Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2667
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: 22027
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1877 original size:46 final size:45
Alignment explanation
Indices: 1824--1997 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
1814 GATTTGAGCA
1824 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
1870 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
1916 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
1962 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1998 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 17
0.80 0.07 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 36 0.33
46 64 0.58
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:9408 original size:46 final size:46
Alignment explanation
Indices: 9358--9533 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
9348 TGATTGAGCA
9358 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
9404 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
9449 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
9497 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
9534 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:9514 original size:93 final size:93
Alignment explanation
Indices: 9355--9526 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
9345 GGATGATTGA
*
9355 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
9420 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
9448 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
9512 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
9527 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:11717 original size:40 final size:40
Alignment explanation
Indices: 11669--11936 Score: 457
Period size: 40 Copynumber: 6.7 Consensus size: 40
11659 CCGCAAACAC
* * *
11669 ATTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATA
1 ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
*
11709 ATTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATA
1 ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
* * *
11749 ATTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATA
1 ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
11789 ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
1 ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
*
11829 ATTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATA
1 ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
11869 ATTGCCTTCGGGTCTTAGCCCGGATATAT-AACTCGCATA
1 ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
11908 ATTGCCTTCGGGTCTTAGCCCGGATATAT
1 ATTGCCTTCGGGTCTTAGCCCGGATATAT
11937 TCCAATGCTC
Statistics
Matches: 216, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
39 39 0.18
40 177 0.82
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (40 bp):
ATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATA
Found at i:20204 original size:40 final size:40
Alignment explanation
Indices: 20120--20382 Score: 449
Period size: 40 Copynumber: 6.6 Consensus size: 40
20110 AACACATGTG
* *
20120 CTTCGGGTCTTAACCCGGACATATCAACT-GCATAATTGC
1 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
*
20159 CTTCGGGTCTTAGCCCGGATATATCATCTCGCATAATTGC
1 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
* * *
20199 CTTCGGGT-ATAGCCCGGACATATTAACTCGCATAATTGC
1 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
20238 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
1 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
*
20278 CTTCGGGTCTTAGCCCGGATATATTAACTCGCATAATTGC
1 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
20318 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
1 CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
20358 CTTCGGGTCTTAGCCCGGATATATC
1 CTTCGGGTCTTAGCCCGGATATATC
20383 CAATGCTCAT
Statistics
Matches: 210, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
39 61 0.29
40 149 0.71
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.30
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGC
Done.