Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002736.1 Kokia drynarioides strain JFW-HI SEQ_115040, 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: 51636
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1756 original size:29 final size:30
Alignment explanation
Indices: 1689--1775 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 30
1679 CTCAAAAGTG
1689 TATATGAACTTTGATTTAATACTTAATTGTA
1 TATATGAACTTTGATTTAATAC-TAATTGTA
** ** *
1720 TGCATGAACTTTGATTTTGTAC-AATTTTA
1 TATATGAACTTTGATTTAATACTAATTGTA
* *
1749 TATATGAAATTTTGATTTGAT-CTAATT
1 TATATG-AACTTTGATTTAATACTAATT
1776 CTCATAAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 11 0.25
30 15 0.34
31 18 0.41
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.49
Consensus pattern (30 bp):
TATATGAACTTTGATTTAATACTAATTGTA
Found at i:15335 original size:10 final size:9
Alignment explanation
Indices: 15315--15341 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
15305 CAACTCGGGA
15315 TTTTTTATT
1 TTTTTTATT
15324 TTTTTTATT
1 TTTTTTATT
15333 TTTTTTATT
1 TTTTTTATT
15342 AATTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTATT
Found at i:16864 original size:42 final size:42
Alignment explanation
Indices: 16805--16888 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
16795 ATATAGAAGA
16805 ATGTTAATGCTTCACATGGCAAGATGAGGATGATGATGGGTT
1 ATGTTAATGCTTCACATGGCAAGATGAGGATGATGATGGGTT
*
16847 ATGTTAATGCTTCACATGGCAAGATGAGGATGGTGATGGGTT
1 ATGTTAATGCTTCACATGGCAAGATGAGGATGATGATGGGTT
16889 GGATTGGATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.31
Consensus pattern (42 bp):
ATGTTAATGCTTCACATGGCAAGATGAGGATGATGATGGGTT
Found at i:17369 original size:3 final size:3
Alignment explanation
Indices: 17363--17387 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17353 AAAAAAAAAA
17363 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
17388 TTAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:18043 original size:2 final size:2
Alignment explanation
Indices: 18036--18066 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18026 ACGATTTGAC
18036 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18067 AATAATGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21097 original size:2 final size:2
Alignment explanation
Indices: 21092--21118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21082 TGTGTGTGTG
21092 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21119 CTGAATTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28306 original size:22 final size:22
Alignment explanation
Indices: 28281--28322 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28271 CAAGTAAGTC
*
28281 AAAAAAGTAAGAAAATTTAATT
1 AAAAAAGTAAGAAAAATTAATT
* *
28303 AAAATAGTAATAAAAATTAA
1 AAAAAAGTAAGAAAAATTAA
28323 AGAGAAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
AAAAAAGTAAGAAAAATTAATT
Found at i:40649 original size:30 final size:30
Alignment explanation
Indices: 40608--40669 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
40598 GAGAGGACCT
*
40608 CCTGGTCCACCACCACCACGCCCTGGAATG
1 CCTGCTCCACCACCACCACGCCCTGGAATG
40638 CCTGCTCCACCACCACCACGCCCTGGAATG
1 CCTGCTCCACCACCACCACGCCCTGGAATG
40668 CC
1 CC
40670 GCCTCCCCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.50, G:0.18, T:0.13
Consensus pattern (30 bp):
CCTGCTCCACCACCACCACGCCCTGGAATG
Found at i:51546 original size:10 final size:11
Alignment explanation
Indices: 51521--51547 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
51511 TTTTTTTAAA
51521 AAAAATACGAC
1 AAAAATACGAC
51532 AAAAATACGAC
1 AAAAATACGAC
51543 AAAAA
1 AAAAA
51548 AATATCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAATACGAC
Done.