Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004350.1 Kokia drynarioides strain JFW-HI SEQ_117690, 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: 5840
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34


Found at i:43 original size:21 final size:21

Alignment explanation


    Indices: 4--49  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

          1 CTA

                    *  *         
          4 CCACTAGTCCACTCCCCACCC
          1 CCACTAGTACAATCCCCACCC

                          *     *
         25 CCACTAGTACAATCTCCACCT
          1 CCACTAGTACAATCCCCACCC

                
         46 CCAC
          1 CCAC

         50 CAATTCCATC


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

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.24, C:0.54, G:0.04, T:0.17


Consensus pattern (21 bp):   
CCACTAGTACAATCCCCACCC

Found at i:1115 original size:23 final size:25

Alignment explanation


    Indices: 1068--1123  Score: 82
    Period size: 23  Copynumber: 2.4  Consensus size: 25

       1058 TAATAGTTTT

                                     
       1068 CCCAAA-AATTATCATTTATCCAAA
          1 CCCAAACAATTATCATTTATCCAAA

                                 *   
       1092 CCCAAACAA-TATCA-TTATCTAAA
          1 CCCAAACAATTATCATTTATCCAAA

                     
       1115 CCCAAACAA
          1 CCCAAACAA

       1124 AAAATTAAAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  23   17  0.57
  24   11  0.37
  25    2  0.07

ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23


Consensus pattern (25 bp):   
CCCAAACAATTATCATTTATCCAAA

Found at i:1213 original size:18 final size:18

Alignment explanation


    Indices: 1190--1225  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1180 AAGTAAACTC

                              
       1190 TAAACAGACCCATTTTGA
          1 TAAACAGACCCATTTTGA

                              
       1208 TAAACAGACCCATTTTGA
          1 TAAACAGACCCATTTTGA

       1226 CTTCTTACCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28


Consensus pattern (18 bp):   
TAAACAGACCCATTTTGA

Found at i:2621 original size:21 final size:21

Alignment explanation


    Indices: 2555--2629  Score: 78
    Period size: 21  Copynumber: 3.6  Consensus size: 21

       2545 GATCCATACC

                       *         
       2555 CCACCCCCACCGGTCCACTCA
          1 CCACCCCCACCAGTCCACTCA

                 *    *         *
       2576 CCACCACCACTAGTCCACTCC
          1 CCACCCCCACCAGTCCACTCA

                          *  *  *
       2597 CCACCCCCACCAGTACAATCT
          1 CCACCCCCACCAGTCCACTCA

                 *      
       2618 CCACCTCCACCA
          1 CCACCCCCACCA

       2630 ATTCCATCTC


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

Matches are distributed among these distances:
  21   44  1.00

ACGTcount: A:0.24, C:0.59, G:0.05, T:0.12


Consensus pattern (21 bp):   
CCACCCCCACCAGTCCACTCA
Done.