Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003395.1 Kokia drynarioides strain JFW-HI SEQ_116135, 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: 27232
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:335 original size:4 final size:4

Alignment explanation


    Indices: 315--400  Score: 77
    Period size: 4  Copynumber: 21.2  Consensus size: 4

        305 AACACATTAC

                       *                     *                         * 
        315 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CTTT CTTT -TTT CTTT CCTCT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT

             *      *                           *          
        363 CCTT CTTC CTTT CTTT CTTT CTTT CCTTT ATTT CTTT C
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C

        401 CCGTTTATTT


Statistics
Matches: 66,  Mismatches: 11, Indels: 10
        0.76            0.13        0.11

Matches are distributed among these distances:
   3    6  0.09
   4   50  0.76
   5   10  0.15

ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66


Consensus pattern (4 bp):   
CTTT

Found at i:355 original size:24 final size:23

Alignment explanation


    Indices: 317--399  Score: 85
    Period size: 24  Copynumber: 3.4  Consensus size: 23

        307 CACATTACCT

                   *  *            
        317 TTCTTTCCTTCTTCTTTCTTTCC
          1 TTCTTTCTTTTTTCTTTCTTTCC

                                 *   
        340 TCTCTTTCTTTTTTCTTTCCTCTCC
          1 T-TCTTTCTTTTTTCTTT-CTTTCC

                 *                  
        365 TTCTTCCTTTCTTTCTTTCTTTCC
          1 TTCTTTCTTT-TTTCTTTCTTTCC

               *       
        389 TTTATTTCTTT
          1 -TTCTTTCTTT

        400 CCCGTTTATT


Statistics
Matches: 49,  Mismatches: 7, Indels: 6
        0.79            0.11        0.10

Matches are distributed among these distances:
  23    1  0.02
  24   27  0.55
  25   21  0.43

ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67


Consensus pattern (23 bp):   
TTCTTTCTTTTTTCTTTCTTTCC

Found at i:1158 original size:13 final size:13

Alignment explanation


    Indices: 1140--1168  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       1130 AGCCTATAGA

                         
       1140 TATCCATCGTAGC
          1 TATCCATCGTAGC

                         
       1153 TATCCATCGTAGC
          1 TATCCATCGTAGC

               
       1166 TAT
          1 TAT

       1169 AGCAACAAGG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34


Consensus pattern (13 bp):   
TATCCATCGTAGC
Done.