Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013398.1 Kokia drynarioides strain JFW-HI SEQ_128422, 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: 14080
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Found at i:6240 original size:22 final size:20
Alignment explanation
Indices: 6215--6265 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
6205 CATGTATATA
6215 AAATATTAATAATTATTTTATT
1 AAATATTAATAATTA-TTTA-T
* *
6237 AAATAATAAAAATTATTTAT
1 AAATATTAATAATTATTTAT
6257 AAA-ATTAAT
1 AAATATTAAT
6266 TTTATTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.16
20 4 0.16
21 4 0.16
22 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATTAATAATTATTTAT
Found at i:6302 original size:36 final size:35
Alignment explanation
Indices: 6225--6291 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
6215 AAATATTAAT
6225 AATT-ATTTTATTAAATAATAAAAATTATTTATAA
1 AATTAATTTTATTAAATAATAAAAATTATTTATAA
* * *
6259 AATTAATTTTATTAAGTAGTAAATACTTATTTA
1 AATTAATTTTATTAAATAATAAA-AATTATTTA
6292 ATAAGATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 4 0.14
35 16 0.57
36 8 0.29
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (35 bp):
AATTAATTTTATTAAATAATAAAAATTATTTATAA
Found at i:6402 original size:23 final size:25
Alignment explanation
Indices: 6376--6429 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
6366 TTTTTGAATC
6376 TAATTAT-AAATACATATA-AATA-T
1 TAATTATAAAAT-CATATATAATATT
6399 TAA-TATAAAATCATATATAATATT
1 TAATTATAAAATCATATATAATATT
6423 TAATTAT
1 TAATTAT
6430 TTAAAGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 9 0.33
23 11 0.41
24 4 0.15
25 3 0.11
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATTATAAAATCATATATAATATT
Found at i:10647 original size:19 final size:19
Alignment explanation
Indices: 10602--10647 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
10592 GAATTAATCA
10602 ATTAAAAATGATTTATTTT
1 ATTAAAAATGATTTATTTT
*
10621 ATTGAAAATGATTTATTCTT
1 ATTAAAAATGATTTATT-TT
10641 -TTAAAAA
1 ATTAAAAA
10648 AATTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (19 bp):
ATTAAAAATGATTTATTTT
Found at i:10889 original size:17 final size:17
Alignment explanation
Indices: 10850--10909 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
10840 ACCCTAACAG
**
10850 AATTTAAATTTATTTTA
1 AATTTAAATTTATAATA
*
10867 AGTTTAAATTTATAATA
1 AATTTAAATTTATAATA
*
10884 AATTTAAAGTTTA-AATT
1 AATTTAAA-TTTATAATA
*
10901 TATTTAAAT
1 AATTTAAAT
10910 AATGTCCAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 1 0.03
17 31 0.86
18 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATAATA
Found at i:11683 original size:3 final size:3
Alignment explanation
Indices: 11675--11761 Score: 86
Period size: 3 Copynumber: 28.0 Consensus size: 3
11665 TAGTTTTATA
* * ** *
11675 AAT AAT AAT AAC ATT AAT AAT AA- ACAGT AAT AAT AATT AGC ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AA-T AAT AAT AAT
11722 AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11762 TATTATTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
2 1 0.01
3 62 0.89
4 6 0.09
5 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11705 original size:13 final size:13
Alignment explanation
Indices: 11677--11710 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11667 GTTTTATAAA
*
11677 TAATAAT-AACAT
1 TAATAATAAACAG
11689 TAATAATAAACAG
1 TAATAATAAACAG
11702 TAATAATAA
1 TAATAATAA
11711 TTAGCATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (13 bp):
TAATAATAAACAG
Done.