Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_746 ID=scaffold_746-JGI_221_v2.0
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: 5901
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.27
Warning! 1808 characters in sequence are not A, C, G, or T
Found at i:1334 original size:27 final size:27
Alignment explanation
Indices: 1304--1360 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1294 ATCTAATGAT
1304 TAATTATGACCCCTTGAAATAAAACAC
1 TAATTATGACCCCTTGAAATAAAACAC
1331 TAATTATGACCCCTTGAAATAAAACAC
1 TAATTATGACCCCTTGAAATAAAACAC
1358 TAA
1 TAA
1361 CTTTTCGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.26
Consensus pattern (27 bp):
TAATTATGACCCCTTGAAATAAAACAC
Found at i:3550 original size:13 final size:12
Alignment explanation
Indices: 3496--3549 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
3486 ATTTTACTTC
3496 ATATAATTAAAA
1 ATATAATTAAAA
* *
3508 AAATTATTAAAA
1 ATATAATTAAAA
*
3520 ATAATAAATAATAA
1 AT-ATAATTAA-AA
3534 ATATAATT-AAA
1 ATATAATTAAAA
3545 ATATA
1 ATATA
3550 TCACTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 7 0.21
12 12 0.35
13 11 0.32
14 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAATTAAAA
Done.