Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006164.1 Kokia drynarioides strain JFW-HI SEQ_120720, 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, 750

Length: 1251
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26


Found at i:16 original size:11 final size:11

Alignment explanation


    Indices: 1--66  Score: 55
    Period size: 11  Copynumber: 5.9  Consensus size: 11

                       
          1 TTAAATTAAAT
          1 TTAAATTAAAT

                         
         12 TTAAATTTAAGA-
          1 TTAAA-TTAA-AT

                *      
         24 TTAATTTAAAT
          1 TTAAATTAAAT

                 *     
         35 TTAAAATAAAT
          1 TTAAATTAAAT

            *           
         46 CTAAATTTAAA-
          1 TTAAA-TTAAAT

            *         
         57 ATAAATTAAA
          1 TTAAATTAAA

         67 AAGGGGGGCC


Statistics
Matches: 45,  Mismatches: 6, Indels: 9
        0.75            0.10        0.15

Matches are distributed among these distances:
  10    6  0.13
  11   26  0.58
  12   12  0.27
  13    1  0.02

ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41


Consensus pattern (11 bp):   
TTAAATTAAAT

Found at i:29 original size:17 final size:17

Alignment explanation


    Indices: 1--63  Score: 90
    Period size: 17  Copynumber: 3.7  Consensus size: 17

                 *           
          1 TTAAATTAAATTTAAAT
          1 TTAAAATAAATTTAAAT

                *  *         
         18 TTAAGATTAATTTAAAT
          1 TTAAAATAAATTTAAAT

                       *     
         35 TTAAAATAAATCTAAAT
          1 TTAAAATAAATTTAAAT

                        
         52 TTAAAATAAATT
          1 TTAAAATAAATT

         64 AAAAAGGGGG


Statistics
Matches: 39,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  17   39  1.00

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43


Consensus pattern (17 bp):   
TTAAAATAAATTTAAAT

Found at i:58 original size:7 final size:6

Alignment explanation


    Indices: 1--56  Score: 57
    Period size: 6  Copynumber: 9.8  Consensus size: 6

                                                              *     
          1 TTAAA- TTAAAT TTAAAT TTAAGA- TT-AAT TTAAAT TTAAA- ATAAAT
          1 TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT

            *           
         46 CTAAAT TTAAA
          1 TTAAAT TTAAA

         57 ATAAATTAAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 9
        0.78            0.05        0.16

Matches are distributed among these distances:
   4    1  0.02
   5   12  0.28
   6   29  0.67
   7    1  0.02

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43


Consensus pattern (6 bp):   
TTAAAT

Found at i:160 original size:26 final size:25

Alignment explanation


    Indices: 129--178  Score: 73
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        119 TATCAAACAC

                                      
        129 TTAAATAAAACATCAAAATCCCAAAT
          1 TTAAAT-AAACATCAAAATCCCAAAT

                  *       *         
        155 TTAAATTAACATCATAATCCCAAA
          1 TTAAATAAACATCAAAATCCCAAA

        179 ATAATATAAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25   16  0.73
  26    6  0.27

ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26


Consensus pattern (25 bp):   
TTAAATAAACATCAAAATCCCAAAT
Done.