Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012380.1 Kokia drynarioides strain JFW-HI SEQ_127384, 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: 10552
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26


Found at i:303 original size:16 final size:18

Alignment explanation


    Indices: 282--318  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 18

        272 AGTGATAAGT

                              
        282 ATTAAT-AG-TAATATTA
          1 ATTAATCAGATAATATTA

                               
        298 ATTAATCAGAATAATATTA
          1 ATTAATCAG-ATAATATTA

              
        317 AT
          1 AT

        319 AATGGACGGC


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  16    6  0.33
  17    2  0.11
  19   10  0.56

ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41


Consensus pattern (18 bp):   
ATTAATCAGATAATATTA

Found at i:1645 original size:58 final size:59

Alignment explanation


    Indices: 1519--1745  Score: 348
    Period size: 59  Copynumber: 3.9  Consensus size: 59

       1509 CTTTCTAAAT

                           *                                           
       1519 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAA
          1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAA

                             *                                         
       1578 ATTACCATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCCCGAACCTTTTGAAA
          1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAA

                           *                   *         *       * *   
       1636 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCTGAACCTTCTAAAA
          1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAA

                    *   *                   *          *       
       1695 ATTACCATGTTATCCCCGAACTTCCAAAAATCTCATTTTTGACTCCGAACC
          1 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC

       1746 CTCCAAAACT


Statistics
Matches: 153,  Mismatches: 14, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
  58   56  0.37
  59   97  0.63

ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31


Consensus pattern (59 bp):   
ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAA

Found at i:1646 original size:30 final size:29

Alignment explanation


    Indices: 1510--1715  Score: 134
    Period size: 30  Copynumber: 6.9  Consensus size: 29

       1500 GTCCCTAAAC

                                            
       1510 TTTCTAAATATTACCATTTTACCCTCGAA-C-
          1 TTTC-AAA-ATTACCATTTTACCC-CGAACCT

              *     * *                    
       1540 TTCCAAAAATCCCATTTTTGACCCCGAACCT
          1 TTTCAAAATTACCA-TTTT-ACCCCGAACCT

               *                   *  *  
       1571 TTTGAAAATTACCATTTTACCCCCAAAC-
          1 TTTCAAAATTACCATTTTACCCCGAACCT

              *     * *                   
       1599 TTCCAAAAATCCCATTTTGACCCCGAACCT
          1 TTTCAAAATTACCATTTT-ACCCCGAACCT

               *                          
       1629 TTTGAAAATTACCATTTTACCCTCGAA-C-
          1 TTTCAAAATTACCATTTTACCC-CGAACCT

              *     * *             *      
       1657 TTCCAAAAATCCCAATTTTGACCCTGAACCT
          1 TTTCAAAATTACC-ATTTT-ACCCCGAACCT

             * *           *            
       1688 TCTAAAAATTACCATGTTATCCCCGAAC
          1 TTTCAAAATTACCATTTTA-CCCCGAAC

       1716 TTCCAAAAAT


Statistics
Matches: 133,  Mismatches: 31, Indels: 24
        0.71            0.16        0.13

Matches are distributed among these distances:
  28   28  0.21
  29   41  0.31
  30   46  0.35
  31   18  0.14

ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32


Consensus pattern (29 bp):   
TTTCAAAATTACCATTTTACCCCGAACCT

Found at i:1725 original size:117 final size:118

Alignment explanation


    Indices: 1519--1745  Score: 366
    Period size: 117  Copynumber: 1.9  Consensus size: 118

       1509 CTTTCTAAAT

                                               *                 * *         
       1519 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAAATTACC
          1 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCCGAACCTTCTAAAAATTACC

              *                                                  
       1584 ATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCCCGAACCTTTTGAAA
         66 ATGTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAA

                                                         *                   
       1636 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCTGAACCTTCTAAAAATTACC
          1 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCCGAACCTTCTAAAAATTACC

                  *    *              *          *       
       1701 ATGTTATCCCCGAACTTCCAAAAATCTCATTTTTGACTCCGAACC
         66 ATGTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC

       1746 CTCCAAAACT


Statistics
Matches: 100,  Mismatches: 9, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
 117   86  0.86
 118   14  0.14

ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31


Consensus pattern (118 bp):   
ATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCCGAACCTTCTAAAAATTACC
ATGTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTGAAA

Done.