Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003679.1 Kokia drynarioides strain JFW-HI SEQ_116604, 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: 18176
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Found at i:169 original size:51 final size:51
Alignment explanation
Indices: 98--199 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
88 GTAAGTTTTC
*
98 ATTTTGCACCCGATTATATAAAATTGCATTGTAATTTTTTGGTCACTCATT
1 ATTTTGCACCCGATTATATAAAATTGCATTGTAATTTGTTGGTCACTCATT
*
149 ATTTTGCACCCTATTATATAAAATTGCATTGTAATTTGTTGGTCACTCATT
1 ATTTTGCACCCGATTATATAAAATTGCATTGTAATTTGTTGGTCACTCATT
200 GTTAACTTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (51 bp):
ATTTTGCACCCGATTATATAAAATTGCATTGTAATTTGTTGGTCACTCATT
Found at i:8894 original size:17 final size:17
Alignment explanation
Indices: 8869--8924 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
8859 AAAAAAAAAG
*
8869 AATTGAATTGAAAAAATT
1 AATTTAATT-AAAAAATT
8887 -ATTTAATTAAAAAATT
1 AATTTAATTAAAAAATT
* *
8903 AATTTATTTAATTAAATT
1 AATTTAATTAA-AAAATT
8921 AATT
1 AATT
8925 AATAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 8 0.24
17 16 0.48
18 9 0.27
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
AATTTAATTAAAAAATT
Found at i:8909 original size:21 final size:22
Alignment explanation
Indices: 8885--8927 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
8875 ATTGAAAAAA
8885 TTATTTAATTAAA-AAATTAAT
1 TTATTTAATTAAATAAATTAAT
*
8906 TTATTTAATTAAATTAATTAAT
1 TTATTTAATTAAATAAATTAAT
8928 AAATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTAATTAAATAAATTAAT
Found at i:13330 original size:17 final size:18
Alignment explanation
Indices: 13305--13347 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
13295 CATTCTAAAA
13305 ATTATAAAT-ATATAAACT
1 ATTATAAATAATA-AAACT
13323 ATTA-AAATAATAAAACT
1 ATTATAAATAATAAAACT
13340 ATTATAAA
1 ATTATAAA
13348 AATTACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTATAAATAATAAAACT
Found at i:13513 original size:22 final size:22
Alignment explanation
Indices: 13488--13530 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13478 ATTATTTTTT
* *
13488 AAAAGCACTTTTAAGATAAAAA
1 AAAAACACTTTAAAGATAAAAA
13510 AAAAACACTTTAAAGATAAAA
1 AAAAACACTTTAAAGATAAAA
13531 TTATTACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAAACACTTTAAAGATAAAAA
Found at i:14178 original size:6 final size:6
Alignment explanation
Indices: 14167--14199 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
14157 ATCAAATCAA
*
14167 TGTATT TGTATT TATATT TGTATT TGTATT TGT
1 TGTATT TGTATT TGTATT TGTATT TGTATT TGT
14200 TGAACTAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
TGTATT
Found at i:18125 original size:17 final size:17
Alignment explanation
Indices: 18097--18166 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
18087 GGTCCAACAG
18097 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
18114 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
18131 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
18148 AATTTAAATTTA-TTTA
1 AATTTAAATTTATTTTA
18164 AAT
1 AAT
18167 AATGTCCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
16 6 0.13
17 41 0.87
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:18152 original size:7 final size:6
Alignment explanation
Indices: 18097--18159 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
18087 GGTCCAACAG
* * * *
18097 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
18142 -ATTTGA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA
18160 TTTAAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.09
5 8 0.18
6 29 0.64
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AATTTA
Done.