Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015303.1 Kokia drynarioides strain JFW-HI SEQ_130348, 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: 387286
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34

Warning! 929 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:373099 original size:89 final size:89

Alignment explanation


    Indices: 372963--373148  Score: 216
    Period size: 89  Copynumber: 2.1  Consensus size: 89

     372953 TAATTGCTTT

                    *      *      *                                * **      
     372963 TTTTTTTTTGAAAAAGTTTGAAGTTTTTTTTATGTATTTAAAAGTTCAAGTA-CTTACTTGAATG
          1 TTTTTTTTGGAAAAAATTTGAACTTTTTTTTATGTATTTAAAAGTTCAAGTATC-CAAATGAATG

                             *       
     373027 CAAAATAAAAACATGAGTTTAATTG
         65 CAAAATAAAAACATGAGCTTAATTG

                                               *                           * 
     373052 TTTTTTTTGGAAAAAATTTGAAAACTTTTTTTT-TTTA-TTAAAAGTTCAAGTATCCAAATGAGT
          1 TTTTTTTTGGAAAAAATTTG--AACTTTTTTTTATGTATTTAAAAGTTCAAGTATCCAAATGAAT

             *         *             *
     373115 GTAAAATAAAAGCATGAGCTTAATTT
         64 GCAAAATAAAAACATGAGCTTAATTG

                    
     373141 TTTTTTTT
          1 TTTTTTTT

     373149 TTTTTTTAAG


Statistics
Matches: 82,  Mismatches: 12, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  89   68  0.83
  90    4  0.05
  91   10  0.12

ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46


Consensus pattern (89 bp):   
TTTTTTTTGGAAAAAATTTGAACTTTTTTTTATGTATTTAAAAGTTCAAGTATCCAAATGAATGC
AAAATAAAAACATGAGCTTAATTG

Found at i:381305 original size:18 final size:18

Alignment explanation


    Indices: 381282--381327  Score: 92
    Period size: 18  Copynumber: 2.6  Consensus size: 18

     381272 AGGCTTGGCC

                              
     381282 ATGAGAGCAGGAGTCGAG
          1 ATGAGAGCAGGAGTCGAG

                              
     381300 ATGAGAGCAGGAGTCGAG
          1 ATGAGAGCAGGAGTCGAG

                      
     381318 ATGAGAGCAG
          1 ATGAGAGCAG

     381328 AAGGGCTTTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.35, C:0.11, G:0.43, T:0.11


Consensus pattern (18 bp):   
ATGAGAGCAGGAGTCGAG

Found at i:385204 original size:24 final size:24

Alignment explanation


    Indices: 385172--385231  Score: 84
    Period size: 24  Copynumber: 2.5  Consensus size: 24

     385162 AATAATCTTC

                            *       
     385172 CAATTAAACTCTATTTGTTTGTTT
          1 CAATTAAACTCTATTTATTTGTTT

                        *           
     385196 CAATTAAACTCTGTTTATTTGTTT
          1 CAATTAAACTCTATTTATTTGTTT

               **       
     385220 CAAACAAACTCT
          1 CAATTAAACTCT

     385232 TATTAGTCTA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47


Consensus pattern (24 bp):   
CAATTAAACTCTATTTATTTGTTT

Found at i:386717 original size:44 final size:44

Alignment explanation


    Indices: 386628--386715  Score: 106
    Period size: 44  Copynumber: 2.0  Consensus size: 44

     386618 TAGTGTCGAG

                  *           *                  *      
     386628 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
          1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA

                          *                    *         
     386672 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
          1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA

     386716 TTCAAGGATT


Statistics
Matches: 37,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  44   25  0.68
  45   12  0.32

ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27


Consensus pattern (44 bp):   
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA

Done.