Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004163.1 Kokia drynarioides strain JFW-HI SEQ_117391, whole genome shotgun sequence
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: 1992
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Found at i:268 original size:17 final size:17
Alignment explanation
Indices: 246--317 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
236 TATTTCAAAT
*
246 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
263 TTTAAACTT--AATAAA
1 TTTAAACTTAAAATAAA
*
278 TTTAAATTTAAAAT-AA
1 TTTAAACTTAAAATAAA
**
294 TTCTAAACTTGGAATAAA
1 TT-TAAACTTAAAATAAA
312 TTTAAA
1 TTTAAA
318 ATAAAGATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
15 14 0.30
16 4 0.09
17 24 0.52
18 4 0.09
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:283 original size:32 final size:33
Alignment explanation
Indices: 246--317 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
236 TATTTCAAAT
246 TTTAAATTTAAAATAAATT-TAAACTT-AATAAA
1 TTTAAATTTAAAAT-AATTCTAAACTTGAATAAA
278 TTTAAATTTAAAATAATTCTAAACTTGGAATAAA
1 TTTAAATTTAAAATAATTCTAAACTT-GAATAAA
312 TTTAAA
1 TTTAAA
318 ATAAAGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
31 4 0.11
32 21 0.57
34 12 0.32
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (33 bp):
TTTAAATTTAAAATAATTCTAAACTTGAATAAA
Found at i:842 original size:11 final size:12
Alignment explanation
Indices: 819--852 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
809 TTGAAACTTA
*
819 AAGAAAGAAAAG
1 AAGAAAAAAAAG
831 AA-AAAAAAAAG
1 AAGAAAAAAAAG
842 AAGAAAAAAAA
1 AAGAAAAAAAA
853 TAAAGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:863 original size:14 final size:13
Alignment explanation
Indices: 826--864 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
816 TTAAAGAAAG
826 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
839 AAGAAGAAAAAAAA
1 AA-AAGAAAAAAAA
*
853 TAAAGATAAAAA
1 AAAAGA-AAAAA
865 CCCACAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:864 original size:16 final size:15
Alignment explanation
Indices: 822--864 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
812 AAACTTAAAG
822 AAAGAAAAGAAAAAAA
1 AAAGAAAA-AAAAAAA
*
838 AAAGAAGAAAAAAAAT
1 AAAGAA-AAAAAAAAA
*
854 AAAGATAAAAA
1 AAAGAAAAAAA
865 CCCACAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 17 0.71
17 2 0.08
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.05
Consensus pattern (15 bp):
AAAGAAAAAAAAAAA
Found at i:1725 original size:18 final size:16
Alignment explanation
Indices: 1700--1739 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
1690 AATTTCACCC
1700 AAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAAGA
*
1716 GAAAAGAAAGGAAAAAGA
1 -AAAA-AAAGAAAAAAGA
1734 AAAAAA
1 AAAAAA
1740 GAGGAGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 8 0.38
18 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGA
Done.