Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002842.1 Corchorus capsularis cultivar CVL-1 contig02850, 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, 710
Length: 1184
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Found at i:55 original size:37 final size:37
Alignment explanation
Indices: 10--80 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1 GGTAAAAAG
10 TAGTAATCA-AAAATTAAATAACTAAGAGTCAAGGTAA
1 TAGTAATCATAAAA-TAAATAACTAAGAGTCAAGGTAA
* * *
47 TAGTAATCATTAAATAAGTAATTAAGAGTCAAGG
1 TAGTAATCATAAAATAAATAACTAAGAGTCAAGG
81 CGAAAATAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 27 0.90
38 3 0.10
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (37 bp):
TAGTAATCATAAAATAAATAACTAAGAGTCAAGGTAA
Found at i:404 original size:7 final size:7
Alignment explanation
Indices: 392--898 Score: 151
Period size: 7 Copynumber: 70.9 Consensus size: 7
382 AGTACTAATC
392 AGTAAAG
1 AGTAAAG
399 AGTAAA-
1 AGTAAAG
*
405 ATGGTGAAG
1 A--GTAAAG
*
414 AGTCAAG
1 AGTAAAG
**
421 AGTAATC
1 AGTAAAG
428 AGTAAAG
1 AGTAAAG
*
435 AGTAAAAT
1 AGT-AAAG
443 AGTGAAA-
1 AGT-AAAG
450 AGTAAAG
1 AGTAAAG
* **
457 ACTAATC
1 AGTAAAG
464 AGTAAA-
1 AGTAAAG
470 AGGTAAA-
1 A-GTAAAG
477 ATGGTAAAG
1 A--GTAAAG
*
486 AGTCAAG
1 AGTAAAG
* **
493 AGCAATC
1 AGTAAAG
500 AGTAAAG
1 AGTAAAG
*
507 AGTAGAAT
1 AGTA-AAG
*
515 AGTAAAA
1 AGTAAAG
*
522 AGTAAAA
1 AGTAAAG
**
529 AGTAATC
1 AGTAAAG
536 AGTAAAG
1 AGTAAAG
*
543 AGTAAAAT
1 AGT-AAAG
551 AGTAAAG
1 AGTAAAG
** *
558 AGTCGAT
1 AGTAAAG
* **
565 AGCAATC
1 AGTAAAG
572 AGTAAAG
1 AGTAAAG
*
579 AGTAGAAT
1 AGTA-AAG
*
587 AGTAAAA
1 AGTAAAG
**
594 AGTAATC
1 AGTAAAG
601 AGTAAAG
1 AGTAAAG
608 -GTAAA-
1 AGTAAAG
613 ATGGTAAAG
1 A--GTAAAG
622 AGTAAAG
1 AGTAAAG
**
629 AGTAATC
1 AGTAAAG
636 AGTAAAG
1 AGTAAAG
643 AGTAAA-
1 AGTAAAG
649 ATGGTAAAG
1 A--GTAAAG
*
658 AGTCAAG
1 AGTAAAG
**
665 AGTAATC
1 AGTAAAG
672 AGTAAAG
1 AGTAAAG
* *
679 ATTAAAAT
1 AGT-AAAG
*
687 AGTAAAA
1 AGTAAAG
694 AG-AAAG
1 AGTAAAG
**
700 AGTAATC
1 AGTAAAG
707 AGT-AAG
1 AGTAAAG
713 AGGTAAA-
1 A-GTAAAG
*
720 ATGATAAAA
1 A-G-TAAAG
729 AGTAAAG
1 AGTAAAG
**
736 AGTAATC
1 AGTAAAG
*
743 AGTAAAA
1 AGTAAAG
*
750 AGTAGAAT
1 AGTA-AAG
*
758 AGTAAAA
1 AGTAAAG
*
765 AGTAAAA
1 AGTAAAG
**
772 AGTAATC
1 AGTAAAG
779 AGTAAAG
1 AGTAAAG
786 AGTAAA-
1 AGTAAAG
792 ATGGTAAAG
1 A--GTAAAG
*
801 AGTCAAG
1 AGTAAAG
* **
808 TGTAATC
1 AGTAAAG
*
815 AGTCAAG
1 AGTAAAG
*
822 AGTAAAAT
1 AGT-AAAG
*
830 AGTAAAA
1 AGTAAAG
837 AG-AAAG
1 AGTAAAG
**
843 AGTAATC
1 AGTAAAG
850 AGT-AAG
1 AGTAAAG
856 AGGTAAA-
1 A-GTAAAG
*
863 ATGGTAAAA
1 A--GTAAAG
872 AGTAAAG
1 AGTAAAG
**
879 AGTAATC
1 AGTAAAG
*
886 AGTAAAA
1 AGTAAAG
893 AGTAAA
1 AGTAAA
899 ATGGTAAAAA
Statistics
Matches: 366, Mismatches: 100, Indels: 68
0.69 0.19 0.13
Matches are distributed among these distances:
6 26 0.07
7 250 0.68
8 83 0.23
9 7 0.02
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (7 bp):
AGTAAAG
Found at i:428 original size:36 final size:36
Alignment explanation
Indices: 387--954 Score: 640
Period size: 36 Copynumber: 16.1 Consensus size: 36
377 TAATCAGTAC
* * *
387 TAATCAGTAAAGAGTAAAATGGTGAAGAGTCAAGAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* * *
423 TAATCAGTAAAGAGTAAAATAGTGAAAAGTAAAGAC
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* *
459 TAATCAGTAAA-AGGTAAAATGGTAAAGAGTCAAGAG
1 TAATCAGTAAAGA-GTAAAATGGTAAAAAGTAAAGAG
* * * *
495 CAATCAGTAAAGAGTAGAATAGTAAAAAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* * ** *
531 TAATCAGTAAAGAGTAAAATAGTAAAGAGTCGATAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* * *
567 CAATCAGTAAAGAGT---A--G--AATAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
*
596 TAATCAGTAAAG-GTAAAATGGTAAAGAGTAAAGAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* *
631 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* *
667 TAATCAGTAAAGATTAAAATAGTAAAAAG-AAAGAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
*
702 TAATCAGT-AAGAGGTAAAATGATAAAAAGTAAAGAG
1 TAATCAGTAAAGA-GTAAAATGGTAAAAAGTAAAGAG
* * * *
738 TAATCAGTAAAAAGTAGAATAGTAAAAAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* * *
774 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGTG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* *
810 TAATCAGTCAAGAGTAAAATAGTAAAAAG-AAAGAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
845 TAATCAGT-AAGAGGTAAAATGGTAAAAAGTAAAGAG
1 TAATCAGTAAAGA-GTAAAATGGTAAAAAGTAAAGAG
* * *
881 TAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAA
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
* * * *
917 TAATCAGCAAAAAGTAAAATGGTAAATAGTAAATAG
1 TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
953 TA
1 TA
955 GTAAAGTGAA
Statistics
Matches: 454, Mismatches: 62, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.00
29 19 0.04
31 2 0.00
33 2 0.00
34 8 0.02
35 76 0.17
36 338 0.74
37 7 0.02
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.20
Consensus pattern (36 bp):
TAATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAG
Found at i:632 original size:28 final size:29
Alignment explanation
Indices: 500--954 Score: 124
Period size: 29 Copynumber: 15.4 Consensus size: 29
490 AAGAGCAATC
* *
500 AGTAAAGAGTAGAATAGTAAAA-AGTAAAA
1 AGTAAACAGTA-AAGAGTAAAATAGTAAAA
*
529 AGTAATCAGTAAAGAGTAAAATAGTAAAGA
1 AGTAAACAGTAAAGAGTAAAATAGTAAA-A
* *
559 GTCGATAGCAATCAGTAAAGAGTAGAATAGTAAAA
1 --AG-TA--AA-CAGTAAAGAGTAAAATAGTAAAA
* *
594 AGTAATCAGTAAAG-GTAAAATGGTAAAGAGTAAAG
1 AGTAAACAGTAAAGAGTAAAA---T----AGTAAAA
* * *
629 AGTAATCAGTAAAGAGTAAAATGGTAAAG
1 AGTAAACAGTAAAGAGTAAAATAGTAAAA
* * **
658 AGTCAAGAGTAATCAGTAAAGAT--TAAAA
1 AGTAAACAGTAAAGAGTAAA-ATAGTAAAA
* *
686 TAGTAAAAAG-AAAGAGT--AATCAGTAAGA
1 -AGTAAACAGTAAAGAGTAAAAT-AGTAAAA
* * * **
714 GGTAAA-ATGATAAAAAGT-AAAGAGTAATC
1 AGTAAACA-G-TAAAGAGTAAAATAGTAAAA
* *
743 AGTAAAAAGTAGAATAGTAAAA-AGTAAAA
1 AGTAAACAGTA-AAGAGTAAAATAGTAAAA
* *
772 AGTAATCAGTAAAGAGTAAAATGGTAAAGAGTCA
1 AGTAAACAGTAAAGAGTAAAATAGT-AA-A---A
* *
806 AGTGTAATCAGTCAAGAGTAAAATAGTAAAA
1 A--GTAAACAGTAAAGAGTAAAATAGTAAAA
* ** * *
837 AG-AAAGAGTAATCAGTAAGA-GGTAAAA
1 AGTAAACAGTAAAGAGTAAAATAGTAAAA
* *
864 TGGTAAAAAGTAAAGAGT--AATCAGTAAAA
1 -AGTAAACAGTAAAGAGTAAAAT-AGTAAAA
893 AGTAAA-A-T---G-GTAAAA-AGTAAAA
1 AGTAAACAGTAAAGAGTAAAATAGTAAAA
* * * * * *
915 AATAATCAGCAAAAAGTAAAATGGTAAAT
1 AGTAAACAGTAAAGAGTAAAATAGTAAAA
*
944 AGTAAATAGTA
1 AGTAAACAGTA
955 GTAAAGTGAA
Statistics
Matches: 316, Mismatches: 61, Indels: 98
0.67 0.13 0.21
Matches are distributed among these distances:
22 13 0.04
23 2 0.01
24 2 0.01
25 2 0.01
26 3 0.01
27 14 0.04
28 62 0.20
29 119 0.38
30 12 0.04
31 4 0.01
32 3 0.01
33 4 0.01
34 3 0.01
35 24 0.08
36 49 0.16
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (29 bp):
AGTAAACAGTAAAGAGTAAAATAGTAAAA
Found at i:815 original size:143 final size:143
Alignment explanation
Indices: 387--942 Score: 675
Period size: 143 Copynumber: 3.9 Consensus size: 143
377 TAATCAGTAC
* * * * *
387 TAATCAGTAAAGAGTAAAATGGTGAAGAGTCAAGAGTAATCAGTAAAGAGTAAAAT-AGTGAAAA
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGTAATCAGTAAAG-GTAAAATGA-TAAAAA
* * * * * * * *
451 GTAAAGACTAATCAGTAAAAGGTAAAATGGTAAAGAGTCAAGAGCAATCAGTAAAGAGTAGAATA
64 GTAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGAGTAAAATG
* * *
516 GTAAAAAGTAAAAAG
129 GTAAAGAGTCAAGAG
* ** * * *
531 TAATCAGTAAAGAGTAAAATAGTAAAGAGTCGATAGCAATCAGTAAA-G----A-G-TAGAATAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGTAATCAGTAAAGGTAAAATGATA-AAAAG
* * * *
589 TAAAAAGTAATCAGT-AAAGGTAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATGG
65 TAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGAGTAAAATGG
653 TAAAGAGTCAAGAG
130 TAAAGAGTCAAGAG
*
667 TAATCAGTAAAGATTAAAATAGTAAAAAG-AAAGAGTAATCAGTAAGAGGTAAAATGATAAAAAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGTAATCAGTAA-AGGTAAAATGATAAAAAG
* *
731 TAAAGAGTAATCAGTAAAAAGTAGAATAGTAAAAAGTAAAAAGTAATCAGTAAAGAGTAAAATGG
65 TAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGAGTAAAATGG
*
796 TAAAGAGTCAAGTG
130 TAAAGAGTCAAGAG
* *
810 TAATCAGTCAAGAGTAAAATAGTAAAAAG-AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGTAATCAGTAA-AGGTAAAATGATAAAAAG
* * *
874 TAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAATAATCAGCAAAAAGTAAAATGG
65 TAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGAGTAAAATGG
939 TAAA
130 TAAA
943 TAGTAAATAG
Statistics
Matches: 363, Mismatches: 38, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
135 12 0.03
136 85 0.23
137 18 0.05
138 1 0.00
141 1 0.00
142 20 0.06
143 184 0.51
144 42 0.12
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.19
Consensus pattern (143 bp):
TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGTAATCAGTAAAGGTAAAATGATAAAAAGT
AAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGAGTAAAATGGT
AAAGAGTCAAGAG
Found at i:905 original size:22 final size:21
Alignment explanation
Indices: 500--913 Score: 126
Period size: 22 Copynumber: 19.6 Consensus size: 21
490 AAGAGCAATC
* *
500 AGTAAAGAGTAGAATAGTAAAA
1 AGTAAAAAGTA-AAGAGTAAAA
** *
522 AGTAAAAAGTAATCAGTAAAG
1 AGTAAAAAGTAAAGAGTAAAA
** *
543 AGTAAAATAGTAAAGAGTCGAT
1 AGTAAAA-AGTAAAGAGTAAAA
* ** *
565 AGCAATCAGTAAAGAGTAGAAT
1 AGTAAAAAGTAAAGAGTA-AAA
**
587 AGTAAAAAGTAATCAGT-AAA
1 AGTAAAAAGTAAAGAGTAAAA
* * *
607 GGTAAAATGGTAAAGAGTAAAG
1 AGTAAAA-AGTAAAGAGTAAAA
**
629 AGTAATCAGTAAAGAGTAAAA
1 AGTAAAAAGTAAAGAGTAAAA
* * * **
650 TGGTAAAGAGTCAAGAGTAATC
1 -AGTAAAAAGTAAAGAGTAAAA
* * *
672 AGTAAAGATTAAAATAGTAAAA
1 AGTAAAAAGT-AAAGAGTAAAA
* ** *
694 AG-AAAGAGTAATCAGTAAGA
1 AGTAAAAAGTAAAGAGTAAAA
*
714 GGT-AAAA-T---GA-TAAAA
1 AGTAAAAAGTAAAGAGTAAAA
* **
729 AGTAAAGAGTAATCAGTAAAA
1 AGTAAAAAGTAAAGAGTAAAA
* *
750 AGTAGAATAGTAAAAAGTAAAA
1 AGTA-AAAAGTAAAGAGTAAAA
**
772 AGTAATCAGTAAAGAGTAAAA
1 AGTAAAAAGTAAAGAGTAAAA
* * * * **
793 TGGTAAAGAGTCAAGTGTAATC
1 -AGTAAAAAGTAAAGAGTAAAA
* * *
815 AGTCAAGAGTAAAATAGTAAAA
1 AGTAAAAAGT-AAAGAGTAAAA
* ** *
837 AG-AAAGAGTAATCAGTAAGA
1 AGTAAAAAGTAAAGAGTAAAA
* * * *
857 GGTAAAATGGTAAAAAGTAAAG
1 AGTAAAA-AGTAAAGAGTAAAA
** *
879 AGTAATCAGTAAAAAGTAAAA
1 AGTAAAAAGTAAAGAGTAAAA
*
900 TGGTAAAAAGTAAA
1 -AGTAAAAAGTAAA
914 AAATAATCAG
Statistics
Matches: 281, Mismatches: 92, Indels: 38
0.68 0.22 0.09
Matches are distributed among these distances:
15 6 0.02
16 4 0.01
17 1 0.00
19 1 0.00
20 30 0.11
21 109 0.39
22 130 0.46
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (21 bp):
AGTAAAAAGTAAAGAGTAAAA
Found at i:1044 original size:24 final size:25
Alignment explanation
Indices: 984--1057 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 25
974 CAGTAAAGTA
*
984 AAAAAG-GTAAAATTGGTATTCAGT
1 AAAAAGAGTAAAAATGGTATTCAGT
** *
1008 AGTAA-AGTGAAAATGGTATTCAGT
1 AAAAAGAGTAAAAATGGTATTCAGT
1032 AAAAAGAGTAAAAATGG--TTCAGT
1 AAAAAGAGTAAAAATGGTATTCAGT
1055 AAA
1 AAA
1058 GTAAAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
23 9 0.22
24 22 0.54
25 10 0.24
ACGTcount: A:0.49, C:0.04, G:0.22, T:0.26
Consensus pattern (25 bp):
AAAAAGAGTAAAAATGGTATTCAGT
Found at i:1062 original size:49 final size:51
Alignment explanation
Indices: 951--1055 Score: 137
Period size: 54 Copynumber: 2.1 Consensus size: 51
941 AATAGTAAAT
*
951 AGTAGTAAAGTGAAAATGGTATTCAGTAAAGTAAAAAAGGTAAAATTGGTATTC
1 AGTAGTAAAGTGAAAATGGTATTCAGT-AAG-AAAAAAGGTAAAAATGG-ATTC
*
1005 AGTAGTAAAGTGAAAATGGTATTCAGT-A-AAAAGA-GTAAAAATGG-TTC
1 AGTAGTAAAGTGAAAATGGTATTCAGTAAGAAAAAAGGTAAAAATGGATTC
1052 AGTA
1 AGTA
1056 AAGTAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
47 7 0.14
49 9 0.18
50 5 0.10
52 1 0.02
54 27 0.55
ACGTcount: A:0.47, C:0.04, G:0.23, T:0.27
Consensus pattern (51 bp):
AGTAGTAAAGTGAAAATGGTATTCAGTAAGAAAAAAGGTAAAAATGGATTC
Found at i:1143 original size:24 final size:25
Alignment explanation
Indices: 1112--1181 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
1102 GGATATTAAG
1112 CAAAAATGGTA-AAGTAAAAAAAGT
1 CAAAAATGGTATAAGTAAAAAAAGT
* **
1136 CAAAAATGGTATCAGTAAAAAGGGT
1 CAAAAATGGTATAAGTAAAAAAAGT
1161 CAAAAAATGGTATCAAGTAAA
1 C-AAAAATGGTAT-AAGTAAA
1182 GTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
24 11 0.28
25 11 0.28
26 11 0.28
27 6 0.15
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (25 bp):
CAAAAATGGTATAAGTAAAAAAAGT
Found at i:1166 original size:26 final size:25
Alignment explanation
Indices: 1112--1181 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 25
1102 GGATATTAAG
*
1112 CAAAAATGGTA-AAGTAAAAAAAGT
1 CAAAAATGGTATCAGTAAAAAAAGT
**
1136 CAAAAATGGTATCAGTAAAAAGGGT
1 CAAAAATGGTATCAGTAAAAAAAGT
1161 CAAAAAATGGTATCAAGTAAA
1 C-AAAAATGGTATC-AGTAAA
1182 GTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 11 0.28
25 11 0.28
26 12 0.30
27 6 0.15
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (25 bp):
CAAAAATGGTATCAGTAAAAAAAGT
Done.