Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1249
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: 5569
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Found at i:4774 original size:39 final size:39
Alignment explanation
Indices: 4678--4935 Score: 283
Period size: 40 Copynumber: 6.6 Consensus size: 39
4668 TTGAATGCTG
* * * * * *
4678 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
4718 TCCGGATTAAGAT-CCGAAGGCCTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTGTGCGAGTTACTAAA
*
4757 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
4797 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
4836 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
*
4876 TCC-GGTT-A-TCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
4912 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
4936 TGAACGAGGA
Statistics
Matches: 189, Mismatches: 21, Indels: 17
0.83 0.09 0.07
Matches are distributed among these distances:
36 15 0.08
37 14 0.07
38 2 0.01
39 78 0.41
40 79 0.42
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:4797 original size:40 final size:40
Alignment explanation
Indices: 4678--4935 Score: 289
Period size: 39 Copynumber: 6.6 Consensus size: 40
4668 TTGAATGCTG
* * * * * *
4678 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * *
4718 TCCGGATTAAGAT-CCGAAGGCCTT-GTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
4757 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
4797 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* **
4836 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
4876 TCC-GGTT-A-TCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
4912 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
4936 TGAACGAGGA
Statistics
Matches: 190, Mismatches: 20, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
36 14 0.07
37 15 0.08
38 2 0.01
39 80 0.42
40 76 0.40
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:4814 original size:79 final size:79
Alignment explanation
Indices: 4678--4935 Score: 312
Period size: 79 Copynumber: 3.3 Consensus size: 79
4668 TTGAATGCTG
* * * * * * *
4678 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
*
4741 TGTGCGAGATACTAAA
64 TGTGCGAGTTACTAAA
*
4757 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-
4822 GTGCGAGTTA-TAAA
65 GTGCGAGTTACTAAA
* * *
4836 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAATCC-GGTT-A-TCCCGAAGGCATTG
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
*
4898 TGTGAGTTACTAAA
66 TGCGAGTTACTAAA
* *
4912 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
4936 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
75 9 0.06
76 37 0.23
77 1 0.01
78 5 0.03
79 92 0.58
80 15 0.09
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
TGCGAGTTACTAAA
Done.