Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021862.1 Corchorus olitorius cultivar O-4 contig21895, 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: 15727
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Found at i:9337 original size:26 final size:26
Alignment explanation
Indices: 9289--9343 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
9279 TTTCTATTAT
* *
9289 TTTAATAATGGTATAATTAAAATGTA
1 TTTAATAATGGAATAATTAAAATATA
*
9315 TTTAATAATGGCAAT-ATTGAAATATA
1 TTTAATAATGG-AATAATTAAAATATA
9341 TTT
1 TTT
9344 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (26 bp):
TTTAATAATGGAATAATTAAAATATA
Found at i:9464 original size:114 final size:114
Alignment explanation
Indices: 9257--9487 Score: 335
Period size: 114 Copynumber: 2.0 Consensus size: 114
9247 CGTTGGATCC
* * *
9257 TAATTAATGAGAATAATCTAAATTTCTATTATTTTAATAATGGTATAATTAAAATGTATTTAATA
1 TAATTAATGAGAATAAGCTAAATTTCTATTATTTTAACAATGGAATAATTAAAATGTATTTAATA
* *
9322 ATGGCAATATTGAAATATATTTGAAAAAATAA-GATACAATCGGAAAACA
66 ATGGCAATATAGAAATATATTTGAAAAAA-AAGGATACAATCGAAAAACA
*
9371 TAATTAATGA-AGATAAGCTAAATTT-TCATTATTTTAACAATGGAATAATTAAAATATTATTTA
1 TAATTAATGAGA-ATAAGCTAAATTTCT-ATTATTTTAACAATGGAATAATTAAAAT-GTATTTA
*
9434 ATAATGGCAATATAGAAATATATTTG-AAAAAAAGGGTACAATCGAAAAACA
63 ATAATGGCAATATAGAAATATATTTGAAAAAAAAGGATACAATCGAAAAACA
9485 TAA
1 TAA
9488 AGTTTCTCGT
Statistics
Matches: 106, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
113 4 0.04
114 71 0.67
115 31 0.29
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (114 bp):
TAATTAATGAGAATAAGCTAAATTTCTATTATTTTAACAATGGAATAATTAAAATGTATTTAATA
ATGGCAATATAGAAATATATTTGAAAAAAAAGGATACAATCGAAAAACA
Found at i:9687 original size:43 final size:44
Alignment explanation
Indices: 9596--9698 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 44
9586 TGAATTTTTT
* * *
9596 TATGAAATTTTGATAATTACCCTATTAAATTTTGATAACTACCC
1 TATGAAATTTTGATAATTACCCTATGAAATTGTGATAACTACCA
*
9640 TATGAAATTTTGATAATTA-CGTATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGATAATTACCCTATGAAATTGTGAT-AACTACCA
*
9683 TATGAAACTTTGATAA
1 TATGAAATTTTGATAA
9699 CCTAACTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 30 0.57
44 23 0.43
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAATTACCCTATGAAATTGTGATAACTACCA
Found at i:9713 original size:65 final size:64
Alignment explanation
Indices: 9596--9720 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 64
9586 TGAATTTTTT
* * * * * *
9596 TATGAAATTTTGATAATTACCCTATTAAATTTTGATAACTACCCTATGAAATTTTGATAATTACG
1 TATGAAATTGTGATAA-TACCCTATGAAACTTTGATAACTACACTATAAAATTTTAATAATTACG
9661 TATGAAATTGTGATAA-ACTCCATATGAAACTTTGATAACCTA-ACTATAAAATTTTAATAA
1 TATGAAATTGTGATAATAC-CC-TATGAAACTTTGATAA-CTACACTATAAAATTTTAATAA
9721 ACCTTCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
63 2 0.04
64 2 0.04
65 44 0.86
66 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (64 bp):
TATGAAATTGTGATAATACCCTATGAAACTTTGATAACTACACTATAAAATTTTAATAATTACG
Found at i:9746 original size:21 final size:22
Alignment explanation
Indices: 9596--9781 Score: 127
Period size: 22 Copynumber: 8.5 Consensus size: 22
9586 TGAATTTTTT
9596 TATGAAATTTTGATAA--TTACCC
1 TATGAAATTTTGATAACCTT--CC
* *
9618 TATTAAATTTTGATAA-CTACCC
1 TATGAAATTTTGATAACCT-TCC
*
9640 TATGAAATTTTGATAA--TTACG
1 TATGAAATTTTGATAACCTT-CC
* *
9661 TATGAAATTGTGATAAAC-TCC
1 TATGAAATTTTGATAACCTTCC
* **
9682 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACCTTCC
* *
9705 TATAAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
9728 TATGAAATTTTG-TAACCTTTC
1 TATGAAATTTTGATAACCTTCC
* *
9749 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
9770 TGTGAGATTTTG
1 TATGAAATTTTG
9782 TTAATAATCC
Statistics
Matches: 128, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.05
21 39 0.30
22 65 0.51
23 18 0.14
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:15703 original size:2 final size:2
Alignment explanation
Indices: 15696--15727 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15686 ACAATTTATG
15696 TA 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 TA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.