Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007434.1 Kokia drynarioides strain JFW-HI SEQ_122055, 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: 7271
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32


Found at i:4402 original size:24 final size:24

Alignment explanation


    Indices: 4316--4390  Score: 123
    Period size: 24  Copynumber: 3.1  Consensus size: 24

       4306 AGAAATAATC

                 *       *      *   
       4316 TTTCAGTTAAACTTTGTTTAATTG
          1 TTTCAATTAAACTCTGTTTATTTG

                                    
       4340 TTTCAATTAAACTCTGTTTATTTG
          1 TTTCAATTAAACTCTGTTTATTTG

                                    
       4364 TTTCAATTAAACTCTGTTTATTTG
          1 TTTCAATTAAACTCTGTTTATTTG

               
       4388 TTT
          1 TTT

       4391 GAGTCAAACT


Statistics
Matches: 48,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  24   48  1.00

ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56


Consensus pattern (24 bp):   
TTTCAATTAAACTCTGTTTATTTG

Found at i:6587 original size:29 final size:28

Alignment explanation


    Indices: 6542--6610  Score: 93
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       6532 AAATTTGAAT

                     *  *                
       6542 TTTTGGAAACTTTAAGGGTCAAATCAAAA
          1 TTTTGGAAAATTCAAGGGTC-AATCAAAA

                                   * *  
       6571 TTTTGGAAAATTCAAGGGTCAATTAGAA
          1 TTTTGGAAAATTCAAGGGTCAATCAAAA

                        
       6599 TTTTGGAAAATT
          1 TTTTGGAAAATT

       6611 TGGGGTCAAA


Statistics
Matches: 36,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  28   18  0.50
  29   18  0.50

ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35


Consensus pattern (28 bp):   
TTTTGGAAAATTCAAGGGTCAATCAAAA

Found at i:6652 original size:30 final size:30

Alignment explanation


    Indices: 6530--6766  Score: 191
    Period size: 29  Copynumber: 8.1  Consensus size: 30

       6520 TAAAACAGGA

                                 *    *   
       6530 TCAAATTTGAATTTTTGGAAACTTTAAGGG
          1 TCAAATTTGAATTTTTGGAAAGTTTAGGGG

                   **  *         *  * *   
       6560 TCAAA-TCAAAATTTTGGAAAATTCAAGGG
          1 TCAAATTTGAATTTTTGGAAAGTTTAGGGG

                   *             *        
       6589 TC-AATTAGAA-TTTTGGAAAATTT-GGGG
          1 TCAAATTTGAATTTTTGGAAAGTTTAGGGG

                                          
       6616 TCAAATTTGAATTTTTGGAAAGTTTAGGGG
          1 TCAAATTTGAATTTTTGGAAAGTTTAGGGG

                           *              
       6646 TCAAATTTGAATTTTCGG-AAGTTTAGGGG
          1 TCAAATTTGAATTTTTGGAAAGTTTAGGGG

             *     **     * **          * *
       6675 TTAAATTCAAATTTCTAAAAAGTTT-GACGA
          1 TCAAATTTGAATTTTTGGAAAGTTTAG-GGG

                                      *   
       6705 TCAAATTTGAATTTTT-GAAAGTTTAAGGG
          1 TCAAATTTGAATTTTTGGAAAGTTTAGGGG

            *    *  *  *               *  
       6734 CCAAACTTAAAATTTTGGAAAGTTTAGAGG
          1 TCAAATTTGAATTTTTGGAAAGTTTAGGGG

               
       6764 TCA
          1 TCA

       6767 TAAAACAATT


Statistics
Matches: 163,  Mismatches: 36, Indels: 16
        0.76            0.17        0.07

Matches are distributed among these distances:
  27    5  0.03
  28   21  0.13
  29   79  0.48
  30   58  0.36

ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36


Consensus pattern (30 bp):   
TCAAATTTGAATTTTTGGAAAGTTTAGGGG

Found at i:6756 original size:59 final size:57

Alignment explanation


    Indices: 6526--6760  Score: 204
    Period size: 59  Copynumber: 4.0  Consensus size: 57

       6516 ACATTAAAAC

                                     *              *             *   *
       6526 AGGATCAAATTTGAATTTTTGGAAACTTTAAGGGTCAAATCAAAATTTTGGAAAATTCA
          1 AGGATCAAATTTGAATTTTT-GAAAGTTTAAGGGTCAAATTAAAATTTTGGAAAGTT-T

               *       *       *    *    *           *  *             
       6585 AGGGTC-AATTAGAATTTTGGAAAATTT-GGGGTCAAATTTGAATTTTTGGAAAGTTT
          1 AGGATCAAATTTGAATTTTTGAAAGTTTAAGGGTCAAA-TTAAAATTTTGGAAAGTTT

                *               * *       *    *     *        **       
       6641 AGGGGTCAAATTTGAATTTTCGGAAGTTTAGGGGTTAAATTCAAATTTCTAAAAAGTTT
          1 A-GGATCAAATTTGAATTTTTGAAAGTTTAAGGGTCAAATTAAAATTT-TGGAAAGTTT

              *                               *                        
       6700 GACGATCAAATTTGAATTTTTGAAAGTTTAAGGGCCAAACTTAAAATTTTGGAAAGTTT
          1 -AGGATCAAATTTGAATTTTTGAAAGTTTAAGGGTCAAA-TTAAAATTTTGGAAAGTTT

              
       6759 AG
          1 AG

       6761 AGGTCATAAA


Statistics
Matches: 139,  Mismatches: 30, Indels: 15
        0.76            0.16        0.08

Matches are distributed among these distances:
  56    9  0.06
  57   26  0.19
  58   36  0.26
  59   59  0.42
  60    9  0.06

ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36


Consensus pattern (57 bp):   
AGGATCAAATTTGAATTTTTGAAAGTTTAAGGGTCAAATTAAAATTTTGGAAAGTTT
Done.