Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013856.1 Corchorus capsularis cultivar CVL-1 contig13877, 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: 8274
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:282 original size:14 final size:14
Alignment explanation
Indices: 260--359 Score: 68
Period size: 14 Copynumber: 7.3 Consensus size: 14
250 CAGTAAAAAG
260 GTAAA-AGTAATCA
1 GTAAAGAGTAATCA
273 GTAAAGAGTAATCA
1 GTAAAGAGTAATCA
* **
287 GTAAAAAGTAAAAA
1 GTAAAGAGTAATCA
* *
301 TGGCAAAGAGTAGT-A
1 --GTAAAGAGTAATCA
*
316 --AAAAAGTAATCA
1 GTAAAGAGTAATCA
328 GGTAAA-AGTAATCA
1 -GTAAAGAGTAATCA
342 GT-AAGAAGTAATCA
1 GTAAAG-AGTAATCA
356 GTAA
1 GTAA
360 GAAGGTCAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
11 8 0.12
12 3 0.04
13 7 0.10
14 37 0.54
15 5 0.07
16 8 0.12
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (14 bp):
GTAAAGAGTAATCA
Found at i:360 original size:14 final size:14
Alignment explanation
Indices: 319--363 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
309 AGTAGTAAAA
319 AAGTAATCAGGTAA-
1 AAGTAATCA-GTAAG
333 AAGTAATCAGTAAG
1 AAGTAATCAGTAAG
347 AAGTAATCAGTAAG
1 AAGTAATCAGTAAG
361 AAG
1 AAG
364 GTCAAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.13
14 26 0.87
ACGTcount: A:0.51, C:0.07, G:0.22, T:0.20
Consensus pattern (14 bp):
AAGTAATCAGTAAG
Found at i:435 original size:43 final size:41
Alignment explanation
Indices: 355--525 Score: 166
Period size: 43 Copynumber: 4.0 Consensus size: 41
345 AGAAGTAATC
* * *
355 AGTAAGAAGGTC-AAAAATGGTATCAAGTGAAATATGGTATTG
1 AGTAA-AAGGTCAAAAAATGGTAT-AAGTAAAAAATGGTATTA
*
397 AGTAAGAAGGTCAAAAAATGGTGTAGAGTAAAAAATGGTATTA
1 AGTAA-AAGGTCAAAAAATGGTATA-AGTAAAAAATGGTATTA
* * *
440 AGTAAAAGAGT-AAAGAATGGTATTAATTAAAAAATGGTGTTA
1 AGTAAAAG-GTCAAAAAATGGTA-TAAGTAAAAAATGGTATTA
* * *
482 AGTAAAAGGGTCAAAAAATGGTATCCAGTAAGAGATGGTATTA
1 AGTAAAA-GGTCAAAAAATGGTAT-AAGTAAAAAATGGTATTA
525 A
1 A
526 ACAAAAATGG
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
42 50 0.46
43 58 0.54
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.25
Consensus pattern (41 bp):
AGTAAAAGGTCAAAAAATGGTATAAGTAAAAAATGGTATTA
Found at i:451 original size:25 final size:25
Alignment explanation
Indices: 421--471 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
411 AAAATGGTGT
421 AGAGTAAAAAATGGTATTAAGTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
* *
446 AGAGTAAAGAATGGTATTAATTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
471 A
1 A
472 AATGGTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (25 bp):
AGAGTAAAAAATGGTATTAAGTAAA
Found at i:472 original size:42 final size:43
Alignment explanation
Indices: 355--505 Score: 150
Period size: 42 Copynumber: 3.6 Consensus size: 43
345 AGAAGTAATC
* * * * *
355 AGTAAGAAG-GTC-AAAAATGGTATCAAGTGAAATATGGTATTG
1 AGTAA-AAGAGTCAAAAAATGGTATTAATTAAAAAATGGTATTA
* *
397 AGTAAGAAG-GTCAAAAAATGGT-GTAGAGTAAAAAATGGTATTA
1 AGTAA-AAGAGTCAAAAAATGGTATTA-ATTAAAAAATGGTATTA
* *
440 AGTAAAAGAGT-AAAGAATGGTATTAATTAAAAAATGGTGTTA
1 AGTAAAAGAGTCAAAAAATGGTATTAATTAAAAAATGGTATTA
*
482 AGTAAAAGGGTCAAAAAATGGTAT
1 AGTAAAAGAGTCAAAAAATGGTAT
506 CCAGTAAGAG
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
42 50 0.54
43 43 0.46
ACGTcount: A:0.48, C:0.03, G:0.25, T:0.25
Consensus pattern (43 bp):
AGTAAAAGAGTCAAAAAATGGTATTAATTAAAAAATGGTATTA
Found at i:475 original size:17 final size:17
Alignment explanation
Indices: 448--488 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
438 TAAGTAAAAG
*
448 AGTAAAGAATGGTATTA
1 AGTAAAAAATGGTATTA
* *
465 ATTAAAAAATGGTGTTA
1 AGTAAAAAATGGTATTA
482 AGTAAAA
1 AGTAAAA
489 GGGTCAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (17 bp):
AGTAAAAAATGGTATTA
Found at i:512 original size:85 final size:85
Alignment explanation
Indices: 370--525 Score: 197
Period size: 85 Copynumber: 1.8 Consensus size: 85
360 GAAGGTCAAA
* * * * *
370 AATGGTATCAAGTGAAATATGGTATTGAGTAAGAAGGTCAAAAAATGGTGTAGAGTAAAAAATGG
1 AATGGTATCAAGTAAAAAATGGTATTAAGTAAGAAGGTCAAAAAATGGTATACAGTAAAAAATGG
435 TATTAAGTAAAAGAGTAAAG
66 TATTAAGTAAAAGAGTAAAG
* * * * * *
455 AATGGTATTAATTAAAAAATGGTGTTAAGTAA-AAGGGTCAAAAAATGGTATCCAGTAAGAGATG
1 AATGGTATCAAGTAAAAAATGGTATTAAGTAAGAA-GGTCAAAAAATGGTATACAGTAAAAAATG
519 GTATTAA
65 GTATTAA
526 ACAAAAATGG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
84 2 0.03
85 57 0.97
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.26
Consensus pattern (85 bp):
AATGGTATCAAGTAAAAAATGGTATTAAGTAAGAAGGTCAAAAAATGGTATACAGTAAAAAATGG
TATTAAGTAAAAGAGTAAAG
Found at i:532 original size:59 final size:59
Alignment explanation
Indices: 452--564 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
442 TAAAAGAGTA
* * *
452 AAGAATGGTATTAATTAAAAAATGGTGTTAAGTAAAAGGGTCA-AAAAATGGTATCCAGT
1 AAGAATGGTATTAA-TAAAAAATGGTATTAAGTAAAAGAGTAAGAAAAATGGTATCCAGT
511 AAGAGATGGTATTAA-ACAAAAATGGTATTAAGTAAAAGAGTAAGAAAAATGGTA
1 AAGA-ATGGTATTAATA-AAAAATGGTATTAAGTAAAAGAGTAAGAAAAATGGTA
565 AAAGTAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 1 0.02
59 27 0.56
60 20 0.42
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.25
Consensus pattern (59 bp):
AAGAATGGTATTAATAAAAAATGGTATTAAGTAAAAGAGTAAGAAAAATGGTATCCAGT
Found at i:547 original size:16 final size:16
Alignment explanation
Indices: 495--547 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
485 AAAAGGGTCA
**
495 AAAAATGGTATCCAGT
1 AAAAATGGTATTAAGT
* **
511 AAGAGATGGTATTAAAC
1 AA-AAATGGTATTAAGT
528 AAAAATGGTATTAAGT
1 AAAAATGGTATTAAGT
544 AAAA
1 AAAA
548 GAGTAAGAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAAATGGTATTAAGT
Found at i:575 original size:15 final size:15
Alignment explanation
Indices: 555--585 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
545 AAAGAGTAAG
*
555 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
570 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
585 A
1 A
586 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Done.