Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001598.1 Kokia drynarioides strain JFW-HI SEQ_113220, 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, 900

Length: 1501
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37


Found at i:369 original size:89 final size:89

Alignment explanation


    Indices: 160--371  Score: 236
    Period size: 89  Copynumber: 2.4  Consensus size: 89

        150 ATTTATCAAC

                              *                        *  *                  
        160 TTTTTCAAAAAAAGCAATCAAGCTCCT-TTTTTTTTTGACACTCAATTACGTAGTTGAACTTTCA
          1 TTTTTC-AAAAAAGCAATTAAGCTCCTCTTTTTTTTTGACACTAAAGTACGTAGTTGAACTTTCA

                 *              *     
        224 AAATATATCAAAAAGGTCCTTAAACT
         65 AAATACATCAAAAA-GTCCTCAAACT

                                                            **   *           
        250 TTTTT-AGAAAAAGCAATTAAGCTCCTCTTTTTTTTT-ACACTAAAGTGGGTATTTGAACTTTCA
          1 TTTTTCA-AAAAAGCAATTAAGCTCCTCTTTTTTTTTGACACTAAAGTACGTAGTTGAACTTTCA

                *                   * 
        313 AAATGCATCAAAAA-TACC-CAAATT
         65 AAATACATCAAAAAGT-CCTCAAACT

                                   *           
        337 TTTTTCAAAAATAGCAATTAAGCGCCTGCTTTTTT
          1 TTTTTCAAAAA-AGCAATTAAGCTCCT-CTTTTTT

        372 CACTCAATTG


Statistics
Matches: 105,  Mismatches: 11, Indels: 13
        0.81            0.09        0.10

Matches are distributed among these distances:
  87   14  0.13
  88   18  0.17
  89   59  0.56
  90   14  0.13

ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38


Consensus pattern (89 bp):   
TTTTTCAAAAAAGCAATTAAGCTCCTCTTTTTTTTTGACACTAAAGTACGTAGTTGAACTTTCAA
AATACATCAAAAAGTCCTCAAACT

Found at i:589 original size:19 final size:20

Alignment explanation


    Indices: 567--622  Score: 60
    Period size: 20  Copynumber: 2.8  Consensus size: 20

        557 AAATTTTAAT

                                
        567 AAAAATATTAAAAATTAGAA
          1 AAAAATATTAAAAATTAGAA

                 *           * * 
        587 AAAAAAATATAAAAA-TCGTA
          1 AAAAATAT-TAAAAATTAGAA

                    *       
        607 AAAAATATAAAAAATT
          1 AAAAATATTAAAAATT

        623 TAAATTTTTA


Statistics
Matches: 29,  Mismatches: 5, Indels: 4
        0.76            0.13        0.11

Matches are distributed among these distances:
  19    5  0.17
  20   18  0.62
  21    6  0.21

ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23


Consensus pattern (20 bp):   
AAAAATATTAAAAATTAGAA

Found at i:1251 original size:34 final size:35

Alignment explanation


    Indices: 1175--1252  Score: 88
    Period size: 36  Copynumber: 2.2  Consensus size: 35

       1165 TTATATCTAT

                       *                 *      
       1175 TATTTATATTATTAAATTAAATTTAACATTTTGTAA
          1 TATTTATATTACTAAATT-AATTTAACATATTGTAA

                         *                      
       1211 TATTTATATTACTGAATT-ATTTAATCATATTG-AA
          1 TATTTATATTACTAAATTAATTTAA-CATATTGTAA

             *      
       1245 TCTTTATA
          1 TATTTATA

       1253 AATTTCTATC


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  34   15  0.41
  35    6  0.16
  36   16  0.43

ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53


Consensus pattern (35 bp):   
TATTTATATTACTAAATTAATTTAACATATTGTAA
Done.