Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009084.1 Kokia drynarioides strain JFW-HI SEQ_123784, 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: 38405
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 68 characters in sequence are not A, C, G, or T
Found at i:5887 original size:4 final size:4
Alignment explanation
Indices: 5878--5903 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5868 TTGCCAATAC
5878 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
5904 GCCTAGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:11777 original size:21 final size:21
Alignment explanation
Indices: 11751--11792 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11741 TATTGCCCTT
11751 AGTGGATTGCTATGATCAATC
1 AGTGGATTGCTATGATCAATC
11772 AGTGGATTGCTATGATCAATC
1 AGTGGATTGCTATGATCAATC
11793 CTAGTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
AGTGGATTGCTATGATCAATC
Found at i:22160 original size:57 final size:57
Alignment explanation
Indices: 22091--22204 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
22081 ATAGATTTGA
22091 ATTGTTAAACATATATGAACTAATTAAATTGAATTAAATCGATTTTCGAATTTATAT
1 ATTGTTAAACATATATGAACTAATTAAATTGAATTAAATCGATTTTCGAATTTATAT
22148 ATTGTTAAACATATATGAACTAATTAAATTGAATTAAATCGATTTTCGAATTTATAT
1 ATTGTTAAACATATATGAACTAATTAAATTGAATTAAATCGATTTTCGAATTTATAT
22205 CAAAATTAGC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (57 bp):
ATTGTTAAACATATATGAACTAATTAAATTGAATTAAATCGATTTTCGAATTTATAT
Found at i:26369 original size:115 final size:115
Alignment explanation
Indices: 26167--26384 Score: 364
Period size: 115 Copynumber: 1.9 Consensus size: 115
26157 TTGTAACACG
* *
26167 TAAACACACCCTAAACAAACTTGAATGACCCAAAATTCTTTCGAGAAACAGCATAAAAGTAACAC
1 TAAACACACACTAAACAAACTCGAATGACCCAAAATTCTTTCGAGAAACAGCATAAAAGTAACAC
*
26232 CTTAAACCCTAATTCAAATGCTACATTTCAATACCAAAACAAAAGGCACA
66 CTTAAACCCTAATCCAAATGCTACATTTCAATACCAAAACAAAAGGCACA
* * *
26282 TAAACACACACTAAACAATCTCGAATGACCCAAAATTCTTTTGAGAAACATCATAAAAGTAACAC
1 TAAACACACACTAAACAAACTCGAATGACCCAAAATTCTTTCGAGAAACAGCATAAAAGTAACAC
* *
26347 CTTAAACCCTAATCCAAATGCTAGATTTCAGTACCAAA
66 CTTAAACCCTAATCCAAATGCTACATTTCAATACCAAA
26385 TAGACCAGAA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 95 1.00
ACGTcount: A:0.46, C:0.25, G:0.08, T:0.22
Consensus pattern (115 bp):
TAAACACACACTAAACAAACTCGAATGACCCAAAATTCTTTCGAGAAACAGCATAAAAGTAACAC
CTTAAACCCTAATCCAAATGCTACATTTCAATACCAAAACAAAAGGCACA
Found at i:29325 original size:26 final size:26
Alignment explanation
Indices: 29296--29360 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
29286 TCAATAAATA
29296 AAAAATATATAAAATTATTAAATA-TT
1 AAAAATATATAAAATTA-TAAATATTT
*
29322 -AAAATA-ATATAA-TATAAATATTT
1 AAAAATATATAAAATTATAAATATTT
*
29345 AAAAAAATA-AAAATTA
1 AAAAATATATAAAATTA
29361 ATATATCCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 6 0.19
23 4 0.12
24 13 0.41
25 9 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATATATAAAATTATAAATATTT
Found at i:29363 original size:22 final size:23
Alignment explanation
Indices: 29314--29364 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
29304 ATAAAATTAT
* *
29314 TAAATA-TTAAAATAATATAATA
1 TAAATATTTAAAAAAATATAAAA
29336 TAAATATTTAAAAAAATA-AAAA
1 TAAATATTTAAAAAAATATAAAA
*
29358 TTAATAT
1 TAAATAT
29365 ATCCGGACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATATTTAAAAAAATATAAAA
Found at i:34229 original size:4 final size:4
Alignment explanation
Indices: 34220--34254 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
34210 TATTAAAGAG
34220 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
34255 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:34271 original size:14 final size:14
Alignment explanation
Indices: 34222--34273 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
34212 TTAAAGAGTG
*
34222 TATGTATGTATGTA
1 TATGTGTGTATGTA
*
34236 TGTATGTATGTATGTA
1 --TATGTGTGTATGTA
* *
34252 TGTGTGTGTGTGTA
1 TATGTGTGTATGTA
34266 TATGTGTG
1 TATGTGTG
34274 GCTCTCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 18 0.56
16 14 0.44
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (14 bp):
TATGTGTGTATGTA
Done.