Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold770
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: 42893
ACGTcount: A:0.08, C:0.04, G:0.05, T:0.08
Warning! 32473 characters in sequence are not A, C, G, or T
Found at i:110 original size:20 final size:19
Alignment explanation
Indices: 46--110 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
36 TATAAATGCA
*
46 AATGAGCTTAAAATGAGTTG
1 AATGAGC-TAAAATGAGCTG
* *
66 ATTGAGCTAAGAGTGAGCTCG
1 AATGAGCTAA-AATGAGCT-G
87 -ATGAGCTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
106 AATGA
1 AATGA
111 ACTTGAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.14
20 30 0.83
21 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:408 original size:12 final size:12
Alignment explanation
Indices: 391--455 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
381 TCACACTCTT
391 TTTTTTTTTGAA
1 TTTTTTTTTGAA
403 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
415 TTTCCTTTTTTTCAA
1 -TT--TTTTTTTGAA
* *
430 -ATTTTTTTAAA
1 TTTTTTTTTGAA
*
441 TTTTTTTTCGAA
1 TTTTTTTTTGAA
453 TTT
1 TTT
456 CCTCTTCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 9 0.21
12 23 0.53
13 2 0.05
15 9 0.21
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:38521 original size:15 final size:15
Alignment explanation
Indices: 38477--38530 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
38467 AAAAGTTCGA
**
38477 AAAAAAAATTTGAA-
1 AAAAAAAATTAAAAG
*
38491 AAAAAAAATTCGAAAG
1 AAAAAAAATT-AAAAG
38507 AAAAAAAATTAAAAG
1 AAAAAAAATTAAAAG
38522 AAAAAAAAT
1 AAAAAAAAT
38531 GTATACGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.29
15 15 0.43
16 10 0.29
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (15 bp):
AAAAAAAATTAAAAG
Found at i:38525 original size:14 final size:14
Alignment explanation
Indices: 38464--38528 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 14
38454 ATAGGTACGT
38464 AAAAAAAGTTCGAAA-
1 AAAAAAA-TT-GAAAG
*
38479 AAAAAATTTGAAA-
1 AAAAAAATTGAAAG
38492 AAAAAAATTCGAAAG
1 AAAAAAATT-GAAAG
*
38507 AAAAAAAATTAAAAG
1 -AAAAAAATTGAAAG
38522 AAAAAAA
1 AAAAAAA
38529 ATGTATACGG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.27
14 13 0.30
15 10 0.23
16 9 0.20
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (14 bp):
AAAAAAATTGAAAG
Found at i:41228 original size:36 final size:33
Alignment explanation
Indices: 41163--41229 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
41153 GTGAATGAAG
*
41163 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
41196 TGAGTGAAGAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
41230 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.12
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Done.