Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold609
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: 31411
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:2884 original size:14 final size:14
Alignment explanation
Indices: 2859--2891 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2849 TATTCTGTAG
2859 TTTAGTTAATTAGT
1 TTTAGTTAATTAGT
2873 TATTAG-TAATTAGT
1 T-TTAGTTAATTAGT
2887 TTTAG
1 TTTAG
2892 ATAAAGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (14 bp):
TTTAGTTAATTAGT
Found at i:4093 original size:13 final size:13
Alignment explanation
Indices: 4075--4103 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4065 TTCCACCAAA
4075 ATTTTAGCAACTC
1 ATTTTAGCAACTC
4088 ATTTTAGCAACTC
1 ATTTTAGCAACTC
4101 ATT
1 ATT
4104 ACTCACACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (13 bp):
ATTTTAGCAACTC
Found at i:7208 original size:23 final size:23
Alignment explanation
Indices: 7182--7226 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
7172 TGGGTATGTG
*
7182 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
7205 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
7227 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:14445 original size:27 final size:27
Alignment explanation
Indices: 14372--14438 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 27
14362 AATTAAAATT
14372 TTAAAAATTCAA-AAAATTATTTTTTAAAAA
1 TTAAAAATT-AATAAAATTA---TTTAAAAA
14402 TTAAAAATTAATAAAATTATTTAAAAA
1 TTAAAAATTAATAAAATTATTTAAAAA
14429 GTATAAAAAT
1 -T-TAAAAAT
14439 CATAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 8 0.24
28 1 0.03
29 9 0.26
30 16 0.47
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
TTAAAAATTAATAAAATTATTTAAAAA
Found at i:17975 original size:2 final size:2
Alignment explanation
Indices: 17968--17996 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17958 TGCACGCCTC
17968 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
17997 CCCAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:19068 original size:43 final size:43
Alignment explanation
Indices: 18992--19107 Score: 162
Period size: 43 Copynumber: 2.7 Consensus size: 43
18982 CGTCGCTAAT
*
18992 TTTAGCGGCGC-TTTTACACAAACGCCGCTATAGATCAAGACC
1 TTTAGCGGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACC
* * * *
19034 TTTAGCGGCGCTTTTTTTATAAACGCCGCTATAGATCATGACT
1 TTTAGCGGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACC
* *
19077 TTTAGCGACGCTTTTTTCGCAAACGCCGCTA
1 TTTAGCGGCGCTTTTTTCACAAACGCCGCTA
19108 AAAGTGCCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 11 0.17
43 53 0.83
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACC
Found at i:23348 original size:27 final size:27
Alignment explanation
Indices: 23181--23358 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
23171 TAAATTGTAC
*
23181 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
23208 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
23234 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
23262 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
23290 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
23317 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
23344 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
23359 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:23349 original size:82 final size:81
Alignment explanation
Indices: 23178--23358 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
23168 GATTAAATTG
* * * *
23178 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
23243 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
23259 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
23323 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
23341 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
23359 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:31319 original size:81 final size:81
Alignment explanation
Indices: 31179--31334 Score: 192
Period size: 81 Copynumber: 1.9 Consensus size: 81
31169 AAATTGTACA
* * * *
31179 GCACTAAGTGTGCGATTCTACTTTGTTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGA-
1 GCACTAAGTGTGCGAGTCTACTATGTTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA-AT
31243 GTGCGAATTGACATACG
65 GTGCGAATTGACATACG
** *
31260 GCACTAAGTGTGCGAGTCTAACTATG-TAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGCGAGTCT-ACTATGTTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
31323 TGTGCGAGTTGA
64 TGTGCGAATTGA
31335 TTATATAGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
80 2 0.03
81 57 0.89
82 5 0.08
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCTACTATGTTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATG
TGCGAATTGACATACG
Found at i:31344 original size:54 final size:53
Alignment explanation
Indices: 31207--31355 Score: 151
Period size: 54 Copynumber: 2.8 Consensus size: 53
31197 TACTTTGTTT
** *
31207 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGAGTGCGAATTGACATACG
1 GCACTAAGTGTGCGAGTTGAATAT-ATAGCACTAAGTGTGCGAATTGACATACG
* * *
31260 GCACTAAGTGTGCGAGTCT-AACTATGTAGCACTAAGTGTGCGATTTGA-TTACGTG
1 GCACTAAGTGTGCGAGT-TGAA-TATATAGCACTAAGTGTGCGAATTGACATAC--G
* * *
31315 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGAATATATAGCACTAAGTGTGCG
31356 GGCTCATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
53 21 0.26
54 41 0.51
55 18 0.22
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (53 bp):
GCACTAAGTGTGCGAGTTGAATATATAGCACTAAGTGTGCGAATTGACATACG
Found at i:31345 original size:27 final size:27
Alignment explanation
Indices: 31207--31355 Score: 115
Period size: 27 Copynumber: 5.5 Consensus size: 27
31197 TACTTTGTTT
** *
31207 GCACTAAGTGTGCGAAATGAATATG-A
1 GCACTAAGTGTGCGAGTTGATTATGTA
* * * *
31233 TGCACTAAGAGTGCGAATTGACATACG--
1 -GCACTAAGTGTGCGAGTTGA-TTATGTA
* *
31260 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAGT-TGATTATGTA
* * *
31288 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGTTGATTATGTA
* *
31315 GCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTGATTATGTA
*
31342 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
31356 GGCTCATATA
Statistics
Matches: 98, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 18 0.18
27 60 0.61
28 20 0.20
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTGATTATGTA
Done.