Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006857.1 Kokia drynarioides strain JFW-HI SEQ_121456, 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: 13128
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:4469 original size:15 final size:16
Alignment explanation
Indices: 4438--4472 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4428 GGTTGTCTTG
4438 AGTTCAAGTCAATTTA
1 AGTTCAAGTCAATTTA
*
4454 AGTTCAAG-CGATTTA
1 AGTTCAAGTCAATTTA
4469 AGTT
1 AGTT
4473 TGAGTTGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (16 bp):
AGTTCAAGTCAATTTA
Found at i:11604 original size:18 final size:18
Alignment explanation
Indices: 11581--11617 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
11571 GCATCTAATA
*
11581 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAAATATT
11599 TTGTTCCTTGTAAATATT
1 TTGTTCCTTGTAAATATT
11617 T
1 T
11618 GGCAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (18 bp):
TTGTTCCTTGTAAATATT
Found at i:12230 original size:99 final size:99
Alignment explanation
Indices: 12059--12519 Score: 611
Period size: 99 Copynumber: 4.7 Consensus size: 99
12049 TCATTACCAC
* * * * *
12059 GAAGGGAAATATTTAAGCCGCAACGACGAATCTAGTACCACGAAGGTAACAAAGGGAAAAGTTTA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAACAAAGGGAAAGGTTTA
12124 AGTCGCAAAGGCGAACCTTATACCTCAGAAGCAT
66 AGTCGCAAAGGCGAACCTTATACCTCAGAAGCAT
* *
12158 GAAGGGAAAGATTTAAGCCGCAACGGCGAATTCAGTACCACGAAGGTAACAAAGGGAAAGGTTTA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAACAAAGGGAAAGGTTTA
* *
12223 AGTCGCAAAGGCGAACCTTATACCTCAGTAGTAT
66 AGTCGCAAAGGCGAACCTTATACCTCAGAAGCAT
** ** *
12257 GAAGGGAAAGATTTAAGCCGCAACGGTAAATCCAGTACCACGAAGATAATGAAGGGAGAGGTTTA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAACAAAGGGAAAGGTTTA
* * * *
12322 AGCCGCAATGGCGAACCTTGTACCTCAAAAGCAT
66 AGTCGCAAAGGCGAACCTTATACCTCAGAAGCAT
* * * * *
12356 GAAAGGAAAAAATTTAAGCCACAACGGCGAATCCAATACCACGAAAAT-ACAAAGGGAAAGGTTT
1 G-AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAACAAAGGGAAAGGTTT
* * *
12420 AAGTCGCAATGGCGAACCTTATACCTCGGGAGACAT
65 AAGTCGCAAAGGCGAACCTTATACCTCAGAAG-CAT
* * * * *
12456 GAAGGGAAAGATTTGAGCCGCAACAGTGAATCCAGTACCACGAAGAT-GCAAAGGGAAAGATTTA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAACAAAGGGAAAGGTTTA
12520 CCTCAAGAGC
Statistics
Matches: 315, Mismatches: 45, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
99 272 0.86
100 43 0.14
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (99 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAACAAAGGGAAAGGTTTA
AGTCGCAAAGGCGAACCTTATACCTCAGAAGCAT
Found at i:12513 original size:149 final size:147
Alignment explanation
Indices: 12060--12519 Score: 403
Period size: 149 Copynumber: 3.1 Consensus size: 147
12050 CATTACCACG
* * * * * *
12060 AAGGGAAATATTTAAGCCGCAACGACGAATCTAGTACCACGAAGGTAACAAAGGGAAAAGTTTAA
1 AAGGGAAAAATTTAAGCCGCAACGGCGAATCCAATACCACGAAAGT-ACAAAGGGAAAGGTTTAA
12125 GTCGCAAAGGCGAACCTTATACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAAT
65 GTCGCAAAGGCGAACCTTATACCTC-GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAAT
* * *
12189 TCAGTACCACGAAGGTAACA
129 CCAGTACCACGAAGAT-GCA
** * * * * * ** *
12209 AAGGGAAAGGTTTAAGTCGCAAAGGCGAA-CCTTATACCTC-AGTAGTATGAAGGGAAAGATTTA
1 AAGGGAAAAATTTAAGCCGCAACGGCGAATCC-AATACCACGA-AAGTACAAAGGGAAAGGTTTA
* * ** * * * * *
12272 AGCCGCAACGGTAAATCC--AGTACCACGAAGATAATGAAGGGAGAGGTTTAAGCCGCAATGGCG
64 AGTCGCAAAGGCGAA-CCTTA-TACCTCGAAGA-CATGAAGGGAAAGATTTAAGCCGCAACGGCG
* * *
12335 AA-CCTTGTACCTCAAAAGCATG-A
126 AATCC-AGTACCAC-GAAG-ATGCA
* * *
12358 AAGGAAAAAATTTAAGCCACAACGGCGAATCCAATACCACGAAAATACAAAGGGAAAGGTTTAAG
1 AAGGGAAAAATTTAAGCCGCAACGGCGAATCCAATACCACGAAAGTACAAAGGGAAAGGTTTAAG
* * * * *
12423 TCGCAATGGCGAACCTTATACCTCGGGAGACATGAAGGGAAAGATTTGAGCCGCAACAGTGAATC
66 TCGCAAAGGCGAACCTTATACCTC-GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
12488 CAGTACCACGAAGATGCA
130 CAGTACCACGAAGATGCA
*
12506 AAGGGAAAGATTTA
1 AAGGGAAAAATTTA
12520 CCTCAAGAGC
Statistics
Matches: 234, Mismatches: 61, Indels: 33
0.71 0.19 0.10
Matches are distributed among these distances:
147 8 0.03
148 50 0.21
149 162 0.69
150 13 0.06
151 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.17
Consensus pattern (147 bp):
AAGGGAAAAATTTAAGCCGCAACGGCGAATCCAATACCACGAAAGTACAAAGGGAAAGGTTTAAG
TCGCAAAGGCGAACCTTATACCTCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
AGTACCACGAAGATGCA
Found at i:12521 original size:27 final size:26
Alignment explanation
Indices: 12491--12544 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
12481 GTGAATCCAG
12491 TACCACGAAGATGCA-AAGGGAAAGATT
1 TACCAC-AAGA-GCAGAAGGGAAAGATT
*
12518 TACCTCAAGAGCATGAAGGGAAAGATT
1 TACCACAAGAGCA-GAAGGGAAAGATT
12545 AAGTCACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 4 0.17
27 17 0.71
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.17
Consensus pattern (26 bp):
TACCACAAGAGCAGAAGGGAAAGATT
Found at i:12971 original size:6 final size:6
Alignment explanation
Indices: 12962--12993 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
12952 TCCCAAAAGT
12962 AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
12994 TGTTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Done.