Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008393.1 Kokia drynarioides strain JFW-HI SEQ_123061, 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: 2022
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30


Found at i:1388 original size:9 final size:9

Alignment explanation


    Indices: 1371--1414  Score: 52
    Period size: 9  Copynumber: 4.9  Consensus size: 9

       1361 GATTGACCTT

                     
       1371 GAAGAGAGA
          1 GAAGAGAGA

              *      
       1380 GAGGAGAGA
          1 GAAGAGAGA

                   * 
       1389 GAAGAGAAA
          1 GAAGAGAGA

             **      
       1398 GGGGAGAGA
          1 GAAGAGAGA

                    
       1407 GAAGAGAG
          1 GAAGAGAG

       1415 GATTTTGAGA


Statistics
Matches: 27,  Mismatches: 8, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
   9   27  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (9 bp):   
GAAGAGAGA

Found at i:1394 original size:18 final size:18

Alignment explanation


    Indices: 1371--1414  Score: 70
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1361 GATTGACCTT

                              
       1371 GAAGAGAGAGAGGAGAGA
          1 GAAGAGAGAGAGGAGAGA

                   *  *       
       1389 GAAGAGAAAGGGGAGAGA
          1 GAAGAGAGAGAGGAGAGA

                    
       1407 GAAGAGAG
          1 GAAGAGAG

       1415 GATTTTGAGA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (18 bp):   
GAAGAGAGAGAGGAGAGA

Found at i:1859 original size:30 final size:30

Alignment explanation


    Indices: 1791--1967  Score: 130
    Period size: 30  Copynumber: 5.9  Consensus size: 30

       1781 CCCTATTTTA

                                 *          
       1791 TTTAAAAATTACATTTTGACGTCC-AAA-TAT
          1 TTTAAAAATTACATTTTGAC-ACCTAAACT-T

                        *   *               
       1821 TTCT-AAAATTATATTATGAC-CCTTAAACTT
          1 TT-TAAAAATTACATTTTGACACC-TAAACTT

                       * *      *  *   *  
       1851 TTTAAAAATTAAAATTTGACTCCCAAATTT
          1 TTTAAAAATTACATTTTGACACCTAAACTT

                     *                    
       1881 TTTAAAAATCACATTTTGACACCTAAACTT
          1 TTTAAAAATTACATTTTGACACCTAAACTT

              **             *  *      *  
       1911 TTCGAAAATTACATTTTAACCCCTAAATTT
          1 TTTAAAAATTACATTTTGACACCTAAACTT

               *     *                  
       1941 TTTTAAAATCACATTTTGATC-CCTAAA
          1 TTTAAAAATTACATTTTGA-CACCTAAA

       1968 GTGTCCCAAA


Statistics
Matches: 117,  Mismatches: 23, Indels: 14
        0.76            0.15        0.09

Matches are distributed among these distances:
  28    2  0.02
  29    1  0.01
  30  109  0.93
  31    5  0.04

ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40


Consensus pattern (30 bp):   
TTTAAAAATTACATTTTGACACCTAAACTT

Found at i:1889 original size:60 final size:59

Alignment explanation


    Indices: 1791--1998  Score: 174
    Period size: 60  Copynumber: 3.5  Consensus size: 59

       1781 CCCTATTTTA

                                             *      * *                   
       1791 TTTAAAAATTACATTTTGACGT-CCAAATATTTCTAAAATTATATTATGAC-CCTTAAACTT
          1 TTTAAAAATTACATTTTGAC-TCCCAAAT-TTTTTAAAATCACATTATGACACC-TAAACTT

                       * *                               *              
       1851 TTTAAAAATTAAAATTTGACTCCCAAATTTTTTAAAAATCACATTTTGACACCTAAACTT
          1 TTTAAAAATTACATTTTGACTCCCAAATTTTTT-AAAATCACATTATGACACCTAAACTT

              **             *                            *            * *
       1911 TTCGAAAATTACATTTTAAC-CCCTAAATTTTTTTAAAATCACATTTTGATC-CCTAAAGTG
          1 TTTAAAAATTACATTTTGACTCCC-AAA-TTTTTTAAAATCACATTATGA-CACCTAAACTT

             ***     *                   
       1971 TCCCAAAATCACATTTTGAC-CCCAAATT
          1 TTTAAAAATTACATTTTGACTCCCAAATT

       1999 ATTCGAAACT


Statistics
Matches: 125,  Mismatches: 17, Indels: 14
        0.80            0.11        0.09

Matches are distributed among these distances:
  58    2  0.02
  59   11  0.09
  60  103  0.82
  61    9  0.07

ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38


Consensus pattern (59 bp):   
TTTAAAAATTACATTTTGACTCCCAAATTTTTTAAAATCACATTATGACACCTAAACTT

Found at i:1959 original size:90 final size:87

Alignment explanation


    Indices: 1791--2021  Score: 205
    Period size: 90  Copynumber: 2.6  Consensus size: 87

       1781 CCCTATTTTA

                     *                       *       *   * *    *            
       1791 TTTAAAAATTACATTTTGACGTCCAAATATTTCTAAAATTATATTATGACCCTTAAACTTTTTAA
          1 TTTAAAAATCACATTTTGAC--CCAAAT-TTTCGAAAATTACATTTTAACCCCTAAACTTTTTAA

                *                  * *
       1856 AAATTAAAATTTGACTCCC-AAATTT
         63 AAATCAAAATTTGA-TCCCTAAAGTG

                                                                     *     * 
       1881 TTTAAAAATCACATTTTGACACCTAAACTTTTCGAAAATTACATTTTAACCCCTAAATTTTTTTA
          1 TTTAAAAATCACATTTTGAC-CC-AAA-TTTTCGAAAATTACATTTTAACCCCTAAACTTTTTAA

                  * *                
       1946 AAATCACATTTTGATCCCTAAAGTG
         63 AAATCAAAATTTGATCCCTAAAGTG

             ***                                *               
       1971 TCCCAAAATCACATTTTGACCCCAAATTATTCGAAACTT-CATTTTCAACCC
          1 TTTAAAAATCACATTTTGA-CCCAAATT-TTCGAAAATTACATTTT-AACCC

       2022 T


Statistics
Matches: 117,  Mismatches: 18, Indels: 13
        0.79            0.12        0.09

Matches are distributed among these distances:
  88    8  0.07
  89   23  0.20
  90   84  0.72
  91    2  0.02

ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38


Consensus pattern (87 bp):   
TTTAAAAATCACATTTTGACCCAAATTTTCGAAAATTACATTTTAACCCCTAAACTTTTTAAAAA
TCAAAATTTGATCCCTAAAGTG
Done.