Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005165.1 Kokia drynarioides strain JFW-HI SEQ_119013, 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: 18236
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:684 original size:24 final size:26
Alignment explanation
Indices: 657--704 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
647 AGAGAAATAT
657 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
681 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
705 TTCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:805 original size:23 final size:22
Alignment explanation
Indices: 770--901 Score: 106
Period size: 23 Copynumber: 5.8 Consensus size: 22
760 CTAGCGCGCT
*
770 TACTGTTCAGCACTGTGTGTGCC
1 TACTGTT-TGCACTGTGTGTGCC
*
793 TACTGTTTCGCACT-TCGTGTGCT
1 TACTGTTT-GCACTGT-GTGTGCC
*
816 TACTGTTTCGCACCT-CGTGTGCC
1 TACTGTTT-GCA-CTGTGTGTGCC
* * *
839 TACTGATTTGCGCTATGTGCGCC
1 TACTG-TTTGCACTGTGTGTGCC
* *
862 TAGTGATTGCACTGTGTGTGCC
1 TACTGTTTGCACTGTGTGTGCC
* *
884 TACTGATTACACTGTGTG
1 TACTGTTTGCACTGTGTG
902 CTTACTGTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
22 32 0.36
23 53 0.59
24 5 0.06
ACGTcount: A:0.13, C:0.25, G:0.25, T:0.37
Consensus pattern (22 bp):
TACTGTTTGCACTGTGTGTGCC
Found at i:13202 original size:15 final size:17
Alignment explanation
Indices: 13182--13219 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
13172 ATTTTCTAAG
*
13182 AATTATTAAGAT-AT-A
1 AATTATTAAAATAATAA
13197 AATTATTAAAATAATAA
1 AATTATTAAAATAATAA
13214 AATTAT
1 AATTAT
13220 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTATTAAAATAATAA
Found at i:13355 original size:6 final size:6
Alignment explanation
Indices: 13344--13393 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
13334 TTTAATTTAT
*
13344 TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
13389 TTTAA
1 TTTAA
13394 TTTCGAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 2 0.05
5 8 0.21
6 29 0.74
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:13395 original size:17 final size:17
Alignment explanation
Indices: 13337--13396 Score: 95
Period size: 17 Copynumber: 3.6 Consensus size: 17
13327 CCCCTTTTTT
*
13337 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
*
13354 AA-TTAATCTAAATTTA
1 AATTTAATTTAAATTTA
13370 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
13387 AATTTAATTT
1 AATTTAATTT
13397 CGAAATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
16 14 0.36
17 25 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:13396 original size:11 final size:11
Alignment explanation
Indices: 13337--13393 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
13327 CCCCTTTTTT
*
13337 AATTTATTTTA
1 AATTTAATTTA
*
13348 AATTTAAATT-
1 AATTTAATTTA
*
13358 AATCTAAATTTA
1 AAT-TTAATTTA
13370 AATTTAATTTA
1 AATTTAATTTA
13381 AATTTAAATTTA
1 AATTT-AATTTA
13393 A
1 A
13394 TTTCGAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
10 3 0.08
11 25 0.66
12 10 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:16932 original size:12 final size:13
Alignment explanation
Indices: 16915--16980 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 13
16905 AAATTGATTC
16915 AAATTTAT-TTTT
1 AAATTTATATTTT
16927 AAATTTAAGTTTATTTT
1 AAATTT-A---TATTTT
*
16944 AAATTTA-AATTT
1 AAATTTATATTTT
*
16956 AAATTTATCTTTT
1 AAATTTATATTTT
*
16969 AAATTTAAATTT
1 AAATTTATATTT
16981 GCTTTAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
12 17 0.40
13 14 0.33
16 2 0.05
17 10 0.23
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
AAATTTATATTTT
Found at i:16933 original size:6 final size:6
Alignment explanation
Indices: 16924--17012 Score: 85
Period size: 6 Copynumber: 15.2 Consensus size: 6
16914 CAAATTTATT
* * **
16924 TTTAAA TTTAAG TTT-AT TTTAAA TTTAAA TTTAAA TTTATCT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA
** *
16972 TTTAAA TTT-GC TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
17013 GGATTTAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
5 11 0.17
6 51 0.77
7 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:16945 original size:17 final size:18
Alignment explanation
Indices: 16915--17012 Score: 83
Period size: 17 Copynumber: 5.2 Consensus size: 18
16905 AAATTGATTC
16915 AAATTTATTTTTAAATTT
1 AAATTTATTTTTAAATTT
*
16933 AAGTTTATTTTAAATTTAAATTT
1 AAATTTA--TT---TTTAAATTT
16956 AAATTTATCTTTTAAATTT
1 AAATTTAT-TTTTAAATTT
**
16975 AAATTT-GCTTTAAATTT
1 AAATTTATTTTTAAATTT
* *
16992 AAATTTA-ATTAAAATTT
1 AAATTTATTTTTAAATTT
17009 AAAT
1 AAAT
17013 GGATTTAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
17 27 0.40
18 6 0.09
19 15 0.22
20 2 0.03
21 1 0.01
22 1 0.01
23 15 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
AAATTTATTTTTAAATTT
Found at i:16969 original size:13 final size:12
Alignment explanation
Indices: 16924--17010 Score: 63
Period size: 11 Copynumber: 7.4 Consensus size: 12
16914 CAAATTTATT
* *
16924 TTTAAATTTAAG
1 TTTAATTTTAAA
16936 TTT-ATTTTAAA
1 TTTAATTTTAAA
*
16947 TTTAAATTTAAA
1 TTTAATTTTAAA
*
16959 TTTATCTTTTAAA
1 TTTA-ATTTTAAA
* **
16972 TTTAAATTT-GC
1 TTTAATTTTAAA
*
16983 TTTAAATTTAAA
1 TTTAATTTTAAA
*
16995 TTTAA-TTAAAA
1 TTTAATTTTAAA
17006 TTTAA
1 TTTAA
17011 ATGGATTTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
11 28 0.47
12 22 0.37
13 10 0.17
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:16972 original size:42 final size:41
Alignment explanation
Indices: 16915--16999 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 41
16905 AAATTGATTC
* *
16915 AAATTTATTTTTAAATTTAAGTTTATTTTAAATTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTACTTTAAATTTAAATTT
*
16956 AAATTTATCTTTTAAATTTAAATTTGCTTTAAATTTAAATTT
1 AAATTTAT-TTTTAAATTTAAATTTACTTTAAATTTAAATTT
16998 AA
1 AA
17000 TTAAAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 8 0.20
42 32 0.80
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (41 bp):
AAATTTATTTTTAAATTTAAATTTACTTTAAATTTAAATTT
Found at i:17726 original size:3 final size:3
Alignment explanation
Indices: 17720--17758 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
17710 AATATTTTTA
17720 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17759 GAATTAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18062 original size:17 final size:18
Alignment explanation
Indices: 18040--18074 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
18030 AACGTTTTTT
*
18040 AAAAAAGGGAA-AAAAGA
1 AAAAAAGGAAAGAAAAGA
18057 AAAAAAGGAAAGAAAAGA
1 AAAAAAGGAAAGAAAAGA
18075 GGGTACTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAAAGGAAAGAAAAGA
Done.