Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003946.1 Corchorus capsularis cultivar CVL-1 contig03954, 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, 605
Length: 1009
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.25
Found at i:544 original size:57 final size:56
Alignment explanation
Indices: 393--623 Score: 362
Period size: 56 Copynumber: 4.2 Consensus size: 56
383 GAAAGGGGGC
393 AATCAGTAATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTA
449 AATCAGTAATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTAA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGT-A
*
506 AATCAGTAATTAAGTAAAAAGGAGATTAATCA-GGGTCAAAGTAGCAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAA-GAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTA
* * * **
562 AATCAGGAATTAAGT-AAAAGAGATTAATCA-GAGTTAAGGTAATAGTAATCAGT-
1 AATCAGTAATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTA
615 AATCAGTAA
1 AATCAGTAA
624 AAAAGAGTAA
Statistics
Matches: 165, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
53 8 0.05
54 29 0.18
55 4 0.02
56 70 0.42
57 43 0.26
58 11 0.07
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (56 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTA
Found at i:638 original size:113 final size:112
Alignment explanation
Indices: 393--628 Score: 336
Period size: 113 Copynumber: 2.1 Consensus size: 112
383 GAAAGGGGGC
** *
393 AATCAGTAATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTAAATCAGTAA
1 AATCAGTAAAAAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTAAATCAGGAA
*
458 TTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTAA
66 TTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAACAGTAATCAGT-A
** *
506 AATCAGTAATTAAGTAAAAAGGAGATTAATCA-GGGTCAAAGTAGCAGTAATCAGTAAATCAGGA
1 AATCAGTAAAAAAGTAAAAA-GAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTAAATCAGGA
* * *
570 ATTAAGT-AAAAGAGATTAATCA-GAGTTAAGGTAATAGTAATCAGT-
65 ATTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAACAGTAATCAGTA
615 AATCAGTAAAAAAG
1 AATCAGTAAAAAAG
629 AGTAAAAAAA
Statistics
Matches: 114, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
109 12 0.11
111 19 0.17
112 15 0.13
113 57 0.50
114 11 0.10
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (112 bp):
AATCAGTAAAAAAGTAAAAAGAGATTAATCATGAGTCAAAGTAGCAGTAATCAGTAAATCAGGAA
TTAAGTAAAAAGAGATTAATCATGAGTCAAAGTAACAGTAATCAGTA
Found at i:710 original size:26 final size:26
Alignment explanation
Indices: 617--824 Score: 228
Period size: 26 Copynumber: 7.8 Consensus size: 26
607 TAATCAGTAA
*
617 TCAGTAAAAAAGAGTAAAAAAACAATAT
1 TCAGT-AAAAAGAGT-AAGAAACAATAT
*
645 TCAGTAAAAAGAGTAAGAAA-AGGGTCA-
1 TCAGTAAAAAGAGTAAGAAACA--AT-AT
*
672 TCAGTAAATAGAGTAAGAAACAATAT
1 TCAGTAAAAAGAGTAAGAAACAATAT
*
698 TCAGTAAAAAGAGTAAGAAA-AGAGCCA-
1 TCAGTAAAAAGAGTAAGAAACA-A--TAT
*
725 TCAGTAAAAAGAGTAAGAAACAGTAT
1 TCAGTAAAAAGAGTAAGAAACAATAT
*
751 TCAGTAAAAAGAGTAAGAAAAAGAGTCAT
1 TCAGTAAAAAGAGTAAGAAACA-A-T-AT
780 T-AGTAAAAAGAGTAAGAAACAATAT
1 TCAGTAAAAAGAGTAAGAAACAATAT
805 TCAGTAAAAAGAGTAAGAAA
1 TCAGTAAAAAGAGTAAGAAA
825 AGCGTAATAG
Statistics
Matches: 155, Mismatches: 11, Indels: 30
0.79 0.06 0.15
Matches are distributed among these distances:
25 7 0.05
26 66 0.43
27 50 0.32
28 29 0.19
29 3 0.02
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (26 bp):
TCAGTAAAAAGAGTAAGAAACAATAT
Found at i:789 original size:16 final size:13
Alignment explanation
Indices: 647--825 Score: 79
Period size: 13 Copynumber: 13.5 Consensus size: 13
637 AACAATATTC
647 AGTAAAAAGAGTA
1 AGTAAAAAGAGTA
*
660 AG--AAAAGGGTCA
1 AGTAAAAAGAGT-A
*
672 TCAGTAAATAGAGTA
1 --AGTAAAAAGAGTA
* * *
687 AG-AAACAATATTC
1 AGTAAA-AAGAGTA
700 AGTAAAAAGAGTA
1 AGTAAAAAGAGTA
*
713 AG--AAAAGAGCCATC
1 AGTAAAAAGAG---TA
727 AGTAAAAAGAGTA
1 AGTAAAAAGAGTA
* * *
740 AG-AAACAGTATTC
1 AGTAAAAAG-AGTA
753 AGTAAAAAGAGTA
1 AGTAAAAAGAGTA
766 AG-AAAAAGAGTCA
1 AGTAAAAAGAGT-A
779 TTAGTAAAAAGAGTA
1 --AGTAAAAAGAGTA
* * *
794 AG-AAACAATATTC
1 AGTAAA-AAGAGTA
807 AGTAAAAAGAGTA
1 AGTAAAAAGAGTA
820 AG-AAAA
1 AGTAAAA
826 GCGTAATAGT
Statistics
Matches: 122, Mismatches: 24, Indels: 41
0.65 0.13 0.22
Matches are distributed among these distances:
11 14 0.11
12 25 0.20
13 41 0.34
14 16 0.13
15 4 0.03
16 22 0.18
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (13 bp):
AGTAAAAAGAGTA
Found at i:797 original size:54 final size:53
Alignment explanation
Indices: 616--826 Score: 341
Period size: 53 Copynumber: 3.9 Consensus size: 53
606 GTAATCAGTA
* *
616 ATCAGTAAAAAAGAGTAAAAAAACAATATTCAGTAAAAAGAGTAAGAAAAGGGTC
1 ATCAGT-AAAAAGAGT-AAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
* *
671 ATCAGTAAATAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
*
724 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAAGAGTC
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAG-AAAAGAGTC
*
778 ATTAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
827 CGTAATAGTA
Statistics
Matches: 146, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
53 82 0.56
54 58 0.40
55 6 0.04
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
Found at i:809 original size:107 final size:108
Alignment explanation
Indices: 616--826 Score: 354
Period size: 107 Copynumber: 2.0 Consensus size: 108
606 GTAATCAGTA
* *
616 ATCAGTAAAAAAGAGTAAAAAAACAATATTCAGTAAAAAGAGTAAGAAAAGGGTCATCAGTAAAT
1 ATCAGTAAAAAAGAGTAAAAAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAA
681 AGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCC
66 AGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCC
* * *
724 ATCAGT-AAAAAGAGT-AAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAAGAGTCATTAGTAAA
1 ATCAGTAAAAAAGAGTAAAAAAACAATATTCAGTAAAAAGAGTAAG-AAAAGAGTCATCAGTAAA
787 AAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
65 AAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
827 CGTAATAGTA
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
106 27 0.28
107 64 0.66
108 6 0.06
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (108 bp):
ATCAGTAAAAAAGAGTAAAAAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAA
AGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCC
Found at i:979 original size:27 final size:28
Alignment explanation
Indices: 905--980 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
895 AAAGGCAATA
905 CAGTAAAGAGTAAAATGGTAAAAAGTAAT
1 CAGTAAAGAGT-AAATGGTAAAAAGTAAT
* **
934 -GGTAATCAGTAAA-GAGTAAAAAGTAAT
1 CAGTAAAGAGTAAATG-GTAAAAAGTAAT
961 CAGTAAAGAG-AAATGGTAAA
1 CAGTAAAGAGTAAATGGTAAA
981 GAGTTATAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
26 1 0.03
27 23 0.61
28 14 0.37
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (28 bp):
CAGTAAAGAGTAAATGGTAAAAAGTAAT
Done.