Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012725.1 Kokia drynarioides strain JFW-HI SEQ_127736, 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: 15729
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Warning! 85 characters in sequence are not A, C, G, or T
Found at i:18 original size:6 final size:6
Alignment explanation
Indices: 4--65 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
1 AAT
* * * * *
4 ATATTA ATATAA ATATAA AAATAT AT-TAA TTATTA ATATAA ATAT-A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
50 ATATTA ATATAA ATAT
1 ATATAA ATATAA ATAT
66 TATTAATTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
5 8 0.18
6 36 0.82
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATATAA
Found at i:56 original size:17 final size:17
Alignment explanation
Indices: 4--65 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
1 AAT
4 ATATTAATATAAATATA
1 ATATTAATATAAATATA
21 A-A--AATAT--AT-TA
1 ATATTAATATAAATATA
32 ATTATTAATATAAATATA
1 A-TATTAATATAAATATA
50 ATATTAATATAAATAT
1 ATATTAATATAAATAT
66 TATTAATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
11 3 0.08
12 2 0.05
13 1 0.03
14 5 0.13
15 5 0.13
16 1 0.03
17 18 0.47
18 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAATATAAATATA
Found at i:66 original size:29 final size:29
Alignment explanation
Indices: 4--67 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1 AAT
4 ATATTAATATAAATATAAAAATATATTAA
1 ATATTAATATAAATATAAAAATATATTAA
* * *
33 TTATTAATATAAATATAATATTA-ATATAA
1 ATATTAATATAAATATAAAAATATAT-TAA
62 ATATTA
1 ATATTA
68 TTAATTACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATTAATATAAATATAAAAATATATTAA
Found at i:3669 original size:30 final size:31
Alignment explanation
Indices: 3612--3673 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3602 AGAAAAAGAT
3612 TGTTTTGTCACATTTTCAAAAGTTGAGGGAC
1 TGTTTTGTCACATTTTCAAAAGTTGAGGGAC
* *
3643 TGTTTTGTCACATTTT-TAATGTTGAGGGAC
1 TGTTTTGTCACATTTTCAAAAGTTGAGGGAC
3673 T
1 T
3674 CAAATGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (31 bp):
TGTTTTGTCACATTTTCAAAAGTTGAGGGAC
Found at i:8351 original size:2 final size:2
Alignment explanation
Indices: 8344--8373 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8334 TAGTATTGAT
*
8344 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8374 GGAAGAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8494 original size:243 final size:243
Alignment explanation
Indices: 8215--8702 Score: 949
Period size: 243 Copynumber: 2.0 Consensus size: 243
8205 TTACAAAAGC
* *
8215 TTGCGTTACTTTTGATTGTCAATCAAACATCATTTTCTTTGAAAAGAAATTACATGATTATAATA
1 TTGCATTACTTTTGATTGTCAATCAAACATCATTTTCTTTGAAAAAAAATTACATGATTATAATA
8280 ACAAGTTTTATAATAAAAATCATGAAAATTAAAACACTTCCAACCTTTAAATCATAGTATTGATT
66 ACAAGTTTTATAATAAAAATCATGAAAATTAAAACACTTCCAACCTTTAAATCATAGTATTGATT
8345 ATATATATATATATGTATATATATATATAGGAAGAAAGTGAAGGGTGGAGGAGATTGTTGAGAGA
131 ATATATATATATATGTATATATATATATAGGAAGAAAGTGAAGGGTGGAGGAGATTGTTGAGAGA
8410 GAAAGCAAAAAAGTTCATATGAGAAATAGTGTAATCATTTTTATTAAG
196 GAAAGCAAAAAAGTTCATATGAGAAATAGTGTAATCATTTTTATTAAG
*
8458 TTGCATTACTTTTGATTGTCAATCAAACATCATTTTCTTTGAAAAAAAATTTCATGATTATAATA
1 TTGCATTACTTTTGATTGTCAATCAAACATCATTTTCTTTGAAAAAAAATTACATGATTATAATA
8523 ACAAGTTTTATAATAAAAATCATGAAAATTAAAACACTTCCAACCTTTAAATCATAGTATTGATT
66 ACAAGTTTTATAATAAAAATCATGAAAATTAAAACACTTCCAACCTTTAAATCATAGTATTGATT
8588 ATATATATATATATGTATATATATATATAGGAAGAAAGTGAAGGGTGGAGGAGATTGTTGAGAGA
131 ATATATATATATATGTATATATATATATAGGAAGAAAGTGAAGGGTGGAGGAGATTGTTGAGAGA
8653 GAAAGCAAAAAAGTTCATATGAGAAATAGTGTAATCATTTTTATTAAG
196 GAAAGCAAAAAAGTTCATATGAGAAATAGTGTAATCATTTTTATTAAG
8701 TT
1 TT
8703 ATTGTAAACG
Statistics
Matches: 242, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
243 242 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (243 bp):
TTGCATTACTTTTGATTGTCAATCAAACATCATTTTCTTTGAAAAAAAATTACATGATTATAATA
ACAAGTTTTATAATAAAAATCATGAAAATTAAAACACTTCCAACCTTTAAATCATAGTATTGATT
ATATATATATATATGTATATATATATATAGGAAGAAAGTGAAGGGTGGAGGAGATTGTTGAGAGA
GAAAGCAAAAAAGTTCATATGAGAAATAGTGTAATCATTTTTATTAAG
Found at i:8594 original size:2 final size:2
Alignment explanation
Indices: 8587--8616 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8577 TAGTATTGAT
*
8587 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8617 GGAAGAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9778 original size:99 final size:99
Alignment explanation
Indices: 9626--9827 Score: 386
Period size: 99 Copynumber: 2.0 Consensus size: 99
9616 TTCAGAGAAG
9626 AAGATGAATCAAGTACACAAGAACTGATGAGCGAATTAGGGATATATATAATATATATGGAGAAA
1 AAGATGAATCAAGTACACAAGAACTGATGAGCGAATTAGGGATATATATAATATATATGGAGAAA
9691 CTTTTTTTTTTACTGAAAAGATGAATTGTCGGCA
66 CTTTTTTTTTTACTGAAAAGATGAATTGTCGGCA
*
9725 AAGATGAATCAAGTACATAAGAACTGATGAGCGAATTAGGGATATATATAATATATATGGAGAAA
1 AAGATGAATCAAGTACACAAGAACTGATGAGCGAATTAGGGATATATATAATATATATGGAGAAA
*
9790 CTTTTTTTTTTACTGAAAAGATGAATTGTCGGCC
66 CTTTTTTTTTTACTGAAAAGATGAATTGTCGGCA
9824 AAGA
1 AAGA
9828 AAAAGGCTTG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (99 bp):
AAGATGAATCAAGTACACAAGAACTGATGAGCGAATTAGGGATATATATAATATATATGGAGAAA
CTTTTTTTTTTACTGAAAAGATGAATTGTCGGCA
Done.