Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: LOC111281690
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, 428
Length: 714
ACGTcount: A:0.24, C:0.12, G:0.45, T:0.19
Found at i:82 original size:22 final size:24
Alignment explanation
Indices: 57--108 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
47 GTGGAGGAAG
57 TGGCTTGCAAGGA-GGAGA-GGCA
1 TGGCTTGCAAGGACGGAGAGGGCA
* *
79 TGGCTCGCAAGGACGGGGAGGGCA
1 TGGCTTGCAAGGACGGAGAGGGCA
103 TGGCTT
1 TGGCTT
109 CTTAGGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.48
23 4 0.16
24 9 0.36
ACGTcount: A:0.21, C:0.17, G:0.46, T:0.15
Consensus pattern (24 bp):
TGGCTTGCAAGGACGGAGAGGGCA
Found at i:162 original size:91 final size:92
Alignment explanation
Indices: 3--451 Score: 569
Period size: 92 Copynumber: 4.9 Consensus size: 92
1 AT
* * *
3 GGGAGGGCATGACTTCCTAAGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGCTTGCAAG
1 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGCTTGCAAG
*
68 GAGGAGA-GGCATGGCTCGCAAGGACG
66 GAGGAGAGGGCATGGCTCGCAAGGAGG
*
94 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGCTTGCACG
1 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGCTTGCAAG
*
159 GAGGGGAGGGCATGGCAT-GCAAGGAGG
66 GAGGAGAGGGCATGGC-TCGCAAGGAGG
*
186 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGC--G-GA-
1 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGCTTGCAAG
247 GAGGA-AGGGCATGGCTCGCAAGGAGG
66 GAGGAGAGGGCATGGCTCGCAAGGAGG
* * *
273 GGGAGGGCATGGCTTCTCAGGGAAAGGAGGAA---TCTTTGGATGTGGAGGATGTGGCTCGCAAG
1 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGCTTGCAAG
* * * *
335 GAAGGGGA-GACAATGGCTTGCAAGGAAG
66 G-AGGAGAGGGC-ATGGCTCGCAAGGAGG
** *
363 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTTGGACGTGGAGGATGTGGAGGATGTGGCT
1 GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATC-TT---C-T-TTGGATGTGGAGGAAGTGGCT
*
428 TGCAAGGAAGGGGAGGGCATGGCT
60 TGCAAGG-AGGAGAGGGCATGGCT
452 TCTTAGGGAA
Statistics
Matches: 317, Mismatches: 21, Indels: 32
0.86 0.06 0.09
Matches are distributed among these distances:
84 22 0.07
86 2 0.01
87 51 0.16
88 5 0.02
89 5 0.02
90 47 0.15
91 67 0.21
92 74 0.23
93 1 0.00
94 1 0.00
97 1 0.00
98 1 0.00
99 38 0.12
100 2 0.01
ACGTcount: A:0.24, C:0.12, G:0.45, T:0.19
Consensus pattern (92 bp):
GGGAGGGCATGGCTTCTTAGGGAAAGGAGGAATCTTCTTTGGATGTGGAGGAAGTGGCTTGCAAG
GAGGAGAGGGCATGGCTCGCAAGGAGG
Found at i:174 original size:23 final size:24
Alignment explanation
Indices: 148--200 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
138 GTGGAGGAAG
*
148 TGGCTTGCACGGA-GGGGAGGGCA
1 TGGCTTGCAAGGAGGGGGAGGGCA
*
171 TGGCATGCAAGGAGGGGGAGGGCA
1 TGGCTTGCAAGGAGGGGGAGGGCA
195 TGGCTT
1 TGGCTT
201 CTTAGGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.19, C:0.15, G:0.51, T:0.15
Consensus pattern (24 bp):
TGGCTTGCAAGGAGGGGGAGGGCA
Found at i:520 original size:15 final size:15
Alignment explanation
Indices: 502--533 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
492 TGGCTTGCAA
502 GGAGGAGGAGGGCAT
1 GGAGGAGGAGGGCAT
*
517 GGAGGGGGAGGGCAT
1 GGAGGAGGAGGGCAT
532 GG
1 GG
534 CTTCTCAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.66, T:0.06
Consensus pattern (15 bp):
GGAGGAGGAGGGCAT
Found at i:593 original size:84 final size:82
Alignment explanation
Indices: 437--599 Score: 249
Period size: 81 Copynumber: 2.0 Consensus size: 82
427 TTGCAAGGAA
* * *
437 GGGGAGGGCATGGCTTCTTAGGGAAAGGAGCAATGTTCTTTGGATGTGGAGGAAGTGGCTTGCAA
1 GGGGAGGGCATGGCTTCTCAGGGAAAGGAG--AGGATCTTTGGATGTGGAGGAAGTGGCTTGCAA
502 GGAGGAGGAGGGCATGGAG
64 GGAGGAGGAGGGCATGGAG
*
521 GGGGAGGGCATGGCTTCTCAGGGAAAGGAG-GGATCTTTGGATGTGGAGGATGTGGCTTGCAAGG
1 GGGGAGGGCATGGCTTCTCAGGGAAAGGAGAGGATCTTTGGATGTGGAGGAAGTGGCTTGCAAGG
585 AAGG-GGAGGGCATGG
66 -AGGAGGAGGGCATGG
600 CTTCTTAGGG
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
81 42 0.57
82 3 0.04
84 29 0.39
ACGTcount: A:0.23, C:0.10, G:0.48, T:0.20
Consensus pattern (82 bp):
GGGGAGGGCATGGCTTCTCAGGGAAAGGAGAGGATCTTTGGATGTGGAGGAAGTGGCTTGCAAGG
AGGAGGAGGGCATGGAG
Found at i:613 original size:150 final size:150
Alignment explanation
Indices: 409--686 Score: 538
Period size: 150 Copynumber: 1.9 Consensus size: 150
399 TGGACGTGGA
409 GGATGTGGAGGATGTGGCTTGCAAGGAAGGGGAGGGCATGGCTTCTTAGGGAAAGGAGCAATGTT
1 GGATGTGGAGGATGTGGCTTGCAAGGAAGGGGAGGGCATGGCTTCTTAGGGAAAGGAGCAATGTT
*
474 CTTTGGATGTGGAGGAAGTGGCTTGCAAGGAGGAGGAGGGCATGGAGGGGGAGGGCATGGCTTCT
66 CTTTGGATGTGGAGGAAGTGGCTTGCAAGGAGGAGGAGGGCATGGAGGGGGAGGGCACGGCTTCT
539 CAGGGAAAGGAGGGATCTTT
131 CAGGGAAAGGAGGGATCTTT
559 GGATGTGGAGGATGTGGCTTGCAAGGAAGGGGAGGGCATGGCTTCTTAGGGAAAGGAGCAATGTT
1 GGATGTGGAGGATGTGGCTTGCAAGGAAGGGGAGGGCATGGCTTCTTAGGGAAAGGAGCAATGTT
*
624 CTTTGGATGTGGAGGAAGTGGCTTGCAGGGAGGAGGAGGGCATGGAGGGGGAGGGCACGGCTT
66 CTTTGGATGTGGAGGAAGTGGCTTGCAAGGAGGAGGAGGGCATGGAGGGGGAGGGCACGGCTT
687 GCAAGGAGGG
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 126 1.00
ACGTcount: A:0.23, C:0.10, G:0.47, T:0.20
Consensus pattern (150 bp):
GGATGTGGAGGATGTGGCTTGCAAGGAAGGGGAGGGCATGGCTTCTTAGGGAAAGGAGCAATGTT
CTTTGGATGTGGAGGAAGTGGCTTGCAAGGAGGAGGAGGGCATGGAGGGGGAGGGCACGGCTTCT
CAGGGAAAGGAGGGATCTTT
Found at i:664 original size:69 final size:66
Alignment explanation
Indices: 521--668 Score: 208
Period size: 69 Copynumber: 2.2 Consensus size: 66
511 GGGCATGGAG
* *
521 GGGGAGGGCATGGCTTCTCAGGGAAAGGAGGGATCTTTGGATGTGGAGGATGTGGCTTGCAAGGA
1 GGGGAGGGCATGGCTTCTCAGGGAAAGGAGGGATCTTTGGATGTGGAGGAAGTGGCTTGCAAGGG
586 A
66 A
* * *
587 GGGGAGGGCATGGCTTCTTAGGGAAAGGAGCAATGTTCTTTGGATGTGGAGGAAGTGGCTTGC-A
1 GGGGAGGGCATGGCTTCTCAGGGAAAGGAG---GGATCTTTGGATGTGGAGGAAGTGGCTTGCAA
651 GGGA
63 GGGA
655 GGAGGAGGGCATGG
1 GG-GGAGGGCATGG
669 AGGGGGAGGG
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
66 29 0.40
68 6 0.08
69 38 0.52
ACGTcount: A:0.22, C:0.10, G:0.47, T:0.21
Consensus pattern (66 bp):
GGGGAGGGCATGGCTTCTCAGGGAAAGGAGGGATCTTTGGATGTGGAGGAAGTGGCTTGCAAGGG
A
Done.