Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2301
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: 132231
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 2
Found at i:121400 original size:32 final size:32
Alignment explanation
Indices: 121307--121400 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 32
121297 AAATAATTTG
*
121307 TTTAATT-TAAAATATATTAAAT-TTAGATATAA
1 TTTAATTATAAAAAATA-TAAATATTA-ATATAA
** **
121339 TTTTTTTA-AAAAAATTATTTATATT--TATAA
1 TTTAATTATAAAAAA-TATAAATATTAATATAA
121369 TTTAATTATAAAAAATATAAATATTAATATAA
1 TTTAATTATAAAAAATATAAATATTAATATAA
121401 AATAATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
30 19 0.40
31 6 0.13
32 18 0.38
33 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
TTTAATTATAAAAAATATAAATATTAATATAA
Found at i:121413 original size:18 final size:18
Alignment explanation
Indices: 121392--121431 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
121382 AATATAAATA
121392 TTAATATAAAATAATTTT
1 TTAATATAAAATAATTTT
**
121410 TTAATATTTAATAATTTT
1 TTAATATAAAATAATTTT
121428 TTAA
1 TTAA
121432 CAATAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATATAAAATAATTTT
Found at i:130371 original size:74 final size:74
Alignment explanation
Indices: 130250--130398 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
130240 CAAAGGCCAG
130250 ATTCATTATTCAACAGAGATTCGTTATTATGTTCAAGTTCTAAATATGATGCAGTGTAAAAGTGC
1 ATTCATTATTCAACAGAGATTCGTTATTATGTTCAAGTTCTAAATATGATGCAGTGTAAAAGTGC
130315 TATATTAGC
66 TATATTAGC
130324 ATTCATTATTCAACAGAGATTCGTTATTATGTTCAAGTTCTAAATATGATGCAGTGTAAAAGTGC
1 ATTCATTATTCAACAGAGATTCGTTATTATGTTCAAGTTCTAAATATGATGCAGTGTAAAAGTGC
130389 TATATTAGC
66 TATATTAGC
130398 A
1 A
130399 CATAATTGGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (74 bp):
ATTCATTATTCAACAGAGATTCGTTATTATGTTCAAGTTCTAAATATGATGCAGTGTAAAAGTGC
TATATTAGC
Found at i:131696 original size:1 final size:1
Alignment explanation
Indices: 131690--131722 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
131680 CCTTGTCTTC
*
131690 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
131723 GTTCCTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Done.