Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6476.1
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: 11483
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.30
Warning! 510 characters in sequence are not A, C, G, or T
Found at i:1682 original size:64 final size:64
Alignment explanation
Indices: 1601--1783 Score: 167
Period size: 67 Copynumber: 2.8 Consensus size: 64
1591 AGACATTATG
* * *
1601 ATGTAGCTAGGTTGCATGGGAGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGAGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * *
1665 ATGTAGCTAGGTCGCATGCGTGATTCCAGGTGAAGGACACCATGTAGACAAAAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGAGATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
1730 AA
63 AA
* * *
1732 ACTG--GCTAGGTCACATGGGTAG-TACTAAGTGTTCACCATGT-GTACAAGAGAG
1 A-TGTAGCTAGGTCGCATGGG-AGATACTATGTGTACACCATGTAG-ACAAGAGAG
1784 TCGAACTATA
Statistics
Matches: 93, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
62 1 0.01
63 17 0.18
64 24 0.26
66 18 0.19
67 31 0.33
68 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGAGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:5096 original size:18 final size:18
Alignment explanation
Indices: 5075--5109 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5065 TTTTTCTTTT
5075 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
5093 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
5110 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:6008 original size:14 final size:14
Alignment explanation
Indices: 5989--6052 Score: 60
Period size: 15 Copynumber: 4.5 Consensus size: 14
5979 AGACTTTTCA
5989 CTTTTTTTTTCCTT
1 CTTTTTTTTTCCTT
**
6003 CTTTTTTTTAAC-T
1 CTTTTTTTTTCCTT
*
6016 CGATTTTTTTGTCACTT
1 C--TTTTTTTTTC-CTT
6033 CTTTTTTTTTCCTT
1 CTTTTTTTTTCCTT
6047 -TTTTTT
1 CTTTTTT
6053 CAATTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 8 0.20
14 13 0.32
15 16 0.40
16 1 0.03
17 2 0.05
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.73
Consensus pattern (14 bp):
CTTTTTTTTTCCTT
Found at i:6071 original size:12 final size:12
Alignment explanation
Indices: 6056--6080 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6046 TTTTTTTCAA
6056 TTTTTTTGAATT
1 TTTTTTTGAATT
6068 TTTTTTTGAATT
1 TTTTTTTGAATT
6080 T
1 T
6081 CTTCTCTTTT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:6965 original size:20 final size:20
Alignment explanation
Indices: 6926--6986 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
6916 CCAATAAAAT
* *
6926 AAATGAGCTGAATTGTAGCT-
1 AAATGACCTCAATTG-AGCTG
*
6946 AAATTGACCTCGATTGAGCTG
1 AAA-TGACCTCAATTGAGCTG
*
6967 AAATGAGCTCAATTGAGCTG
1 AAATGACCTCAATTGAGCTG
6987 GTCGGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATGACCTCAATTGAGCTG
Found at i:10616 original size:30 final size:29
Alignment explanation
Indices: 10582--10665 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
10572 TAAACTAAAA
*
10582 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAG-TTTAGCTCGTGAGCTAAAGC
* * * * * *
10612 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAG-TTTAGCTCGTGAGCTAAAGC
*
10642 TGAGCTAAGTTTAGCTTGTGAGCT
1 TGAGCTAAGTTTAGCTCGTGAGCT
10666 GAATATGAGC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 10 0.25
30 30 0.75
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (29 bp):
TGAGCTAAGTTTAGCTCGTGAGCTAAAGC
Done.