Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 161 of 161
Found at i:50173077 original size:35 final size:37
Alignment explanation
Indices: 50173007--50173086 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 37
50172997 AATATAATTA
* *
50173007 TAATTATAATTTAAAATTATTAATTCACATATAAAAT
1 TAATTATAATATAAAATTATTAATTCACATATAAAAC
* *
50173044 TAATTATAATAT-ACATTA-TAATTGCA-ATTTAAAAC
1 TAATTATAATATAAAATTATTAATT-CACATATAAAAC
50173079 TAATTATA
1 TAATTATA
50173087 GAATATGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 20 0.53
36 7 0.18
37 11 0.29
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.42
Consensus pattern (37 bp):
TAATTATAATATAAAATTATTAATTCACATATAAAAC
Found at i:50179937 original size:19 final size:19
Alignment explanation
Indices: 50179894--50179938 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
50179884 CAAATATATA
* *
50179894 ATTATATTTTTTTAAAAGT
1 ATTATATTATCTTAAAAGT
* *
50179913 AATATATTATCTTAAAATT
1 ATTATATTATCTTAAAAGT
50179932 ATTATAT
1 ATTATAT
50179939 AATTATATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTATATTATCTTAAAAGT
Found at i:50179962 original size:18 final size:19
Alignment explanation
Indices: 50179939--50179984 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
50179929 ATTATTATAT
50179939 AATTATATTT-TAAAAATA
1 AATTATATTTCTAAAAATA
*
50179957 AATTATATTTCTAAAATTA
1 AATTATATTTCTAAAAATA
*
50179976 AAATATATT
1 AATTATATT
50179985 ATTATTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTATATTTCTAAAAATA
Found at i:50179972 original size:43 final size:44
Alignment explanation
Indices: 50179886--50180001 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 44
50179876 TCTAATAACA
*
50179886 AATATATAATTATATTTTTTTAAAAGT-AATATATTATCTTAAAATT
1 AATATATAATTATA---TTTTAAAAATAAATATATTATCTTAAAATT
*
50179932 ATTATATAATTATATTTTAAAAATAAATTATATT-TC-TAAAATT
1 AATATATAATTATATTTTAAAAATAAA-TATATTATCTTAAAATT
*
50179975 AAAATAT-ATTATTATTGTATAAAAATA
1 AATATATAATTA-TATT-T-TAAAAATA
50180002 GCTTTTGTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
42 4 0.07
43 25 0.41
44 5 0.08
45 14 0.23
46 13 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (44 bp):
AATATATAATTATATTTTAAAAATAAATATATTATCTTAAAATT
Found at i:50181113 original size:22 final size:22
Alignment explanation
Indices: 50181088--50181131 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
50181078 TAGTCTTATA
50181088 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* *
50181110 ATAAATTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
50181132 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:50181167 original size:13 final size:14
Alignment explanation
Indices: 50181151--50181192 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
50181141 TTTTAATTTT
50181151 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
50181164 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
50181179 ATTTTAAATAATAT
1 ATTTT-AATAATAT
50181193 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:50181177 original size:16 final size:16
Alignment explanation
Indices: 50181155--50181191 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
50181145 AATTTTATTT
50181155 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
50181172 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
50181187 TAATA
1 TAATA
50181192 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:50183793 original size:26 final size:26
Alignment explanation
Indices: 50183756--50183813 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
50183746 TGATACAAAT
50183756 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
50183782 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
50183808 TGATAA
1 TGATAA
50183814 GGATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Done.