Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008321.1 Kokia drynarioides strain JFW-HI SEQ_122986, 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: 2154
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36


Found at i:1674 original size:29 final size:30

Alignment explanation


    Indices: 1628--1863  Score: 221
    Period size: 30  Copynumber: 7.9  Consensus size: 30

       1618 CCCAAGAGGT

                  *     **     *          
       1628 CCTTAAGCTTTTTAAAAATTACATTTTGAC
          1 CCTTAAACTTTTCCAAAATCACATTTTGAC

                        *        *   *   *
       1658 CCTTAAA-TTTTTCAAAATCATATTCT-AA
          1 CCTTAAACTTTTCCAAAATCACATTTTGAC

                    *                   *  
       1686 CCTCTAAATTTTTCCAAAATCACATTTTAAC
          1 CCT-TAAACTTTTCCAAAATCACATTTTGAC

              *                **      *  
       1717 CCCTAAACTTTTCCAAAATTGCATTTTAAC
          1 CCTTAAACTTTTCCAAAATCACATTTTGAC

               *               *          
       1747 CC-CAAACTTTTCCAAAATTACATTTTGAC
          1 CCTTAAACTTTTCCAAAATCACATTTTGAC

                                            
       1776 ACC-TAAA-TTTTCCAAAAATCACATTTTGAC
          1 -CCTTAAACTTTTCC-AAAATCACATTTTGAC

                *        **                
       1806 ACCTCAAACTTTTTGAAAATCACATTTTGAC
          1 -CCTTAAACTTTTCCAAAATCACATTTTGAC

                               *       
       1837 CCTTAAACTTTTCCAAAATTACATTTT
          1 CCTTAAACTTTTCCAAAATCACATTTT

       1864 CACCATAAAT


Statistics
Matches: 173,  Mismatches: 26, Indels: 14
        0.81            0.12        0.07

Matches are distributed among these distances:
  28    4  0.02
  29   49  0.28
  30   94  0.54
  31   22  0.13
  32    4  0.02

ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39


Consensus pattern (30 bp):   
CCTTAAACTTTTCCAAAATCACATTTTGAC

Found at i:1729 original size:59 final size:58

Alignment explanation


    Indices: 1642--1855  Score: 220
    Period size: 59  Copynumber: 3.6  Consensus size: 58

       1632 AAGCTTTTTA

                 *            *         *                               
       1642 AAAATTACATTTTGACCCTTAAA-TTTTTCAAAATCATATTCTAACCTCTAAATTTTTCC
          1 AAAATCACATTTTGACCCCTAAACTTTTCCAAAATCATATT-TAACCTC-AAATTTTTCC

                         *                                  *    *      
       1701 AAAATCACATTTTAACCCCTAAACTTTTCCAAAATTGCAT-TTTAACCCCAAACTTTTCC
          1 AAAATCACATTTTGACCCCTAAACTTTTCCAAAA-T-CATATTTAACCTCAAATTTTTCC

                 *          *                     *                       *
       1760 AAAATTACATTTTGACACCTAAA-TTTTCCAAAAATCACATTTTGACACCTCAAACTTTTT-G
          1 AAAATCACATTTTGACCCCTAAACTTTTCC-AAAATCATA-TTT-A-ACCTCAAA-TTTTTCC

                              *                
       1821 AAAATCACATTTTGACCCTTAAACTTTTCCAAAAT
          1 AAAATCACATTTTGACCCCTAAACTTTTCCAAAAT

       1856 TACATTTTCA


Statistics
Matches: 129,  Mismatches: 16, Indels: 18
        0.79            0.10        0.11

Matches are distributed among these distances:
  57    2  0.02
  58    7  0.05
  59   56  0.43
  60   16  0.12
  61   35  0.27
  62   13  0.10

ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37


Consensus pattern (58 bp):   
AAAATCACATTTTGACCCCTAAACTTTTCCAAAATCATATTTAACCTCAAATTTTTCC
Done.