Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2616
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: 10312
ACGTcount: A:0.18, C:0.29, G:0.32, T:0.20
Found at i:4477 original size:62 final size:60
Alignment explanation
Indices: 4283--4485 Score: 182
Period size: 62 Copynumber: 3.2 Consensus size: 60
4273 CGGCAACTGT
*
4283 GCGCACCCGGTGCTCCCCACGGTGTGCGCCGCGACCGCCCCC-ACCCCAGGGGGCGGGAAGGGC
1 GCGCA-CC-GTGCTCCGCACGG-GTGCGCCGCGACCGCCCCCGACCCCAGGGGGCGGG-AGGGC
* *
4346 GCGCACCGTGCTCCTGGC-CGGGTGCGTGCCGCGGCCG-CCCCGCACCCCCCAGGGTGG-GCGA-
1 GCGCACCGTGCTCC--GCACGGGTGC--GCCGCGACCGCCCCCG-A--CCCCAGGG-GGCGGGAG
4407 GGC
58 GGC
* * *
4410 GCGCACCGTGCTCCGCATGGCGTGCGCCCCGCCCGCCCCCGACCCCAGGGGGCGGGATGGGC
1 GCGCACCGTGCTCCGCACGG-GTGCGCCGCGACCGCCCCCGACCCCAGGGGGCGGGA-GGGC
*
4472 GCGCACCGTTCTCC
1 GCGCACCGTGCTCC
4486 CGCCCGCAGC
Statistics
Matches: 117, Mismatches: 8, Indels: 31
0.75 0.05 0.20
Matches are distributed among these distances:
59 2 0.02
60 11 0.09
61 11 0.09
62 36 0.31
63 22 0.19
64 22 0.19
65 1 0.01
66 10 0.09
67 2 0.02
ACGTcount: A:0.08, C:0.45, G:0.38, T:0.09
Consensus pattern (60 bp):
GCGCACCGTGCTCCGCACGGGTGCGCCGCGACCGCCCCCGACCCCAGGGGGCGGGAGGGC
Found at i:4574 original size:102 final size:102
Alignment explanation
Indices: 4396--4582 Score: 315
Period size: 102 Copynumber: 1.8 Consensus size: 102
4386 CGCACCCCCC
* *
4396 AGGGTGGGCGAGGCGCGCACCGTGCTCCGCATGGCGTGCGCCCCGCCCGCCCCCGACCCCAGGGG
1 AGGGTGGGCGAGGCGCGCACCGTGCTCCGCATGGCGTGCGCCCCGACCGCCCCCGACACCAGGGG
4461 GCGGGATGGGCGCGCACCGTTCTCCCGCCCGCAGCCG
66 GCGGGATGGGCGCGCACCGTTCTCCCGCCCGCAGCCG
*
4498 AGGGTGGGCGAGGCGCGCACCGGTGCTCCGCATGGTGTGCGCCCCGACCGCCCCC-ACACCAGGG
1 AGGGTGGGCGAGGCGCGCACC-GTGCTCCGCATGGCGTGCGCCCCGACCGCCCCCGACACCAGGG
4562 GGCGGGCA-GGGCGCGCACCGT
65 GGCGGG-ATGGGCGCGCACCGT
4583 GCACCTGGCC
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
102 48 0.60
103 32 0.40
ACGTcount: A:0.10, C:0.41, G:0.41, T:0.09
Consensus pattern (102 bp):
AGGGTGGGCGAGGCGCGCACCGTGCTCCGCATGGCGTGCGCCCCGACCGCCCCCGACACCAGGGG
GCGGGATGGGCGCGCACCGTTCTCCCGCCCGCAGCCG
Found at i:5022 original size:64 final size:64
Alignment explanation
Indices: 4921--5042 Score: 199
Period size: 64 Copynumber: 1.9 Consensus size: 64
4911 CACCGATAGC
*
4921 ACATGCGGAGGCCCAAGCGTGGGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCCTCTCTA
1 ACATGCGGAGGCCCAAGCGTGCGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCCTCTCTA
* * * *
4985 ACATGCGGAGGGCCAAGCGTGCGCAACGAGTCCCTCCCCAGCATCCGTCCCTCCCCCC
1 ACATGCGGAGGCCCAAGCGTGCGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCC
5043 CAACCAAACG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (64 bp):
ACATGCGGAGGCCCAAGCGTGCGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCCTCTCTA
Found at i:5290 original size:63 final size:62
Alignment explanation
Indices: 5102--5296 Score: 200
Period size: 63 Copynumber: 3.1 Consensus size: 62
5092 CGACAACGGT
* *
5102 GCGCACCCGGTGCCCCGCGAGGTGTGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAGGGC
1 GCGCA-CCGGCGCCCCGCGAGGTGCGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAGGGC
* * * * * * * * * *
5165 GCGCCCCGTGCTCCCGCCCG-GGTCCGTGCCGCGGCCGCCCGCA--CCAGAGGGCGGG-CGAGGC
1 GCGCACCG-GCGCCC-CGCGAGGTGCGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAG-GGC
*
5226 GCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCCACCCCAGGGGGCGGGAAGGGC
1 GCGCACCGGCGCCCCGCGAGGTGCGCGCCCCGACCG-CCCCCACCCCAGGGGGCGGGAAGGGC
5289 GCGCACCG
1 GCGCACCG
5297 TGCTCCTGGC
Statistics
Matches: 101, Mismatches: 23, Indels: 16
0.72 0.16 0.11
Matches are distributed among these distances:
59 3 0.03
60 18 0.18
61 26 0.26
62 3 0.03
63 47 0.47
64 4 0.04
ACGTcount: A:0.10, C:0.46, G:0.41, T:0.04
Consensus pattern (62 bp):
GCGCACCGGCGCCCCGCGAGGTGCGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAGGGC
Found at i:5324 original size:103 final size:101
Alignment explanation
Indices: 5203--5391 Score: 297
Period size: 103 Copynumber: 1.9 Consensus size: 101
5193 CCGCGGCCGC
5203 CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCC
1 CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCG-CCCCC
*
5268 ACCCCAGGGGGCGGGAAGGGCGCGCACCGTGCTCCTGG
65 ACCAC-GGGGGCGGGAAGGGCGCGCACCGTGCTCCTGG
* * * * * *
5306 CCGCACCCGAGGGTGGGCGAGGCGCGCACCGGCGCTCCGCGTGGTGTGCGCCCCGGCCGCCCCCA
1 CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCA
5371 CCACGGGGGCGGGAAGGGCGC
66 CCACGGGGGCGGGAAGGGCGC
5392 CCCCGGGCCG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 17 0.22
102 9 0.11
103 53 0.67
ACGTcount: A:0.11, C:0.42, G:0.43, T:0.05
Consensus pattern (101 bp):
CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCA
CCACGGGGGCGGGAAGGGCGCGCACCGTGCTCCTGG
Done.