Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014339.1 Kokia drynarioides strain JFW-HI SEQ_129376, 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, 991
Length: 1652
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.28
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:411 original size:216 final size:215
Alignment explanation
Indices: 1--1148 Score: 1306
Period size: 216 Copynumber: 5.3 Consensus size: 215
* *
1 AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCGTA
1 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTA
* *** * * * * *
66 AAAGTTTGCCAAAGTTTGGTAGTTCATCCAAAAACCAAGATAGAAACAACTCTCACGTAAATAAG
66 AAACTTCATC-AAGTTTGGAAGTTCGTCCAAGAA-CAAGAAAGAAACAACTCTCACGTAAATAAC
* * * * * * ** * *
131 TTTTTCATTCAAAGGCGAAAAGTAGTTTTGATAATGACAAAG-TATTTAGACTAAATTATGCGAT
129 TTTTTAATTTATAGACCAAAAGTTGTTTACA-AATGACAAAGCTATTTAGACCAAATGATGCGAT
* * **
195 TTCCCGAGCATGAAATGTTCAGA
193 TTCACGAGCATGGAATGTTTGGA
* *
218 AAATTGTTGGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTA
1 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTA
* * **
283 AAACTTCATCAAGTTTGGAAGTTCATCCAAGAATAGAGTTAGAAA-AAGCTCTCACGTAAATAAC
66 AAACTTCATCAAGTTTGGAAGTTCGTCCAAGAACA-AGAAAGAAACAA-CTCTCACGTAAATAAC
347 TTTTTAATTTATAGACCAAAAGTTGTTTACAAATTGA-AAAGCTATTTAGACCAAATGATGCGAT
129 TTTTTAATTTATAGACCAAAAGTTGTTTACAAA-TGACAAAGCTATTTAGACCAAATGATGCGAT
*
411 TTCACAAGCATGGAATGTTTGGA
193 TTCACGAGCATGGAATGTTTGGA
* * *
434 AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCATA
1 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTA
* * * * * *
499 AAA-TTTACCAAAGTTTGGAAGTTCGTCCAAAAACCAAGAAAGAAACAACTCTCATGTACATAAG
66 AAACTTCATC-AAGTTTGGAAGTTCGTCCAAGAA-CAAGAAAGAAACAACTCTCACGTAAATAAC
* * * *** * * * * *
563 TTTTTCATTCAAAGGTAAAAAGTAGTTTAGATAATGACAAAG-TATTTAGACTAAATTATGCAAT
129 TTTTTAATTTATAGACCAAAAGTTGTTTACA-AATGACAAAGCTATTTAGACCAAATGATGCGAT
* * **
627 TTCTCGAGCATGAAATGTTCAGA
193 TTCACGAGCATGGAATGTTTGGA
* * *
650 AAATTGTTCGAAGGAATGGATCATCATGAATACATTATGGAACTGAAGTTATAAAAGAACTCGTA
1 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTA
* *
715 AAACTTCATCAAGTTCGGAAGTTCGTCCAAGAACAGAGTAAGAAACAACTCTCACGTAAATAACT
66 AAACTTCATCAAGTTTGGAAGTTCGTCCAAGAACA-AGAAAGAAACAACTCTCACGTAAATAACT
**
780 TTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAA-CTATTTAGACCAAATGATATGATT
130 TTTTAATTTATAGACCAAAAGTTGTTTAC-AAATGACAAAGCTATTTAGACCAAATGATGCGATT
* * *
844 TCCCGTGCATGGAATATTTGGA
194 TCACGAGCATGGAATGTTTGGA
* * * * * *
866 AAATTGCTGGAAGGAATGGATTGTCGTGAATACTTTAAGGAACTAAAGTTCTAAAAGAACTCGTA
1 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTA
* * * * * *** * *
931 AAACTTCATCAAGTTCGAAAGTTCGTCCAAGAATAAAGAGAGAAATAACGAACTCGTAAATATC-
66 AAACTTCATCAAGTTTGGAAGTTCGTCCAAGAA-CAAGAAAGAAACAACTCTCACGTAAATAACT
995 TTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAA-CTATTTAGACCAAATGATGCGATT
130 TTTTAATTTATAGACCAAAAGTTGTTTAC-AAATGACAAAGCTATTTAGACCAAATGATGCGATT
*
1059 TCATGAGCATGGAATGTTTGGA
194 TCACGAGCATGGAATGTTTGGA
* * * * * *
1081 AAATTGCTTGAAGGAATGGATTGTCATGAATACTTTAAGGAAC-GAATGTTATAGATGAACTGGT
1 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAA-GTTATAAAAGAACTCGT
1145 AAAA
65 AAAA
1149 GTTTTCCNNN
Statistics
Matches: 792, Mismatches: 124, Indels: 32
0.84 0.13 0.03
Matches are distributed among these distances:
214 2 0.00
215 153 0.19
216 555 0.70
217 82 0.10
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (215 bp):
AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTA
AAACTTCATCAAGTTTGGAAGTTCGTCCAAGAACAAGAAAGAAACAACTCTCACGTAAATAACTT
TTTAATTTATAGACCAAAAGTTGTTTACAAATGACAAAGCTATTTAGACCAAATGATGCGATTTC
ACGAGCATGGAATGTTTGGA
Found at i:805 original size:432 final size:431
Alignment explanation
Indices: 1--1148 Score: 1567
Period size: 432 Copynumber: 2.7 Consensus size: 431
1 AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCGTA
1 AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCGTA
* * * * *
66 AAAGTTTGCCAAAGTTTGGTAGTTCATCCAAAAACCAAGATAGAAACAACTCTCACGTAAATAAG
66 AAACTTTACCAAAGTTTGGAAGTTCGTCCAAAAACCAAGAAAGAAACAACTCTCA-GTAAATAAG
* *
131 TTTTTCATTCAAAGGCGAAAAGTAGTTTTGATAATGACAAAGTATTTAGACTAAATTATGCGATT
130 TTTTTCATTCAAAGGCAAAAAGTAGTTTAGATAATGACAAAGTATTTAGACTAAATTATGCGATT
*
196 TCCCGAGCATGAAATGTTCAGAAAATTGTTGGAAGGAATGGATCGTCATGAATACTTTATGGAAC
195 TCTCGAGCATGAAATGTTCAGAAAATTGTT-GAAGGAATGGATCGTCATGAATACTTTATGGAAC
* * *
261 TGAAGTTATAAAAGAACTCGTAAAACTTCATCAAGTTTGGAAGTTCATCCAAGAATAGAGTTAGA
259 TGAAGTTATAAAAGAACTCGTAAAACTTCATCAAGTTCGGAAGTTCATCCAAGAACAGAGTAAGA
*
326 AAAAGCTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAATTGA-AAAGCT
324 AAAAGCTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAA-CT
* *
390 ATTTAGACCAAATGATGCGATTTCACAAGCATGGAATGTTTGGA
388 ATTTAGACCAAATGATACGATTTCACAAGCATGGAATATTTGGA
*
434 AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCATA
1 AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCGTA
*
499 AAA-TTTACCAAAGTTTGGAAGTTCGTCCAAAAACCAAGAAAGAAACAACTCTCATGTACATAAG
66 AAACTTTACCAAAGTTTGGAAGTTCGTCCAAAAACCAAGAAAGAAACAACTCTCA-GTAAATAAG
* *
563 TTTTTCATTCAAAGGTAAAAAGTAGTTTAGATAATGACAAAGTATTTAGACTAAATTATGCAATT
130 TTTTTCATTCAAAGGCAAAAAGTAGTTTAGATAATGACAAAGTATTTAGACTAAATTATGCGATT
* *
628 TCTCGAGCATGAAATGTTCAGAAAATTGTTCGAAGGAATGGATCATCATGAATACATTATGGAAC
195 TCTCGAGCATGAAATGTTCAGAAAATTGTT-GAAGGAATGGATCGTCATGAATACTTTATGGAAC
*
693 TGAAGTTATAAAAGAACTCGTAAAACTTCATCAAGTTCGGAAGTTCGTCCAAGAACAGAGTAAGA
259 TGAAGTTATAAAAGAACTCGTAAAACTTCATCAAGTTCGGAAGTTCATCCAAGAACAGAGTAAGA
758 AACAA-CTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
324 AA-AAGCTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
* * **
822 ATTTAGACCAAATGATATGATTTCCCGTGCATGGAATATTTGGA
388 ATTTAGACCAAATGATACGATTTCACAAGCATGGAATATTTGGA
* * * * * * * *
866 AAATTGCTGGAAGGAATGGATTGTCGTGAATACTTTAAGGAACTAAAGTTCTAAAAGAACTCGTA
1 AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCGTA
* * * * * ** * * *
931 AAACTTCATC-AAGTTCGAAAGTTCGTCCAAGAATAAAGAGAGAAATAACGAACTC-GTAAAT-A
66 AAACTTTACCAAAGTTTGGAAGTTCGTCCAAAAACCAAGAAAGAAACAAC--TCTCAGTAAATAA
* * * * * * * * * * *
993 -TCTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
129 GT-TTTTCATTCAAAGGCAAAAAGTAGTTTAGATAATGACAAAGTATTTAGACTAAATTATGCGA
* ** * *
1057 TTTCAT-GAGCATGGAATGTTTGGAAAATTGCTTGAAGGAATGGATTGTCATGAATACTTTAAGG
193 TTTC-TCGAGCATGAAATGTTCAGAAAATTG-TTGAAGGAATGGATCGTCATGAATACTTTATGG
* * *
1121 AAC-GAATGTTATAGATGAACTGGTAAAA
256 AACTGAA-GTTATAAAAGAACTCGTAAAA
1149 GTTTTCCNNN
Statistics
Matches: 637, Mismatches: 69, Indels: 20
0.88 0.10 0.03
Matches are distributed among these distances:
430 4 0.01
431 123 0.19
432 431 0.68
433 76 0.12
434 3 0.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (431 bp):
AAATTGCTCGAAGGAGTGGATCGTCATGAATACTTTATGGAACTGAAGTTATAAATGAACTCGTA
AAACTTTACCAAAGTTTGGAAGTTCGTCCAAAAACCAAGAAAGAAACAACTCTCAGTAAATAAGT
TTTTCATTCAAAGGCAAAAAGTAGTTTAGATAATGACAAAGTATTTAGACTAAATTATGCGATTT
CTCGAGCATGAAATGTTCAGAAAATTGTTGAAGGAATGGATCGTCATGAATACTTTATGGAACTG
AAGTTATAAAAGAACTCGTAAAACTTCATCAAGTTCGGAAGTTCATCCAAGAACAGAGTAAGAAA
AAGCTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATT
TAGACCAAATGATACGATTTCACAAGCATGGAATATTTGGA
Done.