Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013511.1 Kokia drynarioides strain JFW-HI SEQ_128537, 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: 6081
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Found at i:69 original size:15 final size:15
Alignment explanation
Indices: 51--102 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
41 TATAAGACAT
51 AGAAGAATAAAGAAA
1 AGAAGAATAAAGAAA
* * *
66 AGAAAAAGAAACAAA
1 AGAAGAATAAAGAAA
*
81 AGAAAGAATAGAAGAAC
1 AG-AAGAATA-AAGAAA
98 AGAAG
1 AGAAG
103 CTTAAACGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 14 0.50
16 8 0.29
17 6 0.21
ACGTcount: A:0.71, C:0.04, G:0.21, T:0.04
Consensus pattern (15 bp):
AGAAGAATAAAGAAA
Found at i:534 original size:17 final size:18
Alignment explanation
Indices: 512--547 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
502 TAAATGAGTT
512 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
529 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
547 A
1 A
548 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:869 original size:18 final size:18
Alignment explanation
Indices: 846--882 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
836 CTTGTAATCA
846 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
864 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
882 A
1 A
883 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:1032 original size:41 final size:40
Alignment explanation
Indices: 984--1084 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
974 TCGACCTTGA
**
984 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCATTTTACTTCGGATAG
* ** * * *
1024 ATTCGATGAGGTACT--GAGT-ACCATTTTACTTTGGTTAG
1 -GTCGATGAGACACTGGGTGTCACCATTTTACTTCGGATAG
1062 GTCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
1085 TTTATTGCTT
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
37 11 0.24
38 15 0.33
39 6 0.13
40 2 0.04
41 11 0.24
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.34
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCATTTTACTTCGGATAG
Found at i:3303 original size:39 final size:39
Alignment explanation
Indices: 3260--3343 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
3250 GGGATGATTT
*
3260 GTTGTAGCCTTGTTTGAGTTATTTTGGAATGAATATCAC
1 GTTGTAGACTTGTTTGAGTTATTTTGGAATGAATATCAC
*
3299 GTTGTAGACTTGTTTGAGTTATTTTGGAATGAATATCAT
1 GTTGTAGACTTGTTTGAGTTATTTTGGAATGAATATCAC
3338 GTTGTA
1 GTTGTA
3344 TTTATGTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (39 bp):
GTTGTAGACTTGTTTGAGTTATTTTGGAATGAATATCAC
Found at i:5701 original size:31 final size:31
Alignment explanation
Indices: 5660--5767 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
5650 TAAGAAGCCC
5660 TTATTTGAGCACTTTTGAAAAAGTTTGGCTC-
1 TTATTTGAGCACTTTTGAAAAA-TTTGGCTCT
* * **
5691 TTGTTTGAGCACTCTCAAAAAATTTTGGC-CT
1 TTATTTGAGCACTTTTGAAAAA-TTTGGCTCT
*
5722 TTATTTGAGCAC-TTTGAAAGATTTGGCT-T
1 TTATTTGAGCACTTTTGAAAAATTTGGCTCT
* * *
5751 TCATTCGAGCATTTTTG
1 TTATTTGAGCACTTTTG
5768 TAAATGTTAA
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 16 0.26
30 10 0.16
31 35 0.57
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (31 bp):
TTATTTGAGCACTTTTGAAAAATTTGGCTCT
Done.