Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012069.1 Kokia drynarioides strain JFW-HI SEQ_127067, 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: 21376
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:98 original size:20 final size:20
Alignment explanation
Indices: 73--112 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
63 AAATAATTTA
*
73 AATTATAGTAATGCAAACCT
1 AATTATAGTAATACAAACCT
93 AATTATAGTAATACAAACCT
1 AATTATAGTAATACAAACCT
113 GGATTTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (20 bp):
AATTATAGTAATACAAACCT
Found at i:2370 original size:18 final size:18
Alignment explanation
Indices: 2347--2383 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2337 TTCATTGGTC
2347 AAGTCGGGTCGAACTTAA
1 AAGTCGGGTCGAACTTAA
2365 AAGTCGGGTCGAACTTAA
1 AAGTCGGGTCGAACTTAA
2383 A
1 A
2384 TATGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (18 bp):
AAGTCGGGTCGAACTTAA
Found at i:3207 original size:5 final size:5
Alignment explanation
Indices: 3197--3225 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3187 TCTTTATAGC
3197 TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3226 ATTTGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:3307 original size:14 final size:14
Alignment explanation
Indices: 3282--3316 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3272 TTTTGATCAA
*
3282 ATATTTCATTTTCC
1 ATATTCCATTTTCC
*
3296 ATTTTCCATTTTCC
1 ATATTCCATTTTCC
3310 ATATTCC
1 ATATTCC
3317 TTATTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTCCATTTTCC
Found at i:9266 original size:31 final size:31
Alignment explanation
Indices: 9231--9289 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
9221 CAATTTGGTT
**
9231 ATTGAACTATTCGTAAGTTTTCATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTTAAGTC
*
9262 ATTGAACTATTCAAAAGTTTTTATTTAA
1 ATTGAACTATTCAAAAGTTTTCATTTAA
9290 ATCACTAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTTTCATTTAAGTC
Found at i:15203 original size:26 final size:26
Alignment explanation
Indices: 15169--15222 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
15159 ATAGTAGTAA
*
15169 TTTACTTAATTATTTTTTGAAGTTAG
1 TTTAATTAATTATTTTTTGAAGTTAG
*
15195 TTTAATTAATTTTTTTTTGAAGTTAG
1 TTTAATTAATTATTTTTTGAAGTTAG
15221 TT
1 TT
15223 ATTTCAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (26 bp):
TTTAATTAATTATTTTTTGAAGTTAG
Found at i:21345 original size:2 final size:2
Alignment explanation
Indices: 21340--21371 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21330 TTTACATGTC
21340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21372 TTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.