Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2277
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: 13007
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Found at i:3002 original size:40 final size:40
Alignment explanation
Indices: 2936--3201 Score: 446
Period size: 40 Copynumber: 6.7 Consensus size: 40
2926 GAGCATTGGA
*
2936 ATATATCCGGGCT-AGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
2975 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
* *
3015 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
3055 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
3095 ATATATCC-GGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
3134 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
3174 ATATGTCCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
3202 ATGTGTTTGC
Statistics
Matches: 216, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
39 50 0.23
40 166 0.77
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
Found at i:3122 original size:119 final size:119
Alignment explanation
Indices: 2935--3201 Score: 446
Period size: 119 Copynumber: 2.2 Consensus size: 119
2925 TGAGCATTGG
* *
2935 AATATATCCGGGCTAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 AATATATCCGGGCTAGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAAACCCGAAGG
* *
3000 CAATTATGCGAGTTGATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGAT
66 CAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
3054 AATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCC-GGCTAAAACCCGAAG
1 AATATATCCGGGCTA-GACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAAACCCGAAG
*
3118 GCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
65 GCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
* *
3173 GATATGTCCGGGCTAAGACCCGAAGGCAA
1 AATATATCCGGGCT-AGACCCGAAGGCAA
3202 ATGTGTTTGC
Statistics
Matches: 139, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
119 106 0.76
120 33 0.24
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (119 bp):
AATATATCCGGGCTAGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAAACCCGAAGG
CAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
Found at i:11515 original size:40 final size:40
Alignment explanation
Indices: 11456--11721 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
11446 GAGCATTGGA
* *
11456 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
11496 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAG-TG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
* *
11535 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
11575 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
11615 ATATATCCGGGCTAA-ACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
11654 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
11694 ATATGTCCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
11722 ATGTGTTTGC
Statistics
Matches: 217, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
39 77 0.35
40 140 0.65
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
Found at i:11587 original size:79 final size:80
Alignment explanation
Indices: 11456--11721 Score: 455
Period size: 79 Copynumber: 3.4 Consensus size: 80
11446 GAGCATTGGA
*
11456 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
11521 CAATTATGCGAG-TG
66 CAATTATGCGAGATG
* *
11535 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATAATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
11600 CAATTATGCGAGATG
66 CAATTATGCGAGATG
*
11615 ATATATCCGGGCTA-AACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
*
11679 CAATTATGCGAGTTG
66 CAATTATGCGAGATG
* *
11694 ATATGTCCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTATGACCCGAAGGCAA
11722 ATGTGTTTGC
Statistics
Matches: 176, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
79 148 0.84
80 28 0.16
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (80 bp):
ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
CAATTATGCGAGATG
Found at i:11666 original size:119 final size:119
Alignment explanation
Indices: 11455--11721 Score: 464
Period size: 119 Copynumber: 2.2 Consensus size: 119
11445 TGAGCATTGG
*
11455 AATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAG
1 AATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAG
*
11520 GCAATTATGCGAGTGATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGAT
66 GCAATTATGCGAGTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
11574 AATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAA-ACCCGAAG
1 AATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAG
*
11638 GCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
66 GCAATTATGCGAG-TGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
* * *
11693 GATATGTCCGGGCTAAGACCCGAAGGCAA
1 AATATATCCGGGCTATGACCCGAAGGCAA
11722 ATGTGTTTGC
Statistics
Matches: 141, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
118 21 0.15
119 120 0.85
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (119 bp):
AATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAG
GCAATTATGCGAGTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
Done.