Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010456.1 Kokia drynarioides strain JFW-HI SEQ_125354, 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: 5862
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:127 original size:13 final size:13

Alignment explanation


    Indices: 109--171  Score: 69
    Period size: 13  Copynumber: 4.9  Consensus size: 13

         99 TCCTTCTTCC

                      *  
        109 CTTTCTTCTTATT
          1 CTTTCTTCTTTTT

                          
        122 CTTTCTTCTTCTTT
          1 CTTTCTTCTT-TTT

                     *   
        136 CTTTCTT-TCTTT
          1 CTTTCTTCTTTTT

                         
        148 CTTTC-TCTTTTT
          1 CTTTCTTCTTTTT

                         
        160 CCTTTCTT-TTTT
          1 -CTTTCTTCTTTT

        172 CCTTCATTTT


Statistics
Matches: 43,  Mismatches: 3, Indels: 8
        0.80            0.06        0.15

Matches are distributed among these distances:
  11    1  0.02
  12   12  0.28
  13   20  0.47
  14   10  0.23

ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73


Consensus pattern (13 bp):   
CTTTCTTCTTTTT

Found at i:127 original size:22 final size:22

Alignment explanation


    Indices: 102--175  Score: 61
    Period size: 22  Copynumber: 3.5  Consensus size: 22

         92 TTTCCTCTCC

                                    
        102 TTCTTC-CCTTTC-TTCTTATTCT
          1 TTCTTCTCCTTTCTTTC-T-TTCT

                   *              
        124 TTCTTCTTCTTTCTTTCTTTCT
          1 TTCTTCTCCTTTCTTTCTTTCT

                            *      
        146 TTCTT-TCTCTTT-TTCCTTTCT
          1 TTCTTCTC-CTTTCTTTCTTTCT

                       
        167 TT-TT-TCCTT
          1 TTCTTCTCCTT

        176 CATTTTTTGT


Statistics
Matches: 46,  Mismatches: 3, Indels: 9
        0.79            0.05        0.16

Matches are distributed among these distances:
  19    3  0.07
  20    4  0.09
  21   11  0.24
  22   19  0.41
  23    6  0.13
  24    3  0.07

ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70


Consensus pattern (22 bp):   
TTCTTCTCCTTTCTTTCTTTCT

Found at i:137 original size:4 final size:4

Alignment explanation


    Indices: 120--172  Score: 60
    Period size: 4  Copynumber: 13.8  Consensus size: 4

        110 TTTCTTCTTA

                                                                         
        120 TTCT TTC- TTC- TTCT TTCT TTCT TTCT TTCT TTCT CTT-T TTCCT TTCT
          1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TT-CT TTCT

                    
        167 TT-T TTC
          1 TTCT TTC

        173 CTTCATTTTT


Statistics
Matches: 44,  Mismatches: 0, Indels: 10
        0.81            0.00        0.19

Matches are distributed among these distances:
   3   11  0.25
   4   28  0.64
   5    5  0.11

ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74


Consensus pattern (4 bp):   
TTCT

Found at i:183 original size:12 final size:12

Alignment explanation


    Indices: 84--175  Score: 62
    Period size: 13  Copynumber: 7.2  Consensus size: 12

         74 AAACACATTA

                *       
         84 CTTTTTTTTTTC
          1 CTTTCTTTTTTC

                *   *  * 
         96 CTCTCCTTCTTCC
          1 CT-TTCTTTTTTC

                          
        109 CTTTCTTCTTATT-
          1 CTTTCTT-TT-TTC

                         *
        122 CTTTCTTCTTCTTT
          1 CTTTCTT-TT-TTC

                         
        136 CTTTCTTTCTTT-
          1 CTTTCTTT-TTTC

                         
        148 CTTTCTCTTTTTC
          1 CTTTCT-TTTTTC

                        
        161 CTTTCTTTTTTC
          1 CTTTCTTTTTTC

               
        173 CTT
          1 CTT

        176 CATTTTTTGT


Statistics
Matches: 65,  Mismatches: 8, Indels: 14
        0.75            0.09        0.16

Matches are distributed among these distances:
  12   24  0.37
  13   32  0.49
  14    9  0.14

ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70


Consensus pattern (12 bp):   
CTTTCTTTTTTC
Done.