Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold525
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: 45058
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:15149 original size:28 final size:28
Alignment explanation
Indices: 15098--15151 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
15088 TCTTAGGACT
* *
15098 TTTCTTTATTTCTTACTGTTTCGATTTA
1 TTTCTTTATTTCCTACTGTGTCGATTTA
15126 TTTCTTTA-TTCCTACTTGTGTCGATT
1 TTTCTTTATTTCCTAC-TGTGTCGATT
15152 CATTGTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.13, C:0.17, G:0.09, T:0.61
Consensus pattern (28 bp):
TTTCTTTATTTCCTACTGTGTCGATTTA
Found at i:24050 original size:19 final size:21
Alignment explanation
Indices: 24016--24064 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
24006 AAGGAAGACA
24016 CAAAAAGA-AATCAAAAA-AG
1 CAAAAAGAGAATCAAAAAGAG
*
24035 -AAAAAGAGAATGAAAAAGAG
1 CAAAAAGAGAATCAAAAAGAG
24055 CAAAAAGAGA
1 CAAAAAGAGA
24065 TTGAGAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 2 0.08
21 9 0.35
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (21 bp):
CAAAAAGAGAATCAAAAAGAG
Found at i:27564 original size:14 final size:14
Alignment explanation
Indices: 27545--27588 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
27535 CTCTTAATTC
27545 GATTGTGCAGATTT
1 GATTGTGCAGATTT
27559 GATTGTGCAGATTT
1 GATTGTGCAGATTT
*
27573 GATAT-TTCAGATTT
1 GAT-TGTGCAGATTT
27587 GA
1 GA
27589 GGACGAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 27 0.96
15 1 0.04
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (14 bp):
GATTGTGCAGATTT
Found at i:30765 original size:13 final size:13
Alignment explanation
Indices: 30747--30772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30737 GGACATTCCA
30747 GATTTAATTTCAT
1 GATTTAATTTCAT
30760 GATTTAATTTCAT
1 GATTTAATTTCAT
30773 TTGTTTGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
GATTTAATTTCAT
Found at i:31881 original size:23 final size:22
Alignment explanation
Indices: 31855--31907 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31845 TTGAGATTGA
*
31855 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
31878 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
31900 AAAAGAAA
1 AAAAGAAA
31908 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:36371 original size:12 final size:13
Alignment explanation
Indices: 36354--36382 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
36344 TTAAACTAAG
36354 TAAATAAAT-AAA
1 TAAATAAATAAAA
36366 TAAATAAATAAAA
1 TAAATAAATAAAA
36379 TAAA
1 TAAA
36383 ACTTTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:37779 original size:23 final size:22
Alignment explanation
Indices: 37727--37779 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
37717 TCCACGTCTT
*
37727 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
37749 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
37772 TTTCTTTT
1 TTTCTTTT
37780 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Done.