Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008327.1 Kokia drynarioides strain JFW-HI SEQ_122992, 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: 5221
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Found at i:3962 original size:20 final size:20
Alignment explanation
Indices: 3939--3995 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
3929 GAAATATATT
* *
3939 AAAATATAAAAATATTTTCA
1 AAAATATAAAAATAATTTAA
3959 AAAATA-AAATAATAAATTTAA
1 AAAATATAAA-AAT-AATTTAA
3980 AAATATATAAAAATAA
1 AAA-ATATAAAAATAA
3996 AAAATATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 3 0.10
20 9 0.29
21 10 0.32
22 6 0.19
23 3 0.10
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATATAAAAATAATTTAA
Found at i:3981 original size:32 final size:29
Alignment explanation
Indices: 3940--4001 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 29
3930 AAATATATTA
*
3940 AAATATAAAAATATTTTCAAAAATAAAATAAT
1 AAATATAAAAATA-TAT-AAAAATAAAA-AAT
*
3972 AAATTTAAAAATATATAAAAATAAAAAAT
1 AAATATAAAAATATATAAAAATAAAAAAT
4001 A
1 A
4002 TTGTTGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.14
30 10 0.36
31 2 0.07
32 12 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (29 bp):
AAATATAAAAATATATAAAAATAAAAAAT
Found at i:3994 original size:22 final size:23
Alignment explanation
Indices: 3942--3996 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
3932 ATATATTAAA
*
3942 ATATAAAAAT-ATTTTCAAAAAT
1 ATATAAAAATAAATTTCAAAAAT
*
3964 A-A-AATAATAAATTT-AAAAAT
1 ATATAAAAATAAATTTCAAAAAT
3984 ATATAAAAATAAA
1 ATATAAAAATAAA
3997 AAATATTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 12 0.44
21 6 0.22
22 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
ATATAAAAATAAATTTCAAAAAT
Found at i:4000 original size:17 final size:17
Alignment explanation
Indices: 3930--4047 Score: 59
Period size: 17 Copynumber: 7.0 Consensus size: 17
3920 AAATTCAAAG
*
3930 AAATATATTAAAATATAA
1 AAATATATAAAAATA-AA
*
3948 AAATATTTTCAAAAAT--A
1 AAATA-TAT-AAAAATAAA
* *
3965 AAATA-AT-AAATTTAA
1 AAATATATAAAAATAAA
3980 AAATATATAAAAATAAA
1 AAATATATAAAAATAAA
* * *
3997 AAATATTGTTGACAAT-AA
1 AAATA-T-ATAAAAATAAA
* **
4015 ATA-ATATAAAAATTTA
1 AAATATATAAAAATAAA
4031 AAATATATAAAAATAAA
1 AAATATATAAAAATAAA
4048 TATTTTTAAT
Statistics
Matches: 73, Mismatches: 17, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
13 4 0.05
15 12 0.16
16 6 0.08
17 29 0.40
18 10 0.14
19 7 0.10
20 5 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AAATATATAAAAATAAA
Found at i:4040 original size:22 final size:22
Alignment explanation
Indices: 4010--4088 Score: 54
Period size: 23 Copynumber: 3.5 Consensus size: 22
4000 TATTGTTGAC
*
4010 AATAAATAATATAAAAATTTAA
1 AATATATAATATAAAAATTTAA
* * **
4032 AATATATAAAAATAAATATTTTT
1 AATATAT-AATATAAAAATTTAA
* *
4055 AAT-TATAATA-ATAAATCTAA
1 AATATATAATATAAAAATTTAA
4075 AATTTATATAATAT
1 AA--TATATAATAT
4089 TAAATAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
20 7 0.17
21 3 0.07
22 10 0.24
23 21 0.51
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATATAATATAAAAATTTAA
Found at i:4065 original size:51 final size:53
Alignment explanation
Indices: 3930--4047 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 53
3920 AAATTCAAAG
*
3930 AAATATATTAAAATATAAAAATATT-TT--CAA-AAATAAAATAATAAATTTAA
1 AAATATATAAAAATA-AAAAATATTATTGACAATAAATAAAATAATAAATTTAA
* *
3980 AAATATATAAAAATAAAAAATATTGTTGACAATAAATAATATAA-AAATTT-A
1 AAATATATAAAAATAAAAAATATTATTGACAATAAATAAAATAATAAATTTAA
4031 AAATATATAAAAATAAA
1 AAATATATAAAAATAAA
4048 TATTTTTAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
49 9 0.15
50 16 0.26
51 18 0.29
52 9 0.15
53 10 0.16
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (53 bp):
AAATATATAAAAATAAAAAATATTATTGACAATAAATAAAATAATAAATTTAA
Done.