Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018033.1 Corchorus olitorius cultivar O-4 contig18066, 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: 13177
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:6703 original size:47 final size:47
Alignment explanation
Indices: 6649--6738 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
6639 TCCGGCATAT
6649 TTTCTTTGTGATTACTAATATAATAATTACTACTGTTAATTATATAA
1 TTTCTTTGTGATTACTAATATAATAATTACTACTGTTAATTATATAA
* *
6696 TTTCTTTGTGATTATTAATATAATAATTACTATTGTTAATTAT
1 TTTCTTTGTGATTACTAATATAATAATTACTACTGTTAATTAT
6739 TTTTCTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (47 bp):
TTTCTTTGTGATTACTAATATAATAATTACTACTGTTAATTATATAA
Found at i:6721 original size:26 final size:25
Alignment explanation
Indices: 6649--6723 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 25
6639 TCCGGCATAT
6649 TTTCTTTGTGATTACTAATATAATAA
1 TTTCTTTGTGATTA-TAATATAATAA
* ** *
6675 TTAC-TACTG-TTA-ATTAT-ATAA
1 TTTCTTTGTGATTATAATATAATAA
6696 TTTCTTTGTGATTATTAATATAATAA
1 TTTCTTTGTGATTA-TAATATAATAA
6722 TT
1 TT
6724 ACTATTGTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 7 0.19
22 7 0.19
23 3 0.08
24 3 0.08
25 7 0.19
26 9 0.25
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (25 bp):
TTTCTTTGTGATTATAATATAATAA
Found at i:9326 original size:14 final size:14
Alignment explanation
Indices: 9307--9351 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
9297 AACAATACTG
9307 CATCATCAACACTA
1 CATCATCAACACTA
* *
9321 CATCAT---TACTG
1 CATCATCAACACTA
9332 CATCATCAACACTA
1 CATCATCAACACTA
9346 CATCAT
1 CATCAT
9352 TACTGCATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
11 9 0.38
14 15 0.62
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.27
Consensus pattern (14 bp):
CATCATCAACACTA
Found at i:9370 original size:25 final size:25
Alignment explanation
Indices: 9302--9362 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
9292 ACATTAACAA
9302 TACTGCATCATCAACACTACATCAT
1 TACTGCATCATCAACACTACATCAT
9327 TACTGCATCATCAACACTACATCAT
1 TACTGCATCATCAACACTACATCAT
9352 TACTGCATCAT
1 TACTGCATCAT
9363 ATTTACTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (25 bp):
TACTGCATCATCAACACTACATCAT
Found at i:13089 original size:362 final size:363
Alignment explanation
Indices: 12424--13148 Score: 1391
Period size: 362 Copynumber: 2.0 Consensus size: 363
12414 CTCATGATGT
12424 TGAGTGAAATTACCATTGTTCTAAGAGAGGGGCGGCTAAGAAGAGAAAAACACATAAACAATATG
1 TGAGTGAAATTACCATTGTTCTAAGAGAGGGGCGGCTAAGAAGAGAAAAACACATAAACAATATG
12489 ATAATGTAAGGTGCTAATAAGAAGTGGACGGCTAGTGTTATTAGAATACAAGGTATTTATAGGCA
66 ATAATGTAAGGTGCTAATAAGAAGTGGACGGCTAGTGTTATTAGAATACAAGGTATTTATAGGCA
12554 AATACTAGGATTAAGGTTAACTAAGTTGCACATCTTGGGCTTGGATATAGAGTGTAGCTGGCCAT
131 AATACTAGGATTAAGGTTAACTAAGTTGCACATCTTGGGCTTGGATATAGAGTGTAGCTGGCCAT
12619 CAACTTCATTGTGTCATACAGTGGCATAGCCAAAGATTTACTTAAGTGGAGTCAAAAATTTGTAA
196 CAACTTCATTGTGTCATACAGTGGCATAGCCAAAGATTTACTTAAGTGGAGTCAAAAATTTGTAA
12684 TACATTCTTTTTACTAATCAAATAAAAGTTATTTATATGTAAACTTAACAATTCTACATTTATAT
261 TACATTCTTTTTACTAATCAAATAAAAGTTATTTATATGTAAACTTAACAATTCTACATTTATAT
12749 ATATATATA-AGAGAGAGAGAGAGAGAGAGAGA-AGAGA
326 ATATATA-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
12786 TGAGTGAAATTACCATTGTTCTAAGAGAGGGGCGGCTAAGAAGAGAAAAACACATAAACAATATG
1 TGAGTGAAATTACCATTGTTCTAAGAGAGGGGCGGCTAAGAAGAGAAAAACACATAAACAATATG
*
12851 CTAATGTAAGGTGCTAATAAGAAGTGGACGGCTAGTGTTATTAGAATACAAGGTATTTATAGGCA
66 ATAATGTAAGGTGCTAATAAGAAGTGGACGGCTAGTGTTATTAGAATACAAGGTATTTATAGGCA
*
12916 AATACTAGGATTAAGGTTAACTAAGTTGCACATCTTGGGCTTGGATATAGAGTGTGGCTGGCCAT
131 AATACTAGGATTAAGGTTAACTAAGTTGCACATCTTGGGCTTGGATATAGAGTGTAGCTGGCCAT
12981 CAACTTCATTGTGTCATACAGTGGCATAGCCAAAGATTTACTTAAGTGGAGTCAAAAATTTGTAA
196 CAACTTCATTGTGTCATACAGTGGCATAGCCAAAGATTTACTTAAGTGGAGTCAAAAATTTGTAA
* *
13046 TACATTCTTTTTACTAATCAGATAAAAGTTATTTATATGTAAACTTAACAATTCTACGTTTATAT
261 TACATTCTTTTTACTAATCAAATAAAAGTTATTTATATGTAAACTTAACAATTCTACATTTATAT
13111 ATATATAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
326 ATATATAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
13149 GAGAGAGAGA
Statistics
Matches: 357, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
361 1 0.00
362 351 0.98
363 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (363 bp):
TGAGTGAAATTACCATTGTTCTAAGAGAGGGGCGGCTAAGAAGAGAAAAACACATAAACAATATG
ATAATGTAAGGTGCTAATAAGAAGTGGACGGCTAGTGTTATTAGAATACAAGGTATTTATAGGCA
AATACTAGGATTAAGGTTAACTAAGTTGCACATCTTGGGCTTGGATATAGAGTGTAGCTGGCCAT
CAACTTCATTGTGTCATACAGTGGCATAGCCAAAGATTTACTTAAGTGGAGTCAAAAATTTGTAA
TACATTCTTTTTACTAATCAAATAAAAGTTATTTATATGTAAACTTAACAATTCTACATTTATAT
ATATATAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
Found at i:13123 original size:2 final size:2
Alignment explanation
Indices: 13118--13177 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
13108 TATATATATA
13118 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
13160 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.