Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014155.1 Kokia drynarioides strain JFW-HI SEQ_129188, 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: 5064
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:3894 original size:29 final size:28
Alignment explanation
Indices: 3862--3926 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
3852 GATCCCTAGG
3862 GGTAAAATGGTAATTTTGGGAAAATTCGA
1 GGTAAAATGG-AATTTTGGGAAAATTCGA
* * **
3891 GGTAAAATGGGATTTTTGGAAGTTTCGA
1 GGTAAAATGGAATTTTGGGAAAATTCGA
3919 GGTCAAAA
1 GGT-AAAA
3927 AAGGTGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (28 bp):
GGTAAAATGGAATTTTGGGAAAATTCGA
Found at i:3966 original size:29 final size:29
Alignment explanation
Indices: 3860--4303 Score: 365
Period size: 30 Copynumber: 15.0 Consensus size: 29
3850 CGGATCCCTA
* ** *
3860 GGGGT-AAAATGGTAATTTTGGGAAAATTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTG
* * *
3889 GAGGT-AAAATGGGATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
* * **
3917 GAGGTCAAAAAAGGTGTTTTTGGAAGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTG
* * * *
3947 GGGGTTAAAATAGAATTTTTGAAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
* * *
3976 AGGGTTAAAATGGGAATTTTT-GAAGTTCG
1 GGGGTAAAAAT-GGAATTTTTGGAAGTTTG
*
4005 AGGGTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTG
* * ** * *
4035 AGGTTAAAAATGGGTTTTTTTTTGGAAATTTT
1 GGGGTAAAAAT-GG--AATTTTTGGAAGTTTG
* * *
4067 AGGGTCAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
*
4096 GGGGTCAAAAATGGGATTTTTGGAAGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTG
* * *
4126 AGGGTAAAAATGGGATTTTTGGAAGTTTTA
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTG
4156 GGGGTAAAAATGGAATTTTTGGAAGTTTTAG
1 GGGGTAAAAATGGAATTTTTGGAAG-TTT-G
* ** *
4187 GGGTTAAAAATGGGTTTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
*
4216 GGGGTAAAAATGGAATTTTTAGAAGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTG
* *
4246 GGGTTAAAAAT-GAGATTTTTGGAAGTTCG
1 GGGGTAAAAATGGA-ATTTTTGGAAGTTTG
* *
4275 AGGGTAAAAAAAGGAATTTTTGGAAGTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTT
4304 AGGGACTTCC
Statistics
Matches: 341, Mismatches: 59, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
28 26 0.08
29 124 0.36
30 142 0.42
31 28 0.08
32 12 0.04
33 9 0.03
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTG
Found at i:3967 original size:59 final size:58
Alignment explanation
Indices: 3893--4307 Score: 358
Period size: 59 Copynumber: 7.0 Consensus size: 58
3883 AAATTCGAGG
* * ** *
3893 TAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAAAGGTGTTTTTGGAAGTTTGGGGGT
1 TAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * * *
3952 TAAAATAGAATTTTTGAAAGTTT-TAGGGTTAAAATGGGAATTTTT-GAAGTTCGAGGGT
1 TAAAATGGAATTTTTGGAAGTTTCGA-GGTAAAAAT-GGAATTTTTGGAAGTTTGAGGGT
* * ** * *
4010 AAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGTTTTTTTTTGGAAATTTTAGGGT
1 TAAAATGGAATTTTTGGAAGTTTCGAGG-TAAAAAT-GG--AATTTTTGGAAGTTTGAGGGT
* * * *
4072 CAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 TAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * * *
4131 AAAAATGGGATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGGT
1 TAAAATGGAATTTTTGGAAG-TTTCGAGGTAAAAATGGAATTTTTGGAAGTTTGA-GGGT
** * *
4191 TAAAAATGGGTTTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTAGAAGTTTTG-GGGT
1 T-AAAATGGAATTTTTGGAAGTTTC-GAGGTAAAAATGGAATTTTTGGAAG-TTTGAGGGT
*
4250 TAAAAAT-GAGATTTTTGGAAG-TTCGAGGGTAAAAAAAGGAATTTTTGGAAGTTT-AGGG
1 T-AAAATGGA-ATTTTTGGAAGTTTCGA-GGT-AAAAATGGAATTTTTGGAAGTTTGAGGG
4308 ACTTCCGAAG
Statistics
Matches: 298, Mismatches: 41, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
58 40 0.13
59 133 0.45
60 54 0.18
61 29 0.10
62 42 0.14
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (58 bp):
TAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:4086 original size:33 final size:33
Alignment explanation
Indices: 4004--4145 Score: 94
Period size: 29 Copynumber: 4.6 Consensus size: 33
3994 TTTGAAGTTC
* *
4004 GAGGGTAAAAATGGA---ATTTTTGGAAGTTTT
1 GAGGGTAAAAATGGATTTTTTTTTGGAAATTTT
* *
4034 GAGGTTAAAAATGGGTTTTTTTTTGGAAATTTT
1 GAGGGTAAAAATGGATTTTTTTTTGGAAATTTT
* * *
4067 -AGGGTCAAAATGGA---ATTTTTGGAAGTTTT
1 GAGGGTAAAAATGGATTTTTTTTTGGAAATTTT
*
4096 G-GGGTCAAAAATGGGA----TTTTTGG-AAGTTT
1 GAGGGT-AAAAAT-GGATTTTTTTTTGGAAATTTT
4125 GAGGGTAAAAATGGGATTTTT
1 GAGGGTAAAAAT-GGATTTTT
4146 GGAAGTTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
29 32 0.36
30 29 0.33
31 3 0.03
32 11 0.12
33 14 0.16
ACGTcount: A:0.30, C:0.01, G:0.30, T:0.39
Consensus pattern (33 bp):
GAGGGTAAAAATGGATTTTTTTTTGGAAATTTT
Done.