Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1776
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: 26924
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:7155 original size:46 final size:46
Alignment explanation
Indices: 7105--7280 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
7095 TGGTTGAGCA
7105 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
7151 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
7196 CATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
7244 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
7281 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 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:7266 original size:93 final size:93
Alignment explanation
Indices: 7102--7273 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
7092 GGATGGTTGA
* *
7102 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
7167 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
7195 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
7260 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
7274 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:9853 original size:15 final size:15
Alignment explanation
Indices: 9821--9849 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9811 ATTGTCAGTG
9821 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
9836 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
9850 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:15835 original size:39 final size:40
Alignment explanation
Indices: 15790--15957 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
15780 CGGGGTTTAG
* * *
15790 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
15829 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
15869 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
15909 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
15950 CCGGATAT
1 CCGGATAT
15958 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:15940 original size:41 final size:40
Alignment explanation
Indices: 15813--15957 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
15803 CTCGCACAAG
* * * * *
15813 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
15853 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
15893 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
15934 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
15958 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:23846 original size:39 final size:40
Alignment explanation
Indices: 23788--23967 Score: 105
Period size: 40 Copynumber: 4.5 Consensus size: 40
23778 AATCAAGCAT
* * *
23788 CTTCGGGT-TT-AGCCGGATATAACCACTCGCA-CAAGGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
*** *
23825 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
* * ** * * *
23865 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
* ** * ** * * *
23905 CTTCGGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGTCTTAACCCGGATATAACCAC-TAGCATAAAGGC
* *
23946 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAACCCGGATAT
23968 CATTCGAGTA
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
37 8 0.07
38 2 0.02
39 16 0.14
40 63 0.53
41 29 0.25
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
Found at i:23950 original size:41 final size:40
Alignment explanation
Indices: 23823--23967 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
23813 CTCGCACAAG
* * * * *
23823 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
23863 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
23903 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
23944 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
23968 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Done.