Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000273.1 Kokia drynarioides strain JFW-HI SEQ_111019, 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: 7493
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:3238 original size:124 final size:124
Alignment explanation
Indices: 3018--3264 Score: 309
Period size: 124 Copynumber: 2.0 Consensus size: 124
3008 ACTTCCAAAG
* * *
3018 GTCATCTTCTTGATAATATACAGAAAAGTGGACCAAAATAATGAAGCAAAACTCAATATAAGTGA
1 GTCATCTTCTTGATAAGATACAGAAAAGTGGACCAAAATAATAAAGCAAAACTCAACATAAGTGA
* * * *
3083 AACTTCAAAACCCCATCATCTTGATGAGATACAGAGAAGTGGATCAAAACTATGAAGCA
66 AACTTCAAAACCCCATCATCCTGATGAGATACAGAGAAGTCGACCAAAACAATGAAGCA
* * * *** * * *
3142 GTCATCTTCTTGATGAGATACA-AAGAAGTGGTCCAAAATTATAAAGTGGAGCTCAACATGAGTN
1 GTCATCTTCTTGATAAGATACAGAA-AAGTGGACCAAAATAATAAAGCAAAACTCAACATAAGTG
*
3206 AAACTTCAAACCCCCAT-ATTCCTGATGAGATACAGAGAAGTCGACCAAAACAATGAAGC
65 AAACTTCAAAACCCCATCA-TCCTGATGAGATACAGAGAAGTCGACCAAAACAATGAAGC
3265 GAGGCTCAAT
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
123 3 0.03
124 101 0.97
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.22
Consensus pattern (124 bp):
GTCATCTTCTTGATAAGATACAGAAAAGTGGACCAAAATAATAAAGCAAAACTCAACATAAGTGA
AACTTCAAAACCCCATCATCCTGATGAGATACAGAGAAGTCGACCAAAACAATGAAGCA
Found at i:3280 original size:76 final size:75
Alignment explanation
Indices: 3144--3417 Score: 280
Period size: 76 Copynumber: 3.6 Consensus size: 75
3134 ATGAAGCAGT
* * * * * * * * * ** *
3144 CATCTTCTTGATGAGATACAAAGAAGTGGTCCAAAATTATAAAGTGGAGCTCAACATGAGTNAAA
1 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAAA-AATGAAGCGAAACTCAATGTGAGTAAAA
3209 CTTCAAACCCC
65 CTTCAAACCCC
* * * **
3220 CATATTCCTGATGAGATACAGAGAAGTCGACCAAAACAATGAAGCGAGGCTCAATGTGAGTAAAA
1 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAAA-AATGAAGCGAAACTCAATGTGAGTAAAA
*
3285 CTTCAAACCCA
65 CTTCAAACCCC
** * *
3296 CATCTTTTTGATGAGATATAGAGAAGTGGATCGAAAAAATGAAGCGAAACTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATATAGAGAAGTGGA-CCAAAAAATGAAGCGAAACTCAATGTGAGTAAAA
*
3361 CTTTAAA-CCC
65 CTTCAAACCCC
* *
3371 CATCTTCCTAATGAGATATAGAGAAGTGGATCAAAATAATGAAGCGA
1 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAAA-AATGAAGCGA
3418 TTATCTTCCT
Statistics
Matches: 165, Mismatches: 31, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
74 4 0.02
75 39 0.24
76 117 0.71
77 5 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (75 bp):
CATCTTCCTGATGAGATATAGAGAAGTGGACCAAAAAATGAAGCGAAACTCAATGTGAGTAAAAC
TTCAAACCCC
Found at i:3413 original size:75 final size:74
Alignment explanation
Indices: 3200--3417 Score: 283
Period size: 76 Copynumber: 2.9 Consensus size: 74
3190 GAGCTCAACA
* * * * *
3200 TGAGTNAAACTTCAAACCCCCATATTCCTGATGAGATACAGAGAAGTCGACCAAAACAATGAAGC
1 TGAGTAAAACTTCAAA-CCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAA-AATGAAGC
**
3265 GAGGCTCAATG
64 GAAACTCAATG
**
3276 TGAGTAAAACTTCAAACCCACATCTTTTTGATGAGATATAGAGAAGTGGATCGAAAAAATGAAGC
1 TGAGTAAAACTTCAAACCC-CATCTTCCTGATGAGATATAGAGAAGTGGATC-AAAAAATGAAGC
3341 GAAACTCAATG
64 GAAACTCAATG
* * *
3352 TGAGTGAAACTTTAAACCCCATCTTCCTAATGAGATATAGAGAAGTGGATCAAAATAATGAAGCG
1 TGAGTAAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAA-AATGAAGCG
3417 A
65 A
3418 TTATCTTCCT
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
74 4 0.03
75 42 0.34
76 75 0.60
77 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (74 bp):
TGAGTAAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAAAATGAAGCGA
AACTCAATG
Found at i:3529 original size:123 final size:123
Alignment explanation
Indices: 3304--3529 Score: 267
Period size: 123 Copynumber: 1.8 Consensus size: 123
3294 CACATCTTTT
* * * * *
3304 TGATGAGATATAGAGAAGTGGATCGAAAAAATGAAGCGAAACTCAATGTGAGTGAAACTTTAAAC
1 TGATGAGATATAGAGAAGTAGACCGAAAAAATAAAGCGAAACTCAATGAGAGTGAAACTTCAAAC
* * * * * *
3369 CCCATCTTCCTAATGAGATATAGAGAAGTGGATCAAAATAATGAAGCGATTATCTTCC
66 CCCATCTTCCTAATAAGATACAAAAAAGAGGACCAAAATAATGAAGCGATTATCTTCC
* * *
3427 TGATGAGATATAGAGAAGTAGACC-AGAATAATAAAGTCG-AGCTCAATGAGAGTGAAACTTCGA
1 TGATGAGATATAGAGAAGTAGACCGA-AAAAATAAAG-CGAAACTCAATGAGAGTGAAACTTCAA
* * *
3490 ACCCTATCTTCCTGATAAGGTACAAAAAAGAGGACCAAAA
64 ACCCCATCTTCCTAATAAGATACAAAAAAGAGGACCAAAA
3530 GATGAAGATA
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
122 1 0.01
123 81 0.96
124 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (123 bp):
TGATGAGATATAGAGAAGTAGACCGAAAAAATAAAGCGAAACTCAATGAGAGTGAAACTTCAAAC
CCCATCTTCCTAATAAGATACAAAAAAGAGGACCAAAATAATGAAGCGATTATCTTCC
Found at i:5265 original size:30 final size:30
Alignment explanation
Indices: 5214--5419 Score: 165
Period size: 30 Copynumber: 6.9 Consensus size: 30
5204 ATAAATTACA
* *
5214 TTTTAACCTTCAAACTATCCAAAAATTATG
1 TTTTAACCCTCAAACTTTCCAAAAATTATG
* * *
5244 TTTTGACCCTCGAACTGTCCAAAAATT-TGG
1 TTTTAACCCTCAAACTTTCCAAAAATTAT-G
** * * *
5274 AATTAACCCCCAAAATTTCCAAAAATTATA
1 TTTTAACCCTCAAACTTTCCAAAAATTATG
*
5304 TTTTAACCCT-AAACTTTCCAAAAATTAAG
1 TTTTAACCCTCAAACTTTCCAAAAATTATG
*
5333 TTTTAACCC-CTAAACTTAT-C-AAAATTAAG
1 TTTTAACCCTC-AAACTT-TCCAAAAATTATG
* *
5362 TTTTGACCCCCAAACTTTCCAAAAAATT-TGG
1 TTTTAACCCTCAAACTTTCC-AAAAATTAT-G
* *
5393 ATTTAA-CCTCTAAATTTTCCAAAAATT
1 TTTTAACCCTC-AAACTTTCCAAAAATT
5420 TAAATTTAGC
Statistics
Matches: 141, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
28 1 0.01
29 50 0.35
30 69 0.49
31 21 0.15
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (30 bp):
TTTTAACCCTCAAACTTTCCAAAAATTATG
Found at i:5322 original size:29 final size:29
Alignment explanation
Indices: 5206--5441 Score: 130
Period size: 30 Copynumber: 7.9 Consensus size: 29
5196 TTTTATTTAT
* * *
5206 AAATTACATTTTAACCTTCAAACTATCCAA
1 AAATTATATTTTAACCCT-AAACTTTCCAA
* * * *
5236 AAATTATGTTTTGACCCTCGAACTGTCCAA
1 AAATTATATTTTAACCCT-AAACTTTCCAA
* * *
5266 AAATT-TGGA-ATTAACCCCCAAAATTTCCAA
1 AAATTAT--ATTTTAA-CCCTAAACTTTCCAA
5296 AAATTATATTTTAACCCTAAACTTTCCAA
1 AAATTATATTTTAACCCTAAACTTTCCAA
5325 AAATTA-AGTTTTAACCCCTAAACTTAT-C-A
1 AAATTATA-TTTTAA-CCCTAAACTT-TCCAA
* *
5354 AAATTA-AGTTTTGACCCCCAAACTTTCCAAA
1 AAATTATA-TTTT-AACCCTAAACTTTCC-AA
*
5385 AAATT-TGGA-TTTAACCTCTAAATTTTCCAA
1 AAATTAT--ATTTTAACC-CTAAACTTTCCAA
* *
5415 AAATT-TAAATTTAGCCCCTAAACTTTC
1 AAATTAT-ATTTTA-ACCCTAAACTTTC
5442 TAAACTTTCT
Statistics
Matches: 164, Mismatches: 24, Indels: 36
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.01
29 51 0.31
30 85 0.52
31 25 0.15
33 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (29 bp):
AAATTATATTTTAACCCTAAACTTTCCAA
Found at i:5420 original size:30 final size:30
Alignment explanation
Indices: 5256--5441 Score: 164
Period size: 30 Copynumber: 6.2 Consensus size: 30
5246 TTGACCCTCG
* * * *
5256 AACTGTCCAAAAATTTGGAATTAACCCCCA
1 AACTTTCCAAAAATTTAGATTTAACCCCTA
* *
5286 AAATTTCCAAAAATTATA-TTTTAA-CCCTA
1 AACTTTCCAAAAATT-TAGATTTAACCCCTA
* *
5315 AACTTTCCAAAAATTAAGTTTTAACCCCTA
1 AACTTTCCAAAAATTTAGATTTAACCCCTA
* * * *
5345 AACTTAT-C-AAAATTAAGTTTTGACCCCCA
1 AACTT-TCCAAAAATTTAGATTTAACCCCTA
* *
5374 AACTTTCCAAAAAATTTGGATTTAACCTCTA
1 AACTTTCC-AAAAATTTAGATTTAACCCCTA
* * *
5405 AATTTTCCAAAAATTTAAATTTAGCCCCTA
1 AACTTTCCAAAAATTTAGATTTAACCCCTA
5435 AACTTTC
1 AACTTTC
5442 TAAACTTTCT
Statistics
Matches: 127, Mismatches: 22, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.02
29 49 0.39
30 52 0.41
31 24 0.19
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (30 bp):
AACTTTCCAAAAATTTAGATTTAACCCCTA
Done.