Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5275.1
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: 27675
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.23
Warning! 7456 characters in sequence are not A, C, G, or T
Found at i:14828 original size:12 final size:12
Alignment explanation
Indices: 14813--14859 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
14803 AAGAGGAAAG
14813 TTGAAAAAAAAA
1 TTGAAAAAAAAA
14825 TTG-AAAAAAAA
1 TTGAAAAAAAAA
*
14836 TCGAAAAAAAAA
1 TTGAAAAAAAAA
*
14848 TTTAAAAAAAAA
1 TTGAAAAAAAAA
14860 ATCGAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:14833 original size:11 final size:11
Alignment explanation
Indices: 14817--14858 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
14807 GGAAAGTTGA
14817 AAAAAAAATTG
1 AAAAAAAATTG
*
14828 AAAAAAAATCG
1 AAAAAAAATTG
*
14839 AAAAAAAAATTT
1 -AAAAAAAATTG
14851 AAAAAAAA
1 AAAAAAAA
14859 AATCGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:14841 original size:23 final size:25
Alignment explanation
Indices: 14815--14868 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
14805 GAGGAAAGTT
*
14815 GAAAAAAAAA-TT-GAAAAAAAATC
1 GAAAAAAAAATTTAAAAAAAAAATC
14838 GAAAAAAAAATTTAAAAAAAAAATC
1 GAAAAAAAAATTTAAAAAAAAAATC
14863 GAAAAA
1 GAAAAA
14869 TCGAAGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 10 0.36
24 2 0.07
25 16 0.57
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (25 bp):
GAAAAAAAAATTTAAAAAAAAAATC
Found at i:14867 original size:12 final size:12
Alignment explanation
Indices: 14815--14868 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
14805 GAGGAAAGTT
*
14815 GAAAAAAAAATT
1 GAAAAAAAAATC
14827 G-AAAAAAAATC
1 GAAAAAAAAATC
*
14838 GAAAAAAAAATTT
1 GAAAAAAAAA-TC
*
14851 AAAAAAAAAATC
1 GAAAAAAAAATC
14863 GAAAAA
1 GAAAAA
14869 TCGAAGTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 10 0.29
12 15 0.43
13 10 0.29
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (12 bp):
GAAAAAAAAATC
Done.