Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005485.1 Kokia drynarioides strain JFW-HI SEQ_119546, 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, 802

Length: 1337
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38


Found at i:393 original size:30 final size:28

Alignment explanation


    Indices: 310--510  Score: 152
    Period size: 30  Copynumber: 6.8  Consensus size: 28

        300 AAAGGTCCCT

                                    *     *
        310 AAACTATCCAAAAATTCCATTTTCCACCTCG
          1 AAACT-TCCAAAAATTCCATTTT-TACC-CA

                           *              
        341 AAACTTCCAAAAATTTCATTTTTGACCTCA
          1 AAACTTCCAAAAATTCCATTTTT-ACC-CA

                  *                       
        371 AAACTTTCAAAAATTCCATTTTTATTCCC-
          1 AAACTTCCAAAAATTCCATTTTTA--CCCA

            *                *     *      
        400 GAACTTCCAAAAATTCTAATTTTAACCCTA
          1 AAACTTCCAAAAATTC-CATTTTTACCC-A

                  *      *              *
        430 AAACTTTCAAAAAATCCATTTTTACCCCC
          1 AAACTTCCAAAAATTCCATTTTTA-CCCA

            *   *       *                 
        459 GAACCTCCAAAATTTCCATTTTTGACCCTA
          1 AAACTTCCAAAAATTCCATTTTT-ACCC-A

                  *               
        489 AAACTTTCAAAAATTACCATTT
          1 AAACTTCCAAAAATT-CCATTT

        511 CACCCCCGAA


Statistics
Matches: 135,  Mismatches: 25, Indels: 20
        0.75            0.14        0.11

Matches are distributed among these distances:
  28    3  0.02
  29   42  0.31
  30   77  0.57
  31   13  0.10

ACGTcount: A:0.37, C:0.26, G:0.02, T:0.34


Consensus pattern (28 bp):   
AAACTTCCAAAAATTCCATTTTTACCCA

Found at i:434 original size:59 final size:59

Alignment explanation


    Indices: 318--529  Score: 238
    Period size: 59  Copynumber: 3.6  Consensus size: 59

        308 CTAAACTATC

                                                                            
        318 CAAAAATTCCA-TTTT-CCACCTCGAAACTTCCAAAAATT-TCATTTTTGA-CCTCAAAACTTT
          1 CAAAAATTCCATTTTTACC-CC-CG-AACTTCCAAAAATTCT-ATTTTTGACCCT-AAAACTTT

                             **                     *    *             
        378 CAAAAATTCCATTTTTATTCCCGAACTTCCAAAAATTCTAATTTTAACCCTAAAACTTT
          1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCTAAAACTTT

                  *                   *       *   *                    
        437 CAAAAAATCCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTGACCCTAAAACTTT
          1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCTAAAACTTT

                            *                   
        496 CAAAAATTACCA-TTTCACCCCCGAA-TGTCCAAAA
          1 CAAAAATT-CCATTTTTACCCCCGAACT-TCCAAAA

        530 CTCAATTTTC


Statistics
Matches: 131,  Mismatches: 15, Indels: 13
        0.82            0.09        0.08

Matches are distributed among these distances:
  59  105  0.80
  60   20  0.15
  61    6  0.05

ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33


Consensus pattern (59 bp):   
CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCTAAAACTTT
Done.