Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007889.1 Kokia drynarioides strain JFW-HI SEQ_122530, 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: 71132
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:20043 original size:28 final size:29
Alignment explanation
Indices: 20001--20068 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
19991 TTTTTAATGG
*
20001 TAAAAATATATTTTAAT-TCTAAAAATAA
1 TAAAAATATAATTTAATCTCTAAAAATAA
* * *
20029 TAAAAATTTAATTTAATCCTTTAAAAATTA
1 TAAAAATATAATTTAAT-CTCTAAAAATAA
20059 T-AAAATATAA
1 TAAAAATATAA
20069 ACTATTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 15 0.45
29 8 0.24
30 10 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATAATTTAATCTCTAAAAATAA
Found at i:24605 original size:24 final size:24
Alignment explanation
Indices: 24577--24807 Score: 284
Period size: 24 Copynumber: 9.6 Consensus size: 24
24567 TATTAGTTGG
* *
24577 CGAGCGTAAACGTAAAGTGACTGA
1 CGAGCATAAACGTAAAGTGGCTGA
* *
24601 TGAGCATAAACGTAAAGTGGCTAA
1 CGAGCATAAACGTAAAGTGGCTGA
*
24625 CGATCATAAACGTAAAGTGGCTGA
1 CGAGCATAAACGTAAAGTGGCTGA
*
24649 CGATCATAAACGTAAAGTGGCTGA
1 CGAGCATAAACGTAAAGTGGCTGA
*
24673 CGAGCATAAACGTAAAGTGGAT-A
1 CGAGCATAAACGTAAAGTGGCTGA
*
24696 GCGAGCATAAACGTAAAGTGGCTGG
1 -CGAGCATAAACGTAAAGTGGCTGA
**
24721 CGAGCATAAACGTAAAGTGATTGA
1 CGAGCATAAACGTAAAGTGGCTGA
* * * *
24745 CAAGCACAAACATAAAGTGGCTGG
1 CGAGCATAAACGTAAAGTGGCTGA
* *
24769 CTAGCATAAACGTATAGTGGCTGA
1 CGAGCATAAACGTAAAGTGGCTGA
* *
24793 CGTGCATAAATGTAA
1 CGAGCATAAACGTAA
24808 CTAAAACTTA
Statistics
Matches: 176, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
23 1 0.01
24 175 0.99
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (24 bp):
CGAGCATAAACGTAAAGTGGCTGA
Found at i:34691 original size:22 final size:22
Alignment explanation
Indices: 34665--34708 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
34655 GGTTTGAATT
34665 TAAAGAACATAAAAATAAAAGA
1 TAAAGAACATAAAAATAAAAGA
34687 TAAAGAACATAAAAATAAAAGA
1 TAAAGAACATAAAAATAAAAGA
34709 AATAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (22 bp):
TAAAGAACATAAAAATAAAAGA
Found at i:34713 original size:15 final size:15
Alignment explanation
Indices: 34677--34715 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
34667 AAGAACATAA
34677 AAATAAAAGATAAAG
1 AAATAAAAGATAAAG
34692 AACATAAAA-ATAAAAG
1 AA-ATAAAAGAT-AAAG
34708 AAATAAAA
1 AAATAAAA
34716 CAAAGGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (15 bp):
AAATAAAAGATAAAG
Found at i:34717 original size:22 final size:22
Alignment explanation
Indices: 34665--34717 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
34655 GGTTTGAATT
*
34665 TAAAGAACATAAAAATAAAAGA
1 TAAAAAACATAAAAATAAAAGA
*
34687 TAAAGAACATAAAAATAAAAGA
1 TAAAAAACATAAAAATAAAAGA
34709 -AATAAAACA
1 TAA-AAAACA
34718 AAGGAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.13
Consensus pattern (22 bp):
TAAAAAACATAAAAATAAAAGA
Found at i:42908 original size:24 final size:24
Alignment explanation
Indices: 42880--42938 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
42870 TAGACTAATA
* *
42880 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
* **
42904 AGAGTTTAATTGTAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
42928 AGAGTTTAACT
1 AGAGTTTAACT
42939 AAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:45877 original size:93 final size:92
Alignment explanation
Indices: 45773--45963 Score: 303
Period size: 93 Copynumber: 2.1 Consensus size: 92
45763 GATCATATTT
* * *
45773 AATAAATAATAAGTTAATTGAGGTAACTTTATTAAATATGATCGATTGGATTTAGTATTTTTATG
1 AATAAACAATAAATTAATTGAGGCAACTTTATTAAATATGATCGATTGGATTTAGTATTTTTATG
*
45838 GTAAATGTTTTTT-TTAAATGATTGATTG
66 GT-AAT-TTTTTTCTTAAATAATTGATTG
* *
45866 AATAAACAATAAATTAATTTAGGCAACTTTATTAAATATGATTGATTGGATTTAGTATTTTTATG
1 AATAAACAATAAATTAATTGAGGCAACTTTATTAAATATGATCGATTGGATTTAGTATTTTTATG
45931 GTAATTTTTTTCTTAAATAATTGATTG
66 GTAATTTTTTTCTTAAATAATTGATTG
45958 AATAAA
1 AATAAA
45964 AAATGCTTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
91 6 0.07
92 23 0.25
93 62 0.68
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (92 bp):
AATAAACAATAAATTAATTGAGGCAACTTTATTAAATATGATCGATTGGATTTAGTATTTTTATG
GTAATTTTTTTCTTAAATAATTGATTG
Found at i:48341 original size:24 final size:24
Alignment explanation
Indices: 48290--48344 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
48280 TATTTCTGTT
*
48290 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* *
48314 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
48338 AAACTCT
1 AAACTCT
48345 TATTAGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:52762 original size:18 final size:16
Alignment explanation
Indices: 52731--52764 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
52721 TGATGTCCCA
52731 TTGTTGGATAAATTTC
1 TTGTTGGATAAATTTC
52747 TTGTTAGGAGTAAATTTC
1 TTGTT-GGA-TAAATTTC
52765 CAATTCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (16 bp):
TTGTTGGATAAATTTC
Found at i:55972 original size:29 final size:30
Alignment explanation
Indices: 55926--55983 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
55916 AGTATAAAAA
*
55926 TAAATTTTTATTATTTTTAAAGGA-TTAAAT
1 TAAATTTTTATCATTTTT-AAGGAGTTAAAT
55956 TAAATTTTTATCA-TTTTAAGGAGTTAAA
1 TAAATTTTTATCATTTTTAAGGAGTTAAA
55984 GTGTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 9 0.35
30 12 0.46
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.50
Consensus pattern (30 bp):
TAAATTTTTATCATTTTTAAGGAGTTAAAT
Found at i:66182 original size:17 final size:18
Alignment explanation
Indices: 66156--66190 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
66146 AGAATATATA
*
66156 TATATATATATTATTTTG
1 TATATATATATTAATTTG
66174 TATAT-TATATTAATTTG
1 TATATATATATTAATTTG
66191 ACTACTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TATATATATATTAATTTG
Found at i:68856 original size:14 final size:14
Alignment explanation
Indices: 68824--68856 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
68814 GCCTAGAATC
*
68824 AAGCCCATAAAATG
1 AAGCTCATAAAATG
68838 AAGCTCATAAAATG
1 AAGCTCATAAAATG
68852 AAGCT
1 AAGCT
68857 ATTTGAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (14 bp):
AAGCTCATAAAATG
Done.