Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004285.1 Kokia drynarioides strain JFW-HI SEQ_117582, 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: 4024
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38


Found at i:1391 original size:52 final size:52

Alignment explanation


    Indices: 1335--1473  Score: 179
    Period size: 52  Copynumber: 2.7  Consensus size: 52

       1325 CTTCTCTTTT

                                        *               *       
       1335 CATTATTATTACTATAATTTTTCTTATTCTTATTCCATGGGCTCTATAGTGC
          1 CATTATTATTACTATAATTTTTCTTATTATTATTCCATGGGCTCCATAGTGC

                     *                  *                  *    
       1387 CATTATTATCACTATAATTTTTCTTATTTTTATTCCATGGGCTCCATGGTGC
          1 CATTATTATTACTATAATTTTTCTTATTATTATTCCATGGGCTCCATAGTGC

            *           *   *   *  *           
       1439 AACTTATTATTATTATTATTATTATTATTATTATT
          1 CA-TTATTATTACTATAATTTTTCTTATTATTATT

       1474 ATTATTATTA


Statistics
Matches: 75,  Mismatches: 11, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  52   49  0.65
  53   26  0.35

ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53


Consensus pattern (52 bp):   
CATTATTATTACTATAATTTTTCTTATTATTATTCCATGGGCTCCATAGTGC

Found at i:1450 original size:3 final size:3

Alignment explanation


    Indices: 1442--1485  Score: 88
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       1432 ATGGTGCAAC

                                                                      
       1442 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       1486 GTAGTGCTGC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   41  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:2062 original size:29 final size:28

Alignment explanation


    Indices: 2042--2105  Score: 76
    Period size: 29  Copynumber: 2.2  Consensus size: 28

       2032 TTTTAAATTA

                       *                 
       2042 AAAAATAGAAAGAATAAATTTATAATAGT
          1 AAAAATA-AAAAAATAAATTTATAATAGT

                                    *     
       2071 AAAAATAAAAAAATAAAATTTAATTATA-T
          1 AAAAATAAAAAAAT-AAATTT-ATAATAGT

                  
       2100 AAAAAT
          1 AAAAAT

       2106 GAGCTTATTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  28    6  0.19
  29   20  0.65
  30    5  0.16

ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28


Consensus pattern (28 bp):   
AAAAATAAAAAAATAAATTTATAATAGT
Done.