Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007298.1 Corchorus capsularis cultivar CVL-1 contig07319, 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: 7533
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Found at i:223 original size:22 final size:22
Alignment explanation
Indices: 198--847 Score: 216
Period size: 22 Copynumber: 29.9 Consensus size: 22
188 AAGGAGCCAG
198 AAAATAGTAATCAGTAAAAGGT
1 AAAATAGTAATCAGTAAAAGGT
*
220 AAAATGGTAATCAGT-AAAGAGT
1 AAAATAGTAATCAGTAAAAG-GT
*
242 AAAGT-GATAATCAGT-AAAGAGT
1 AAAATAG-TAATCAGTAAAAG-GT
264 --AATAG-AAGTCAGTAAGAA-G-
1 AAAATAGTAA-TCAGTAA-AAGGT
* * *
283 -CAATGGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGTAAAAGGT
* *
304 AAAA-AGGTAATTAGTAAAAAGT
1 AAAATA-GTAATCAGTAAAAGGT
*
326 AAAATAGTAATTAG-AAAAGAGT
1 AAAATAGTAATCAGTAAAAG-GT
* **
348 AAAATGGTAAAGAGT-AAAGAGT
1 AAAATAGTAATCAGTAAAAG-GT
** ** *
370 --AATCAGTAAAGACAAAAATGAT
1 AAAAT-AGTAATCAGTAAAA-GGT
* * *
392 AAAGAAAGAGTGAT-AGTAAGA-GT
1 --A-AAATAGTAATCAGTAAAAGGT
* *
415 AAAA-AGGTAAAAT-GGTAAAAAGT
1 AAAATA-GT--AATCAGTAAAAGGT
* *
438 AAAA-GGTAATCAGTAAAGGGT
1 AAAATAGTAATCAGTAAAAGGT
* * *
459 AAAATGGTAATTAGTAAAAAGT
1 AAAATAGTAATCAGTAAAAGGT
* **
481 AAAATGGTAATCAGTAAAAATT
1 AAAATAGTAATCAGTAAAAGGT
*
503 AAAAGAGTAATCAGTAGAAA-GT
1 AAAATAGTAATCAGTA-AAAGGT
525 --AATAGTAATCAGTAAGAA-G-
1 AAAATAGTAATCAGTAA-AAGGT
* *
544 -CAATAGTAGTCAGTGAAAA-GT
1 AAAATAGTAATCAGT-AAAAGGT
*
565 -AAATAGTAATCAGTAAGA-GT
1 AAAATAGTAATCAGTAAAAGGT
* *
585 AAAAAAGTAATAAGTAAGAA-GT
1 AAAATAGTAATCAGTAA-AAGGT
* * *
607 AAAA-GGAAATCAGTAAGA-GT
1 AAAATAGTAATCAGTAAAAGGT
627 AAAA-AGGTAATCAGT-AAAGAGT
1 AAAATA-GTAATCAGTAAAAG-GT
*
649 AAAA-AGCTAATCAGCAAGAA-GT
1 AAAATAG-TAATCAGTAA-AAGGT
* *
671 AAAA-AGGTAATCAGTAAAAAGC
1 AAAATA-GTAATCAGTAAAAGGT
* * *
693 AAAA-GGCAATCAGTAAAAAGT
1 AAAATAGTAATCAGTAAAAGGT
* *
714 AAAAGAGTAATCAGTAAAAAAGGAGCAG
1 AAAATAGTAATCAGT--AAAA-G-G--T
*
742 AAAATAGTAATAAGTAAAAGAGT
1 AAAATAGTAATCAGTAAAAG-GT
* *
765 AAAATGGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGTAAAAGGT
* *
787 AAGAA-GGTAATCA--ACAAGAGT
1 AA-AATAGTAATCAGTAAAAG-GT
808 AAAATAGTAATCAGTACAAA-GT
1 AAAATAGTAATCAGTA-AAAGGT
830 AAAGA-A-TAATCAGTAAAA
1 AAA-ATAGTAATCAGTAAAA
848 TAGTGATGGT
Statistics
Matches: 498, Mismatches: 72, Indels: 118
0.72 0.10 0.17
Matches are distributed among these distances:
19 6 0.01
20 84 0.17
21 118 0.24
22 216 0.43
23 35 0.07
24 8 0.02
25 7 0.01
26 9 0.02
27 2 0.00
28 13 0.03
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.20
Consensus pattern (22 bp):
AAAATAGTAATCAGTAAAAGGT
Found at i:313 original size:8 final size:7
Alignment explanation
Indices: 294--733 Score: 56
Period size: 7 Copynumber: 62.1 Consensus size: 7
284 AATGGTAATC
294 AGTAAAA
1 AGTAAAA
301 AGTAAAA
1 AGTAAAA
**
308 AGGTAATT
1 A-GTAAAA
316 AGTAAAA
1 AGTAAAA
323 AGTAAAA
1 AGTAAAA
**
330 TAGTAATT
1 -AGTAAAA
338 AG-AAAA
1 AGTAAAA
344 GAGTAAAA
1 -AGTAAAA
* *
352 TGGTAAAG
1 -AGTAAAA
*
360 AGTAAAG
1 AGTAAAA
**
367 AGTAATC
1 AGTAAAA
*
374 AGTAAAG
1 AGTAAAA
*
381 A-CAAAA
1 AGTAAAA
*
387 A-TGATAA
1 AGT-AAAA
*
394 AG-AAAG
1 AGTAAAA
* *
400 AGT-GAT
1 AGTAAAA
*
406 AGT-AAG
1 AGTAAAA
412 AGTAAAA
1 AGTAAAA
419 AGGTAAAA
1 A-GTAAAA
*
427 TGGTAAAA
1 -AGTAAAA
435 AGTAAAA
1 AGTAAAA
* **
442 GGTAATC
1 AGTAAAA
*
449 AGTAAAG
1 AGTAAAA
*
456 GGTAAAA
1 AGTAAAA
* **
463 TGGTAATT
1 -AGTAAAA
471 AGTAAAA
1 AGTAAAA
478 AGTAAAA
1 AGTAAAA
* **
485 TGGTAATC
1 -AGTAAAA
493 AGTAAAA
1 AGTAAAA
*
500 ATTAAAA
1 AGTAAAA
**
507 GAGTAATC
1 -AGTAAAA
*
515 AGTAGAA
1 AGTAAAA
*
522 AGT-AAT
1 AGTAAAA
**
528 AGTAATC
1 AGTAAAA
*
535 AGTAAGA
1 AGTAAAA
* *
542 AG-CAAT
1 AGTAAAA
***
548 AGTAGTC
1 AGTAAAA
*
555 AGTGAAA
1 AGTAAAA
*
562 AGTAAAT
1 AGTAAAA
**
569 AGTAATC
1 AGTAAAA
*
576 AGT-AAG
1 AGTAAAA
582 AGTAAAAA
1 AGT-AAAA
*
590 AGTAATA
1 AGTAAAA
*
597 AGTAAGA
1 AGTAAAA
604 AGT-AAA
1 AGTAAAA
* *
610 AGGAAATC
1 AGTAAA-A
*
618 AGT-AAG
1 AGTAAAA
624 AGTAAAA
1 AGTAAAA
**
631 AGGTAATC
1 A-GTAAAA
*
639 AGTAAAG
1 AGTAAAA
646 AGTAAAA
1 AGTAAAA
**
653 AGCTAATC
1 AG-TAAAA
* *
661 AGCAAGA
1 AGTAAAA
668 AGTAAAA
1 AGTAAAA
**
675 AGGTAATC
1 A-GTAAAA
683 AGTAAAA
1 AGTAAAA
*
690 AGCAAAA
1 AGTAAAA
* * **
697 GGCAATC
1 AGTAAAA
704 AGTAAAA
1 AGTAAAA
711 AGTAAAA
1 AGTAAAA
**
718 GAGTAATC
1 -AGTAAAA
726 AGTAAAA
1 AGTAAAA
733 A
1 A
734 AGGAGCAGAA
Statistics
Matches: 294, Mismatches: 115, Indels: 48
0.64 0.25 0.11
Matches are distributed among these distances:
6 36 0.12
7 187 0.64
8 71 0.24
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (7 bp):
AGTAAAA
Found at i:333 original size:15 final size:15
Alignment explanation
Indices: 294--335 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
284 AATGGTAATC
294 AGTAAAA-AGTAAAA
1 AGTAAAATAGTAAAA
*
308 AGGT-AATTAGTAAAA
1 A-GTAAAATAGTAAAA
323 AGTAAAATAGTAA
1 AGTAAAATAGTAA
336 TTAGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (15 bp):
AGTAAAATAGTAAAA
Found at i:381 original size:36 final size:36
Alignment explanation
Indices: 317--482 Score: 115
Period size: 36 Copynumber: 4.5 Consensus size: 36
307 AAGGTAATTA
* * *
317 GTAAAAAGTAAAATAGTAATTAGAAAAGAGTAAAATG
1 GTAAAAAGT-AAAGAGTAATCAGTAAAGAGTAAAATG
* **
354 GTAAAGAGTAAAGAGTAATCAGTAAAGACAAAAAT-
1 GTAAAAAGTAAAGAGTAATCAGTAAAGAGTAAAATG
* * *
389 G-ATAAAG-AAAGAGTGATAGTAAGAGTAAAAAGGTAAAATG
1 GTAAAAAGTAAAGAGT-A-A-T--CAGTAAAGA-GTAAAATG
*
429 GTAAAAAGTAAA-AGGTAATCAGTAAAGGGTAAAATG
1 GTAAAAAGTAAAGA-GTAATCAGTAAAGAGTAAAATG
** *
465 GTAATTAGTAAAAAGTAA
1 GTAAAAAGTAAAGAGTAA
483 AATGGTAATC
Statistics
Matches: 100, Mismatches: 18, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
33 7 0.07
34 5 0.05
35 2 0.02
36 44 0.44
37 15 0.15
38 7 0.07
39 6 0.06
40 2 0.02
41 7 0.07
42 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (36 bp):
GTAAAAAGTAAAGAGTAATCAGTAAAGAGTAAAATG
Found at i:533 original size:20 final size:20
Alignment explanation
Indices: 508--579 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
498 AAATTAAAAG
508 AGTAATCAGTAGAAAGTAAT
1 AGTAATCAGTAGAAAGTAAT
*
528 AGTAATCAGTA-AGAAGCAAT
1 AGTAATCAGTAGA-AAGTAAT
*
548 AGTAGTCAGT-GAAAAGTAAAT
1 AGTAATCAGTAG-AAAGT-AAT
569 AGTAATCAGTA
1 AGTAATCAGTA
580 AGAGTAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 1 0.02
20 29 0.67
21 13 0.30
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.24
Consensus pattern (20 bp):
AGTAATCAGTAGAAAGTAAT
Found at i:845 original size:94 final size:93
Alignment explanation
Indices: 565--823 Score: 227
Period size: 94 Copynumber: 2.9 Consensus size: 93
555 AGTGAAAAGT
* * * * * * * *
565 AAATAGTAATCAGT--AAGAGTAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCAGTAAGAGTA
1 AAATAGTAATAAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGAAAAAGTA
*
628 AAA-AGGTAATCAGT---AAA-GAG--TA
66 AAAGA-GTAATCAGTAAAAAAGGAGAAGA
* * *
650 AAA-AGCTAATCAGCAAGA-AGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGTAAAAAG
1 AAATAG-TAATAAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAG-AAAAAG
*
713 TAAAAGAGTAATCAGTAAAAAAGGAGCAGA
64 TAAAAGAGTAATCAGTAAAAAAGGAGAAGA
* * * *
743 AAATAGTAATAAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCA-ACAAGAG
1 AAATAGTAATAAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAA-AAGGCAATCAGA-AAAAG
*
807 TAAAATAGTAATCAGTA
64 TAAAAGAGTAATCAGTA
824 CAAAGTAAAG
Statistics
Matches: 141, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
84 2 0.01
85 10 0.07
86 33 0.23
87 19 0.13
88 1 0.01
90 3 0.02
91 3 0.02
93 14 0.10
94 47 0.33
95 9 0.06
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.17
Consensus pattern (93 bp):
AAATAGTAATAAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGAAAAAGTA
AAAGAGTAATCAGTAAAAAAGGAGAAGA
Found at i:877 original size:116 final size:114
Alignment explanation
Indices: 633--847 Score: 265
Period size: 116 Copynumber: 1.9 Consensus size: 114
623 GAGTAAAAAG
*
633 GTAATCAGT-AAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAAAGGTAATCAGTAAAAAGCAAAA
1 GTAATCAGTAAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCAG-AAAAAGCAAAA
* *
697 GGCAATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATA
65 AGCAATCAGTAAAAAGTAAAAGAATAATCAGTAAAAAAGGAG-AGAAAATA
* * * * * * *
748 GTAATAAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCA-ACAAGAGTAAAA
1 GTAATCAGTAAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCAGA-AAAAGCAAAA
* *
812 TAGTAATCAGTACAAAGT-AAAGAATAATCAGTAAAA
65 -AGCAATCAGTAAAAAGTAAAAGAATAATCAGTAAAA
848 TAGTGATGGT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
114 1 0.01
115 33 0.39
116 51 0.60
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.17
Consensus pattern (114 bp):
GTAATCAGTAAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCAGAAAAAGCAAAAA
GCAATCAGTAAAAAGTAAAAGAATAATCAGTAAAAAAGGAGAGAAAATA
Found at i:1748 original size:25 final size:25
Alignment explanation
Indices: 1714--1761 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1704 TATTTTCTAC
*
1714 CTCTCTCTATTGTAATGGCTTATAT
1 CTCTCTCTATTGTAATAGCTTATAT
*
1739 CTCTCTCTATTGTGATAGCTTAT
1 CTCTCTCTATTGTAATAGCTTAT
1762 TGAAGAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (25 bp):
CTCTCTCTATTGTAATAGCTTATAT
Found at i:4505 original size:19 final size:20
Alignment explanation
Indices: 4471--4510 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4461 ATGAGATGTC
4471 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
4491 TTAAAAACCCA-TTAACATA
1 TTAAAAACCCACTTAACATA
4510 T
1 T
4511 CAATAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAAAAACCCACTTAACATA
Found at i:4565 original size:72 final size:73
Alignment explanation
Indices: 4464--4599 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 73
4454 TACCGAAATG
4464 AGATGTCTTAAAAACCCACTTAACATATTAAAAACCCA-TTAACATATCAATAATTAAAGGGAAT
1 AGATGTCTTAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAAT
4528 CTTACTGA
66 CTTACTGA
* * *
4536 AGATGTCTTAAAAACCCACTTAACATATTAAAAACCTACTTAATATTTCAATAATTAAAGGGAA
1 AGATGTCTTAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAA
4600 CCTCAAATTA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
72 37 0.62
73 23 0.38
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (73 bp):
AGATGTCTTAAAAACCCACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAAT
CTTACTGA
Done.