Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008762.1 Kokia drynarioides strain JFW-HI SEQ_123445, 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: 6808
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35


Found at i:1644 original size:38 final size:39

Alignment explanation


    Indices: 1585--1775  Score: 181
    Period size: 38  Copynumber: 4.9  Consensus size: 39

       1575 GTTGTAAGCA

                         *  *       *          *   
       1585 GTGTTTATCGGGCCTAATGCCTAGTAGGCTTCGTGTC-G
          1 GTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCTG

                     *              *      *   *   
       1623 GTGTTTATCTGGCTTAGTGCCTAGAAGGCTTTGT-ACTG
          1 GTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCTG

                       *              *     *      
       1661 GTGTTTATCGGTCTTAGTGCCTAGCAAGCTTCATGCC-G
          1 GTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCTG

             *               * *                   
       1699 GAGTTTATCGGGCTTAGAGTCTAGCAGGCTTCGTGCCTG
          1 GTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCTG

               *      **    *        *            
       1738 TGTATTTATCTAGCTTTGTGCCTAGTAGGCTTCGTGCC
          1 -GTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCC

       1776 AGTGTATATT


Statistics
Matches: 122,  Mismatches: 27, Indels: 6
        0.79            0.17        0.04

Matches are distributed among these distances:
  37    1  0.01
  38   90  0.74
  39    2  0.02
  40   29  0.24

ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36


Consensus pattern (39 bp):   
GTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCTG

Found at i:1768 original size:40 final size:41

Alignment explanation


    Indices: 1719--1823  Score: 115
    Period size: 41  Copynumber: 2.6  Consensus size: 41

       1709 GGCTTAGAGT

                             *                        
       1719 CTAGCAGGCTTCGTGCCTGTGTAT-TTATCTA-GCTTTGTGC
          1 CTAGCAGGCTTCGTGCCAGTGTATATTATC-AGGCTTTGTGC

                *                                 *  
       1759 CTAGTAGGCTTCGTGCCAGTGTATATTATCAGGCTTTGAGC
          1 CTAGCAGGCTTCGTGCCAGTGTATATTATCAGGCTTTGTGC

             *    * *      * *      
       1800 CCAGCAAGTTTCGTGTCGGTGTAT
          1 CTAGCAGGCTTCGTGCCAGTGTAT

       1824 TGTATTAGGT


Statistics
Matches: 54,  Mismatches: 9, Indels: 3
        0.82            0.14        0.05

Matches are distributed among these distances:
  40   23  0.43
  41   31  0.57

ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36


Consensus pattern (41 bp):   
CTAGCAGGCTTCGTGCCAGTGTATATTATCAGGCTTTGTGC

Found at i:5510 original size:10 final size:11

Alignment explanation


    Indices: 5475--5521  Score: 60
    Period size: 11  Copynumber: 4.3  Consensus size: 11

       5465 ATAATTTTAT

                *      
       5475 ATTTAAAAATA
          1 ATTTTAAAATA

                    *  
       5486 ATTTTAAATTA
          1 ATTTTAAAATA

                       
       5497 ATTTTAAAAT-
          1 ATTTTAAAATA

                        
       5507 ATTTTAAAAATA
          1 ATTTT-AAAATA

               
       5519 ATT
          1 ATT

       5522 AATTTTTGCT


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  10    5  0.16
  11   23  0.74
  12    3  0.10

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (11 bp):   
ATTTTAAAATA

Done.