Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006538.1 Kokia drynarioides strain JFW-HI SEQ_121123, 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: 5498
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34


Found at i:2418 original size:30 final size:29

Alignment explanation


    Indices: 2347--2455  Score: 103
    Period size: 30  Copynumber: 3.8  Consensus size: 29

       2337 GAACTATCCA

                   *     *    *   *      
       2347 AAAATCATATTTTGACCCCAAACTTTTAT
          1 AAAATCACATTTTAACCCTAAAATTTTAT

                 * *                    * 
       2376 AAAATTATATTTTAACCCTTAAAATTTTCT
          1 AAAATCACATTTTAACCC-TAAAATTTTAT

                               *    *   *
       2406 AAAATCACATTTTAACCCTCAAA-GTTAA
          1 AAAATCACATTTTAACCCTAAAATTTTAT

                        *         
       2434 AAAATCACATTTCAACCCTAAA
          1 AAAATCACATTTTAACCCTAAA

       2456 CTTCCTAAAA


Statistics
Matches: 66,  Mismatches: 13, Indels: 3
        0.80            0.16        0.04

Matches are distributed among these distances:
  28   22  0.33
  29   20  0.30
  30   24  0.36

ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35


Consensus pattern (29 bp):   
AAAATCACATTTTAACCCTAAAATTTTAT

Found at i:2444 original size:28 final size:29

Alignment explanation


    Indices: 2406--2567  Score: 116
    Period size: 29  Copynumber: 5.7  Consensus size: 29

       2396 AAAATTTTCT

                                   *     
       2406 AAAATCACATTTTAACCCTCAAAGTT-AA
          1 AAAATCACATTTTAACCCTCAAACTTCAA

                        *              **
       2434 AAAATCACATTTCAACCCT-AAACTTCCT
          1 AAAATCACATTTTAACCCTCAAACTTCAA

                 *       **            * 
       2462 AAAATTACATTTTTGCCCTCAAACTTCTA
          1 AAAATCACATTTTAACCCTCAAACTTCAA

                 *       *       *    * * 
       2491 AAAATTACATTTTTACCCTCTGAACTACCA
          1 AAAATCACATTTTAACCCTC-AAACTTCAA

              *          *              **
       2521 AAGATCACATTTTTA-CCTCAAACTTTCTC
          1 AAAATCACATTTTAACCCTCAAAC-TTCAA

                 *             
       2550 AAAATAACATTTT-ACCCT
          1 AAAATCACATTTTAACCCT

       2568 TAAAACTTTC


Statistics
Matches: 107,  Mismatches: 22, Indels: 9
        0.78            0.16        0.07

Matches are distributed among these distances:
  27    5  0.05
  28   37  0.35
  29   46  0.43
  30   19  0.18

ACGTcount: A:0.38, C:0.26, G:0.02, T:0.33


Consensus pattern (29 bp):   
AAAATCACATTTTAACCCTCAAACTTCAA

Found at i:2486 original size:29 final size:29

Alignment explanation


    Indices: 2449--2582  Score: 105
    Period size: 29  Copynumber: 4.6  Consensus size: 29

       2439 CACATTTCAA

                                         
       2449 CCCT-AAACTTCCT-AAAATTACATTTTT
          1 CCCTCAAACTTCCTAAAAATTACATTTTT

                                          
       2476 GCCCTCAAACTT-CTAAAAATTACATTTTT
          1 -CCCTCAAACTTCCTAAAAATTACATTTTT

                   *    *      *  *        
       2505 ACCCTCTGAACTACC-AAAGATCACATTTTT
          1 -CCCTC-AAACTTCCTAAAAATTACATTTTT

            *          *  *     *       *
       2535 ACCTCAAACTTTCTCAAAATAACATTTTA
          1 CCCTCAAACTTCCTAAAAATTACATTTTT

                 *      *      
       2564 CCCTTAAAACTTTCTAAAA
          1 CCC-TCAAACTTCCTAAAA

       2583 TATGTTTTAA


Statistics
Matches: 84,  Mismatches: 16, Indels: 10
        0.76            0.15        0.09

Matches are distributed among these distances:
  28   11  0.13
  29   42  0.50
  30   30  0.36
  31    1  0.01

ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35


Consensus pattern (29 bp):   
CCCTCAAACTTCCTAAAAATTACATTTTT

Found at i:4901 original size:24 final size:23

Alignment explanation


    Indices: 4848--4903  Score: 58
    Period size: 24  Copynumber: 2.3  Consensus size: 23

       4838 GAAAAATTTG

                 *       *     *   
       4848 AAAATTTAACAATTTAACATTGT
          1 AAAATGTAACAATGTAACAATGT

              *                      
       4871 AGTAATGTAACAATGTAACAATGTT
          1 A-AAATGTAACAATGTAACAATG-T

                    
       4896 AAAATGTA
          1 AAAATGTA

       4904 TACCGTGTCA


Statistics
Matches: 26,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  23    1  0.04
  24   23  0.88
  25    2  0.08

ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34


Consensus pattern (23 bp):   
AAAATGTAACAATGTAACAATGT
Done.