Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013569.1 Kokia drynarioides strain JFW-HI SEQ_128595, 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: 4686
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Found at i:3920 original size:49 final size:49
Alignment explanation
Indices: 3858--4432 Score: 458
Period size: 49 Copynumber: 11.7 Consensus size: 49
3848 GTACCACGAA
* *
3858 ACATGAAGGGAAAGATTTAAGTCACAATGGCGAATCC-AGTACCATAAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCATAAAG
* * * * * *
3907 ATAGGGAGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACC-TCAGAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAT-A-AAG
* * * *
3957 AGATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACC-TCAAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAT-AAAG
* * * * **
4006 ACATGAAGGGAAGGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCATAAAG
* * *
4055 ACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACC-TCAAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAT-AAAG
* ** * * * **
4104 ACAAGAAGGGAGGGATTTAAGCCGTAACGACGAATCC-AGTACCACGAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCATAAAG
* * * *
4153 ACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACC-TCAAAA
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAT-AAAG
* ***
4202 ACATGAAGGGAAGGATTTAAGTCGCAACGGCGAATCC-AGTACCGCGAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCATAAAG
* * *
4251 ACATG-AGGAGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACC-TCGGAAG
1 ACATGAAGG-GAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAT--AAAG
* * * * *
4301 -CATAAAGGGAAATATTTAAGCCGCAAAGGCGAATCC-AGTACCATGAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCATAAAG
* * *
4349 ACATGAAGGGAAGGGTTTAAGTCGCAATGGCGAACCTTA-TACC-TCAGAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACC-TAGTACCAT-A-AAG
* *
4399 -CATGAAAGGAAAAGATTTAAGCCGCAACGGCGAA
1 ACATG-AAGGGAAAGATTTAAGTCGCAACGGCGAA
4433 TCCGGTACCA
Statistics
Matches: 417, Mismatches: 85, Indels: 47
0.76 0.15 0.09
Matches are distributed among these distances:
48 17 0.04
49 316 0.76
50 84 0.20
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (49 bp):
ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCATAAAG
Found at i:4089 original size:98 final size:98
Alignment explanation
Indices: 3846--4461 Score: 737
Period size: 98 Copynumber: 6.3 Consensus size: 98
3836 CTACAGGTCT
* * *
3846 CAGTACCACGAA-ACATGAAGGGAAAGATTTAAGTCACAATGGCGAATCC-AGTACCAT-AAAGA
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTAGTACC-TCAAAGA
* * * * *
3908 TAGGGAGGGAAAGG-TTTAAGTCTCAACGGCGAA-C
64 CATGAAGGG-AAGGATTTAAGCCGCAACGGCGAATC
* * *
3942 CTTGTACCTCAGAAGAGATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGA
1 C-AGTACCAC-GAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGA
*
4007 CATGAAGGGAAGGATTTAAGCCGCAACGGTGAATC
64 CATGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
*
4042 TAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGACA
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGACA
* * * *
4107 AGAAGGGAGGGATTTAAGCCGTAACGACGAATC
66 TGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
*
4140 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAAAACA
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGACA
*
4205 TGAAGGGAAGGATTTAAGTCGCAACGGCGAATC
66 TGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
* * * * *
4238 CAGTACCGCGAAGACAT-GAGGAGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCGGAAG-
1 CAGTACCACGAAGACATAAAGG-GAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTC-AAAGA
* ** *
4301 CATAAAGGGAAATATTTAAGCCGCAAAGGCGAATC
64 CATGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
* * *
4336 CAGTACCATGAAGACATGAAGGGAAGGGTTTAAGTCGCAATGGCGAACCTTA-TACCTCAGAAG-
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACC-TAGTACCTCA-AAGA
* *
4399 CATGAAAGGAAAAGATTTAAGCCGCAACGGCGAATC
64 CATG-AAGGGAAGGATTTAAGCCGCAACGGCGAATC
* * * * *
4435 CGGTACCATGAAAACACAAAGAGAAAG
1 CAGTACCACGAAGACATAAAGGGAAAG
4462 ATTAAAGCAG
Statistics
Matches: 451, Mismatches: 56, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
96 1 0.00
97 9 0.02
98 316 0.70
99 124 0.27
100 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (98 bp):
CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGACA
TGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
Done.