Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1114
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: 2762
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.25
Warning! 228 characters in sequence are not A, C, G, or T
Found at i:406 original size:7 final size:7
Alignment explanation
Indices: 396--460 Score: 57
Period size: 7 Copynumber: 9.9 Consensus size: 7
386 AAAAAAAAGG
396 AAAAAAC
1 AAAAAAC
403 -AAAAA-
1 AAAAAAC
*
408 AAATAAC
1 AAAAAAC
*
415 AAAACA-
1 AAAAAAC
421 AAAAAAC
1 AAAAAAC
428 -AAAAAC
1 AAAAAAC
434 AAAAAAC
1 AAAAAAC
**
441 AAAAATT
1 AAAAAAC
*
448 AAAAATC
1 AAAAAAC
455 AAAAAA
1 AAAAAA
461 ATCGAAGTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
6 20 0.43
7 26 0.57
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (7 bp):
AAAAAAC
Found at i:407 original size:8 final size:8
Alignment explanation
Indices: 396--445 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
386 AAAAAAAAGG
396 AAAAAACA
1 AAAAAACA
404 AAAAAA-A
1 AAAAAACA
411 TAACAAAACA
1 -AA-AAAACA
421 AAAAAAC-
1 AAAAAACA
428 -AAAAAC-
1 AAAAAACA
434 AAAAAACA
1 AAAAAACA
442 AAAA
1 AAAA
446 TTAAAAATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.16
7 7 0.19
8 17 0.46
9 6 0.16
10 1 0.03
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (8 bp):
AAAAAACA
Found at i:408 original size:17 final size:17
Alignment explanation
Indices: 386--426 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
376 TTCAGACTCA
386 AAAAAAAAGGAA-AAAAC
1 AAAAAAAA-GAACAAAAC
*
403 AAAAAAAATAACAAAAC
1 AAAAAAAAGAACAAAAC
420 AAAAAAA
1 AAAAAAA
427 CAAAAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.85, C:0.07, G:0.05, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAACAAAAC
Found at i:423 original size:14 final size:14
Alignment explanation
Indices: 396--459 Score: 64
Period size: 13 Copynumber: 4.9 Consensus size: 14
386 AAAAAAAAGG
396 AAAAAAC-AAAA-A
1 AAAAAACAAAAACA
*
408 AAATAAC-AAAACA
1 AAAAAACAAAAACA
421 AAAAAACAAAAAC-
1 AAAAAACAAAAACA
**
434 AAAAAACAAAAATT
1 AAAAAACAAAAACA
*
448 AAAAATCAAAAA
1 AAAAAACAAAAA
460 AATCGAAGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.22
13 19 0.42
14 16 0.36
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAAAACAAAAACA
Found at i:486 original size:13 final size:12
Alignment explanation
Indices: 470--512 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
460 AATCGAAGTC
*
470 AAAAAAAAAGGA
1 AAAAAAAAAAGA
482 AAAAAAAGAGAAGA
1 AAAAAAA-A-AAGA
496 AAAAAGAAAAAGA
1 AAAAA-AAAAAGA
509 AAAA
1 AAAA
513 GGAGAAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 9 0.33
15 2 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:494 original size:27 final size:26
Alignment explanation
Indices: 455--523 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 26
445 ATTAAAAATC
**
455 AAAAAAATCGAAGTCAAAAAA-AAAGGA
1 AAAAAAAGAGAAGTCAAAAAAGAAA--A
482 AAAAAAAGAGAAG--AAAAAAGAAAA
1 AAAAAAAGAGAAGTCAAAAAAGAAAA
*
506 AGAAAAAGGAGAAGTCAA
1 A-AAAAAAGAGAAGTCAA
524 GGCGAAAACC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 17 0.49
26 3 0.09
27 13 0.37
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.04
Consensus pattern (26 bp):
AAAAAAAGAGAAGTCAAAAAAGAAAA
Found at i:518 original size:22 final size:22
Alignment explanation
Indices: 473--518 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
463 CGAAGTCAAA
*
473 AAAAAAGGAAAAAAAAGAGAAG
1 AAAAAAGGAAAAAAAAAAGAAG
*
495 AAAAAA-GAAAAAGAAAAAGGAG
1 AAAAAAGGAAAAA-AAAAAGAAG
517 AA
1 AA
519 GTCAAGGCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAAAAGGAAAAAAAAAAGAAG
Found at i:2742 original size:132 final size:132
Alignment explanation
Indices: 2505--2762 Score: 426
Period size: 132 Copynumber: 2.0 Consensus size: 132
2495 TGTATTTGGC
* * * *
2505 AGTGGAATAGGTTGAAGATTACAGATTCTGTCACCCTATGCAATAGTGGAGCAGATCGAAGATGG
1 AGTGGAATAGGTTGAAGATTACAAATTCTGCCACCCTAAGCAATAGTGGAGAAGATCGAAGATGG
2570 TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCA
66 TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCA
2635 GT
131 GT
* * * *
2637 AGTGGAGTAGGTTGAAGATTGCAAATTCTGCCACCCTAAGCAGTAGTGGAGAATATCGAAGATGG
1 AGTGGAATAGGTTGAAGATTACAAATTCTGCCACCCTAAGCAATAGTGGAGAAGATCGAAGATGG
* *
2702 TGAATCTTATCTTCCCAATGCAGTGTAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTA
66 TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTA
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 116 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (132 bp):
AGTGGAATAGGTTGAAGATTACAAATTCTGCCACCCTAAGCAATAGTGGAGAAGATCGAAGATGG
TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCA
GT
Done.