Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003018.1 Kokia drynarioides strain JFW-HI SEQ_115533, 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: 5083
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35


Found at i:444 original size:29 final size:29

Alignment explanation


    Indices: 397--639  Score: 141
    Period size: 29  Copynumber: 8.3  Consensus size: 29

        387 CAAAAATCAT

                                          
        397 ATTTTGACCCTCAAGCTTTTCCAAAATTAC
          1 ATTTTGACCCTCAA-CTTTTCCAAAATTAC

                                 *      * 
        427 ATTTT-ACCCTCGAAC-TTTCTAAAATTCC
          1 ATTTTGACCCTC-AACTTTTCCAAAATTAC

                  *      * *    **        
        455 ATTTTTAACCC-CGATTTTTATAAAATTAC
          1 A-TTTTGACCCTCAACTTTTCCAAAATTAC

                  *    *                   
        484 ATTTTTTACCCCCAAAC-TTTCCAAAATT-C
          1 A-TTTTGACCCTC-AACTTTTCCAAAATTAC

                                            
        513 TATTTTGACCCT-AA-TTTTCCTAAAAATTAC
          1 -ATTTTGACCCTCAACTTTTCC--AAAATTAC

                                          * 
        543 ACTTTT-ACACC-CAAACTTTT-CAAAATTCC
          1 A-TTTTGAC-CCTC-AACTTTTCCAAAATTAC

                          *      *        
        572 ATTTTGA-CCTCAATTTTTCTAAAAATTAC
          1 ATTTTGACCCTCAACTTTTC-CAAAATTAC

                 *               *      * 
        601 ATTTTTACCCTCGAAC-TTTCAAAAATTTC
          1 ATTTTGACCCTC-AACTTTTCCAAAATTAC

                      
        630 ATTTTTGACC
          1 A-TTTTGACC

        640 TCGATTCTTC


Statistics
Matches: 169,  Mismatches: 21, Indels: 46
        0.72            0.09        0.19

Matches are distributed among these distances:
  27   15  0.09
  28   18  0.11
  29   82  0.49
  30   44  0.26
  31    6  0.04
  32    4  0.02

ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41


Consensus pattern (29 bp):   
ATTTTGACCCTCAACTTTTCCAAAATTAC

Found at i:558 original size:58 final size:59

Alignment explanation


    Indices: 397--655  Score: 252
    Period size: 58  Copynumber: 4.4  Consensus size: 59

        387 CAAAAATCAT

                                                        *       *        
        397 ATTTTGACCCTCAAGCTTTTCC--AAAATTACA-TTTTACCCTCGAACTTTCTAAAATTCC
          1 ATTTTGACCCTCAA--TTTTCCTAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCC

                  *      *                             *                 *
        455 ATTTTTAACCC-CGATTTT--TATAAAATTACATTTTTTACCCCCAAACTTTCCAAAATTCT
          1 A-TTTTGACCCTCAATTTTCCTA-AAAATTACA-TTTTTACCCTCAAACTTTCCAAAATTCC

                                           *                  *         
        514 ATTTTGACCCT-AATTTTCCTAAAAATTACACTTTTACACC-CAAACTTTTCAAAATTCC
          1 ATTTTGACCCTCAATTTTCCTAAAAATTACATTTTTAC-CCTCAAACTTTCCAAAATTCC

                              *                       *       *      * 
        572 ATTTTGA-CCTCAATTTTTCTAAAAATTACATTTTTACCCTCGAACTTTCAAAAATTTC
          1 ATTTTGACCCTCAATTTTCCTAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCC

                         *              
        630 ATTTTTGA-CCTCGATTCTTCC-AAAAA
          1 A-TTTTGACCCTCAATT-TTCCTAAAAA

        656 GACCATTTTA


Statistics
Matches: 168,  Mismatches: 19, Indels: 27
        0.79            0.09        0.13

Matches are distributed among these distances:
  56    4  0.02
  57   14  0.08
  58   84  0.50
  59   61  0.36
  60    5  0.03

ACGTcount: A:0.32, C:0.24, G:0.03, T:0.40


Consensus pattern (59 bp):   
ATTTTGACCCTCAATTTTCCTAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCC

Found at i:654 original size:29 final size:29

Alignment explanation


    Indices: 564--655  Score: 82
    Period size: 29  Copynumber: 3.1  Consensus size: 29

        554 CAAACTTTTC

                  *             *   *     
        564 AAAATTCCA-TTTTGACCTCAATTTTTCTA
          1 AAAATTACATTTTTGACCTCGATTCTTC-A

                                    *      
        593 AAAATTACATTTTT-ACCCTCGA-ACTTTCA
          1 AAAATTACATTTTTGA-CCTCGATTC-TTCA

                  *                       
        622 AAAATTTCATTTTTGACCTCGATTCTTCCA
          1 AAAATTACATTTTTGACCTCGATTCTT-CA

                
        652 AAAA
          1 AAAA

        656 GACCATTTTA


Statistics
Matches: 51,  Mismatches: 6, Indels: 11
        0.75            0.09        0.16

Matches are distributed among these distances:
  29   31  0.61
  30   20  0.39

ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40


Consensus pattern (29 bp):   
AAAATTACATTTTTGACCTCGATTCTTCA

Done.