Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014983.1 Kokia drynarioides strain JFW-HI SEQ_130027, 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: 486004
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 339 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:458847 original size:12 final size:12
Alignment explanation
Indices: 458832--458871 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
458822 GTTGTTTTCG
*
458832 TGTTGTTTTTGT
1 TGTTATTTTTGT
458844 TGTTATTTTTGT
1 TGTTATTTTTGT
*
458856 TGCTATTTTTGT
1 TGTTATTTTTGT
458868 TGTT
1 TGTT
458872 TTTAATGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.05, C:0.03, G:0.20, T:0.72
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:459077 original size:11 final size:12
Alignment explanation
Indices: 459043--459107 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
459033 TTAATATAAA
459043 ATTTTTTAATGT
1 ATTTTTTAATGT
459055 ATTTTAAATTTAAT-T
1 A-TTT---TTTAATGT
459070 ATTTTTTAATGT
1 ATTTTTTAATGT
*
459082 TTTTTTTAATG-
1 ATTTTTTAATGT
*
459093 -TTTTTAAATGT
1 ATTTTTTAATGT
459104 ATTT
1 ATTT
459108 GATATATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
10 9 0.20
11 6 0.14
12 15 0.34
13 3 0.07
14 3 0.07
15 2 0.05
16 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (12 bp):
ATTTTTTAATGT
Found at i:459088 original size:12 final size:12
Alignment explanation
Indices: 459044--459097 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 12
459034 TAATATAAAA
459044 TTTTTTAATGTAT
1 TTTTTTAATGT-T
*
459057 TTTAAATTTAAT-TA
1 TTT---TTTAATGTT
459071 TTTTTTAATGTT
1 TTTTTTAATGTT
459083 TTTTTTAATGTT
1 TTTTTTAATGTT
459095 TTT
1 TTT
459098 AAATGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 6 0.17
12 16 0.46
13 3 0.09
14 3 0.09
15 1 0.03
16 6 0.17
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (12 bp):
TTTTTTAATGTT
Found at i:459125 original size:38 final size:39
Alignment explanation
Indices: 459043--459128 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 39
459033 TTAATATAAA
* * * *
459043 ATTTTTTAATGTATTTTAAATTTAATTATTTTTTAATGT
1 ATTTTTTAATGTATTTTAAATGTAATTATATATTAATAT
* *
459082 TTTTTTTAATGT-TTTTAAATGTATTTGATATATT-ATAT
1 ATTTTTTAATGTATTTTAAATGTAATT-ATATATTAATAT
459120 ATTTTTTAA
1 ATTTTTTAA
459129 ATTTGTTGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 23 0.59
39 16 0.41
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (39 bp):
ATTTTTTAATGTATTTTAAATGTAATTATATATTAATAT
Found at i:462894 original size:29 final size:28
Alignment explanation
Indices: 462841--462902 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
462831 AATAGTCTAT
462841 ATTTTTATTTTTTTAAGAATTAAAT-TAA
1 ATTTTTATTTTTTTAAGAATTAAATGT-A
* **
462869 ATTTTTATTTTTTTTAGTGTTAAAATGTA
1 ATTTTTATTTTTTTAAGAATT-AAATGTA
462898 ATTTT
1 ATTTT
462903 ACCATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 18 0.62
29 10 0.34
30 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (28 bp):
ATTTTTATTTTTTTAAGAATTAAATGTA
Found at i:463571 original size:95 final size:95
Alignment explanation
Indices: 463465--463660 Score: 322
Period size: 95 Copynumber: 2.1 Consensus size: 95
463455 AATCATATTT
*
463465 AATAAATAATAAATTAATTTAGGTAACTTTATTAAATATGATTGATCGGATTTAATATTTTTATG
1 AATAAACAATAAATTAATTTAGGTAACTTTATTAAATATGATTGATCGGATTTAATATTTTTATG
463530 GT-AAATAATTTTTTCTTAAATGATTGATTG
66 GTAAAAT-ATTTTTTCTTAAATGATTGATTG
* *
463560 AATAAACAATAAATTAATTTAGGTAACTTTATTAAATATGATTTATTGGATTTAATATTTTTATG
1 AATAAACAATAAATTAATTTAGGTAACTTTATTAAATATGATTGATCGGATTTAATATTTTTATG
* * *
463625 TTAAAATTTTTTTTTTTAAATGATTGATTG
66 GTAAAATATTTTTTCTTAAATGATTGATTG
463655 AATAAA
1 AATAAA
463661 AAAATTAAGA
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 90 0.96
96 4 0.04
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (95 bp):
AATAAACAATAAATTAATTTAGGTAACTTTATTAAATATGATTGATCGGATTTAATATTTTTATG
GTAAAATATTTTTTCTTAAATGATTGATTG
Done.