Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003468.1 Kokia drynarioides strain JFW-HI SEQ_116267, 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: 15955
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Found at i:959 original size:50 final size:52
Alignment explanation
Indices: 832--980 Score: 176
Period size: 50 Copynumber: 2.8 Consensus size: 52
822 TAGATGTGCT
* ** * *
832 ACATAACAATCGATTTAAACATATAAATTATAGATTTAAAAGAAGTAGTATTCCA
1 ACATAACAATCAATTTAAACATATAAAAAATAGATTCAAAAGAAGCAG--TT-CA
* *
887 ACATAGCAATCAATTTAAACATATAAAAAATTGATTCAAAAGAAGCAG-T-A
1 ACATAACAATCAATTTAAACATATAAAAAATAGATTCAAAAGAAGCAGTTCA
**
937 ACATAACAATCAATTTAAACATATAAACGATAGATTCAAAAGAA
1 ACATAACAATCAATTTAAACATATAAAAAATAGATTCAAAAGAA
981 AAAGAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
50 41 0.49
52 1 0.01
55 41 0.49
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (52 bp):
ACATAACAATCAATTTAAACATATAAAAAATAGATTCAAAAGAAGCAGTTCA
Found at i:5879 original size:95 final size:95
Alignment explanation
Indices: 5776--5974 Score: 296
Period size: 95 Copynumber: 2.1 Consensus size: 95
5766 GCAAAAGTTT
* *
5776 GAAGGGAAGGAAAGTAAAAT-AGAGTAAAACTTTTGGAGGGAAAGTAGAAAGGAAAAAGTTTTAT
1 GAAGGGAAGGAAAGTAAAATGA-AATAAAACTTTTGGAAGGAAAGTAGAAAGGAAAAAGTTTTAT
*
5840 TGGTTTGG-GGAGAAGTAAAAGTGTTTGAAGG-
65 TAGTTTGGAGG-GAAGTAAAAGTGTTTG-AGGA
* *
5871 GAAGGGAAGGAAAGTAAAATGAAATAAAAGTTTTTGAAGGAAAGTAGAAAGGAAAAAGTTTTATT
1 GAAGGGAAGGAAAGTAAAATGAAATAAAACTTTTGGAAGGAAAGTAGAAAGGAAAAAGTTTTATT
*
5936 AGTTTGGAGGGAAGTAAAAGTGTTTGGGGA
66 AGTTTGGAGGGAAGTAAAAGTGTTTGAGGA
5966 GAAGGGAAG
1 GAAGGGAAG
5975 TAAAAGGGTT
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
94 2 0.02
95 90 0.95
96 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.34, T:0.23
Consensus pattern (95 bp):
GAAGGGAAGGAAAGTAAAATGAAATAAAACTTTTGGAAGGAAAGTAGAAAGGAAAAAGTTTTATT
AGTTTGGAGGGAAGTAAAAGTGTTTGAGGA
Found at i:6842 original size:43 final size:43
Alignment explanation
Indices: 6781--6871 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
6771 CCATGTTAGG
6781 CCTAAAGTTTGTAAATGTAGTAGAATTGACTATTTTTTCCTTT
1 CCTAAAGTTTGTAAATGTAGTAGAATTGACTATTTTTTCCTTT
6824 CCTAAAGTTTGTAAATGTAGTAGAATTGACTATTTTTTCCTTT
1 CCTAAAGTTTGTAAATGTAGTAGAATTGACTATTTTTTCCTTT
6867 CCTAA
1 CCTAA
6872 TGAAGAGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (43 bp):
CCTAAAGTTTGTAAATGTAGTAGAATTGACTATTTTTTCCTTT
Found at i:6892 original size:42 final size:43
Alignment explanation
Indices: 6797--6893 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
6787 GTTTGTAAAT
* ** * *
6797 GTAGTAGAATTGACTATTTTTTCCTTTCCTAAAGTTTGTAAAT
1 GTAGAAGAATTGACTATTTTTTCCTTTCCTAAAGTAAGGAAAA
* *
6840 GTAGTAGAATTGACTATTTTTTCCTTTCCTAATG-AAGAGAAAA
1 GTAGAAGAATTGACTATTTTTTCCTTTCCTAAAGTAAG-GAAAA
6883 GTA-AAGAATTG
1 GTAGAAGAATTG
6894 CCTACAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 8 0.17
43 39 0.83
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.40
Consensus pattern (43 bp):
GTAGAAGAATTGACTATTTTTTCCTTTCCTAAAGTAAGGAAAA
Found at i:10927 original size:18 final size:19
Alignment explanation
Indices: 10904--10942 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
10894 AACATTTGTT
10904 AACAACACTC-TACTTGGA
1 AACAACACTCGTACTTGGA
* *
10922 AACAACATTCGTATTTGGA
1 AACAACACTCGTACTTGGA
10941 AA
1 AA
10943 GTTATGGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (19 bp):
AACAACACTCGTACTTGGA
Done.