Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2376
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, 581
Length: 969
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Found at i:268 original size:147 final size:147
Alignment explanation
Indices: 1--301 Score: 593
Period size: 147 Copynumber: 2.0 Consensus size: 147
1 TTTTTTCGTTTTGAACAAAACGACGCCGTTTTGCTATTCTAGAAATTTTTTATTTTTTTTATAAG
1 TTTTTTCGTTTTGAACAAAACGACGCCGTTTTGCTATTCTAGAAATTTTTTATTTTTTTTATAAG
66 TTGATTTATTTTTTGCGACGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCT
66 TTGATTTATTTTTTGCGACGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCT
131 TATAAAGCGCCGCAAAA
131 TATAAAGCGCCGCAAAA
148 TTTTTTCGTTTTGAACAAAACGACGCCGTTTTGCTATTCTAGAAATTTTTTATTTTTTTTATAAG
1 TTTTTTCGTTTTGAACAAAACGACGCCGTTTTGCTATTCTAGAAATTTTTTATTTTTTTTATAAG
*
213 TTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCT
66 TTGATTTATTTTTTGCGACGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCT
278 TATAAAGCGCCGCAAAA
131 TATAAAGCGCCGCAAAA
295 TTTTTTC
1 TTTTTTC
302 TGGGCATTAG
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 153 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (147 bp):
TTTTTTCGTTTTGAACAAAACGACGCCGTTTTGCTATTCTAGAAATTTTTTATTTTTTTTATAAG
TTGATTTATTTTTTGCGACGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCT
TATAAAGCGCCGCAAAA
Found at i:456 original size:114 final size:113
Alignment explanation
Indices: 301--751 Score: 624
Period size: 114 Copynumber: 4.0 Consensus size: 113
291 AAAATTTTTT
*
301 CTGGGCATTAGCGGCGCTTTACCAAAAACGCCGCTAAATCCCTGAAAGTTCAGAAAACGGCGTCG
1 CTGGGCATTAGCGGCGCTTT-CCAAAAACGCCGCTAAATCCCCGAAAGTTCAGAAAACGGCGTCG
366 TTGGGCTTAGGTTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
65 TTGGGCTTAGGTTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
* *
415 CTGGGCATTAGCGGCGCTTTACCAAAAACGCCGCTAAATCCCTGAAAGTTCAGAAAACGGCATCG
1 CTGGGCATTAGCGGCGCTTT-CCAAAAACGCCGCTAAATCCCCGAAAGTTCAGAAAACGGCGTCG
*
480 TTGGGCTTAGGTTTTTTTGCGGCGCTTTAT-CAAAAATGCCGCTAAAGCC
65 TTGGGCTTAGGTTTTTTTGCGGCGCTTT-TCCAAAAACGCCGCTAAAGCC
* * * * *
529 CTAGGCATTAGCGACGC-ATCCTTAAAAACGCCGCTAAATCCCCAAAAGCTT-AAAAAACGGCGT
1 CTGGGCATTAGCGGCGCTTTCC--AAAAACGCCGCTAAATCCCCGAAAG-TTCAGAAAACGGCGT
* * *
592 CGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAATGCCGCTAAAACC
63 CGTTGGGCTTAGGTTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
* * * * *
643 CCGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATGGCGTCG
1 CTGGGCATTAGCGGCGCTTTC-CAAAAACGCCGCTAAATCCCCGAAAGTTCAGAAAACGGCGTCG
* *
708 TTGGGCTTAGG-TTTTTTGCGGCAC-TTTCTCAACAACGCCGCTAA
65 TTGGGCTTAGGTTTTTTTGCGGCGCTTTTC-CAAAAACGCCGCTAA
752 TGCTTTTTTT
Statistics
Matches: 303, Mismatches: 25, Indels: 19
0.87 0.07 0.05
Matches are distributed among these distances:
112 5 0.02
113 27 0.09
114 266 0.88
115 5 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (113 bp):
CTGGGCATTAGCGGCGCTTTCCAAAAACGCCGCTAAATCCCCGAAAGTTCAGAAAACGGCGTCGT
TGGGCTTAGGTTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
Found at i:811 original size:12 final size:12
Alignment explanation
Indices: 794--819 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
784 TTTTTTATCC
794 AAACGCCGCTAA
1 AAACGCCGCTAA
806 AAACGCCGCTAA
1 AAACGCCGCTAA
818 AA
1 AA
820 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Done.