Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015442.1 Corchorus capsularis cultivar CVL-1 contig15463, 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: 8320
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Found at i:369 original size:38 final size:38
Alignment explanation
Indices: 339--506 Score: 197
Period size: 38 Copynumber: 4.6 Consensus size: 38
329 AATTAAGGAC
* *
339 CAAAGTAATAGTAATCAGTAAAATTGAAAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGAAAATTAAGAGT
* *
377 CAAAGTAAGAATAATCAGTAAAATTGATAATTACGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGAAAATTAAGAGT
*
415 C--A--AAG--TAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGAAAATTAAGAGT
* *
447 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGAAAATTAAGAGT
* *
485 CAAGGTAACG-GTAATCAGTAAA
1 CAAAGTAA-GAATAATCAGTAAA
507 TCAGTAATTA
Statistics
Matches: 115, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
32 27 0.23
34 4 0.03
36 4 0.03
38 79 0.69
39 1 0.01
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.25
Consensus pattern (38 bp):
CAAAGTAAGAATAATCAGTAAAATTGAAAATTAAGAGT
Found at i:431 original size:70 final size:70
Alignment explanation
Indices: 348--492 Score: 254
Period size: 70 Copynumber: 2.1 Consensus size: 70
338 CCAAAGTAAT
* *
348 AGTAATCAGTAAAATTGAAAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTACGA
1 AGTAATCAGTAAAATTGAAAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
413 GTCAA
66 GTCAA
*
418 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
1 AGTAATCAGTAAAATTGAAAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
483 GTCAA
66 GTCAA
*
488 GGTAA
1 AGTAA
493 CGGTAATCAG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.26
Consensus pattern (70 bp):
AGTAATCAGTAAAATTGAAAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
GTCAA
Found at i:598 original size:41 final size:39
Alignment explanation
Indices: 527--628 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 39
517 AGTAGAAAGG
* * * *
527 GATTAATCAGTAATTCGGTAATCAAGAGTCAAGGTAATA
1 GATTAATCAGTAAATCGGTAATAAAGAGTCAAAGTAAAA
*
566 GATTAATTAGTGAAATCGGTAATTAAAGAGTCAAAGTAAAA
1 GATTAATCAGT-AAATCGGTAA-TAAAGAGTCAAAGTAAAA
*
607 GAAGTAATCAGTAAATCGGTAA
1 G-ATTAATCAGTAAATCGGTAA
629 AGAGTAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 10 0.19
40 9 0.17
41 26 0.49
42 8 0.15
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (39 bp):
GATTAATCAGTAAATCGGTAATAAAGAGTCAAAGTAAAA
Found at i:645 original size:16 final size:17
Alignment explanation
Indices: 619--653 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
609 AGTAATCAGT
*
619 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
636 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
652 AA
1 AA
654 GGGTAATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:694 original size:43 final size:43
Alignment explanation
Indices: 641--1041 Score: 292
Period size: 43 Copynumber: 9.4 Consensus size: 43
631 AGTAAAAATG
* ** * * *
641 GTAAAAAGTAAAAGGGTAATCGGTAAGACCAAAATGGTAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
* *
684 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAATCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
**
727 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAAAATA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGT-AACCA
* * * * *
771 GTAAAAAGT--GAT-GATAATCCGTAAAAGGTAAAATGGTAATCA
1 GTAAAGAGTAAAATAG-TAATCAGTAAAA-GCAAAATGGTAACCA
* * *
813 GT-AAGAGCAAAATAGTAATCAGTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAACCA
** **
856 GTAAAGAGTAAAATAGTAA--A--AAAAG--TGATGACAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
* * * * * *
893 ATAAA-AGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCA
1 GTAAAGA-GTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
* *
936 GTAAAGAGCAAAA-AGGTAATCAGTAAGAA-CAAAATGGTAATCA
1 GTAAAGAGTAAAATA-GTAATCAGTAA-AAGCAAAATGGTAACCA
* * * * *
979 ATAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAA-GATGATCA
1 GTAAAGAGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAACCA
1023 GTAAAGAGTAAAATAGTAA
1 GTAAAGAGTAAAATAGTAA
1042 AAAGTAATCA
Statistics
Matches: 286, Mismatches: 48, Indels: 47
0.75 0.13 0.12
Matches are distributed among these distances:
36 2 0.01
37 20 0.07
39 6 0.02
41 9 0.03
42 19 0.07
43 164 0.57
44 64 0.22
45 2 0.01
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.19
Consensus pattern (43 bp):
GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
Found at i:696 original size:22 final size:22
Alignment explanation
Indices: 641--1041 Score: 275
Period size: 22 Copynumber: 18.9 Consensus size: 22
631 AGTAAAAATG
* * *
641 GTAAAAAGTAAAAGGGTAATCG
1 GTAAAGAGTAAAATGGTAATCA
** *
663 GT-AAGACCAAAATGGTAACCA
1 GTAAAGAGTAAAATGGTAATCA
*
684 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
706 GTAAA-AGCAAAATGGGAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
727 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
749 GTAAA-AGCAAAATGGTAAAAT-A
1 GTAAAGAGTAAAATGGT--AATCA
* * * *
771 GTAAAAAGT--GATGATAATCC
1 GTAAAGAGTAAAATGGTAATCA
791 GTAAA-AGGTAAAATGGTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
* *
813 GT-AAGAGCAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
834 GTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAA-AATGGTAATCA
*
856 GTAAAGAGTAAAATAGTAA--A
1 GTAAAGAGTAAAATGGTAATCA
* ** *
876 --AAA-AGT--GATGACAACCA
1 GTAAAGAGTAAAATGGTAATCA
*
893 ATAAAAG-GTAAAATGGTAATCA
1 GT-AAAGAGTAAAATGGTAATCA
** *
915 GT-AAGAGCGAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
936 GTAAAGAGCAAAAAGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
**
958 GT-AAGAACAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
979 ATAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
1001 GTAAAAAGTAAGAA-GATGATCA
1 GTAAAGAGTAA-AATGGTAATCA
*
1023 GTAAAGAGTAAAATAGTAA
1 GTAAAGAGTAAAATGGTAA
1042 AAAGTAATCA
Statistics
Matches: 291, Mismatches: 62, Indels: 52
0.72 0.15 0.13
Matches are distributed among these distances:
15 4 0.01
17 4 0.01
18 3 0.01
19 4 0.01
20 16 0.05
21 99 0.34
22 152 0.52
23 9 0.03
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.19
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:928 original size:102 final size:101
Alignment explanation
Indices: 686--961 Score: 333
Period size: 102 Copynumber: 2.6 Consensus size: 101
676 GGTAACCAGT
* * * * *
686 AAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAATCAGTAAAGAGTAAAATAGTAATCAGT
1 AAAG-GTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAAAA-GGTAATCAGT
* *
751 AAAAGCAAAATGGTAAAATAGTAAAAAGTGATGATAATCCGTA
64 -AAAG---AA-GGTAAAATAGTAAAAAGTGATGACAATCCATA
*
794 AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
1 AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAA-AAGGTAATCAGTA
859 AAG-A-GTAAAATAGTAAAAAAAGTGATGACAA-CCAATA
65 AAGAAGGTAAAATAGT--AAAAAGTGATGACAATCC-ATA
* *
896 AAAGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAAAGGTAATCAGTA
1 AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAG-TAAAAGGTAATCAGTA
961 A
65 A
962 GAACAAAATG
Statistics
Matches: 152, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
100 10 0.07
101 2 0.01
102 77 0.51
103 2 0.01
106 4 0.03
107 51 0.34
108 6 0.04
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (101 bp):
AAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAAAAGGTAATCAGTAA
AGAAGGTAAAATAGTAAAAAGTGATGACAATCCATA
Found at i:1023 original size:65 final size:64
Alignment explanation
Indices: 902--1026 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 64
892 AATAAAAGGT
* * * *
902 AAAATGGTAATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAAAGGTAATCAGTAAGAAC
1 AAAATGGTAATCAATAAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAAGAAC
* * * *
966 AAAATGGTAATCAATAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGATGATCAGTAA
1 AAAATGGTAATCAAT-AAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAA
1027 AGAGTAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
64 14 0.27
65 38 0.73
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (64 bp):
AAAATGGTAATCAATAAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAAGAAC
Found at i:1047 original size:22 final size:21
Alignment explanation
Indices: 980--1070 Score: 56
Period size: 22 Copynumber: 4.1 Consensus size: 21
970 TGGTAATCAA
**
980 TAAAGAGTAAAATAGTAATCAG
1 TAAAGAGTAAAA-AGTAAAAAG
* * * **
1002 TAAAAAGTAAGAAGATGATCAG
1 TAAAGAGTAAAAAG-TAAAAAG
1024 TAAAGAGTAAAATAGTAAAAAG
1 TAAAGAGTAAAA-AGTAAAAAG
** *
1046 TAATCAGTAAAAGGTAAAATAG
1 TAAAGAGTAAAAAGTAAAA-AG
1068 TAA
1 TAA
1071 TCAGTAGGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
21 8 0.15
22 45 0.82
23 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.19, T:0.21
Consensus pattern (21 bp):
TAAAGAGTAAAAAGTAAAAAG
Found at i:1076 original size:29 final size:29
Alignment explanation
Indices: 1000--1070 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
990 AATAGTAATC
* *
1000 AGTAAAA-AGTAAGAAGATGATCAGTAAAG
1 AGTAAAATAGTAAAAAG-TAATCAGTAAAG
1029 AGTAAAATAGTAAAAAGTAATCAGTAAA-
1 AGTAAAATAGTAAAAAGTAATCAGTAAAG
1057 AGGTAAAATAGTAA
1 A-GTAAAATAGTAA
1071 TCAGTAGGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 1 0.03
29 29 0.76
30 8 0.21
ACGTcount: A:0.58, C:0.03, G:0.20, T:0.20
Consensus pattern (29 bp):
AGTAAAATAGTAAAAAGTAATCAGTAAAG
Done.