Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010117.1 Corchorus capsularis cultivar CVL-1 contig10138, 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: 21178
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:5943 original size:27 final size:27
Alignment explanation
Indices: 5909--5969 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
5899 AAGTCACCAT
5909 CCCCTCCTCCATACGTGTATAAATCAC
1 CCCCTCCTCCATACGTGTATAAATCAC
*
5936 CCCCTCCTCCATATGTGTATAAATCAC
1 CCCCTCCTCCATACGTGTATAAATCAC
5963 CCCCTCC
1 CCCCTCC
5970 ACCACCATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.23, C:0.44, G:0.07, T:0.26
Consensus pattern (27 bp):
CCCCTCCTCCATACGTGTATAAATCAC
Found at i:5980 original size:30 final size:29
Alignment explanation
Indices: 5917--6011 Score: 95
Period size: 30 Copynumber: 3.3 Consensus size: 29
5907 ATCCCCTCCT
* *
5917 CCATACGTGTATAAATCACCCCCT--CCT
1 CCATATGTGTATAAATCACCCCCTCCCCA
5944 CCATATGTGTATAAATCACCCCCTCCACCA
1 CCATATGTGTATAAATCACCCCCTCC-CCA
* * * * *
5974 CCATATGTCTACAAGTGACCACCTCCTCCA
1 CCATATGTGTATAAATCACCCCCTCC-CCA
6004 CCATATGT
1 CCATATGT
6012 CTACAAGTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 23 0.40
30 34 0.60
ACGTcount: A:0.27, C:0.39, G:0.08, T:0.25
Consensus pattern (29 bp):
CCATATGTGTATAAATCACCCCCTCCCCA
Found at i:6012 original size:30 final size:30
Alignment explanation
Indices: 5933--6023 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
5923 GTGTATAAAT
* * * * *
5933 CACCCCCTCCTCCATATGTGTATAAATCAC
1 CACCTCCTCCACCATATGTCTACAAGTCAC
* * *
5963 CCCCTCCACCACCATATGTCTACAAGTGAC
1 CACCTCCTCCACCATATGTCTACAAGTCAC
5993 CACCTCCTCCACCATATGTCTACAAGTCAC
1 CACCTCCTCCACCATATGTCTACAAGTCAC
6023 C
1 C
6024 TCCACACCCC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.26, C:0.43, G:0.08, T:0.23
Consensus pattern (30 bp):
CACCTCCTCCACCATATGTCTACAAGTCAC
Found at i:10078 original size:2 final size:2
Alignment explanation
Indices: 10071--10095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10061 TTAGGTTTAC
10071 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 T
10096 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14215 original size:97 final size:98
Alignment explanation
Indices: 14045--14238 Score: 345
Period size: 97 Copynumber: 2.0 Consensus size: 98
14035 CCTAATAAAC
14045 AAAAAAAAAATTCAATGGTCCTTGTAATTAATTGATCTTAACAAAACTACTGAAGGTTAATGTAT
1 AAAAAAAAAATTCAATGGTCCTTGTAATTAATTGATCTTAACAAAACTACTGAAGGTTAATGTAT
* *
14110 GATTTGGTAATTGTTCAATGACTAAAATATTGG
66 GATATGGTAATTGTCCAATGACTAAAATATTGG
* *
14143 AAAAAGAAAA-TCAATGGTCCTTGTAATTAATTGATCTTAACAAAACTATTGAAGGTTAATGTAT
1 AAAAAAAAAATTCAATGGTCCTTGTAATTAATTGATCTTAACAAAACTACTGAAGGTTAATGTAT
14207 GATATGGTAATTGTCCAATGACTAAAATATTG
66 GATATGGTAATTGTCCAATGACTAAAATATTG
14239 TTGGAAAAGA
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 83 0.90
98 9 0.10
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (98 bp):
AAAAAAAAAATTCAATGGTCCTTGTAATTAATTGATCTTAACAAAACTACTGAAGGTTAATGTAT
GATATGGTAATTGTCCAATGACTAAAATATTGG
Found at i:16709 original size:109 final size:108
Alignment explanation
Indices: 16513--16806 Score: 417
Period size: 109 Copynumber: 2.6 Consensus size: 108
16503 ACTATTATAT
* * *
16513 TTTTATTCTATTAGAAACTCTATTTTTATTCAATTAAATTAAAATTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATT-AAATTAATATCTTTATAATTACTT
16578 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
60 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
16627 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TAATATCTTTATAATTACTTTATTT
* * *
16692 TTACCAAAAAATTTGGATATATTAAATTTTTTTCTAATATATAA
65 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
16736 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATATAATTTTTTTTAT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATT-AATATCTT-TATAA-TTACTTTAT
16801 TTTTAC
63 TTTTAC
16807 AATTTTTAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
108 5 0.03
109 119 0.71
110 8 0.05
111 15 0.09
114 20 0.12
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (108 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTAATATCTTTATAATTACTTTATTTT
TACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:20273 original size:30 final size:30
Alignment explanation
Indices: 20239--21176 Score: 843
Period size: 30 Copynumber: 31.4 Consensus size: 30
20229 CAAATACGAA
20239 TCACCTCCACCTCCACCATAT-TATTACAAG
1 TCACCTCCACCTCCACCATATGT-TTACAAG
* * *
20269 TCACCTCCGCCTCCTCCATAT-TATTACAAA
1 TCACCTCCACCTCCACCATATGT-TTACAAG
* * * *
20299 TCACCTCCTCCACCTCCATACGTTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * * *
20329 TCACCTCCACCACCTCCATACGTGTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20359 TCACCACCACCACCACCCTATGTTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * * *
20389 TCACCACCTCCTCCTCCATACGTTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20419 TCACCTCCACCCCCACCATACGTGTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * * *
20449 TCACCTCCACCTCCTCCATATGTGTATAAA
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * **
20479 TCACCTCCTCCACCACCATACATTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * * *
20509 TCACCGCCACCTCCTCCATATGTGTATAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
*
20539 -----T-CACCTCCACCATATGTCTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20563 TCACCACCACCTCCTCCATACGTTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20593 TCACCTCTACCACCTCCATATGTTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20623 TCACCACCACCACCTCCACCGTATGTCTACAAG
1 T---CACCTCCACCTCCACCATATGTTTACAAG
* * * ** *
20656 TCACCACCACCACCTCCATACATTTATAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
*
20686 TCACCTCCACCACCACCATATGTTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
*
20716 TCACCTCCACCACCACCATATGTTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20746 TCACCTCCACCACCACCATATGTGTACAAC
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * **
20776 TCACCACCACCTCCTCCATACATTTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20806 TCACCCCCACCTCCACCATACGTCTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * * * *
20836 TCACCTCCTCCTCCTCCATACGTGTATAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* *
20866 TCACCTCCACCACCACCATATGTCTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* *
20896 TCACCACCACCTCCACCATATGTCTAC-AG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
20925 CTCCCCTCCCCCTCCACCATATGTCTACAAG
1 -TCACCTCCACCTCCACCATATGTTTACAAG
* ** *
20956 TCACCCCCACCTCCACCATACATCTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * * * * * *
20986 TCACCACCTCCTCCTCCATACGTGTATAAA
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
21016 TCACCCCCACCTCCACCATACGTCTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
21046 TCACCACCTCCTCCACCATATGTCTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * * *
21076 TCACCTCCACCACCGCCATACGTCTACAAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
21106 TCACCACCACCTCCACCATATGTCTA-TAG
1 TCACCTCCACCTCCACCATATGTTTACAAG
* * *
21135 CTCCCCTCCCCCTCCACCATATGTCTACAAG
1 -TCACCTCCACCTCCACCATATGTTTACAAG
21166 TCACCTCCACC
1 TCACCTCCACC
21177 AC
Statistics
Matches: 753, Mismatches: 141, Indels: 28
0.82 0.15 0.03
Matches are distributed among these distances:
24 20 0.03
29 4 0.01
30 700 0.93
31 5 0.01
33 24 0.03
ACGTcount: A:0.27, C:0.43, G:0.07, T:0.23
Consensus pattern (30 bp):
TCACCTCCACCTCCACCATATGTTTACAAG
Found at i:20551 original size:24 final size:24
Alignment explanation
Indices: 20516--20573 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
20506 AAGTCACCGC
* * *
20516 CACCTCCTCCATATGTGTATAAGT
1 CACCTCCACCATATGTCTACAAGT
20540 CACCTCCACCATATGTCTACAAGT
1 CACCTCCACCATATGTCTACAAGT
*
20564 CACCACCACC
1 CACCTCCACC
20574 TCCTCCATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.40, G:0.09, T:0.24
Consensus pattern (24 bp):
CACCTCCACCATATGTCTACAAGT
Done.