Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009453.1 Kokia drynarioides strain JFW-HI SEQ_124160, 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: 4241
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27


Found at i:571 original size:29 final size:29

Alignment explanation


    Indices: 538--695  Score: 128
    Period size: 29  Copynumber: 5.3  Consensus size: 29

        528 TCCTTAAACT

                                         
        538 TTCCAAAAATTACCATTTTACCCCCGAAC
          1 TTCCAAAAATTACCATTTTACCCCCGAAC

                      *               *    
        567 TTCCAAAAATCA-CATTTTTGA-CCCTGAAC
          1 TTCCAAAAATTACCA-TTTT-ACCCCCGAAC

               *                    ***   
        596 TCTACAAAAATTACCATTTTACCCTTAAAC
          1 T-TCCAAAAATTACCATTTTACCCCCGAAC

                                            
        626 TTCCAAAAA-T-CCAATTTT-CGACCCCGAAC
          1 TTCCAAAAATTACC-ATTTTAC--CCCCGAAC

                                    ** *   
        655 TCTCCAAAAAATTACCATTTTACCATCAAAC
          1 T-TCC-AAAAATTACCATTTTACCCCCGAAC

                      
        686 TTCCAAAAAT
          1 TTCCAAAAAT

        696 CTCATTTTCG


Statistics
Matches: 103,  Mismatches: 13, Indels: 26
        0.73            0.09        0.18

Matches are distributed among these distances:
  27    3  0.03
  28    8  0.08
  29   43  0.42
  30   27  0.26
  31   13  0.13
  32    6  0.06
  33    3  0.03

ACGTcount: A:0.38, C:0.30, G:0.03, T:0.29


Consensus pattern (29 bp):   
TTCCAAAAATTACCATTTTACCCCCGAAC

Found at i:633 original size:59 final size:58

Alignment explanation


    Indices: 541--717  Score: 255
    Period size: 60  Copynumber: 3.0  Consensus size: 58

        531 TTAAACTTTC

                                * *                     *     *        
        541 CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTGACCCTGAACTCTA
          1 CAAAAATTACCATTTTACCCTCAAACTTCCAAAAATC-CATTTTCGACCCCGAACTCTA

                                 *                                    *
        600 CAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCCAATTTTCGACCCCGAACTCTC
          1 CAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCC-ATTTTCGACCCCGAACTCTA

                                *                                      
        659 CAAAAAATTACCATTTTACCATCAAACTTCCAAAAATCTCATTTTCGACCCCGAACTCT
          1 C-AAAAATTACCATTTTACCCTCAAACTTCCAAAAATC-CATTTTCGACCCCGAACTCT

        718 CCAATAATCG


Statistics
Matches: 107,  Mismatches: 8, Indels: 5
        0.89            0.07        0.04

Matches are distributed among these distances:
  58    1  0.01
  59   52  0.49
  60   53  0.50
  61    1  0.01

ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29


Consensus pattern (58 bp):   
CAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCATTTTCGACCCCGAACTCTA

Found at i:694 original size:60 final size:59

Alignment explanation


    Indices: 534--721  Score: 263
    Period size: 59  Copynumber: 3.2  Consensus size: 59

        524 AAGGTCCTTA

                *                      * *                      *     * 
        534 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CACATTTTTGACCCTG
          1 AACTCTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCA-ATTTTCGACCCCG

                  *                     *                              
        593 AACTCTACAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCCAATTTTCGACCCCG
          1 AACTCTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCAATTTTCGACCCCG

                                       *                                 
        652 AACTCTCCAAAAAATTACCATTTTACCATCAAACTTCCAAAAATCTC-ATTTTCGACCCCG
          1 AACTCTCC-AAAAATTACCATTTTACCCTCAAACTTCCAAAAATC-CAATTTTCGACCCCG

                      
        712 AACTCTCCAA
          1 AACTCTCCAA

        722 TAATCGAATA


Statistics
Matches: 116,  Mismatches: 10, Indels: 6
        0.88            0.08        0.05

Matches are distributed among these distances:
  59   58  0.50
  60   57  0.49
  61    1  0.01

ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29


Consensus pattern (59 bp):   
AACTCTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCAATTTTCGACCCCG

Found at i:721 original size:30 final size:28

Alignment explanation


    Indices: 538--726  Score: 104
    Period size: 29  Copynumber: 6.4  Consensus size: 28

        528 TCCTTAAACT

                                           
        538 TTCCAAAAAT-TACCATTTT-ACCCCCGAAC
          1 TTCCAAAAATCT--CATTTTGA-CCCCGAAC

                       *            *    
        567 TTCCAAAAATCACATTTTTGACCCTGAAC
          1 TTCCAAAAATCTCA-TTTTGACCCCGAAC

               *                       **   
        596 TCTACAAAAAT-TACCATTTT-ACCCTTAAAC
          1 T-TCCAAAAATCT--CATTTTGACCC-CGAAC

                                          
        626 TTCCAAAAATC-CAATTTTCGACCCCGAAC
          1 TTCCAAAAATCTC-ATTTT-GACCCCGAAC

                                       * *   
        655 TCTCCAAAAAAT-TACCATTTT-ACCATCAAAC
          1 T-TCC-AAAAATCT--CATTTTGACC-CCGAAC

                                         
        686 TTCCAAAAATCTCATTTTCGACCCCGAAC
          1 TTCCAAAAATCTCATTTT-GACCCCGAAC

                   *    
        715 TCTCCAATAATC
          1 T-TCCAAAAATC

        727 GAATATCCTT


Statistics
Matches: 126,  Mismatches: 13, Indels: 41
        0.70            0.07        0.23

Matches are distributed among these distances:
  27    1  0.01
  28   13  0.10
  29   49  0.39
  30   44  0.35
  31   13  0.10
  32    5  0.04
  33    1  0.01

ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29


Consensus pattern (28 bp):   
TTCCAAAAATCTCATTTTGACCCCGAAC
Done.