Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1017
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1024007
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 32449 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1001898 original size:2 final size:2
Alignment explanation
Indices: 1001891--1001946 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1001881 ACACTGGCAC
1001891 AG AG AG AG AG 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 AG AG AG AG AG
1001933 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
1001947 TGGCAAGTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1014438 original size:2 final size:2
Alignment explanation
Indices: 1014431--1014501 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1014421 ATTAACTCGT
1014431 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1014473 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1014502 GCACATGCGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1020395 original size:2 final size:2
Alignment explanation
Indices: 1020390--1020439 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1020380 ACGAGAGATA
1020390 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1020432 TG TG TG TG
1 TG TG TG TG
1020440 AGAGAGAGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1020444 original size:2 final size:2
Alignment explanation
Indices: 1020439--1020472 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1020429 GTGTGTGTGT
1020439 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1020473 TTTTATAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.