Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012095.1 Kokia drynarioides strain JFW-HI SEQ_127094, 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: 46572
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7604 original size:16 final size:17
Alignment explanation
Indices: 7580--7614 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
7570 CTACTCCTAC
*
7580 AAATTATAAGTCT-AAA
1 AAATGATAAGTCTCAAA
7596 AAATGATAAGTCTCAAA
1 AAATGATAAGTCTCAAA
7613 AA
1 AA
7615 CACTTTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (17 bp):
AAATGATAAGTCTCAAA
Found at i:10059 original size:56 final size:56
Alignment explanation
Indices: 9862--10052 Score: 249
Period size: 56 Copynumber: 3.4 Consensus size: 56
9852 TTGAACCAAA
* ** *
9862 ATAGCTTTACGCTCTAACCGAGACATAAGCAACCCAAAGCTTTAC-CAGAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTCTACTC-GAGCTATAC
* * * *
9918 ATAGTATTACGCTGTAACCGAGACGTAAGCATTCCAAAGCTCTACTTGAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTCTACTCGAGCTATAC
* * *
9974 ATAGCATTATGCTCCAACCGAGACATAAGCGTTCCAAAGCTCTACTCGAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTCTACTCGAGCTATAC
* *
10030 ATGGCATTACGCTCTAATCGAGA
1 ATAGCATTACGCTCTAACCGAGA
10053 TGTAAGCAGA
Statistics
Matches: 115, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
56 115 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (56 bp):
ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTCTACTCGAGCTATAC
Found at i:12941 original size:38 final size:38
Alignment explanation
Indices: 12862--12941 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
12852 GTGCAACAAA
* * * *
12862 AATTTTGGGCATGCTCATGCAGTGATAATTTTGGGCAC
1 AATTTTGGACATGCTCATGCAGTGACAATTCTAGGCAC
* *
12900 AATTTTGGACAT-CATCATGTAGTGACAATTCTAGGCGC
1 AATTTTGGACATGC-TCATGCAGTGACAATTCTAGGCAC
12938 AATT
1 AATT
12942 CTGAATAGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 1 0.03
38 34 0.97
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (38 bp):
AATTTTGGACATGCTCATGCAGTGACAATTCTAGGCAC
Found at i:13949 original size:28 final size:27
Alignment explanation
Indices: 13917--13969 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
13907 TCTTCCTTAG
* *
13917 GCATGAGTTCTTTTTTTTTTCCAATGTA
1 GCATGACTTC-TTCTTTTTTCCAATGTA
*
13945 GCATGTCTTCTTCTTTTTTCCAATG
1 GCATGACTTCTTCTTTTTTCCAATG
13970 CCTCTTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.53
Consensus pattern (27 bp):
GCATGACTTCTTCTTTTTTCCAATGTA
Found at i:16119 original size:13 final size:12
Alignment explanation
Indices: 16089--16123 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
16079 ATTCCTTAGA
16089 TTTAGTTTTTAC
1 TTTAGTTTTTAC
*
16101 TTTAGTTTTTAT
1 TTTAGTTTTTAC
16113 TTGTAGTTTTT
1 TT-TAGTTTTT
16124 GAAACAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.14, C:0.03, G:0.11, T:0.71
Consensus pattern (12 bp):
TTTAGTTTTTAC
Found at i:28426 original size:12 final size:11
Alignment explanation
Indices: 28394--28422 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
28384 ATAGCAATAA
28394 TTTCTTTTCT-
1 TTTCTTTTCTC
28404 TTTCTTTTCTC
1 TTTCTTTTCTC
28415 TTTCTTTT
1 TTTCTTTT
28423 TCTCATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTCTC
Found at i:29516 original size:15 final size:15
Alignment explanation
Indices: 29493--29526 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29483 ATTCTCTTAT
*
29493 TCTTTTTCTTCCTTC
1 TCTTCTTCTTCCTTC
29508 TCTTCTTCTTCCTTC
1 TCTTCTTCTTCCTTC
29523 TCTT
1 TCTT
29527 TCTCCTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTTCTTCTTCCTTC
Found at i:40995 original size:26 final size:24
Alignment explanation
Indices: 40936--40995 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
40926 TTCTATTTTC
*
40936 TAATTTTTAATTTATTTAATTTAT
1 TAATTTTTAATTTATTTAAATTAT
* *
40960 TAACTCTTTAATTTATTTTAAATTGT
1 TAA-TTTTTAATTTA-TTTAAATTAT
40986 TAATATTTTA
1 TAAT-TTTTA
40996 TACTAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 3 0.10
25 11 0.38
26 15 0.52
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:43211 original size:7 final size:7
Alignment explanation
Indices: 43199--43230 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
43189 TGCTCAAGAA
43199 AAAAATG
1 AAAAATG
43206 AAAAATG
1 AAAAATG
43213 AAAAA-G
1 AAAAATG
43219 AAAAA-G
1 AAAAATG
43225 AAAAAT
1 AAAAAT
43231 ATAGAGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (7 bp):
AAAAATG
Done.