Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004500.1 Kokia drynarioides strain JFW-HI SEQ_117938, 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: 28970
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1950 original size:18 final size:19
Alignment explanation
Indices: 1908--1950 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1898 TGTTTACCAA
1908 AAAAATTTATGACCAAGTT
1 AAAAATTTATGACCAAGTT
1927 AGAAAATTT-T-ACCAAGTT
1 A-AAAATTTATGACCAAGTT
1945 CAAAAA
1 -AAAAA
1951 CTGAAGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 12 0.55
19 3 0.14
20 7 0.32
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (19 bp):
AAAAATTTATGACCAAGTT
Found at i:5564 original size:24 final size:25
Alignment explanation
Indices: 5513--5609 Score: 69
Period size: 24 Copynumber: 4.0 Consensus size: 25
5503 GTCAGTTGAT
*
5513 GACGACGAGGACGA-GGATGATGAA
1 GACGACGAGGACGACGGATGAAGAA
**
5537 GACGACGAGGACGACGG-TGAAGGC
1 GACGACGAGGACGACGGATGAAGAA
* * * * *
5561 GACGGCGATGACGAC-GACGACGAT
1 GACGACGAGGACGACGGATGAAGAA
*
5585 GACGAC-AGTGATGAC-GATGAAGAA
1 GACGACGAG-GACGACGGATGAAGAA
5609 G
1 G
5610 GTGAAGAAGA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.40, T:0.08
Consensus pattern (25 bp):
GACGACGAGGACGACGGATGAAGAA
Found at i:5578 original size:15 final size:15
Alignment explanation
Indices: 5540--5590 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
5530 TGATGAAGAC
* *
5540 GACGAGGACGACGGT
1 GACGACGACGACGAT
* * *
5555 GAAGGCGACGGCGAT
1 GACGACGACGACGAT
5570 GACGACGACGACGAT
1 GACGACGACGACGAT
5585 GACGAC
1 GACGAC
5591 AGTGATGACG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.41, T:0.06
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:6385 original size:21 final size:21
Alignment explanation
Indices: 6336--6385 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
6326 ATTTTGAACC
* * *
6336 AGAAGAAAATGGTGAAGAGGA
1 AGAAGAAGATGATGAAGACGA
6357 AGAAGAAGATGATGAAGACGA
1 AGAAGAAGATGATGAAGACGA
*
6378 TGAAGAAG
1 AGAAGAAG
6386 GTAGTGGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.36, T:0.10
Consensus pattern (21 bp):
AGAAGAAGATGATGAAGACGA
Found at i:6706 original size:9 final size:9
Alignment explanation
Indices: 6692--6718 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6682 TGTGGTAATT
6692 ATATTTTGG
1 ATATTTTGG
6701 ATATTTTGG
1 ATATTTTGG
6710 ATATTTTGG
1 ATATTTTGG
6719 TTAATGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (9 bp):
ATATTTTGG
Found at i:8148 original size:27 final size:26
Alignment explanation
Indices: 8100--8152 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
8090 AAAAAATGTT
*
8100 AAATTGTTTAAATTTAATTTTATAAAA
1 AAATTATTTAAATTTAATTTTA-AAAA
8127 AAATTATTTAAATATTAA-TTTAAAAA
1 AAATTATTTAAAT-TTAATTTTAAAAA
8153 TAACATAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATTATTTAAATTTAATTTTAAAAA
Found at i:9661 original size:49 final size:49
Alignment explanation
Indices: 9589--9686 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
9579 TATTATTATT
9589 ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
1 ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
* * *
9638 ATTAAAAAAAAGTTATTGGATTCAAAGGTTATGATTTGCATGAAAACCA
1 ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
9687 GAAAAATACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (49 bp):
ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
Found at i:14078 original size:30 final size:30
Alignment explanation
Indices: 14037--14112 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
14027 GGGTACTTTC
* **
14037 ACTTCTAAATAGTTTAATGACTTAATTGAA
1 ACTTTTAAATAGTTTAATGACTTAATAAAA
*
14067 ACTTTTAAATAGTTCAATGACTTAATAAAA
1 ACTTTTAAATAGTTTAATGACTTAATAAAA
*
14097 ACTTTTGAATAGTTTA
1 ACTTTTAAATAGTTTA
14113 GTGATCATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (30 bp):
ACTTTTAAATAGTTTAATGACTTAATAAAA
Found at i:15997 original size:10 final size:11
Alignment explanation
Indices: 15977--16001 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15967 TCGATCTTGT
15977 AAATAAAAAAA
1 AAATAAAAAAA
15988 AAATAAAAAAA
1 AAATAAAAAAA
15999 AAA
1 AAA
16002 CACCATCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAATAAAAAAA
Done.