Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008944.1 Kokia drynarioides strain JFW-HI SEQ_123638, 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: 8201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:762 original size:19 final size:19

Alignment explanation


    Indices: 724--762  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        714 CATAGGCTTC

                      * *  *   
        724 ATTACTGGTTTCGAATCAA
          1 ATTACTGGTTCCAAACCAA

                               
        743 ATTACTGGTTCCAAACCAA
          1 ATTACTGGTTCCAAACCAA

             
        762 A
          1 A

        763 CTCTCTCCTA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31


Consensus pattern (19 bp):   
ATTACTGGTTCCAAACCAA

Found at i:1495 original size:24 final size:24

Alignment explanation


    Indices: 1461--1651  Score: 125
    Period size: 24  Copynumber: 8.0  Consensus size: 24

       1451 AAAACAACAC

                       *            
       1461 ATATACGTTTATGCTCGTCAGCTT
          1 ATATACGTTTACGCTCGTCAGCTT

                  *        *    *   
       1485 ATATACATTTACGCTTGTCATCTT
          1 ATATACGTTTACGCTCGTCAGCTT

            ** *               *     
       1509 GCACA-GTTTTACGCTCGTTAGCTT
          1 ATATACG-TTTACGCTCGTCAGCTT

                 *          *       
       1533 ATATATGTTTACGCTCATCAGCTT
          1 ATATACGTTTACGCTCGTCAGCTT

            ** *    *  *   *    *   
       1557 GCACACGTCTATGCTAGTCAACTT
          1 ATATACGTTTACGCTCGTCAGCTT

                   *                
       1581 ATATAC-ATTACGCTCGTCAGCTT
          1 ATATACGTTTACGCTCGTCAGCTT

              *         *   *       
       1604 ATGTACGTTTACACTCATCAGCTT
          1 ATATACGTTTACGCTCGTCAGCTT

            * **       *    *       
       1628 TTGCACGTTTATGCTCATCAGCTT
          1 ATATACGTTTACGCTCGTCAGCTT

       1652 GCACATATAC


Statistics
Matches: 123,  Mismatches: 41, Indels: 6
        0.72            0.24        0.04

Matches are distributed among these distances:
  23   17  0.14
  24  105  0.85
  25    1  0.01

ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39


Consensus pattern (24 bp):   
ATATACGTTTACGCTCGTCAGCTT

Found at i:1544 original size:48 final size:48

Alignment explanation


    Indices: 1468--1656  Score: 143
    Period size: 48  Copynumber: 4.0  Consensus size: 48

       1458 CACATATACG

                *                           **   *          
       1468 TTTATGCTCGTCAGCTTATATACATTTACGCTTGTCATCTTGCACAGT
          1 TTTACGCTCGTCAGCTTATATACATTTACGCTCATCAGCTTGCACAGT

                       *          **                         
       1516 TTTACGCTCGTTAGCTTATATATGTTTACGCTCATCAGCTTGCACACG-
          1 TTTACGCTCGTCAGCTTATATACATTTACGCTCATCAGCTTGCACA-GT

             *  *   *    *                   *          *     
       1564 TCTATGCTAGTCAACTTATATACA-TTACGCTCGTCAGCTTATGTAC-G-
          1 TTTACGCTCGTCAGCTTATATACATTTACGCTCATCAGC-T-TGCACAGT

                 *   *       * **  *    *                 
       1611 TTTACACTCATCAGCTTTTGCACGTTTATGCTCATCAGCTTGCACA
          1 TTTACGCTCGTCAGCTTATATACATTTACGCTCATCAGCTTGCACA

       1657 TATACATATT


Statistics
Matches: 107,  Mismatches: 29, Indels: 11
        0.73            0.20        0.07

Matches are distributed among these distances:
  46    4  0.04
  47   29  0.27
  48   69  0.64
  49    5  0.05

ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38


Consensus pattern (48 bp):   
TTTACGCTCGTCAGCTTATATACATTTACGCTCATCAGCTTGCACAGT
Done.