Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009398.1 Kokia drynarioides strain JFW-HI SEQ_124105, 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: 247437
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 14 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:234740 original size:48 final size:48
Alignment explanation
Indices: 234664--234824 Score: 187
Period size: 48 Copynumber: 3.4 Consensus size: 48
234654 TATCTGAGTG
* *
234664 GCTGACGAGCGTAAACATATAGTAGCTGACGAGCATAAACGTACAGTA
1 GCTGACGAGCATAAACATATAGTAGCTGACGAGCATAAACGTACAATA
* * *
234712 GCTGACGAGCATAAACATATAGTGGCTGACGAGCATAAACGTATAATG
1 GCTGACGAGCATAAACATATAGTAGCTGACGAGCATAAACGTACAATA
* * * ** * *
234760 GCTGACGAGCATAAACGTACATTAATTGAAGAGCATAAACGTACATTA
1 GCTGACGAGCATAAACATATAGTAGCTGACGAGCATAAACGTACAATA
* * *
234808 GTTGGCGAGCGTAAACA
1 GCTGACGAGCATAAACA
234825 CACTAAACTT
Statistics
Matches: 94, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (48 bp):
GCTGACGAGCATAAACATATAGTAGCTGACGAGCATAAACGTACAATA
Found at i:234776 original size:24 final size:24
Alignment explanation
Indices: 234660--234778 Score: 175
Period size: 24 Copynumber: 5.0 Consensus size: 24
234650 TTTTTATCTG
* *
234660 AGTGGCTGACGAGCGTAAACATAT
1 AGTGGCTGACGAGCATAAACGTAT
* *
234684 AGTAGCTGACGAGCATAAACGTAC
1 AGTGGCTGACGAGCATAAACGTAT
* *
234708 AGTAGCTGACGAGCATAAACATAT
1 AGTGGCTGACGAGCATAAACGTAT
234732 AGTGGCTGACGAGCATAAACGTAT
1 AGTGGCTGACGAGCATAAACGTAT
*
234756 AATGGCTGACGAGCATAAACGTA
1 AGTGGCTGACGAGCATAAACGTA
234779 CATTAATTGA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (24 bp):
AGTGGCTGACGAGCATAAACGTAT
Found at i:234777 original size:72 final size:72
Alignment explanation
Indices: 234660--234799 Score: 208
Period size: 72 Copynumber: 1.9 Consensus size: 72
234650 TTTTTATCTG
* * * *
234660 AGTGGCTGACGAGCGTAAACATATAGTAGCTGACGAGCATAAACGTACAGTAGCTGACGAGCATA
1 AGTGGCTGACGAGCATAAACATATAATAGCTGACGAGCATAAACGTACAGTAACTGAAGAGCATA
234725 AACATAT
66 AACATAT
* * * *
234732 AGTGGCTGACGAGCATAAACGTATAATGGCTGACGAGCATAAACGTACATTAATTGAAGAGCATA
1 AGTGGCTGACGAGCATAAACATATAATAGCTGACGAGCATAAACGTACAGTAACTGAAGAGCATA
234797 AAC
66 AAC
234800 GTACATTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (72 bp):
AGTGGCTGACGAGCATAAACATATAATAGCTGACGAGCATAAACGTACAGTAACTGAAGAGCATA
AACATAT
Found at i:234817 original size:24 final size:24
Alignment explanation
Indices: 234664--234823 Score: 167
Period size: 24 Copynumber: 6.7 Consensus size: 24
234654 TATCTGAGTG
* * *
234664 GCTGACGAGCGTAAACATATAGTA
1 GCTGACGAGCATAAACGTACAGTA
234688 GCTGACGAGCATAAACGTACAGTA
1 GCTGACGAGCATAAACGTACAGTA
* * *
234712 GCTGACGAGCATAAACATATAGTG
1 GCTGACGAGCATAAACGTACAGTA
* * *
234736 GCTGACGAGCATAAACGTATAATG
1 GCTGACGAGCATAAACGTACAGTA
*
234760 GCTGACGAGCATAAACGTACATTA
1 GCTGACGAGCATAAACGTACAGTA
** * *
234784 ATTGAAGAGCATAAACGTACATTA
1 GCTGACGAGCATAAACGTACAGTA
* * *
234808 GTTGGCGAGCGTAAAC
1 GCTGACGAGCATAAAC
234824 ACACTAAACT
Statistics
Matches: 118, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 118 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (24 bp):
GCTGACGAGCATAAACGTACAGTA
Found at i:234817 original size:72 final size:72
Alignment explanation
Indices: 234664--234824 Score: 196
Period size: 72 Copynumber: 2.2 Consensus size: 72
234654 TATCTGAGTG
* * *
234664 GCTGACGAGCGTAAACATATAGTAGCTGACGAGCATAAACGTACAGTAGCTGACGAGCATAAACA
1 GCTGACGAGCGTAAACATATAATAGCTGACGAGCATAAACGTACAGTAACTGAAGAGCATAAACA
* *
234729 TATAGTG
66 TACAGTA
* * * * * *
234736 GCTGACGAGCATAAACGTATAATGGCTGACGAGCATAAACGTACATTAATTGAAGAGCATAAACG
1 GCTGACGAGCGTAAACATATAATAGCTGACGAGCATAAACGTACAGTAACTGAAGAGCATAAACA
*
234801 TACATTA
66 TACAGTA
* *
234808 GTTGGCGAGCGTAAACA
1 GCTGACGAGCGTAAACA
234825 CACTAAACTT
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (72 bp):
GCTGACGAGCGTAAACATATAATAGCTGACGAGCATAAACGTACAGTAACTGAAGAGCATAAACA
TACAGTA
Found at i:236430 original size:40 final size:40
Alignment explanation
Indices: 236385--236593 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
236375 CCATGACTTG
*
236385 GCTTGAATTTCAACACCGGCTCATAGCCTGCTAAGCCGTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTGCTAAGCCGTA
* * * *
236425 GCTTGAGTTTTAACACCGACTCATAGCTTGCTAAGTCGTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTGCTAAGCCGTA
* *
236465 GCTTGAATTTCAACACCGGCTCATA-CCTGCTAAGCTGTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTGCTAAGCCGTA
* ** * *
236504 GCTTTAATTTTAACACTAGCTCATAACCTGCTAAGTCGTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTGCTAAGCCGTA
* * * * *
236544 GCTTGAGTTTTAACACTGGTTCATACCCTGCTAAGCCGAA
1 GCTTGAATTTTAACACCGGCTCATAGCCTGCTAAGCCGTA
*
236584 GTTTGAATTT
1 GCTTGAATTT
236594 ATTCAAACGT
Statistics
Matches: 142, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 32 0.23
40 110 0.77
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (40 bp):
GCTTGAATTTTAACACCGGCTCATAGCCTGCTAAGCCGTA
Found at i:236518 original size:79 final size:80
Alignment explanation
Indices: 236385--236593 Score: 278
Period size: 79 Copynumber: 2.6 Consensus size: 80
236375 CCATGACTTG
* *
236385 GCTTGAATTTCAACACCGGCTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAACACCGA-CTCAT
1 GCTTGAATTTCAACACCGGCTCATACCCTGCTAAGCCGTAGCTTGAATTTTAACA-CGAGCTCAT
* *
236449 AGCTTGCTAAGTCGTA
65 AACCTGCTAAGTCGTA
* * *
236465 GCTTGAATTTCAACACCGGCTCATA-CCTGCTAAGCTGTAGCTTTAATTTTAACACTAGCTCATA
1 GCTTGAATTTCAACACCGGCTCATACCCTGCTAAGCCGTAGCTTGAATTTTAACACGAGCTCATA
236529 ACCTGCTAAGTCGTA
66 ACCTGCTAAGTCGTA
* * * * * *
236544 GCTTGAGTTTTAACACTGGTTCATACCCTGCTAAGCCGAAGTTTGAATTT
1 GCTTGAATTTCAACACCGGCTCATACCCTGCTAAGCCGTAGCTTGAATTT
236594 ATTCAAACGT
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
78 2 0.02
79 66 0.58
80 45 0.40
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (80 bp):
GCTTGAATTTCAACACCGGCTCATACCCTGCTAAGCCGTAGCTTGAATTTTAACACGAGCTCATA
ACCTGCTAAGTCGTA
Found at i:243503 original size:13 final size:13
Alignment explanation
Indices: 243487--243525 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
243477 GATAAAAAGG
243487 GAAAAGAAAAAAA
1 GAAAAGAAAAAAA
*
243500 GAAAAGAAAAGAA
1 GAAAAGAAAAAAA
243513 GAAGAAGATAAAA
1 GAA-AAGA-AAAA
243526 TTAGGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 15 0.68
14 4 0.18
15 3 0.14
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
GAAAAGAAAAAAA
Found at i:246053 original size:59 final size:59
Alignment explanation
Indices: 245936--246056 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 59
245926 TTTCATATCT
* * * * * * **
245936 TATATTTATAATCTCGTTTTTTTTTTTCATAAATTATATATACATTCAAATATTTTATA
1 TATATTTATAATCTCATTTTTTTTCTTAATAAATCATATATAAATTCAAAAAAATTATA
* *
245995 TATATTTATAGTCT-ATTTTTTTTCTTAATAAATCATATATAAATTTGAAAAAAATTATA
1 TATATTTATAATCTCATTTTTTTTCTTAATAAATCATATATAAA-TTCAAAAAAATTATA
246054 TAT
1 TAT
246057 TATATATACA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 24 0.47
59 27 0.53
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (59 bp):
TATATTTATAATCTCATTTTTTTTCTTAATAAATCATATATAAATTCAAAAAAATTATA
Done.