Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002441.1 Kokia drynarioides strain JFW-HI SEQ_114553, 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: 6348
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38


Found at i:63 original size:18 final size:19

Alignment explanation


    Indices: 42--83  Score: 68
    Period size: 18  Copynumber: 2.3  Consensus size: 19

         32 ATTAGTGTTA

                            *  
         42 TTATTAATATTAA-AATAG
          1 TTATTAATATTAATAAAAG

                               
         60 TTATTAATATTAATAAAAG
          1 TTATTAATATTAATAAAAG

                 
         79 TTATT
          1 TTATT

         84 GAAATGTTTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  18   13  0.59
  19    9  0.41

ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48


Consensus pattern (19 bp):   
TTATTAATATTAATAAAAG

Found at i:76 original size:21 final size:21

Alignment explanation


    Indices: 38--77  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

         28 GGTCATTAGT

                   *     *       
         38 GTTATTATTAATATTAAAATA
          1 GTTATTAATAATAATAAAATA

                      *        
         59 GTTATTAATATTAATAAAA
          1 GTTATTAATAATAATAAAA

         78 GTTATTGAAA


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45


Consensus pattern (21 bp):   
GTTATTAATAATAATAAAATA

Found at i:767 original size:17 final size:17

Alignment explanation


    Indices: 722--819  Score: 115
    Period size: 17  Copynumber: 5.6  Consensus size: 17

        712 TTGTTTATTT

                               
        722 TAAATTTTAAATTTGAAAA
          1 TAAA-TTTAAATTT-AAAA

               *      *     *
        741 TAATTTTAAACTTAAAT
          1 TAAATTTAAATTTAAAA

                             
        758 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTAAAA

                          *   
        775 TAAATTTAAATTTTTAAA
          1 TAAATTTAAA-TTTAAAA

            *        *       
        793 CAAATTTAATTTTAAAA
          1 TAAATTTAAATTTAAAA

                      
        810 TAAATTTAAA
          1 TAAATTTAAA

        820 GTGAGTATGA


Statistics
Matches: 66,  Mismatches: 12, Indels: 4
        0.80            0.15        0.05

Matches are distributed among these distances:
  17   41  0.62
  18   22  0.33
  19    3  0.05

ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAA

Found at i:769 original size:35 final size:35

Alignment explanation


    Indices: 721--819  Score: 121
    Period size: 35  Copynumber: 2.8  Consensus size: 35

        711 TTTGTTTATT

                                   *             
        721 TTAAATTTTAAATTTGAAAATAATTTTAAA-CTTAAA
          1 TTAAA-TTTAAATTT-AAAATAAATTTAAATCTTAAA

                                          *     
        757 TTAAATTTAAATTTAAAATAAATTTAAATTTTTAAA
          1 TTAAATTTAAATTTAAAATAAATTTAAA-TCTTAAA

             *        *                 
        793 -CAAATTTAATTTTAAAATAAATTTAAA
          1 TTAAATTTAAATTTAAAATAAATTTAAA

        820 GTGAGTATGA


Statistics
Matches: 57,  Mismatches: 4, Indels: 5
        0.86            0.06        0.08

Matches are distributed among these distances:
  34   13  0.23
  35   34  0.60
  36   10  0.18

ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44


Consensus pattern (35 bp):   
TTAAATTTAAATTTAAAATAAATTTAAATCTTAAA

Found at i:819 original size:6 final size:6

Alignment explanation


    Indices: 720--787  Score: 61
    Period size: 6  Copynumber: 11.5  Consensus size: 6

        710 ATTTGTTTAT

                                    *   *        *                   
        720 TTTAAA TTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA
          1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

                    *               
        768 TTTAAA -ATAAA TTTAAA TTT
          1 TTTAAA TTTAAA TTTAAA TTT

        788 TTAAACAAAT


Statistics
Matches: 50,  Mismatches: 7, Indels: 9
        0.76            0.11        0.14

Matches are distributed among these distances:
   5   11  0.22
   6   30  0.60
   7    9  0.18

ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47


Consensus pattern (6 bp):   
TTTAAA
Done.