Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2401
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: 26737
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Found at i:847 original size:40 final size:40
Alignment explanation
Indices: 795--1026 Score: 365
Period size: 40 Copynumber: 5.8 Consensus size: 40
785 ATAACCACAA
* * * *
795 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
835 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
875 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
915 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATGTCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATA--TCAACTC
*
957 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
997 GCATAAATGCCTTCGGGTCTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
1027 GTATTCAAAT
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
40 138 0.78
42 40 0.22
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:986 original size:122 final size:120
Alignment explanation
Indices: 795--1026 Score: 392
Period size: 122 Copynumber: 1.9 Consensus size: 120
785 ATAACCACAA
* * *
795 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
*
860 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
66 CGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
915 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATGTCAACTCGCACAAATGCCTTCGGGTCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATA-G-CAACTCGCACAAATGCCTTCGGGTCTTAG
*
980 CCCGGATATATCAACTTGCATAAATGCCTTCGGGTCTTAGCCCGGAT
64 CCCGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGAT
1027 GTATTCAAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 30 0.29
121 1 0.01
122 73 0.70
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (120 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
CGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:990 original size:82 final size:81
Alignment explanation
Indices: 795--1034 Score: 383
Period size: 82 Copynumber: 3.0 Consensus size: 81
785 ATAACCACAA
* * * *
795 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
*
860 CGGATATA-TCAACTT
66 CGGATATATTCAACTC
875 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
940 CGGATATATGTCAACTC
66 CGGATATAT-TCAACTC
* * *
957 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAAATGCCTTCGGGTCTTAGCC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
*
1022 CGGATGTATTCAA
66 CGGATATATTCAA
1035 ATGCTCATGC
Statistics
Matches: 149, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
80 69 0.46
81 4 0.03
82 76 0.51
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (81 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
CGGATATATTCAACTC
Found at i:9253 original size:40 final size:40
Alignment explanation
Indices: 9208--9436 Score: 388
Period size: 40 Copynumber: 5.8 Consensus size: 40
9198 ATAACCACAA
* * * *
9208 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
9248 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
9287 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
9327 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
9367 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
9407 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
9437 GTATTCAAAT
Statistics
Matches: 179, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 34 0.19
40 145 0.81
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:14728 original size:40 final size:41
Alignment explanation
Indices: 14668--14763 Score: 167
Period size: 40 Copynumber: 2.4 Consensus size: 41
14658 CGGATGTAAC
* *
14668 AACCAGCACGAATGCCTTCGGGACTTAACCCGGT-TATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTATAAAAT
14708 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTATAAAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTATAAAAT
14749 AACCCGCACGAATGC
1 AACCCGCACGAATGC
14764 TATGCACATA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
40 33 0.62
41 20 0.38
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (41 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTATAAAAT
Found at i:23120 original size:39 final size:40
Alignment explanation
Indices: 23048--23141 Score: 163
Period size: 39 Copynumber: 2.4 Consensus size: 40
23038 CGGATGTAAC
*
23048 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
23088 AACCCGTACGAATGCCTTC-GGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
23127 AACCCGCACGAATGC
1 AACCCGCACGAATGC
23142 TATGCACATA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 34 0.67
40 17 0.33
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Done.