Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009399.1 Kokia drynarioides strain JFW-HI SEQ_124106, 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: 4919
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35


Found at i:3681 original size:45 final size:44

Alignment explanation


    Indices: 3630--3722  Score: 177
    Period size: 45  Copynumber: 2.1  Consensus size: 44

       3620 TTATCATTTT

                                                        
       3630 TTTACCTCAATGTAATAATTTGCACATTCTTTCACTTTTCACAA
          1 TTTACCTCAATGTAATAATTTGCACATTCTTTCACTTTTCACAA

                                                         
       3674 CTTTACCTCAATGTAATAATTTGCACATTCTTTCACTTTTCACAA
          1 -TTTACCTCAATGTAATAATTTGCACATTCTTTCACTTTTCACAA

                
       3719 TTTA
          1 TTTA

       3723 GTCATCATAG


Statistics
Matches: 48,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  44    4  0.08
  45   44  0.92

ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44


Consensus pattern (44 bp):   
TTTACCTCAATGTAATAATTTGCACATTCTTTCACTTTTCACAA

Found at i:3889 original size:23 final size:23

Alignment explanation


    Indices: 3830--3904  Score: 80
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       3820 GAGAGTACCG

                *                 *
       3830 AAGTACTAAACAGAGAGCACA-T
          1 AAGTGCTAAACAGAGAGCACACA

                      *               
       3852 AAGTGCTGGGCAACAGAGAGCACACA
          1 AAGTGCT---AAACAGAGAGCACACA

                             *     
       3878 AAGTGCTAAACAGAGAGTACACA
          1 AAGTGCTAAACAGAGAGCACACA

                
       3901 AAGT
          1 AAGT

       3905 ACTGAGCATA


Statistics
Matches: 44,  Mismatches: 5, Indels: 7
        0.79            0.09        0.12

Matches are distributed among these distances:
  22    6  0.14
  23   18  0.41
  25   13  0.30
  26    7  0.16

ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12


Consensus pattern (23 bp):   
AAGTGCTAAACAGAGAGCACACA

Found at i:4058 original size:24 final size:26

Alignment explanation


    Indices: 4020--4067  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

       4010 TCTACATGGG

                                       
       4020 CATAATCTCTCATAT-TCAACATTTCT
          1 CATAATCTCTCATATATC-ACATTTCT

                                    
       4046 CATAAT-T-TCATATATCACATTT
          1 CATAATCTCTCATATATCACATTT

       4068 ACATTTCTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   12  0.57
  25    3  0.14
  26    6  0.29

ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44


Consensus pattern (26 bp):   
CATAATCTCTCATATATCACATTTCT
Done.