Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 196 of 196
Found at i:58838579 original size:45 final size:45
Alignment explanation
Indices: 58838513--58838610 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
58838503 TCGACTACTG
* * * *
58838513 TTACTGTTACCGATTCGACACTTTGTGTGTCGGATACTGTTACCA
1 TTACTGTTACAGATTCAACACTTTGTATGTCGAATACTGTTACCA
* * *
58838558 TTACTGTTATAGATTCAACACTTTGTATGTTGAATACTGTTACTA
1 TTACTGTTACAGATTCAACACTTTGTATGTCGAATACTGTTACCA
58838603 TTACTGTT
1 TTACTGTT
58838611 GCCGTTACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.43
Consensus pattern (45 bp):
TTACTGTTACAGATTCAACACTTTGTATGTCGAATACTGTTACCA
Found at i:58848434 original size:59 final size:59
Alignment explanation
Indices: 58848362--58848484 Score: 246
Period size: 59 Copynumber: 2.1 Consensus size: 59
58848352 TAAAGCATAA
58848362 AAATTACAATATTTATATTTATATTCACATACTCTTTTAGATATTACAAATGTGTCTTT
1 AAATTACAATATTTATATTTATATTCACATACTCTTTTAGATATTACAAATGTGTCTTT
58848421 AAATTACAATATTTATATTTATATTCACATACTCTTTTAGATATTACAAATGTGTCTTT
1 AAATTACAATATTTATATTTATATTCACATACTCTTTTAGATATTACAAATGTGTCTTT
58848480 AAATT
1 AAATT
58848485 CTTACCATTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (59 bp):
AAATTACAATATTTATATTTATATTCACATACTCTTTTAGATATTACAAATGTGTCTTT
Found at i:58851195 original size:12 final size:12
Alignment explanation
Indices: 58851178--58851202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58851168 CCTGTTTGTT
58851178 GTAGATATTGAA
1 GTAGATATTGAA
58851190 GTAGATATTGAA
1 GTAGATATTGAA
58851202 G
1 G
58851203 AGGTACCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GTAGATATTGAA
Found at i:58852711 original size:20 final size:20
Alignment explanation
Indices: 58852688--58852743 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
58852678 TTTTTATAAA
*
58852688 TATTTTGAAATTTTGAAAAT
1 TATTTTGAAATTTTGAAAAC
* *
58852708 TATTTCG-AATTTCTAAAAAC
1 TATTTTGAAATTT-TGAAAAC
*
58852728 TATTTTAAAATATTTG
1 TATTTTGAAAT-TTTG
58852744 GTTGAAAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.19
20 16 0.59
21 4 0.15
22 2 0.07
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (20 bp):
TATTTTGAAATTTTGAAAAC
Found at i:58856265 original size:22 final size:21
Alignment explanation
Indices: 58856213--58856269 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
58856203 CCCTTTTCCC
* *
58856213 TTTTCTCTTTTCTCTTATTCT
1 TTTTTTCTTTTCTCTCATTCT
58856234 TCTTCCTTTCTTTTCATCTCATTCT
1 T-TT--TTTCTTTTC-TCTCATTCT
58856259 TTTTTTCTTTT
1 TTTTTTCTTTT
58856270 TTCCCTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
24 10 0.33
25 9 0.30
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTCTTTTCTCTCATTCT
Found at i:58857596 original size:13 final size:13
Alignment explanation
Indices: 58857580--58857606 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58857570 TAAATTAATA
58857580 AATGTAATTATAT
1 AATGTAATTATAT
58857593 AATGTAATTATAT
1 AATGTAATTATAT
58857606 A
1 A
58857607 TTTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AATGTAATTATAT
Found at i:58860535 original size:82 final size:82
Alignment explanation
Indices: 58860388--58860556 Score: 311
Period size: 82 Copynumber: 2.1 Consensus size: 82
58860378 TTGTGAGATG
*
58860388 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATATATCTTAGG
1 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATATATCATAGG
*
58860453 ATTGTCAAATTCCAACT
66 ATTGCCAAATTCCAACT
*
58860470 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATGTATCATAGG
1 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATATATCATAGG
58860535 ATTGCCAAATTCCAACT
66 ATTGCCAAATTCCAACT
58860552 TCTTT
1 TCTTT
58860557 TGAGTAACTT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (82 bp):
TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATATATCATAGG
ATTGCCAAATTCCAACT
Found at i:58869691 original size:12 final size:12
Alignment explanation
Indices: 58869674--58869700 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58869664 ACTAAAAAAA
58869674 TAAAATACTATC
1 TAAAATACTATC
58869686 TAAAATACTATC
1 TAAAATACTATC
58869698 TAA
1 TAA
58869701 CGATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAATACTATC
Found at i:58871822 original size:2 final size:2
Alignment explanation
Indices: 58871815--58871846 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
58871805 ATCATATGTC
58871815 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
58871847 TACATTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.