Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003264.1 Kokia drynarioides strain JFW-HI SEQ_115920, 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: 12655
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:4400 original size:23 final size:23
Alignment explanation
Indices: 4374--4426 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
4364 TTTGAAATTT
*
4374 AATTTTTTATTTTTATTTTCAAA
1 AATTTTATATTTTTATTTTCAAA
* **
4397 AATTTAATATTTTTATTTTTTAA
1 AATTTTATATTTTTATTTTCAAA
4420 AATTTTA
1 AATTTTA
4427 AAATTCAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
AATTTTATATTTTTATTTTCAAA
Found at i:5184 original size:25 final size:23
Alignment explanation
Indices: 5155--5204 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
5145 GTTTAAAATA
5155 AATTTATTAATTTCATTATATTTTT
1 AATTTATTAATTT-ATTA-ATTTTT
* *
5180 AATTTTTTAATTTTTTAATTTTT
1 AATTTATTAATTTATTAATTTTT
5203 AA
1 AA
5205 AGGACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 3 0.13
25 12 0.52
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
AATTTATTAATTTATTAATTTTT
Found at i:5186 original size:8 final size:8
Alignment explanation
Indices: 5175--5202 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5165 TTTCATTATA
5175 TTTTTAAT
1 TTTTTAAT
5183 TTTTTAAT
1 TTTTTAAT
5191 TTTTTAAT
1 TTTTTAAT
5199 TTTT
1 TTTT
5203 AAAGGACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTAAT
Found at i:5734 original size:5 final size:5
Alignment explanation
Indices: 5724--5766 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
5714 TTAAATTATC
*
5724 TGAAA TGAAA TGAAA TGAAA TTGTAA TGAAAA TGAAA TGAAA T
1 TGAAA TGAAA TGAAA TGAAA -TGAAA TG-AAA TGAAA TGAAA T
5767 TATTTTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 26 0.76
6 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.26
Consensus pattern (5 bp):
TGAAA
Found at i:5753 original size:11 final size:11
Alignment explanation
Indices: 5724--5767 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
5714 TTAAATTATC
5724 TGAAATGAAA-
1 TGAAATGAAAT
5734 TGAAATGAAAT
1 TGAAATGAAAT
* *
5745 TGTAATGAAAA
1 TGAAATGAAAT
5756 TGAAATGAAAT
1 TGAAATGAAAT
5767 T
1 T
5768 ATTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (11 bp):
TGAAATGAAAT
Found at i:5759 original size:22 final size:21
Alignment explanation
Indices: 5727--5767 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
5717 AATTATCTGA
5727 AATGAAATGAAATGAAATTGT
1 AATGAAATGAAATGAAATTGT
5748 AATGAAAATGAAATGAAATT
1 AATG-AAATGAAATGAAATT
5768 ATTTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (21 bp):
AATGAAATGAAATGAAATTGT
Found at i:6385 original size:33 final size:31
Alignment explanation
Indices: 6325--6385 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
6315 TAAATAATAT
*
6325 TTAAAAATTTTAATTTTAATTTTAAATAGAC
1 TTAAAAATTTTAATGTTAATTTTAAATAGAC
6356 TTAAAAATATATTATATGTTAA-TTTAAATA
1 TTAAAAAT-T-TTA-ATGTTAATTTTAAATA
6386 AATAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 8 0.31
32 1 0.04
33 11 0.42
34 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
TTAAAAATTTTAATGTTAATTTTAAATAGAC
Found at i:10499 original size:27 final size:27
Alignment explanation
Indices: 10469--10520 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
10459 TAAAAAATAT
* *
10469 AAAA-AATAAACCTTTTTATTTTTTTAA
1 AAAACAATAAA-CTTATAATTTTTTTAA
10496 AAAACAATAAACTTATAATTTTTTT
1 AAAACAATAAACTTATAATTTTTTT
10521 TATTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (27 bp):
AAAACAATAAACTTATAATTTTTTTAA
Done.