Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012560.1 Kokia drynarioides strain JFW-HI SEQ_127569, 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: 577970
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 376 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:518031 original size:31 final size:31
Alignment explanation
Indices: 517993--518072 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
517983 TGTTGCAAGA
517993 AACAAGTATACTGGAGTTTTCTTTTACGATC
1 AACAAGTATACTGGAGTTTTCTTTTACGATC
518024 AACAAGTATACTGGAGTTTTCTTTTACGATC
1 AACAAGTATACTGGAGTTTTCTTTTACGATC
*
518055 AACAAGTATACTAGAGTT
1 AACAAGTATACTGGAGTT
518073 GAATACACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (31 bp):
AACAAGTATACTGGAGTTTTCTTTTACGATC
Found at i:521144 original size:24 final size:24
Alignment explanation
Indices: 521117--521174 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
521107 CAAATCTGAA
521117 GCATCTTCACTTTGATAGTTTTCC
1 GCATCTTCACTTTGATAGTTTTCC
521141 GCATCTTCACTTTGATAGTTTTCC
1 GCATCTTCACTTTGATAGTTTTCC
*
521165 ACATCATTCA
1 GCATC-TTCA
521175 AAAATCCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (24 bp):
GCATCTTCACTTTGATAGTTTTCC
Found at i:534387 original size:17 final size:16
Alignment explanation
Indices: 534332--534397 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
534322 AATATATATG
* *
534332 GAAATGCAATGATAAT
1 GAAATGCAATGACAAA
*
534348 GAAGATGCAGTGACAAGA
1 GAA-ATGCAATGACAA-A
*
534366 AAAATGCAATGACAAA
1 GAAATGCAATGACAAA
534382 CGAAATG-AGATGACAA
1 -GAAATGCA-ATGACAA
534398 CTACATGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
16 5 0.12
17 33 0.82
18 2 0.05
ACGTcount: A:0.52, C:0.11, G:0.23, T:0.15
Consensus pattern (16 bp):
GAAATGCAATGACAAA
Found at i:534396 original size:34 final size:34
Alignment explanation
Indices: 534333--534397 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
534323 ATATATATGG
* *
534333 AAATGCAATGATAATGAAGATGCAGTGACAAGAA
1 AAATGCAATGAAAACGAAGATGCAGTGACAAGAA
534367 AAATGCAATGACAAACGAA-ATG-AGATGACAA
1 AAATGCAATGA-AAACGAAGATGCAG-TGACAA
534398 CTACATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 2 0.07
34 20 0.74
35 5 0.19
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (34 bp):
AAATGCAATGAAAACGAAGATGCAGTGACAAGAA
Found at i:540079 original size:91 final size:91
Alignment explanation
Indices: 539922--540098 Score: 264
Period size: 91 Copynumber: 1.9 Consensus size: 91
539912 GGTCTGCTGG
* * * * * *
539922 GAACATAAACTTATCTATGCTGACGAGGAAATCTTTAATTTGTCCCTCAGGTTGCGCTAACGATC
1 GAACACAAACTTATCTACGCTAACGAGGAAATCTTTAATTTGTCCCTCAAGTTGCACTAACAATC
539987 TATCTGCCAACTACAATGTCATTGTA
66 TATCTGCCAACTACAATGTCATTGTA
** *
540013 GAACACAAACTTATCTACGCTAACGAGGACGTCTTTAATTTGTCCCTCAAGTTGCACTAATAATC
1 GAACACAAACTTATCTACGCTAACGAGGAAATCTTTAATTTGTCCCTCAAGTTGCACTAACAATC
*
540078 TATCTGCCAACTGCAATGTCA
66 TATCTGCCAACTACAATGTCA
540099 CTGCAATAGG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (91 bp):
GAACACAAACTTATCTACGCTAACGAGGAAATCTTTAATTTGTCCCTCAAGTTGCACTAACAATC
TATCTGCCAACTACAATGTCATTGTA
Found at i:552939 original size:24 final size:24
Alignment explanation
Indices: 552907--552953 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
552897 AAAATCTTTA
*
552907 AATTAAACTCTGTTTTTTTGTTTC
1 AATTAAACTCTGTTTATTTGTTTC
*
552931 AATTAAACTTTGTTTATTTGTTT
1 AATTAAACTCTGTTTATTTGTTT
552954 GAGTCAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (24 bp):
AATTAAACTCTGTTTATTTGTTTC
Found at i:552962 original size:24 final size:24
Alignment explanation
Indices: 552911--552965 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
552901 TCTTTAAATT
* *
552911 AAACTCTGTTTTTTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* * *
552935 AAACTTTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
552959 AAACTCT
1 AAACTCT
552966 TATTACTCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:554831 original size:24 final size:24
Alignment explanation
Indices: 554799--554845 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
554789 ATAATCTTTA
*
554799 AATTAAACTCTATTTTTTTGTTTC
1 AATTAAACTCTATTTATTTGTTTC
* *
554823 AATTAAACTTTGTTTATTTGTTT
1 AATTAAACTCTATTTATTTGTTT
554846 GAGTCAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (24 bp):
AATTAAACTCTATTTATTTGTTTC
Found at i:559935 original size:39 final size:39
Alignment explanation
Indices: 559878--559958 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
559868 AATTATGACG
559878 TGATAAATAGTTGACTTACCACTTTTGACATCAAACACA
1 TGATAAATAGTTGACTTACCACTTTTGACATCAAACACA
*
559917 TGATAAATAGTTGCCTTACCACTTTTGACATCAAACACA
1 TGATAAATAGTTGACTTACCACTTTTGACATCAAACACA
559956 TGA
1 TGA
559959 GTTCGGTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (39 bp):
TGATAAATAGTTGACTTACCACTTTTGACATCAAACACA
Found at i:562576 original size:62 final size:62
Alignment explanation
Indices: 562479--562599 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
562469 TCACACAACA
*
562479 TGCTTTTCACAAGTATACGGTTTGGGATAAATACTTACTTGATAAAAATCTATGAGGATACG
1 TGCTTTTCACAAGTATACGGTTTGGGATAAATACTTACTTGATAAAAATCCATGAGGATACG
*
562541 TGCTTTTCACAAGTATATGGTTTGGGATAAATACTTACTTGATAAAAATCCATGAGGAT
1 TGCTTTTCACAAGTATACGGTTTGGGATAAATACTTACTTGATAAAAATCCATGAGGAT
562600 TGCTTATTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (62 bp):
TGCTTTTCACAAGTATACGGTTTGGGATAAATACTTACTTGATAAAAATCCATGAGGATACG
Found at i:573846 original size:15 final size:15
Alignment explanation
Indices: 573826--573857 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
573816 TTGTGAAGGG
573826 AATTAATCTAAATTA
1 AATTAATCTAAATTA
*
573841 AATTAATCTAAGTTA
1 AATTAATCTAAATTA
573856 AA
1 AA
573858 AATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
AATTAATCTAAATTA
Done.