Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011882.1 Kokia drynarioides strain JFW-HI SEQ_126879, 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: 10163
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3008 original size:56 final size:55
Alignment explanation
Indices: 2922--3032 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 55
2912 ACACTCCATC
2922 GAAAATTGTATCGCTTTCAAGAAGATAGTGGAAAGATTAATTAAGATGAAGCGTA
1 GAAAATTGTATCGCTTTCAAGAAGATAGTGGAAAGATTAATTAAGATGAAGCGTA
* *
2977 NGAAAATTGTTTTGCTTTCAAGAAGATAGTGGAAAGATTAATTAAGATGAAGCGTA
1 -GAAAATTGTATCGCTTTCAAGAAGATAGTGGAAAGATTAATTAAGATGAAGCGTA
3033 TAAGATCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.29
Consensus pattern (55 bp):
GAAAATTGTATCGCTTTCAAGAAGATAGTGGAAAGATTAATTAAGATGAAGCGTA
Found at i:4671 original size:18 final size:19
Alignment explanation
Indices: 4645--4687 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4635 AGATGTGAAG
4645 GAAAAGAAGAAAGAGAT-A
1 GAAAAGAAGAAAGAGATGA
* **
4663 GAAAGGAAGCGAGAGATGA
1 GAAAAGAAGAAAGAGATGA
4682 GAAAAG
1 GAAAAG
4688 CACGATTGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.58, C:0.02, G:0.35, T:0.05
Consensus pattern (19 bp):
GAAAAGAAGAAAGAGATGA
Found at i:9619 original size:98 final size:98
Alignment explanation
Indices: 9389--9852 Score: 557
Period size: 98 Copynumber: 4.8 Consensus size: 98
9379 CAAAACACGG
* ** * *
9389 AGGGAAAGGTTTAAGTAGCAACGGTTAACCTTATACCTCAGAAGCATAAAGGAAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* *
9454 CGCAATGGCAATTCCAATACCAC---GA-A-GA
66 CGCAACGGCAAATCCAATACCACGAAGATATGA
* *
9482 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAG-AGACAGGAAGGGAAAGATTTCAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAGAAG-CATGAAGGGAAAGATTTAAG
*
9546 CCGTAACGGCAAATCCAATACCACGAAGATATGA
65 CCGCAACGGCAAATCCAATACCACGAAGATATGA
* * *
9580 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATGCCTCAGAAGCATGAAAGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * *
9645 CGCAACGGCAAATCCAGTACCACAAAGATATGG
66 CGCAACGGCAAATCCAATACCACGAAGATATGA
* ** *
9678 AGGGAAAGGTTTAAGTCGCAACAGTAAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * * * * * *
9743 TGTAACGGCGAATCCAGTACAATGAAGACACGA
66 CGCAACGGCAAATCCAATACCACGAAGATATGA
* * * *
9776 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATCCCTC-GAAAGCATGAAAGGAAA-TTTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAG-AAGCATGAAGGGAAAGATTTAAG
*
9839 CCGCAACGGTAAAT
65 CCGCAACGGCAAAT
9853 TTAGTACCAT
Statistics
Matches: 316, Mismatches: 47, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
92 2 0.01
93 75 0.24
96 2 0.01
97 18 0.06
98 217 0.69
99 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAAGC
CGCAACGGCAAATCCAATACCACGAAGATATGA
Found at i:9831 original size:49 final size:49
Alignment explanation
Indices: 9389--9847 Score: 272
Period size: 49 Copynumber: 9.5 Consensus size: 49
9379 CAAAACACGG
* ** *
9389 AGGGAAAGGTTTAAGTAGCAACGGTTAACCTTATACCTCAGAAG-CATAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCA-AAGACATGA
* * * * * *
9438 AGGAAAAGATTTAAGCCGCAATGGC-AATTCC-AATA-C-C-ACGA-A-GA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAA--CCTTATACCTCAAAGACATGA
* *
9482 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAGAGACAGGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAAAGACATGA
* * * * * * * * *
9531 AGGGAAAGATTTCAGCCGTAACGGCAAATCC-AATACCACGAAGATATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTATACCTCAAAGACATGA
* *
9580 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATGCCTCAGAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCA-AAGACATGA
* * * * * * *
9629 AAGGAAAGATTTAAGCCGCAACGGCAAATCC--AGTACCACAAAGATATGG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTA-TACCTCAAAGACATGA
* ** *
9678 AGGGAAAGGTTTAAGTCGCAACAGTAAACCTTGTACCTCAGAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCA-AAGACATGA
* * * * *
9727 AGGGAAAGATTTAAG-CTGTAACGGCGAATCC--AGTACAAT-GAAGACACGA
1 AGGGAAAGGTTTAAGTC-GCAACGGCGAA-CCTTA-TAC-CTCAAAGACATGA
* *
9776 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATCCCTCGAAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTC-AAAGACATGA
* * *
9825 AAGGAAA-TTTTAAGCCGCAACGG
1 AGGGAAAGGTTTAAGTCGCAACGG
9848 TAAATTTAGT
Statistics
Matches: 305, Mismatches: 76, Indels: 59
0.69 0.17 0.13
Matches are distributed among these distances:
43 2 0.01
44 25 0.08
45 6 0.02
46 1 0.00
47 3 0.01
48 32 0.10
49 216 0.71
50 20 0.07
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (49 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAAAGACATGA
Done.