Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014600.1 Kokia drynarioides strain JFW-HI SEQ_129639, 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: 8733
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34

Warning! 30 characters in sequence are not A, C, G, or T


Found at i:2703 original size:21 final size:21

Alignment explanation


    Indices: 2677--2726  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       2667 AAAATTAAAT

                     *            
       2677 CGATTAAACTAGATTAAAAA-C
          1 CGATTAAACCAGA-TAAAAAGC

                  *              
       2698 CGATTAGACCAGATAAAAAGC
          1 CGATTAAACCAGATAAAAAGC

             *      
       2719 CAATTAAA
          1 CGATTAAA

       2727 TCTAAGAAAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  20    6  0.25
  21   18  0.75

ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20


Consensus pattern (21 bp):   
CGATTAAACCAGATAAAAAGC

Found at i:7766 original size:17 final size:16

Alignment explanation


    Indices: 7731--7768  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       7721 TTTATTTTTA

                            
       7731 TAAAATAAATAAGAAT
          1 TAAAATAAATAAGAAT

                             
       7747 TAAAATATAATAA-AAT
          1 TAAAATA-AATAAGAAT

             *    
       7763 TTAAAT
          1 TAAAAT

       7769 TTAAAATATA


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

Matches are distributed among these distances:
  16   15  0.75
  17    5  0.25

ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32


Consensus pattern (16 bp):   
TAAAATAAATAAGAAT

Found at i:7792 original size:22 final size:23

Alignment explanation


    Indices: 7746--7792  Score: 78
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       7736 TAAATAAGAA

                                   
       7746 TTAAAATATAATAAAATTTAAAT
          1 TTAAAATATAATAAAATTTAAAT

                           *       
       7769 TTAAAATATAAT-AACTTTAAAT
          1 TTAAAATATAATAAAATTTAAAT

              
       7791 TT
          1 TT

       7793 TTAATTTTAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  22   11  0.48
  23   12  0.52

ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43


Consensus pattern (23 bp):   
TTAAAATATAATAAAATTTAAAT

Found at i:8521 original size:25 final size:25

Alignment explanation


    Indices: 8493--8540  Score: 62
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       8483 GTTATTTTTT

                    *         *       
       8493 AAAA-GTATTTTTAGAAAGTTTTATA
          1 AAAAGGTAATTTT-GAAAATTTTATA

                                   
       8518 AAAAGGTAATTTTGAAAATTTTA
          1 AAAAGGTAATTTTGAAAATTTTA

       8541 ATTTAAGATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  25   13  0.65
  26    7  0.35

ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42


Consensus pattern (25 bp):   
AAAAGGTAATTTTGAAAATTTTATA
Done.