Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3161
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: 32505
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5807 original size:79 final size:80
Alignment explanation
Indices: 5709--5891 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
5699 TACTCGTTCA
* *
5709 AATGCCTTCGGGACATAGCCCGG-TTATAGCAACTCGCACAAATGCCTTCGGGA-CTTAACCCAG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGCAACTCGCACAAATGCCTTC-GGATCTTAACCCAG
* *
5772 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
* ** *
5789 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGCAACTCGCACAAATGCCTTCGGATCTTAACCCAGAT
*
5853 ATAGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
5868 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
5892 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGCAACTCGCACAAATGCCTTCGGATCTTAACCCAGAT
ATAGTAACTTAGCAC
Found at i:5891 original size:40 final size:40
Alignment explanation
Indices: 5688--5891 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
5678 CGGAATTTAA
** *
5688 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
5728 CCGGTTATAGCAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
5768 CCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
5807 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
5847 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5887 CCGGA
1 CCGGA
5892 CATCATTCGA
Statistics
Matches: 138, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 31 0.22
40 93 0.67
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:13862 original size:39 final size:39
Alignment explanation
Indices: 13776--13957 Score: 208
Period size: 39 Copynumber: 4.6 Consensus size: 39
13766 GCTACTCGTT
* * *
13776 CAAATGCCTTCGGGACATAGCCCGGTTATAGCAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCA
*
13816 CAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCA
* *
13855 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCA
* * * *
13894 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCCGATTTAGTAAC-TCGCA
13935 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
13958 GACATCATTC
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
38 9 0.07
39 52 0.43
40 48 0.39
41 13 0.11
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCA
Found at i:13959 original size:40 final size:40
Alignment explanation
Indices: 13757--13959 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
13747 TCGAATTTAA
** *
13757 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
13797 CCGGTTATAGCAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
13837 CC-GATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
13875 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
13915 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
13955 CCGGA
1 CCGGA
13960 CATCATTCGA
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
38 9 0.07
39 50 0.36
40 67 0.49
41 12 0.09
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28957 original size:93 final size:92
Alignment explanation
Indices: 28799--28969 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
28789 GGATGGTTGA
* *
28799 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
28864 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
*
28891 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28956 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
28970 CTTATGGGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 24 0.32
93 51 0.68
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28967 original size:46 final size:46
Alignment explanation
Indices: 28803--28976 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
28793 GGTTGAGCAT
* *
28803 CCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
28848 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
28893 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
28941 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28977 GGGGTTACAT
Statistics
Matches: 109, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 23 0.21
46 41 0.38
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Done.