Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000516.1 Kokia drynarioides strain JFW-HI SEQ_111401, 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: 15559
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:114 original size:4 final size:4
Alignment explanation
Indices: 107--158 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
97 CCCCTTCCTC
* *
107 TCTT TC-T TCCT T-TT TCTT TCTT TCTT TCTT TCTTT TTTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT
154 T-TT TC
1 TCTT TC
159 CTTCAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
3 8 0.20
4 30 0.73
5 3 0.07
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:168 original size:25 final size:25
Alignment explanation
Indices: 117--168 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
107 TCTTTCTTCC
* *
117 TTTTTCTTTCTTTCTTTCTTTCTTT
1 TTTTTCTTTCTTTCTTTCCTTCATT
*
142 TTTTTCTTTCTTT-TTTCCTTCAAT
1 TTTTTCTTTCTTTCTTTCCTTCATT
166 TTT
1 TTT
169 CGTTGGGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTCTTTCTTTCTTTCCTTCATT
Found at i:1070 original size:25 final size:25
Alignment explanation
Indices: 1049--1095 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1039 TTTTATATTC
*
1049 ATATTTATATTAAATAAATATAATT
1 ATATTAATATTAAATAAATATAATT
*
1074 GTATTAATATTAAATAAA-ATAA
1 ATATTAATATTAAATAAATATAA
1096 AAATCCCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATATTAATATTAAATAAATATAATT
Found at i:3002 original size:20 final size:21
Alignment explanation
Indices: 2965--3005 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2955 GTTGACTCGA
*
2965 GTTGACTTTGACCCATTGACC
1 GTTGAATTTGACCCATTGACC
2986 GTTGAATTTGA-CCATTGACC
1 GTTGAATTTGACCCATTGACC
3006 TTTTTTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (21 bp):
GTTGAATTTGACCCATTGACC
Found at i:3419 original size:28 final size:28
Alignment explanation
Indices: 3387--3440 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3377 CAACTTTCTC
3387 CAAGACGTTAGAGCTTCTGCCCATTTTT
1 CAAGACGTTAGAGCTTCTGCCCATTTTT
3415 CAAGACGTTAGAGCTTCTGCCCATTT
1 CAAGACGTTAGAGCTTCTGCCCATTT
3441 GAGGTGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (28 bp):
CAAGACGTTAGAGCTTCTGCCCATTTTT
Found at i:15138 original size:4 final size:4
Alignment explanation
Indices: 15125--15170 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
15115 AAAAATAAAG
*
15125 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA G-AA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAA
15171 GAAGGAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 6 0.16
4 28 0.76
5 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:15139 original size:11 final size:11
Alignment explanation
Indices: 15115--15170 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
15105 GGGACCAACG
*
15115 AAAAATAAAGGA
1 AAAAAGAAA-GA
15127 AAAAAGAAAGA
1 AAAAAGAAAGA
15138 AAAAAG--AGA
1 AAAAAGAAAGA
15147 AAGAAAGAAAGA
1 AA-AAAGAAAGA
*
15159 AAGAAGAAAGA
1 AAAAAGAAAGA
15170 A
1 A
15171 GAAGGAGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 5 0.13
10 4 0.10
11 17 0.44
12 13 0.33
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:15140 original size:21 final size:22
Alignment explanation
Indices: 15116--15160 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
15106 GGACCAACGA
15116 AAAATAAAG-GAAA-AAAGAAAG
1 AAAA-AAAGAGAAAGAAAGAAAG
15137 -AAAAAAGAGAAAGAAAGAAAG
1 AAAAAAAGAGAAAGAAAGAAAG
15158 AAA
1 AAA
15161 GAAGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 8 0.38
22 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAGAAAGAAAGAAAG
Found at i:15157 original size:25 final size:26
Alignment explanation
Indices: 15125--15203 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 26
15115 AAAAATAAAG
15125 GAAA-AAAGAAAGAAAAAAG-AGAAA
1 GAAAGAAAGAAAGAAAAAAGAAGAAA
* *
15149 GAAAGAAAGAAAGAAGAAAGAAGAAG
1 GAAAGAAAGAAAGAAAAAAGAAGAAA
*
15175 GAGAAGAAGGAGAATGAAAAAA-AA-AAA
1 GA-AAGAA--AGAAAGAAAAAAGAAGAAA
15202 GA
1 GA
15204 TAATGTGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 4 0.09
25 14 0.31
26 6 0.13
27 9 0.20
28 2 0.04
29 10 0.22
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (26 bp):
GAAAGAAAGAAAGAAAAAAGAAGAAA
Found at i:15171 original size:7 final size:7
Alignment explanation
Indices: 15125--15173 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
15115 AAAAATAAAG
*
15125 GAAAAAA
1 GAAAGAA
15132 GAAAGAA
1 GAAAGAA
*
15139 AAAAG-A
1 GAAAGAA
15145 GAAAGAA
1 GAAAGAA
*
15152 -AGA-AA
1 GAAAGAA
15157 GAAAGAA
1 GAAAGAA
15164 GAAAGAA
1 GAAAGAA
15171 GAA
1 GAA
15174 GGAGAAGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
5 2 0.06
6 9 0.26
7 23 0.68
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Done.