Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013377.1 Kokia drynarioides strain JFW-HI SEQ_128400, 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: 72915
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:361 original size:25 final size:23
Alignment explanation
Indices: 333--378 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
323 GTAGGGTCTA
333 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAATT-T-AAAAAATAATTAG
*
358 AATTAAATTTAAACAATAATT
1 AATTAAATTTAAAAAATAATT
379 CTCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 1 0.05
25 9 0.45
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTAG
Found at i:10937 original size:12 final size:12
Alignment explanation
Indices: 10920--10949 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10910 GATTGTTAAA
10920 AATTAATATTTT
1 AATTAATATTTT
10932 AATTAATATTTT
1 AATTAATATTTT
*
10944 TATTAA
1 AATTAA
10950 AAAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AATTAATATTTT
Found at i:29435 original size:19 final size:20
Alignment explanation
Indices: 29399--29437 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29389 GGAAAACATC
*
29399 CAAAGTTTCACTCTTTAAAA
1 CAAAATTTCACTCTTTAAAA
29419 CAAAATTTCAC-CTTTAAAA
1 CAAAATTTCACTCTTTAAAA
29438 GAAGAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (20 bp):
CAAAATTTCACTCTTTAAAA
Found at i:32574 original size:25 final size:25
Alignment explanation
Indices: 32546--32605 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
32536 TTTATTGGAA
*
32546 ATTTTTATTTTAATATTTTT-AGTGT
1 ATTTTTATATT-ATATTTTTAAGTGT
* * *
32571 ATTTATGTATTATATTTTTAAGTTT
1 ATTTTTATATTATATTTTTAAGTGT
32596 ATTTTATATA
1 ATTTT-TATA
32606 AAAAATAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 8 0.30
25 16 0.59
26 3 0.11
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (25 bp):
ATTTTTATATTATATTTTTAAGTGT
Found at i:33417 original size:6 final size:6
Alignment explanation
Indices: 33401--33431 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
33391 TTTTTTACCA
33401 ATAACAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAA-AT ATAAAT ATAAAT ATAAAT ATAAAT
33432 TGACAACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:36879 original size:29 final size:29
Alignment explanation
Indices: 36812--36880 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
36802 GTAACAAAAT
*
36812 AATAACATAAGTAACTAAAATGTAACATTTC
1 AATAA-ATAAATAACTAAAATGTAACA-TTC
* *
36843 AA-ATATAAATAACTAAAATGTAAC-TTG
1 AATAAATAAATAACTAAAATGTAACATTC
36870 AGATAAATAAA
1 A-ATAAATAAA
36881 AATGACTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 25 0.78
30 1 0.03
31 2 0.06
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.28
Consensus pattern (29 bp):
AATAAATAAATAACTAAAATGTAACATTC
Found at i:39386 original size:29 final size:29
Alignment explanation
Indices: 39331--39429 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 29
39321 AAAATTATAA
*
39331 ATTAATAAA-AATAAAATTATACA-TTAAAC
1 ATTAA-AAATAATAAAAATATA-ATTTAAAC
* *
39360 CTTAAAAATAATAAAAATATAATTTAATC
1 ATTAAAAATAATAAAAATATAATTTAAAC
* *
39389 ATTAAAATATTATAAATAATAAAATATTAAA-
1 ATTAAAA-ATAATAAA-AATATAAT-TTAAAC
39420 ATTATAAAAT
1 ATTA-AAAAT
39430 TATATTTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
28 4 0.07
29 26 0.46
30 7 0.12
31 13 0.23
32 7 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (29 bp):
ATTAAAAATAATAAAAATATAATTTAAAC
Found at i:39412 original size:37 final size:35
Alignment explanation
Indices: 39319--39425 Score: 110
Period size: 35 Copynumber: 2.9 Consensus size: 35
39309 TTGAAATTTT
39319 TTAAA-ATTATAAATTAATAAAAATAAAATTATACA
1 TTAAACATTATAAA-TAATAAAAATAAAATTATACA
* * *
39354 TTAAACCTTAAAAATAATAAAAATATAATT-TAATCA
1 TTAAACATTATAAATAATAAAAATAAAATTAT-A-CA
*
39390 TTAAAATATTATAAATAATAAAATATTAAAATTATA
1 TT-AAACATTATAAATAATAAAA-A-TAAAATTATA
39426 AAATTATATT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
34 1 0.02
35 21 0.36
36 10 0.17
37 17 0.29
38 1 0.02
39 7 0.12
40 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (35 bp):
TTAAACATTATAAATAATAAAAATAAAATTATACA
Found at i:39426 original size:16 final size:17
Alignment explanation
Indices: 39391--39429 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
39381 ATTTAATCAT
39391 TAAAATATTATAAATAA
1 TAAAATATTATAAATAA
*
39408 TAAAATATTA-AAATTA
1 TAAAATATTATAAATAA
39424 TAAAAT
1 TAAAAT
39430 TATATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATATTATAAATAA
Found at i:50464 original size:18 final size:17
Alignment explanation
Indices: 50441--50474 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
50431 TTAAAAAAAA
50441 ATAAAAATGAAAAGATAG
1 ATAAAAAT-AAAAGATAG
50459 ATAAAAATAAAAGATA
1 ATAAAAATAAAAGATA
50475 AAATAGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
ATAAAAATAAAAGATAG
Done.