Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014184.1 Kokia drynarioides strain JFW-HI SEQ_129217, 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: 345611
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:326131 original size:20 final size:20
Alignment explanation
Indices: 326048--326127 Score: 94
Period size: 19 Copynumber: 4.0 Consensus size: 20
326038 AGGACCAAGA
*
326048 GAAGAAGAGAAAGAAGAAAAG
1 GAAGAGGAG-AAGAAGAAAAG
326069 GAAGAGGAGAAGAA-AAAAGG
1 GAAGAGGAGAAGAAGAAAA-G
* *
326089 GAAG-GAATAAGAAGAAAAG
1 GAAGAGGAGAAGAAGAAAAG
326108 GAAGAGGAGAAGAA-AAAAG
1 GAAGAGGAGAAGAAGAAAAG
326127 G
1 G
326128 GAAGGAATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 22 0.43
20 21 0.41
21 8 0.16
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.01
Consensus pattern (20 bp):
GAAGAGGAGAAGAAGAAAAG
Found at i:326673 original size:18 final size:20
Alignment explanation
Indices: 326630--326674 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 20
326620 TTAGTAAGAT
326630 AAAAAAAGAGAGAAAATGAA
1 AAAAAAAGAGAGAAAATGAA
326650 AGAAAAAAG-GA-AAAA-GAA
1 A-AAAAAAGAGAGAAAATGAA
326668 GAAAAAA
1 -AAAAAA
326675 TATATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 3 0.13
21 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAGAGAAAATGAA
Found at i:331816 original size:21 final size:21
Alignment explanation
Indices: 331770--331829 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
331760 ATAAGCACAC
331770 TCAGATGCATCCACAACAAAG
1 TCAGATGCATCCACAACAAAG
* *
331791 CCAGATGCATCCACACCAGAA-
1 TCAGATGCATCCACAACA-AAG
331812 TCAGATGCAGT-CACAACA
1 TCAGATGCA-TCCACAACA
331830 CTCGTCAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.40, C:0.32, G:0.15, T:0.13
Consensus pattern (21 bp):
TCAGATGCATCCACAACAAAG
Found at i:339857 original size:30 final size:30
Alignment explanation
Indices: 339817--339877 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
339807 CAAATAGGAC
*
339817 TATACGAGATTTTGTAGTACATGTCTTGGA
1 TATACAAGATTTTGTAGTACATGTCTTGGA
*
339847 TATACAAGATTTTGTAGTACCTGTCTTGGA
1 TATACAAGATTTTGTAGTACATGTCTTGGA
339877 T
1 T
339878 GATTTACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41
Consensus pattern (30 bp):
TATACAAGATTTTGTAGTACATGTCTTGGA
Found at i:340946 original size:21 final size:21
Alignment explanation
Indices: 340900--340950 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
340890 ATAAGCATGC
*
340900 TCAGATGCATCCACAATAAAG
1 TCAGATGCATCCACAACAAAG
* *
340921 CCAGATGCATCCACACCAGAA-
1 TCAGATGCATCCACAACA-AAG
340942 TCAGATGCA
1 TCAGATGCA
340951 GTCATAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (21 bp):
TCAGATGCATCCACAACAAAG
Found at i:342512 original size:95 final size:95
Alignment explanation
Indices: 342345--342576 Score: 383
Period size: 95 Copynumber: 2.4 Consensus size: 95
342335 ACCTTAACTA
* *
342345 AAGCACAGGTAAACTATACGACTACTGAGAAGGAATTACTAGCACTAGCTTTTCCCTCTAATTCG
1 AAGCACAGGTAAACTATACGACTACTGAGAAGGAATTACTAGCACTAGCTTTTCACTCTAATTCA
342410 TTAACTCGTCAATGCAAAATCAACATGTTC
66 TTAACTCGTCAATGCAAAATCAACATGTTC
* * * * *
342440 AAGGACAGGTAAACTATACGACTACTGAGAAGGAATTACTATCAGTAGTTTTTCAGTCTAATTCA
1 AAGCACAGGTAAACTATACGACTACTGAGAAGGAATTACTAGCACTAGCTTTTCACTCTAATTCA
342505 TTAACTCGTCAATGCAAAATCAACATGTTC
66 TTAACTCGTCAATGCAAAATCAACATGTTC
* *
342535 AAGCACAAGTAAACTATATGACTACTGAGAAGGAATTACTAG
1 AAGCACAGGTAAACTATACGACTACTGAGAAGGAATTACTAG
342577 TAAAACCTTA
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 126 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (95 bp):
AAGCACAGGTAAACTATACGACTACTGAGAAGGAATTACTAGCACTAGCTTTTCACTCTAATTCA
TTAACTCGTCAATGCAAAATCAACATGTTC
Done.