Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009647.1 Kokia drynarioides strain JFW-HI SEQ_124365, 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: 12538
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Found at i:711 original size:29 final size:28

Alignment explanation


    Indices: 662--950  Score: 238
    Period size: 29  Copynumber: 9.7  Consensus size: 28

        652 GTCTCGAAAT

                        **               
        662 TTCCAAAAATCCTGTTTTTACGCCCAAAC
          1 TTCCAAAAATCCCATTTTTAC-CCCAAAC

                            *           *
        691 TTCCAAAAATCCCATTCTTACCCCCAAAT
          1 TTCCAAAAATCCCATTTTTA-CCCCAAAC

                      *                  
        720 TTCCAAAAATTCCATTTTTACCCTCAAAC
          1 TTCCAAAAATCCCATTTTTACCC-CAAAC

                                      *    
        749 TTCCAAAAATCCCATTTTTTGACTCCAAAAC
          1 TTCCAAAAATCCCA-TTTTT-AC-CCCAAAC

                           *          *    
        780 TTCCAAAAATCCCTTTTTTTTATCCCAAAAC
          1 TTCCAAAAATCCC--ATTTTTA-CCCCAAAC

                 *               *          
        811 TTCAAAATAAAATCCCATTTTAACCCCAAAAC
          1 TTC--CA-AAAATCCCATTTTTACCCC-AAAC

                                          
        843 TTCCAAAAATCCCATTTTTAACCCCAAAAC
          1 TTCCAAAAATCCCATTTTT-ACCCC-AAAC

                               *    *    
        873 TTCCAAAAATCCCATTTTCAACCCTAAAC
          1 TTCCAAAAATCCCATTTT-TACCCCAAAC

              * *       **             *   
        902 ATACTAAAAATTATCA-TTTTACCCTCGAAC
          1 -TTCCAAAAA-TCCCATTTTTACCC-CAAAC

                         *     
        932 TTCCAAAAATCCCGTTTTT
          1 TTCCAAAAATCCCATTTTT

        951 TTCTCCGAAC


Statistics
Matches: 212,  Mismatches: 30, Indels: 36
        0.76            0.11        0.13

Matches are distributed among these distances:
  28    5  0.02
  29   90  0.42
  30   52  0.25
  31   36  0.17
  32   20  0.09
  33    1  0.00
  34    8  0.04

ACGTcount: A:0.36, C:0.30, G:0.02, T:0.31


Consensus pattern (28 bp):   
TTCCAAAAATCCCATTTTTACCCCAAAC

Found at i:797 original size:30 final size:29

Alignment explanation


    Indices: 662--890  Score: 255
    Period size: 29  Copynumber: 7.6  Consensus size: 29

        652 GTCTCGAAAT

                        **                
        662 TTCCAAAAATCCTGTTTTTACGCCC-AAAC
          1 TTCCAAAAATCCCATTTTTAC-CCCAAAAC

                            *       *   *
        691 TTCCAAAAATCCCATTCTTACCCCCAAAT
          1 TTCCAAAAATCCCATTTTTACCCCAAAAC

                      *                   
        720 TTCCAAAAATTCCATTTTTACCCTC-AAAC
          1 TTCCAAAAATCCCATTTTTACCC-CAAAAC

                                   *       
        749 TTCCAAAAATCCCATTTTTTGACTCCAAAAC
          1 TTCCAAAAATCCCA-TTTTT-ACCCCAAAAC

                           *      *        
        780 TTCCAAAAATCCCTTTTTTTTATCCCAAAAC
          1 TTCCAAAAATCCC--ATTTTTACCCCAAAAC

                 *               *          
        811 TTCAAAATAAAATCCCATTTTAACCCCAAAAC
          1 TTC--CA-AAAATCCCATTTTTACCCCAAAAC

                                          
        843 TTCCAAAAATCCCATTTTTAACCCCAAAAC
          1 TTCCAAAAATCCCATTTTT-ACCCCAAAAC

                              
        873 TTCCAAAAATCCCATTTT
          1 TTCCAAAAATCCCATTTT

        891 CAACCCTAAA


Statistics
Matches: 171,  Mismatches: 18, Indels: 21
        0.81            0.09        0.10

Matches are distributed among these distances:
  28    3  0.02
  29   71  0.42
  30   36  0.21
  31   31  0.18
  32   21  0.12
  33    1  0.01
  34    8  0.05

ACGTcount: A:0.36, C:0.31, G:0.01, T:0.31


Consensus pattern (29 bp):   
TTCCAAAAATCCCATTTTTACCCCAAAAC

Found at i:2734 original size:21 final size:20

Alignment explanation


    Indices: 2706--2747  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 20

       2696 CAAAAAGTCA

                                 
       2706 AACATCAAC-AGTCAATGGTC
          1 AACATCAACGA-TCAATGGTC

                                 
       2726 AACAGTCAACGATCAATGGTC
          1 AACA-TCAACGATCAATGGTC

             
       2747 A
          1 A

       2748 GGTTCGATTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  20    4  0.20
  21   15  0.75
  22    1  0.05

ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19


Consensus pattern (20 bp):   
AACATCAACGATCAATGGTC

Found at i:4722 original size:20 final size:22

Alignment explanation


    Indices: 4699--4741  Score: 63
    Period size: 20  Copynumber: 2.0  Consensus size: 22

       4689 TTAGTACAAG

                                  
       4699 TATTTTAACATG-TTT-AAAAT
          1 TATTTTAACATGATTTGAAAAT

                     *            
       4719 TATTTTAACTTGATTTGAAAAT
          1 TATTTTAACATGATTTGAAAAT

             
       4741 T
          1 T

       4742 GTTTCAAACT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  20   11  0.55
  21    3  0.15
  22    6  0.30

ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51


Consensus pattern (22 bp):   
TATTTTAACATGATTTGAAAAT
Done.