Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010563.1 Kokia drynarioides strain JFW-HI SEQ_125485, 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: 20869
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Warning! 98 characters in sequence are not A, C, G, or T
Found at i:1331 original size:20 final size:19
Alignment explanation
Indices: 1295--1333 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1285 TCAATGAATA
* *
1295 ATTTAAAAATTATAAAATT
1 ATTTAAAAAATAAAAAATT
1314 ATTTCAAAAAATAAAAAATT
1 ATTT-AAAAAATAAAAAATT
1334 CATAAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTAAAAAATAAAAAATT
Found at i:3278 original size:2 final size:2
Alignment explanation
Indices: 3271--3306 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3261 TAAAAGCGGC
3271 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3307 AGATGCTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4889 original size:19 final size:21
Alignment explanation
Indices: 4850--4891 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
4840 TATATAGTAA
*
4850 AAATAATATAACATTTGTATT
1 AAATAATATAACATTTATATT
4871 AAATAAT-TAA-ATTTATATT
1 AAATAATATAACATTTATATT
4890 AA
1 AA
4892 TGTTAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 3 0.15
21 7 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATAATATAACATTTATATT
Found at i:10013 original size:63 final size:63
Alignment explanation
Indices: 9914--10036 Score: 219
Period size: 63 Copynumber: 2.0 Consensus size: 63
9904 TCAATAGGTT
*
9914 CAGATTCATATTTTTATGCTCATATACATATTGAATATGAATATTAAATAACTCAAATTTTTA
1 CAGATTCATATTTCTATGCTCATATACATATTGAATATGAATATTAAATAACTCAAATTTTTA
* *
9977 CAGATTCGTATTTCTATGCTCATATACATATTGAATATGAATATTAAATAATTCAAATTT
1 CAGATTCATATTTCTATGCTCATATACATATTGAATATGAATATTAAATAACTCAAATTT
10037 ACTTGTAGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.42
Consensus pattern (63 bp):
CAGATTCATATTTCTATGCTCATATACATATTGAATATGAATATTAAATAACTCAAATTTTTA
Found at i:11493 original size:43 final size:43
Alignment explanation
Indices: 11445--11543 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
11435 GGAAAGATAT
* * * *
11445 TGGCACATATAGTGCATTATCGGGCAATCCGAAATAATTATAC
1 TGGCACATATAGTGCATCATCGGACAAACCGAAACAATTATAC
* * * * *
11488 TGGCACACATAATGCATCATCGGATAAACCGAAGCAATTTTAC
1 TGGCACATATAGTGCATCATCGGACAAACCGAAACAATTATAC
11531 TGGCACATA-AGTG
1 TGGCACATATAGTG
11544 TTTACCTAAG
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 3 0.07
43 42 0.93
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (43 bp):
TGGCACATATAGTGCATCATCGGACAAACCGAAACAATTATAC
Found at i:18195 original size:15 final size:15
Alignment explanation
Indices: 18177--18228 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
18167 AGAGGAAGAG
*
18177 GAGGAAGTGGAAGTT
1 GAGGAAGTGGAAGTA
* * *
18192 GAGGAAGAGGTAGAA
1 GAGGAAGTGGAAGTA
18207 GAGGAAGTGGAAGTA
1 GAGGAAGTGGAAGTA
18222 GAGGAAG
1 GAGGAAG
18229 AAGAGGACGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (15 bp):
GAGGAAGTGGAAGTA
Found at i:18200 original size:24 final size:24
Alignment explanation
Indices: 18168--18235 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
18158 TGAAGAAATA
*
18168 GAGGAAGAGG-AGGAAGTGGAAGTT
1 GAGGAAGAGGTA-GAAGAGGAAGTT
*
18192 GAGGAAGAGGTAGAAGAGGAAGTG
1 GAGGAAGAGGTAGAAGAGGAAGTT
* * *
18216 GAAGTAGAGGAAGAAGAGGA
1 GAGGAAGAGGTAGAAGAGGA
18236 CGAGGACGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.49, T:0.09
Consensus pattern (24 bp):
GAGGAAGAGGTAGAAGAGGAAGTT
Found at i:18211 original size:30 final size:30
Alignment explanation
Indices: 18167--18229 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
18157 ATGAAGAAAT
* *
18167 AGAGGAAGAGGAGGAAGTGGAAGTTGAGGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAGGA
*
18197 AGAGGTAGAAGAGGAAGTGGAAGTAGAGGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAGGA
18227 AGA
1 AGA
18230 AGAGGACGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.48, T:0.10
Consensus pattern (30 bp):
AGAGGAAGAAGAGGAAGTGGAAGTAGAGGA
Done.