Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001680.1 Kokia drynarioides strain JFW-HI SEQ_113351, 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: 16215
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:9512 original size:31 final size:31

Alignment explanation


    Indices: 9470--9544  Score: 105
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       9460 AAAATTTGTT

                  *            *           
       9470 ATTTTAATCACTCATGTTAGATAAGGTATCA
          1 ATTTTAGTCACTCATGTTACATAAGGTATCA

                        *            * *   
       9501 ATTTTAGTCACTTATGTTACATAAGTTGTCA
          1 ATTTTAGTCACTCATGTTACATAAGGTATCA

                         
       9532 ATTTTAGTCACTC
          1 ATTTTAGTCACTC

       9545 TACCGTTACA


Statistics
Matches: 38,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   38  1.00

ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43


Consensus pattern (31 bp):   
ATTTTAGTCACTCATGTTACATAAGGTATCA

Found at i:9764 original size:20 final size:18

Alignment explanation


    Indices: 9719--9772  Score: 56
    Period size: 20  Copynumber: 2.8  Consensus size: 18

       9709 TTTAAAAATT

                          *   
       9719 AAAAAATATATAAATTAC
          1 AAAAAATATATAAAATAC

                                  
       9737 AATTAAAATATATAAAATACTC
          1 AA--AAAATATATAAAATA--C

                           
       9759 AAAAAAT-TATAAAA
          1 AAAAAATATATAAAA

       9773 AAAATAATAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 7
        0.79            0.03        0.18

Matches are distributed among these distances:
  18    2  0.06
  19    7  0.23
  20   19  0.61
  22    3  0.10

ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28


Consensus pattern (18 bp):   
AAAAAATATATAAAATAC

Found at i:10881 original size:21 final size:22

Alignment explanation


    Indices: 10839--10886  Score: 53
    Period size: 22  Copynumber: 2.2  Consensus size: 22

      10829 TGATTATCTT

                             *    
      10839 TTATTTATAAAAACACCCATAA
          1 TTATTTATAAAAACACCAATAA

                  *         *     
      10861 TTATTTTTAAAAA-ACTAATAA
          1 TTATTTATAAAAACACCAATAA

            *    
      10882 ATATT
          1 TTATT

      10887 AATACAAATA


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  21   10  0.45
  22   12  0.55

ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40


Consensus pattern (22 bp):   
TTATTTATAAAAACACCAATAA

Found at i:11291 original size:13 final size:15

Alignment explanation


    Indices: 11275--11311  Score: 51
    Period size: 13  Copynumber: 2.5  Consensus size: 15

      11265 ATTCAAAACA

                           
      11275 ATAATTAA-T-TAAT
          1 ATAATTAACTCTAAT

                           
      11288 ATAATTAACTCTAAT
          1 ATAATTAACTCTAAT

                     
      11303 ATTAATTAA
          1 A-TAATTAA

      11312 GTGATAATTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  13    8  0.38
  14    1  0.05
  15    5  0.24
  16    7  0.33

ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43


Consensus pattern (15 bp):   
ATAATTAACTCTAAT

Found at i:16196 original size:6 final size:6

Alignment explanation


    Indices: 16187--16215  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      16177 ACAATATACA

                                             
      16187 TATATG TATATG TATATG TATATG TATAT
          1 TATATG TATATG TATATG TATATG TATAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52


Consensus pattern (6 bp):   
TATATG

Done.