Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000496.1 Kokia drynarioides strain JFW-HI SEQ_111371, 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: 5702
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:156 original size:18 final size:18
Alignment explanation
Indices: 133--229 Score: 58
Period size: 18 Copynumber: 5.2 Consensus size: 18
123 TAAAATTTAT
133 AAATATAAAATTCGTAAA
1 AAATATAAAATTCGTAAA
151 AAATATAAAAAATT-GT-AA
1 AAATAT--AAAATTCGTAAA
* * *
169 AATTTTATAAAGTCGTAAAA
1 AAATATA-AAATTCGT-AAA
*
189 AAATTATATAAATAT--AAAA
1 AAA-TATA-AAAT-TCGTAAA
208 AATATATAAAATTCGTAAA
1 AA-ATATAAAATTCGTAAA
227 AAA
1 AAA
230 ATTTATAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
16 1 0.02
17 5 0.08
18 19 0.32
19 16 0.27
20 11 0.18
21 7 0.12
22 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
AAATATAAAATTCGTAAA
Found at i:193 original size:21 final size:19
Alignment explanation
Indices: 174--238 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
164 TGTAAAATTT
174 TATAAAGTCGTAAAAAAATTA
1 TATAAA-TCGTAAAAAAA-TA
*
195 TATAAAT-AT-AAAAAATA
1 TATAAATCGTAAAAAAATA
*
212 TATAAAATTCGTAAAAAAATT
1 TAT-AAA-TCGTAAAAAAATA
233 TATAAA
1 TATAAA
239 AATTATCGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 5 0.14
18 9 0.24
19 2 0.05
20 5 0.14
21 16 0.43
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (19 bp):
TATAAATCGTAAAAAAATA
Found at i:195 original size:19 final size:19
Alignment explanation
Indices: 136--239 Score: 72
Period size: 19 Copynumber: 5.4 Consensus size: 19
126 AATTTATAAA
136 TATAAAATTCGT-AAAAAAT
1 TATAAAA-TCGTAAAAAAAT
* * **
155 ATAAAAAATTGT-AAAATTT
1 -TATAAAATCGTAAAAAAAT
*
174 TATAAAGTCGTAAAAAAAT
1 TATAAAATCGTAAAAAAAT
*
193 TATATAAAT-AT-AAAAAAT
1 TATA-AAATCGTAAAAAAAT
211 ATATAAAATTCGTAAAAAAATT
1 -TATAAAA-TCGTAAAAAAA-T
233 TATAAAA
1 TATAAAA
240 ATTATCGTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
18 18 0.28
19 23 0.35
20 10 0.15
21 13 0.20
22 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
TATAAAATCGTAAAAAAAT
Found at i:1833 original size:22 final size:24
Alignment explanation
Indices: 1808--1856 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
1798 CAATGGAGAG
1808 AAAGGAAACA-AA-ATCAAAGAAA-
1 AAAGGAAACACAATAT-AAAGAAAT
1830 AAA-GAAACACAATATAAAGAAAT
1 AAAGGAAACACAATATAAAGAAAT
1853 AAAG
1 AAAG
1857 AAAGGAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.08
Consensus pattern (24 bp):
AAAGGAAACACAATATAAAGAAAT
Found at i:3818 original size:6 final size:6
Alignment explanation
Indices: 3807--3837 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3797 AAAGTGATTT
3807 TTATAA TTATAA TTATAA TTATAA TTATAA T
1 TTATAA TTATAA TTATAA TTATAA TTATAA T
3838 GTTTTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Done.