Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1930
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: 24826
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Found at i:2011 original size:23 final size:23
Alignment explanation
Indices: 1985--2082 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
1975 ATAAGTGCCA
1985 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2008 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
2031 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2053 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2076 CACTGAT
1 CACTGAT
2083 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:2050 original size:45 final size:45
Alignment explanation
Indices: 1992--2080 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
1982 CCACACTGAT
* *
1992 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
2037 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
2081 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:6466 original size:46 final size:46
Alignment explanation
Indices: 6416--6588 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
6406 TGGTTGAGCA
6416 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
6462 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
6507 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
6555 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
6589 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:6572 original size:93 final size:93
Alignment explanation
Indices: 6413--6583 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
6403 GGATGGTTGA
* *
6413 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
6478 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
6506 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
6571 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
6584 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:13959 original size:46 final size:46
Alignment explanation
Indices: 13909--14081 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 46
13899 TGGTTGAGCA
13909 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
13955 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
14000 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGTGGGTGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
14048 -CTCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
14082 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 4 0.04
46 58 0.56
47 29 0.28
48 2 0.02
50 2 0.02
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:14065 original size:93 final size:93
Alignment explanation
Indices: 13906--14076 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
13896 GGATGGTTGA
*
13906 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
13971 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
13999 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGTGGGTGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGAG
*
14063 TTGAGTTCGAGTTC
65 TTGAGTCCGAGTTC
14077 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:23219 original size:24 final size:24
Alignment explanation
Indices: 23187--23249 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
23177 AAAATCCAAT
* * *
23187 GCACTATGTGTGCG-GTTTACTATG
1 GCACTATGTGTGCGAGTGTAAT-TA
23211 GCACTATGTGTGCGAGTGTAATTA
1 GCACTATGTGTGCGAGTGTAATTA
23235 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
23250 ATACGGTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (24 bp):
GCACTATGTGTGCGAGTGTAATTA
Done.