Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1426
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: 23242
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:11904 original size:39 final size:40
Alignment explanation
Indices: 11823--11912 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 40
11813 GGGTGTTACA
* * * *
11823 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCAAGTCACTAAAACCGGGCTAAGTC
* * *
11863 CCGAAGGCATT-GTGTAAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCAAGTCACTAAAACCGGGCTAAGTC
11902 CCGAAGGCATT
1 CCGAAGGCATT
11913 TGAACGAGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 32 0.74
40 11 0.26
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCAAGTCACTAAAACCGGGCTAAGTC
Found at i:16285 original size:21 final size:21
Alignment explanation
Indices: 16240--16302 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
16230 TTTTAACCAT
* *
16240 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
16262 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
16283 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
16303 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:16629 original size:21 final size:21
Alignment explanation
Indices: 16602--16658 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
16592 TAGGTACGTA
16602 AAAAAAAGAGTTCGAAAAAAAAG
1 AAAAAAA-A-TTCGAAAAAAAAG
*
16625 AAAAAAAATTTGAAAAAAAAATTG
1 AAAAAAAATTCG-AAAAAAAA--G
16649 AAAAAAAATT
1 AAAAAAAATT
16659 GCATACGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.10
22 9 0.30
23 7 0.23
24 11 0.37
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.16
Consensus pattern (21 bp):
AAAAAAAATTCGAAAAAAAAG
Found at i:16641 original size:13 final size:12
Alignment explanation
Indices: 16616--16656 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
16606 AAAGAGTTCG
16616 AAAAAAAA--GA
1 AAAAAAAATTGA
*
16626 AAAAAAATTTGA
1 AAAAAAAATTGA
16638 AAAAAAAATTGA
1 AAAAAAAATTGA
16650 AAAAAAA
1 AAAAAAA
16657 TTGCATACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 7 0.26
12 20 0.74
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:16657 original size:11 final size:11
Alignment explanation
Indices: 16615--16659 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
16605 AAAAGAGTTC
16615 GAAAAAAAA--
1 GAAAAAAAATT
16624 GAAAAAAAATTT
1 GAAAAAAAA-TT
16636 GAAAAAAAAATT
1 G-AAAAAAAATT
16648 GAAAAAAAATT
1 GAAAAAAAATT
16659 G
1 G
16660 CATACGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.28
11 11 0.34
12 4 0.12
13 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (11 bp):
GAAAAAAAATT
Found at i:17460 original size:15 final size:15
Alignment explanation
Indices: 17428--17461 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17418 GTTCAACGAA
*
17428 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
17443 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
17458 GAGG
1 GAGG
17462 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:19885 original size:8 final size:8
Alignment explanation
Indices: 19845--19874 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
19835 TTAAGAGCTG
19845 TAACTAAAT
1 TAACT-AAT
19854 TAACTAAT
1 TAACTAAT
19862 TAACTAAT
1 TAACTAAT
19870 TAACT
1 TAACT
19875 TAAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (8 bp):
TAACTAAT
Found at i:21953 original size:36 final size:35
Alignment explanation
Indices: 21905--21981 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
21895 TCTCAATTTC
* *
21905 TTTTTTGAATTTCTTCTTTCTTTTTCTCTTCACTTCA
1 TTTTTTGAATTTCTT-GTTCCTTTTCT-TTCACTTCA
* *
21942 TTTTTTG-ATTTCTTGTTCCTTTTCTTTCATTTCT
1 TTTTTTGAATTTCTTGTTCCTTTTCTTTCACTTCA
21976 TTTTTT
1 TTTTTT
21982 CGTTCTCTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 13 0.36
35 9 0.25
36 7 0.19
37 7 0.19
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.70
Consensus pattern (35 bp):
TTTTTTGAATTTCTTGTTCCTTTTCTTTCACTTCA
Done.