Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2166
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: 41600
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:11423 original size:13 final size:14
Alignment explanation
Indices: 11398--11428 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
11388 TCTTTTTTTG
11398 TTTTCACGAAATTT
1 TTTTCACGAAATTT
11412 TTTTCACG-AATTT
1 TTTTCACGAAATTT
11425 TTTT
1 TTTT
11429 TTCACTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTTCACGAAATTT
Found at i:11429 original size:14 final size:14
Alignment explanation
Indices: 11393--11429 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11383 CTTCTTCTTT
11393 TTTTGTTTTCACGAA
1 TTTT-TTTTCACGAA
*
11408 ATTTTTTTCACGAA
1 TTTTTTTTCACGAA
11422 TTTTTTTT
1 TTTTTTTT
11430 TCACTGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (14 bp):
TTTTTTTTCACGAA
Found at i:11429 original size:15 final size:15
Alignment explanation
Indices: 11392--11433 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
11382 TCTTCTTCTT
11392 TTTTTGTTTTCACGAA
1 TTTTT-TTTTCACGAA
*
11408 -ATTTTTTTCACGAA
1 TTTTTTTTTCACGAA
11422 TTTTTTTTTCAC
1 TTTTTTTTTCAC
11434 TGATACAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:13036 original size:18 final size:17
Alignment explanation
Indices: 13012--13054 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
13002 GATATAAGTT
13012 GAAAAAAAAATTCGTGG
1 GAAAAAAAAATTCGTGG
* *
13029 GCAAAAAAAATTTGTGG
1 GAAAAAAAAATTCGTGG
13046 GAAAAAAAA
1 GAAAAAAAA
13055 GAAAGCTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.21, T:0.16
Consensus pattern (17 bp):
GAAAAAAAAATTCGTGG
Found at i:32755 original size:11 final size:11
Alignment explanation
Indices: 32739--32781 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
32729 ATGAAACTAG
32739 TTTTTTCGATT
1 TTTTTTCGATT
32750 TTTTTT-GAATT
1 TTTTTTCG-ATT
*
32761 TTTTTTCGAGGT
1 TTTTTTCGA-TT
32773 TTTTTTCGA
1 TTTTTTCGA
32782 GAAACTACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 1 0.04
11 16 0.57
12 11 0.39
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (11 bp):
TTTTTTCGATT
Found at i:34314 original size:17 final size:17
Alignment explanation
Indices: 34285--34317 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34275 AAGGCGAGGC
34285 CCAATAAGCAAATTCCG
1 CCAATAAGCAAATTCCG
34302 CCAATCAAG-AAATTCC
1 CCAAT-AAGCAAATTCC
34318 ACTCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.18
Consensus pattern (17 bp):
CCAATAAGCAAATTCCG
Found at i:41304 original size:4 final size:4
Alignment explanation
Indices: 41295--41325 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
41285 TAAACTTAAG
41295 TAAA TAAA TAAA TAAA TAAA TAAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
41326 AATAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Done.