Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003787.1 Corchorus capsularis cultivar CVL-1 contig03795, 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, 711
Length: 1186
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Found at i:193 original size:40 final size:42
Alignment explanation
Indices: 114--206 Score: 120
Period size: 40 Copynumber: 2.3 Consensus size: 42
104 GGCAAGAGAT
* *
114 TAATCAGTGAAATCAGTAATTAAAGAGTCAAAGTAAAAGAAG
1 TAATCAGTAAAATCAGTAATTAAAGAATCAAAGTAAAAGAAG
*
156 TAATCAGTAAAAT-GGTAATTAAA-AAT-AAGAGTAAAAGAAG
1 TAATCAGTAAAATCAGTAATTAAAGAATCAA-AGTAAAAGAAG
*
196 CAATCAGTAAA
1 TAATCAGTAAA
207 TCGATAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 2 0.04
40 23 0.50
41 9 0.20
42 12 0.26
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.22
Consensus pattern (42 bp):
TAATCAGTAAAATCAGTAATTAAAGAATCAAAGTAAAAGAAG
Found at i:250 original size:22 final size:22
Alignment explanation
Indices: 222--505 Score: 212
Period size: 22 Copynumber: 13.1 Consensus size: 22
212 AAAGAGTAAA
222 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAAAGTAA-AATGGT
* *
244 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAATGGT
* ** *
266 AATCAGT-GAGGGCAAAATGGT
1 AATCAGTAAAAAGTAAAATGGT
*
287 AATCAGTAGAAAGTAAGAA-GGT
1 AATCAGTAAAAAGTAA-AATGGT
* *
309 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAATGGT
* * *
331 AATTAGTAAAAGGT--AATCAGT
1 AATCAGTAAAAAGTAAAAT-GGT
* * * *
352 AA-GAGCAAAATGGTAAAATAGT
1 AATCAGTAAAA-AGTAAAATGGT
374 AATCAGTAAAAAGTAAAATGGT
1 AATCAGTAAAAAGTAAAATGGT
* *
396 AATCAGTAAAGAGTAAAATCGT
1 AATCAGTAAAAAGTAAAATGGT
*
418 AAAATC-GTAAAAAGTGATAA---T
1 --AATCAGTAAAAAGT-AAAATGGT
*
439 AATCAGTAAAAGGTAAAATGGT
1 AATCAGTAAAAAGTAAAATGGT
* *
461 AATCAGT-AAGAGCAAAATGGT
1 AATCAGTAAAAAGTAAAATGGT
* *
482 AATCAGTAAAGAGTAAAATCGT
1 AATCAGTAAAAAGTAAAATGGT
504 AA
1 AA
506 AAAGTGATAA
Statistics
Matches: 213, Mismatches: 32, Indels: 34
0.76 0.11 0.12
Matches are distributed among these distances:
19 7 0.03
20 17 0.08
21 48 0.23
22 115 0.54
23 19 0.09
24 7 0.03
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.21
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAAATGGT
Found at i:291 original size:65 final size:65
Alignment explanation
Indices: 222--685 Score: 305
Period size: 65 Copynumber: 7.4 Consensus size: 65
212 AAAGAGTAAA
* *
222 AATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT-GAGGGCAAAATGG
1 AATCAGTAAAAAGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATGG
286 T
65 T
* * ** *
287 AATCAGTAGAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATTAGTAAA-AG-GTAATCA
1 AATCAGTAAAAAGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAAT-G
350 GT
64 GT
* * * * * * * *
352 AA-GAGCAAAATGGTAAAATAGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATC
1 AATCAGTAAAA-AGTAAAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATG
416 GT
64 GT
* *
418 AAAATC-GTAAAAAGTGATAA--TAATCAGTAAA-AGGTAAAATGGTAATCAGT-AAGAGCAAAA
1 --AATCAGTAAAAAGT-AAAAGGTAATCAGTAAAGA-GTAAAATAGTAATCAGTAAAGAGCAAAA
478 TGGT
62 TGGT
* * * * *
482 AATCAGTAAAGAGT--AA---AATC-GTAAAAAGT--GATAATAATCAGTAAA-AGGTAAAATGG
1 AATCAGTAAAAAGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAGA-GCAAAATGG
538 T
65 T
* * * *
539 AATCAGT-AAGAGCAAAATGGTAATCAGTAAAGGGTAAAA-GGTAATCAGT-AAGAGCAAAATGG
1 AATCAGTAAAAAGTAAAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATGG
601 T
65 T
* * * * * * *
602 AATCACTAAAGAGT-AAA---AATCAGTAAAAAGTAAGAA-GGTTATCAGTAAAGAGTAAAATAG
1 AATCAGTAAAAAGTAAAAGGTAATCAGTAAAGAGTAA-AATAGTAATCAGTAAAGAGCAAAATGG
662 T
65 T
** **
663 AAAAAGTAATCAGTAAAAGGTAA
1 AATCAGTAAAAAGTAAAAGGTAA
686 AATAGTAATC
Statistics
Matches: 319, Mismatches: 48, Indels: 64
0.74 0.11 0.15
Matches are distributed among these distances:
56 16 0.05
57 18 0.06
58 9 0.03
59 19 0.06
60 13 0.04
61 21 0.07
62 11 0.03
63 35 0.11
64 37 0.12
65 120 0.38
66 5 0.02
67 5 0.02
68 10 0.03
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (65 bp):
AATCAGTAAAAAGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATGGT
Found at i:371 original size:43 final size:44
Alignment explanation
Indices: 321--603 Score: 127
Period size: 43 Copynumber: 6.1 Consensus size: 44
311 TCAGTAAAGA
321 GTAAAATAGTAATTAGTAAAA-GGTAATCAGTAAGAGCAAAATG
1 GTAAAATAGTAATTAGTAAAATGGTAATCAGTAAGAGCAAAATG
* *
364 GTAAAATAGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATC
1 GTAAAATAGTAAT---T----AGTAAAATGGTAATCAGT-AAGAGCAAAATG
* ** * * *
416 GTAAAATCGTAAAAAGTGATAA---TAATCAGTAAAAGGTAAAATG
1 GTAAAATAGTAATTAGT-AAAATGGTAATCAGTAAGA-GCAAAATG
* * * *
459 GT--AATCAGTAA-GAGCAAAATGGTAATCAGTAAAGAGTAAAATC
1 GTAAAAT-AGTAATTAGTAAAATGGTAATCAGT-AAGAGCAAAATG
*
502 GTAAAAAGTGATAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATG
1 GT--AAA---ATAGTAAT---T---A-GTAAAATGGTAATCAGTAAGAGCAAAATG
***
558 GT--AATCAGTAAAGGGTAAAA-GGTAATCAGTAAGAGCAAAATG
1 GTAAAAT-AGTAATTAGTAAAATGGTAATCAGTAAGAGCAAAATG
600 GTAA
1 GTAA
604 TCACTAAAGA
Statistics
Matches: 183, Mismatches: 23, Indels: 67
0.67 0.08 0.25
Matches are distributed among these distances:
40 3 0.02
41 5 0.03
42 31 0.17
43 53 0.29
44 3 0.02
45 3 0.02
46 4 0.02
47 1 0.01
49 6 0.03
50 13 0.07
51 10 0.05
52 22 0.12
56 13 0.07
57 16 0.09
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.22
Consensus pattern (44 bp):
GTAAAATAGTAATTAGTAAAATGGTAATCAGTAAGAGCAAAATG
Found at i:374 original size:36 final size:37
Alignment explanation
Indices: 298--375 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 37
288 ATCAGTAGAA
* *
298 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATT
1 AGTAAGAAGGTAATCAGTAAAGAGCAAAATAGTAAAT
*
335 AGTAA-AAGGTAATCAGT-AAGAGCAAAATGGTAAAAT
1 AGTAAGAAGGTAATCAGTAAAGAGCAAAATAGT-AAAT
371 AGTAA
1 AGTAA
376 TCAGTAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 12 0.32
36 20 0.54
37 5 0.14
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.22
Consensus pattern (37 bp):
AGTAAGAAGGTAATCAGTAAAGAGCAAAATAGTAAAT
Found at i:457 original size:35 final size:35
Alignment explanation
Indices: 407--540 Score: 126
Period size: 35 Copynumber: 3.6 Consensus size: 35
397 ATCAGTAAAG
*
407 AGTAAAATCGTAAAATCGTAAAAAGTGATAATAATC
1 AGTAAAA-GGTAAAATCGTAAAAAGTGATAATAATC
* * *
443 AGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATC
1 AGTAAAAGGTAAAATCGTAA--A--AAGTG-ATAA---TAATC
486 AGT-AAAGAGTAAAATCGTAAAAAGTGATAATAATC
1 AGTAAAAG-GTAAAATCGTAAAAAGTGATAATAATC
*
521 AGTAAAAGGTAAAATGGTAA
1 AGTAAAAGGTAAAATCGTAA
541 TCAGTAAGAG
Statistics
Matches: 80, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
35 30 0.38
36 11 0.14
37 1 0.01
38 3 0.04
39 8 0.10
40 3 0.04
41 1 0.01
42 4 0.05
43 19 0.24
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.22
Consensus pattern (35 bp):
AGTAAAAGGTAAAATCGTAAAAAGTGATAATAATC
Found at i:504 original size:78 final size:78
Alignment explanation
Indices: 416--577 Score: 315
Period size: 78 Copynumber: 2.1 Consensus size: 78
406 GAGTAAAATC
416 GTAAAATCGTAAAAAGTGATAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
1 GTAAAATCGTAAAAAGTGATAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
481 TAATCAGTAAAGA
66 TAATCAGTAAAGA
494 GTAAAATCGTAAAAAGTGATAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
1 GTAAAATCGTAAAAAGTGATAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
*
559 TAATCAGTAAAGG
66 TAATCAGTAAAGA
572 GTAAAA
1 GTAAAA
578 GGTAATCAGT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.22
Consensus pattern (78 bp):
GTAAAATCGTAAAAAGTGATAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
TAATCAGTAAAGA
Found at i:557 original size:21 final size:21
Alignment explanation
Indices: 516--606 Score: 121
Period size: 21 Copynumber: 4.3 Consensus size: 21
506 AAAGTGATAA
* *
516 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAGA-GCAAAATGG
538 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGCAAAATGG
* *
559 TAATCAGTAAAGGGTAAAA-GG
1 TAATCAGT-AAGAGCAAAATGG
580 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGCAAAATGG
601 TAATCA
1 TAATCA
607 CTAAAGAGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
20 8 0.13
21 34 0.56
22 19 0.31
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (21 bp):
TAATCAGTAAGAGCAAAATGG
Found at i:584 original size:42 final size:43
Alignment explanation
Indices: 516--619 Score: 174
Period size: 42 Copynumber: 2.4 Consensus size: 43
506 AAAGTGATAA
*
516 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
559 TAATCAGTAAAGGGTAAAA-GGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
* *
601 TAATCACTAAAGAGTAAAA
1 TAATCAGTAAAGGGTAAAA
620 ATCAGTAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
42 40 0.69
43 18 0.31
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.20
Consensus pattern (43 bp):
TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
Found at i:678 original size:61 final size:59
Alignment explanation
Indices: 374--680 Score: 176
Period size: 63 Copynumber: 5.0 Consensus size: 59
364 GTAAAATAGT
* * * *
374 AATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATCGTAAAATCGTAAAAAGTGATAA
1 AATCAGTAAAAAGTAAAA-GGTAATCAGT-AAGAGCAAAATAGTAAAAAC-TAAACAGT-A-AA
* * ** * *
438 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGT-AA
1 -AATCAGTAAAAAGTAAAA-GGTAATCAGTAAGAGCAAAATAGTAAAAACTAAACAGTAAA
* * * * ** *
498 AATC-GTAAAAAGTGATAA--TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCA--AAA
1 AATCAGTAAAAAGT-AAAAGGTAATCAGTAAGA-GCAAAATAGTAAAAACTAA-A-CAGTAAA
** * ** *
556 TGGTAATCAGTAAAGGGTAAAAGGTAATCAGTAAGAGCAAAATGGTAATCACTAAAGAGTAAA
1 ----AATCAGTAAAAAGTAAAAGGTAATCAGTAAGAGCAAAATAGTAAAAACTAAACAGTAAA
* * * *
619 AATCAGTAAAAAGTAAGAAGGTTATCAGTAAAGAGTAAAATAGTAAAAAGTAATCAGTAAA
1 AATCAGTAAAAAGTAA-AAGGTAATCAGT-AAGAGCAAAATAGTAAAAACTAAACAGTAAA
680 A
1 A
681 GGTAAAATAG
Statistics
Matches: 196, Mismatches: 30, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
56 11 0.06
57 18 0.09
58 11 0.06
59 22 0.11
60 13 0.07
61 26 0.13
62 8 0.04
63 34 0.17
64 25 0.13
65 28 0.14
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (59 bp):
AATCAGTAAAAAGTAAAAGGTAATCAGTAAGAGCAAAATAGTAAAAACTAAACAGTAAA
Found at i:700 original size:29 final size:29
Alignment explanation
Indices: 623--693 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
613 AGTAAAAATC
* *
623 AGTAAAA-AGTAAGAAGGTTATCAGTAAAG
1 AGTAAAATAGTAA-AAAGTAATCAGTAAAG
652 AGTAAAATAGTAAAAAGTAATCAGTAAA-
1 AGTAAAATAGTAAAAAGTAATCAGTAAAG
680 AGGTAAAATAGTAA
1 A-GTAAAATAGTAA
694 TCAGTAAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 1 0.03
29 32 0.84
30 5 0.13
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.21
Consensus pattern (29 bp):
AGTAAAATAGTAAAAAGTAATCAGTAAAG
Found at i:709 original size:22 final size:22
Alignment explanation
Indices: 516--710 Score: 69
Period size: 22 Copynumber: 8.9 Consensus size: 22
506 AAAGTGATAA
** *
516 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAAAGCAAAAATAG
* *
538 TAATCAGTAAGAGC-AAAATGG
1 TAATCAGTAAAAGCAAAAATAG
* ** *
559 TAATCAGTAAAGGGTAAAA-GG
1 TAATCAGTAAAAGCAAAAATAG
* *
580 TAATCAGTAAGAGC-AAAATGG
1 TAATCAGTAAAAGCAAAAATAG
* *
601 TAATCACTAAAGAGTAAAAATCAG
1 TAATCAGTAAA-AGCAAAAAT-AG
** ***
625 TAAAAAGTAAGAAG--GTTATCAG
1 TAATCAGTAA-AAGCAAAAAT-AG
** * * *
647 TAAAGAGTAAAA-TAGTAAAAAG
1 TAATCAGTAAAAGCA-AAAATAG
**
669 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGCAAAAATAG
*
691 TAATCAGTAAGAGCAAAAAT
1 TAATCAGTAAAAGCAAAAAT
711 GGTTATTAGA
Statistics
Matches: 131, Mismatches: 32, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
20 4 0.03
21 44 0.34
22 66 0.50
23 6 0.05
24 10 0.08
25 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGCAAAAATAG
Done.