Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013044.1 Kokia drynarioides strain JFW-HI SEQ_128062, 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: 21305
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Found at i:436 original size:17 final size:17
Alignment explanation
Indices: 416--449 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
406 TTTTACATGA
*
416 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
433 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
450 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:748 original size:24 final size:25
Alignment explanation
Indices: 694--757 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
684 CATGCAGGTT
694 GCAGCATGCATTGGGGCAGCACACG
1 GCAGCATGCATTGGGGCAGCACACG
719 GCAGCA-GCAATTGGGGCAGCA-ACG
1 GCAGCATGC-ATTGGGGCAGCACACG
743 GCAGCATGCATTGGG
1 GCAGCATGCATTGGG
758 AACAGGTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 17 0.46
25 20 0.54
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (25 bp):
GCAGCATGCATTGGGGCAGCACACG
Found at i:1685 original size:39 final size:41
Alignment explanation
Indices: 1605--1688 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 41
1595 AGTTGTGTTG
*
1605 TAATAGTTTGATTCTACATTGTGATTCTTGAACACTATATTTA
1 TAATAGTTTGA-T-TACATTGTGATTCTTAAACACTATATTTA
*
1648 TAATAGTTTGA-TAC-TTGTGATTCTTTAAACA-TGTATTTA
1 TAATAGTTTGATTACATTGTGATTC-TTAAACACTATATTTA
1687 TA
1 TA
1689 CTTTGATTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
39 18 0.47
40 9 0.24
43 11 0.29
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (41 bp):
TAATAGTTTGATTACATTGTGATTCTTAAACACTATATTTA
Found at i:1702 original size:39 final size:38
Alignment explanation
Indices: 1611--1702 Score: 87
Period size: 39 Copynumber: 2.3 Consensus size: 38
1601 GTTGTAATAG
* *
1611 TTTGATTCTACATTGTGATTCTTGAACACTATATTTATA
1 TTTGATTGTAC-TTGTGATTCTTAAACACTATATTTATA
* * * *
1650 ATAGTTTGATACTTGTGATTCTTTAAACA-TGTATTTATA
1 TTTGATTG-TACTTGTGATTC-TTAAACACTATATTTATA
1689 CTTTGATTGTACTT
1 -TTTGATTGTACTT
1703 ATAACACTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
39 27 0.66
40 14 0.34
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (38 bp):
TTTGATTGTACTTGTGATTCTTAAACACTATATTTATA
Found at i:5595 original size:44 final size:44
Alignment explanation
Indices: 5506--5593 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
5496 TAGTGTCGAG
* * *
5506 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
5550 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
5594 TTCAAAGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:7266 original size:18 final size:18
Alignment explanation
Indices: 7243--7277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7233 TTTGTGATCG
7243 AAATTGAAAGTGAAAGTA
1 AAATTGAAAGTGAAAGTA
* *
7261 AAATTGGAATTGAAAGT
1 AAATTGAAAGTGAAAGT
7278 GATATGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTA
Done.