTT
1 TTTTA-T-T-CTACTAAAAACTCTATTTTTATTTAATTAAATTC-AATAT-TTTATAATAT-TTT
* * *
450 ATTTTTACCATTTTACTATTTTTCAATAAA-A--ACTG-GATAT-AT-TAAAATTTTTA-ATGTA
60 ATTTTTACCATTTTA--A---TT-AA-AAAGATTATTGTGAT-TGATCT---ATTTCTATTTG-A
*
508 CAG
113 TAG
*
511 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAAT-TATTATTTTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAATATTTTA-TTTT
* * * *
575 TACCATTTTAATTTAAAAGGTTATTGTGTTTGATCTGTTTCTATTTGATA
65 TACCATTTTAATTAAAAAGATTATTGTGATTGATCTATTTCTATTTGATA
625 ATTTGATGTA
Statistics
Matches: 193, Mismatches: 17, Indels: 57
0.72 0.06 0.21
Matches are distributed among these distances:
113 3 0.02
114 1 0.01
115 13 0.07
116 7 0.04
117 7 0.04
118 38 0.20
119 28 0.15
120 15 0.08
121 10 0.05
122 40 0.21
123 9 0.05
124 12 0.06
125 7 0.04
126 3 0.02
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (115 bp):
TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATTCAATATTTTATAATATTTTATTTTT
ACCATTTTAATTAAAAAGATTATTGTGATTGATCTATTTCTATTTGATAG
Found at i:1375 original size:2 final size:2
Alignment explanation
Indices: 1368--1397 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1358 ATGACTAGTG
1368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1398 AAGTATGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3466 original size:16 final size:16
Alignment explanation
Indices: 3435--3465 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3425 AAAACAAGGG
3435 CTTTTTCTTTTCTTTT
1 CTTTTTCTTTTCTTTT
3451 CTTTTTCTTTT-TTTT
1 CTTTTTCTTTTCTTTT
3466 TAAATAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTTTCTTTTCTTTT
Found at i:3988 original size:3 final size:3
Alignment explanation
Indices: 3980--4010 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3970 CAGAACAGAG
3980 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4011 TTTTTGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:8217 original size:15 final size:15
Alignment explanation
Indices: 8193--8225 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
8183 TATTTCCATC
8193 TCACTGTTATTTATA
1 TCACTGTTATTTATA
*
8208 TCACTTTTATTTATA
1 TCACTGTTATTTATA
8223 TCA
1 TCA
8226 ACATTGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.03, T:0.55
Consensus pattern (15 bp):
TCACTGTTATTTATA
Found at i:10310 original size:7 final size:7
Alignment explanation
Indices: 10298--10328 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
10288 AATATATTTA
10298 TATATAT
1 TATATAT
10305 TATATAT
1 TATATAT
*
10312 AATATAT
1 TATATAT
10319 TATATAT
1 TATATAT
10326 TAT
1 TAT
10329 TAAAATGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TATATAT
Found at i:12208 original size:22 final size:21
Alignment explanation
Indices: 12158--12208 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
12148 ATTTATTAAA
12158 AACTAATTTAATCTTTAAATT
1 AACTAATTTAATCTTTAAATT
*
12179 AGCTTAATTTAA-CTTCTAAACTT
1 AAC-TAATTTAATCTT-TAAA-TT
12202 AACTAAT
1 AACTAAT
12209 AAACCCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 5 0.20
22 16 0.64
23 4 0.16
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (21 bp):
AACTAATTTAATCTTTAAATT
Found at i:12310 original size:20 final size:20
Alignment explanation
Indices: 12273--12324 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
12263 CCAAATAAAC
* *
12273 AAACCCAAAAAGAAT-AAAGT
1 AAACCC-AAATGAATAAAAGG
12293 AAACCCAAATGAATTAAAAGG
1 AAACCCAAATGAA-TAAAAGG
12314 AAAGCCCAAAT
1 AAA-CCCAAAT
12325 AAATGTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.22
20 7 0.26
21 7 0.26
22 7 0.26
ACGTcount: A:0.60, C:0.17, G:0.12, T:0.12
Consensus pattern (20 bp):
AAACCCAAATGAATAAAAGG
Found at i:20443 original size:60 final size:61
Alignment explanation
Indices: 20350--20470 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 61
20340 GGCATGGAAG
* *
20350 TATGTTTCAAGTGGTTTTGTTCTCATATCTGCTTAATTTCTTGT-CAGTTTTCTTTTGTGT
1 TATGTTTCAAGTGGTTTTGTTCTCATATCTGCTTAATGTCTCGTGCAGTTTTCTTTTGTGT
*
20410 TATGTTTCAAGTGGTTTTGTTCTCATATCTGCTTACTGTCTCGTGCAGTTTTCTTTTGTGT
1 TATGTTTCAAGTGGTTTTGTTCTCATATCTGCTTAATGTCTCGTGCAGTTTTCTTTTGTGT
20471 ATATTATTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 41 0.72
61 16 0.28
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (61 bp):
TATGTTTCAAGTGGTTTTGTTCTCATATCTGCTTAATGTCTCGTGCAGTTTTCTTTTGTGT
Done.