Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006638.1 Kokia drynarioides strain JFW-HI SEQ_121228, 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: 7153
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37


Found at i:3370 original size:19 final size:18

Alignment explanation


    Indices: 3310--3371  Score: 56
    Period size: 19  Copynumber: 3.4  Consensus size: 18

       3300 GACATGTGGC

                              
       3310 AAAAAAATT-ATAAAAA-
          1 AAAAAAATTAATAAAAAT

             *      *          
       3326 ATAAAAATCAATAAAAATT
          1 AAAAAAATTAATAAAAA-T

             **                
       3345 ATTAAAATTAATAAAAAGT
          1 AAAAAAATTAATAAAAA-T

                    
       3364 AAAAAAAT
          1 AAAAAAAT

       3372 AAAATTAGAA


Statistics
Matches: 36,  Mismatches: 7, Indels: 3
        0.78            0.15        0.07

Matches are distributed among these distances:
  16    7  0.19
  17    7  0.19
  19   22  0.61

ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24


Consensus pattern (18 bp):   
AAAAAAATTAATAAAAAT

Found at i:3648 original size:90 final size:90

Alignment explanation


    Indices: 3537--3715  Score: 243
    Period size: 90  Copynumber: 2.0  Consensus size: 90

       3527 TTGTTTCGTT

                            *         **     *                 *             
       3537 TGAAAAAGTTTGAGGATCTTTTTGATGTA-TTTGAAAGTTTAAATACCCAATTGAGTACAAAATA
          1 TGAAAAAGTTTGAGGACCTTTTTGATACATTTTAAAAGTTTAAATACCCAAGTGAGTACAAAATA

                *    *                
       3601 AAAGTAAGGGGCTTAATTGCTTTTTC
         66 AAAGCAA-GAGCTTAATTGCTTTTTC

                           *                              *          *       
       3627 TGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTTAAATATCCAAGTGAGTGCAAAATA
          1 TGAAAAAGTTTGAGGACCTTTTTGATACATTTTAAAAGTTTAAATACCCAAGTGAGTACAAAATA

                              *     
       3692 AAAGCAAGAGCTTAATTGTTTTTT
         66 AAAGCAAGAGCTTAATTGCTTTTT

       3716 TTTTTAAATT


Statistics
Matches: 77,  Mismatches: 11, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  90   40  0.52
  91   37  0.48

ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36


Consensus pattern (90 bp):   
TGAAAAAGTTTGAGGACCTTTTTGATACATTTTAAAAGTTTAAATACCCAAGTGAGTACAAAATA
AAAGCAAGAGCTTAATTGCTTTTTC
Done.