Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000437.1 Kokia drynarioides strain JFW-HI SEQ_111273, 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: 24285
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:6912 original size:30 final size:31
Alignment explanation
Indices: 6844--6929 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 31
6834 ATAGGGGTCG
* **
6844 AAATTAAATTATATATTT-TTATTATTTATTT
1 AAATTAAATTATATATTTATAATT-TTTATAA
*
6875 TAA-TAAATTATATATTTATAATTTTTA-AA
1 AAATTAAATTATATATTTATAATTTTTATAA
* *
6904 AAATTAAATTAAAT-TTTATCATTTTT
1 AAATTAAATTATATATTTATAATTTTT
6930 TATTGGTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 13 0.28
30 27 0.59
31 6 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
AAATTAAATTATATATTTATAATTTTTATAA
Found at i:6974 original size:16 final size:17
Alignment explanation
Indices: 6953--6985 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6943 GTAATTTTAC
*
6953 TTTTATTAA-TTTAAAA
1 TTTTATAAATTTTAAAA
6969 TTTTATAAATTTTAAAA
1 TTTTATAAATTTTAAAA
6986 GAGTTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATAAATTTTAAAA
Found at i:15377 original size:10 final size:9
Alignment explanation
Indices: 15348--15419 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
15338 TTTGTTTTTG
15348 AAAATTATA
1 AAAATTATA
15357 AAAATTATA
1 AAAATTATA
* *
15366 AAAATTCTT
1 AAAATTATA
15375 AAAATATATA
1 AAAAT-TATA
15385 AAATATTCA-A
1 AAA-ATT-ATA
* *
15395 AAAGTAGATA
1 AAAAT-TATA
15405 AAAATTATTA
1 AAAATTA-TA
15415 AAAAT
1 AAAAT
15420 GTTATTTATA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
9 24 0.49
10 22 0.45
11 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:18403 original size:19 final size:19
Alignment explanation
Indices: 18381--18425 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
18371 TTTTATTAGA
18381 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
18400 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
18419 ATTTAAT
1 ATTTAAT
18426 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:20068 original size:27 final size:27
Alignment explanation
Indices: 20038--20121 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
20028 GTAATCCGGT
20038 ACTTTATGTACTGACGAGTTAATACAC
1 ACTTTATGTACTGACGAGTTAATACAC
*
20065 ACTTTGATG--C-GACGAG--CATA-AC
1 ACTTT-ATGTACTGACGAGTTAATACAC
20087 GGTACTTTATGTACTGACGAGTTAATACAC
1 ---ACTTTATGTACTGACGAGTTAATACAC
20117 ACTTT
1 ACTTT
20122 GGTGCGACGA
Statistics
Matches: 45, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
22 2 0.04
23 3 0.07
24 3 0.07
25 11 0.24
26 2 0.04
27 16 0.36
28 3 0.07
29 3 0.07
30 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (27 bp):
ACTTTATGTACTGACGAGTTAATACAC
Found at i:20102 original size:52 final size:52
Alignment explanation
Indices: 20034--20162 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
20024 ACGAGTAATC
20034 CGGTACTTTATGTACTGACGAGTTAATACACACTTTGATGCGACGAGCATAA
1 CGGTACTTTATGTACTGACGAGTTAATACACACTTTGATGCGACGAGCATAA
* *
20086 CGGTACTTTATGTACTGACGAGTTAATACACACTTTGGTGCGACGAGCATTA
1 CGGTACTTTATGTACTGACGAGTTAATACACACTTTGATGCGACGAGCATAA
*
20138 CGGTACTTTGTGTACTGACGAGTTA
1 CGGTACTTTATGTACTGACGAGTTA
20163 TGCACTTTGT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (52 bp):
CGGTACTTTATGTACTGACGAGTTAATACACACTTTGATGCGACGAGCATAA
Found at i:20159 original size:27 final size:27
Alignment explanation
Indices: 20075--20159 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
20065 ACTTTGATGC
* *
20075 GACGAGCATAACGGTACTTTATGTACT
1 GACGAGCATTACGGTACTTTGTGTACT
* * ** *
20102 GACGAGTTAATAC-ACACTTTG-GTGC-
1 GACGAG-CATTACGGTACTTTGTGTACT
20127 GACGAGCATTACGGTACTTTGTGTACT
1 GACGAGCATTACGGTACTTTGTGTACT
20154 GACGAG
1 GACGAG
20160 TTATGCACTT
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
24 4 0.10
25 12 0.29
26 6 0.14
27 17 0.40
28 3 0.07
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (27 bp):
GACGAGCATTACGGTACTTTGTGTACT
Found at i:20741 original size:22 final size:24
Alignment explanation
Indices: 20716--20763 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
20706 AGTATGGTAC
*
20716 TTACAAG-AATTTTTATG-AGATT
1 TTACAAGTAATTTTGATGCAGATT
*
20738 TTACAAGTGATTTTGATGCAGATT
1 TTACAAGTAATTTTGATGCAGATT
20762 TT
1 TT
20764 TGAGAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 8 0.36
24 7 0.32
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (24 bp):
TTACAAGTAATTTTGATGCAGATT
Found at i:22128 original size:20 final size:21
Alignment explanation
Indices: 22086--22134 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
22076 TTCACCAAAA
22086 TATTATTTTAACATTTTTCTTT
1 TATT-TTTTAACATTTTTCTTT
22108 TATATTTTTAAC-TTTTT-TTT
1 TAT-TTTTTAACATTTTTCTTT
22128 TATTTTT
1 TATTTTT
22135 CATTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.15
20 6 0.23
21 5 0.19
22 10 0.38
23 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTTTTTAACATTTTTCTTT
Found at i:22145 original size:18 final size:20
Alignment explanation
Indices: 22100--22145 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
22090 ATTTTAACAT
22100 TTTTCTTTTATATTTTTAAC
1 TTTTCTTTTATATTTTTAAC
*
22120 TTTT-TTTT-TATTTTTCA-
1 TTTTCTTTTATATTTTTAAC
22137 TTTTCTTTT
1 TTTTCTTTT
22146 GCTTCTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 4 0.17
20 4 0.17
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTATATTTTTAAC
Found at i:22747 original size:22 final size:22
Alignment explanation
Indices: 22722--22770 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
22712 AGGAGGTCAT
22722 GATGATGATGAAAGTGTTAGTG
1 GATGATGATGAAAGTGTTAGTG
22744 GATGATGATGAAAGTGTTAGTG
1 GATGATGATGAAAGTGTTAGTG
22766 GATGA
1 GATGA
22771 AATGAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.31
Consensus pattern (22 bp):
GATGATGATGAAAGTGTTAGTG
Done.