Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1700
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: 33240
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:3488 original size:27 final size:26
Alignment explanation
Indices: 3457--3510 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
3447 TTTGGCTGAG
*
3457 ATATGAGTGGTAA-TGTGGTTTGAAAAA
1 ATATG-GTGGAAAGTGTGG-TTGAAAAA
*
3484 ATATGGTTGAAAGTGTGGTTGAAAAA
1 ATATGGTGGAAAGTGTGGTTGAAAAA
3510 A
1 A
3511 GATTGAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.31
Consensus pattern (26 bp):
ATATGGTGGAAAGTGTGGTTGAAAAA
Found at i:7107 original size:22 final size:22
Alignment explanation
Indices: 7082--7130 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
7072 GCTAATATAC
* *
7082 AAGGATAGAGATCACTATAATT
1 AAGGATAGAGATAACAATAATT
7104 AAGGATAGAGATAACAATAATT
1 AAGGATAGAGATAACAATAATT
7126 AAGGA
1 AAGGA
7131 GATTACAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.22
Consensus pattern (22 bp):
AAGGATAGAGATAACAATAATT
Found at i:12959 original size:32 final size:32
Alignment explanation
Indices: 12887--12959 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
12877 ATAAGAGAGA
* * *
12887 AATAAGAAAAAATGATATCTAAATATATTTAT
1 AATAATAAAAAATGATATATAAATATATTGAT
* *
12919 CATAATAAAAAATTATATAT-AATATATTGAT
1 AATAATAAAAAATGATATATAAATATATTGAT
12950 AATATATAAA
1 AATA-ATAAA
12960 TTTATATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (32 bp):
AATAATAAAAAATGATATATAAATATATTGAT
Found at i:14859 original size:12 final size:12
Alignment explanation
Indices: 14842--14866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14832 TTATTATTTT
14842 TATTTAAAAATA
1 TATTTAAAAATA
14854 TATTTAAAAATA
1 TATTTAAAAATA
14866 T
1 T
14867 TACAATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTTAAAAATA
Found at i:15719 original size:21 final size:23
Alignment explanation
Indices: 15659--15719 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 23
15649 TTGAGTAATT
*
15659 AATTAAATTTTATTAATTTTAAATAA
1 AATTAAATTATATT-A--TTAAATAA
15685 AATTAAATT-T-TTATTAAAT-A
1 AATTAAATTATATTATTAAATAA
15705 AA-TAAATTATATTAT
1 AATTAAATTATATTAT
15720 CCAAATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.18
20 4 0.12
21 10 0.30
23 1 0.03
24 2 0.06
25 1 0.03
26 9 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTAAATTATATTATTAAATAA
Found at i:22052 original size:18 final size:17
Alignment explanation
Indices: 22004--22053 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
21994 CATATTTTTA
* *
22004 TTAAATTTTTATTATAT
1 TTAAATTTTTTTTATAG
*
22021 TTAATATTTATTTTATAG
1 TTAA-ATTTTTTTTATAG
22039 TTAAATTCTTTTTTA
1 TTAAATT-TTTTTTA
22054 ATGTAATCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTAAATTTTTTTTATAG
Found at i:28739 original size:2 final size:2
Alignment explanation
Indices: 28685--28726 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28675 CCTGAGTATG
28685 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28727 TAATCGGTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:32949 original size:23 final size:22
Alignment explanation
Indices: 32917--32977 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
32907 AGGACATAGG
*
32917 TTATTCTTAAAAAAAAATATCAA
1 TTATTTTTAAAAAAAAATAT-AA
32940 TTATTTTT--AAAAAAATATAA
1 TTATTTTTAAAAAAAAATATAA
32960 TT-TTTTTAAAAAATAAAT
1 TTATTTTTAAAAAA-AAAT
32978 TATTTTATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 14 0.41
22 4 0.12
23 7 0.21
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTTTTAAAAAAAAATATAA
Found at i:32953 original size:21 final size:20
Alignment explanation
Indices: 32927--32983 Score: 84
Period size: 18 Copynumber: 3.0 Consensus size: 20
32917 TTATTCTTAA
32927 AAAAAAATATCAATTATTTTT
1 AAAAAAATAT-AATTATTTTT
32948 AAAAAAATATAATT-TTTTT
1 AAAAAAATATAATTATTTTT
32967 -AAAAAATA-AATTATTTT
1 AAAAAAATATAATTATTTT
32984 ATCAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.11
18 12 0.34
19 5 0.14
20 4 0.11
21 10 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAAAATATAATTATTTTT
Found at i:32990 original size:18 final size:17
Alignment explanation
Indices: 32928--32994 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 17
32918 TATTCTTAAA
32928 AAAAAATATCAATTATTTTT
1 AAAAAATA--AATTA-TTTT
*
32948 AAAAAAATATAATTTTTTT
1 -AAAAAATA-AATTATTTT
32967 AAAAAATAAATTATTTT
1 AAAAAATAAATTATTTT
*
32984 ATCAAAATAAA
1 A-AAAAATAAA
32995 CAATTGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 9 0.22
18 16 0.39
19 4 0.10
20 4 0.10
21 8 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAAAATAAATTATTTT
Done.