Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001247.1 Kokia drynarioides strain JFW-HI SEQ_112617, 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: 26024
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:12911 original size:41 final size:42
Alignment explanation
Indices: 12848--12931 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
12838 TATTAAAGTA
12848 GTTGACTCTTTTGAATTAAAAAAAAAAATATTCAAGCAGACT
1 GTTGACTCTTTTGAATTAAAAAAAAAAATATTCAAGCAGACT
12890 GTTGACTCTTTTGAATT-AAAAAAAAAATATTCAAGCAGACT
1 GTTGACTCTTTTGAATTAAAAAAAAAAATATTCAAGCAGACT
12931 G
1 G
12932 AGAAAGTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 25 0.60
42 17 0.40
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (42 bp):
GTTGACTCTTTTGAATTAAAAAAAAAAATATTCAAGCAGACT
Found at i:16906 original size:76 final size:76
Alignment explanation
Indices: 16826--16970 Score: 263
Period size: 76 Copynumber: 1.9 Consensus size: 76
16816 ATTTTTATCG
*
16826 AAACGTTTATTTTCGGGAAAACAAACAAGTCTCGAAAATATTTTAAAATTAAAAAAAGGGAGTCG
1 AAACGTTTATTTTCGAGAAAACAAACAAGTCTCGAAAATATTTTAAAATTAAAAAAAGGGAGTCG
16891 CCACGTTGTCA
66 CCACGTTGTCA
* *
16902 AAACGTTTATTTTCGAGAAAACAAATAAGTGTCGAAAATATTTTAAAATTAAAAAAAGGGAGTCG
1 AAACGTTTATTTTCGAGAAAACAAACAAGTCTCGAAAATATTTTAAAATTAAAAAAAGGGAGTCG
16967 CCAC
66 CCAC
16971 CAATTTTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (76 bp):
AAACGTTTATTTTCGAGAAAACAAACAAGTCTCGAAAATATTTTAAAATTAAAAAAAGGGAGTCG
CCACGTTGTCA
Found at i:18022 original size:29 final size:28
Alignment explanation
Indices: 17990--18266 Score: 138
Period size: 29 Copynumber: 9.7 Consensus size: 28
17980 GATACCCAAA
*
17990 GGTAAAATGGTAATTTTTGGATATTTGGG
1 GGTAAAATGGTAATTTTTGGA-ATTTGAG
* * * *
18019 GGTAAAACGGTAATTTTTTGACACTCGAG
1 GGTAAAATGGTAATTTTTGGA-ATTTGAG
** **
18048 GACAAAAATAAT-ATTTTTGGAAGTTTGAG
1 G-GTAAAATGGTAATTTTTGGAA-TTTGAG
* * *
18077 GTTAAAATGGTAATTTTTGGACA-CTCAG
1 GGTAAAATGGTAATTTTTGGA-ATTTGAG
* * * *
18105 GGAAAAATGAT-A-TTTTGGAAGTTCAG
1 GGTAAAATGGTAATTTTTGGAATTTGAG
* * *
18131 GGTTAAATGGTAATTTTTGGAAGTTCGGG
1 GGTAAAATGGTAATTTTTGGAA-TTTGAG
* *
18160 GGTGAAAAT-GTGATTTTTGGAAGTTCGAG
1 GGT-AAAATGGTAATTTTTGGAA-TTTGAG
*
18189 AGTAAAATGGTAATTTTTGGAAGTTT-AG
1 GGTAAAATGGTAATTTTTGGAA-TTTGAG
* * *
18217 GGACAAAAAT-GTAATTTTTAAAGATTTTGAG
1 GG--TAAAATGGTAATTTTT--GGAATTTGAG
*
18248 GGTCAAAAT-ATAATTTTTG
1 GGT-AAAATGGTAATTTTTG
18267 AAAAGTTTAG
Statistics
Matches: 188, Mismatches: 44, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
25 1 0.01
26 19 0.10
27 2 0.01
28 34 0.18
29 95 0.51
30 31 0.16
31 6 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (28 bp):
GGTAAAATGGTAATTTTTGGAATTTGAG
Found at i:18064 original size:58 final size:56
Alignment explanation
Indices: 18002--18151 Score: 171
Period size: 58 Copynumber: 2.7 Consensus size: 56
17992 TAAAATGGTA
* *
18002 ATTTTTGGATA-TTTGGGGGTAAAACGGTAATTTTTTGACACTCGAGGACAAAAATAAT
1 ATTTTTGGA-AGTTTGAGGGTAAAACGGTAATTTTTGGACACTC-AGG-CAAAAATAAT
* * * *
18060 ATTTTTGGAAGTTTGAGGTTAAAATGGTAATTTTTGGACACTCAGGGAAAAATGAT
1 ATTTTTGGAAGTTTGAGGGTAAAACGGTAATTTTTGGACACTCAGGCAAAAATAAT
* * *
18116 A-TTTTGGAAG-TTCAGGGTTAAATGGTAATTTTTGGA
1 ATTTTTGGAAGTTTGAGGGTAAAACGGTAATTTTTGGA
18152 AGTTCGGGGG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
54 23 0.28
55 9 0.11
56 9 0.11
57 4 0.05
58 37 0.45
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (56 bp):
ATTTTTGGAAGTTTGAGGGTAAAACGGTAATTTTTGGACACTCAGGCAAAAATAAT
Found at i:19299 original size:3 final size:3
Alignment explanation
Indices: 19286--19341 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
19276 CTCTTTTTAT
** *
19286 TTA TT- TTA TTA TTA AAA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19333 TTA TTA TTA
1 TTA TTA TTA
19342 AGGATATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:20018 original size:17 final size:17
Alignment explanation
Indices: 19996--20042 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
19986 AACTTTTGAT
19996 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
20013 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
20030 TAAATTAAAATTT
1 TAAATTTAAATTT
20043 TTAAAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:20245 original size:18 final size:18
Alignment explanation
Indices: 20218--20252 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20208 TATTTTCATG
*
20218 GAAAATAATTTGGTCAAT
1 GAAAACAATTTGGTCAAT
20236 GAAAACAATTTGGTCAA
1 GAAAACAATTTGGTCAA
20253 CAAAAAACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (18 bp):
GAAAACAATTTGGTCAAT
Found at i:20258 original size:18 final size:18
Alignment explanation
Indices: 20219--20258 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20209 ATTTTCATGG
* **
20219 AAAATAATTTGGTCAATG
1 AAAACAATTTGGTCAACA
20237 AAAACAATTTGGTCAACA
1 AAAACAATTTGGTCAACA
20255 AAAA
1 AAAA
20259 ACGACTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (18 bp):
AAAACAATTTGGTCAACA
Found at i:20570 original size:22 final size:21
Alignment explanation
Indices: 20536--20578 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
20526 ATATAATAAA
*
20536 TTATTAATATAATTAATATATT
1 TTATTAATATAATAAAT-TATT
* *
20558 TTATTATTTTAATAAATTATT
1 TTATTAATATAATAAATTATT
20579 CAATATTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTAATATAATAAATTATT
Found at i:20620 original size:16 final size:16
Alignment explanation
Indices: 20599--20629 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20589 ATTTTATTTG
20599 AATAATAAATTTAAAA
1 AATAATAAATTTAAAA
*
20615 AATAATAATTTTAAA
1 AATAATAAATTTAAA
20630 GTTGTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATAAATTTAAAA
Found at i:25498 original size:3 final size:3
Alignment explanation
Indices: 25492--25530 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25482 TAATAATAAA
25492 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25531 ATGACAATAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.