Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009800.1 Corchorus capsularis cultivar CVL-1 contig09821, 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: 30907
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:8587 original size:39 final size:39
Alignment explanation
Indices: 8533--8613 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
8523 CCTTTTAGGA
8533 AAATTCCAACTTAATACCAAACCTCTAATTTTTGATACT
1 AAATTCCAACTTAATACCAAACCTCTAATTTTTGATACT
*
8572 AAATTCCAACTTAATACCAAACCTTTAATTTTTGATACT
1 AAATTCCAACTTAATACCAAACCTCTAATTTTTGATACT
8611 AAA
1 AAA
8614 CGTTTCAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (39 bp):
AAATTCCAACTTAATACCAAACCTCTAATTTTTGATACT
Found at i:8733 original size:9 final size:9
Alignment explanation
Indices: 8716--8751 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
8706 GTTATCTACG
*
8716 TATTTTTTT
1 TATTATTTT
8725 TATTATTTT
1 TATTATTTT
8734 TATTA-TTT
1 TATTATTTT
8742 TATTATTTT
1 TATTATTTT
8751 T
1 T
8752 CACTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TATTATTTT
Found at i:8856 original size:2 final size:2
Alignment explanation
Indices: 8849--8880 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
8839 ATTTTAACTA
8849 AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A
8881 CCAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13843 original size:17 final size:17
Alignment explanation
Indices: 13805--13837 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13795 CTCATAGTAC
13805 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
13822 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
13838 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:17487 original size:20 final size:21
Alignment explanation
Indices: 17459--17513 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
17449 CCTGATCTTG
*
17459 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
* *
17479 AGTCGTTTGACTCCTTAAGTTG
1 AGTCATTTGACTCCTTAAG-TA
17501 AG-CATTTGACTCC
1 AGTCATTTGACTCC
17514 ATTATTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Found at i:20471 original size:135 final size:135
Alignment explanation
Indices: 20228--20522 Score: 423
Period size: 135 Copynumber: 2.2 Consensus size: 135
20218 CAGAGGCAGA
* * * *
20228 GCACCAAGCGGCTGTTGGTTTTG-CCCCCGAGTCCTTACCCCCCAAGTCTTTCATCGATGAGACC
1 GCACCAAGCAGTTGTTGGTTTTGCCCCCCGAGTCCTTACCCCCCAAATCTTTCATCAATGAGACC
* * ** * *
20292 AACCTGAGCCATGACCTGTTGATTGTTCACCTGATGGTTAACTTGTCGAAGGGGAAGAGGATCGG
66 AACCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACTTGTCGAAAAGGAAGAGCACCGG
20357 GCTGG
131 GCTGG
*
20362 GCACCAAGCAGTTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAATCTTTCATCAATGAGACC
1 GCACCAAGCAGTTGTTGGTTTTGCCCCCCGAGTCCTTACCCCCCAAATCTTTCATCAATGAGACC
* * * * * *
20427 AATCTCAGCCATGACTTGTGGGTTGTTCACCTGATGGTTGACTTGTTGAAAAGGCAGAGCACCGG
66 AACCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACTTGTCGAAAAGGAAGAGCACCGG
20492 GCTGG
131 GCTGG
20497 GCACCAAGCAGTTGTTGGTTTT-CCCC
1 GCACCAAGCAGTTGTTGGTTTTGCCCC
20523 TCCAAGTATT
Statistics
Matches: 143, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
134 25 0.17
135 118 0.83
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.26
Consensus pattern (135 bp):
GCACCAAGCAGTTGTTGGTTTTGCCCCCCGAGTCCTTACCCCCCAAATCTTTCATCAATGAGACC
AACCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACTTGTCGAAAAGGAAGAGCACCGG
GCTGG
Found at i:24062 original size:166 final size:168
Alignment explanation
Indices: 23685--24075 Score: 536
Period size: 168 Copynumber: 2.3 Consensus size: 168
23675 GGTATAAACA
* * * *
23685 CCTAACTTTTGATTATTGAGGGGATTAAATAACTAGAA-TTTTTGGTCATTTCTCAATTGACTTT
1 CCTAACTTTTGATTCTTGAGGGGATTAAATAAATA-AACTTTTTGGTCATTTCTCAATGGACTTG
* * * * * ** * * *
23749 AATAGAGTAGTGGAATTACTAAAAGATCTCTACCAAGGCTTGCTTTTAGAGTTAGAGAACTTATT
65 AATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATAGAGCTAGAGAACTAATC
*
23814 TTTTTCCGTATTTTCCTACTTGGCAGATTACTTAAATAT
130 TTTTTCCGTATTTACCTACTTGGCAGATTACTTAAATAT
* * *
23853 CCTAACTTTTGATTCTTGAGGGGATTAGATAAGTAATCTTTTTGGTCATTTCTCAATGGACTTGA
1 CCTAACTTTTGATTCTTGAGGGGATTAAATAAATAAACTTTTTGGTCATTTCTCAATGGACTTGA
*
23918 ATAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGGATTGATGAT-GAGCTAGAGAACTAATCT
66 ATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATAGAGCTAGAGAACTAATCT
* * *
23982 TTTT-CGTCTTTACCTACTTGGTAGATTACTTAAATGT
131 TTTTCCGTATTTACCTACTTGGCAGATTACTTAAATAT
* *
24019 CCTAACTTTTAATTCTTGAGGAGATTAAATAAATAAACTTTTTGGTCATTTCTCAAT
1 CCTAACTTTTGATTCTTGAGGGGATTAAATAAATAAACTTTTTGGTCATTTCTCAAT
24076 TGACAAATAA
Statistics
Matches: 196, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
166 81 0.41
167 20 0.10
168 95 0.48
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (168 bp):
CCTAACTTTTGATTCTTGAGGGGATTAAATAAATAAACTTTTTGGTCATTTCTCAATGGACTTGA
ATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATAGAGCTAGAGAACTAATCT
TTTTCCGTATTTACCTACTTGGCAGATTACTTAAATAT
Done.