Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006393.1 Kokia drynarioides strain JFW-HI SEQ_120970, 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, 968

Length: 1614
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39


Found at i:168 original size:50 final size:50

Alignment explanation


    Indices: 62--158  Score: 176
    Period size: 50  Copynumber: 1.9  Consensus size: 50

         52 TATGGGTTTG

                                    *                         
         62 TAAGGTTGGACTTAAGTTTGAGCTGTTTGGTTTTGTTTAGGTATTGGATA
          1 TAAGGTTGGACTTAAGTTTGAGCTATTTGGTTTTGTTTAGGTATTGGATA

                                *                          
        112 TAAGGTTGGACTTAAGTTTGGGCTATTTGGTTTTGTTTAGGTATTGG
          1 TAAGGTTGGACTTAAGTTTGAGCTATTTGGTTTTGTTTAGGTATTGG

        159 TAGTTAGGTT


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  50   45  1.00

ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46


Consensus pattern (50 bp):   
TAAGGTTGGACTTAAGTTTGAGCTATTTGGTTTTGTTTAGGTATTGGATA

Found at i:210 original size:16 final size:18

Alignment explanation


    Indices: 189--229  Score: 50
    Period size: 19  Copynumber: 2.3  Consensus size: 18

        179 GTTATTAAAA

                              
        189 TGGGTTGTTT-GG-GTAT
          1 TGGGTTGTTTAGGAGTAT

                  *            
        205 TGGGTTTTTTAGGTAGTAT
          1 TGGGTTGTTTAGG-AGTAT

                  
        224 TGGGTT
          1 TGGGTT

        230 ATTTTAATTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  16    9  0.43
  17    2  0.10
  19   10  0.48

ACGTcount: A:0.10, C:0.00, G:0.39, T:0.51


Consensus pattern (18 bp):   
TGGGTTGTTTAGGAGTAT

Found at i:1240 original size:50 final size:50

Alignment explanation


    Indices: 1133--1273  Score: 112
    Period size: 50  Copynumber: 2.8  Consensus size: 50

       1123 TACTACTATG

                       *         *       *    *         *    *
       1133 AGTTTCAATTCGCCCCTCTATGACTTTAGGGGTATAAGATTTACTTCTGT
          1 AGTTTCAATTCACCCCTCTATAACTTTAGAGGTAAAAGATTTACATCTGC

              *       *      *                         *       
       1183 AGCTTCAATTTACCCCTTTATAACTTTAGAGGTAAAAGATTTGTCAT-TGC
          1 AGTTTCAATTCACCCCTCTATAACTTTAGAGGTAAAAGATTT-ACATCTGC

                                                         
       1233 AGTTTCAATCTGCA--CCTCTA-AAGCTTTAG-GTGTAAAAGATT
          1 AGTTTCAAT-T-CACCCCTCTATAA-CTTTAGAG-GTAAAAGATT

       1274 GGACTGCCAC


Statistics
Matches: 73,  Mismatches: 13, Indels: 10
        0.76            0.14        0.10

Matches are distributed among these distances:
  49    3  0.04
  50   66  0.90
  51    3  0.04
  52    1  0.01

ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38


Consensus pattern (50 bp):   
AGTTTCAATTCACCCCTCTATAACTTTAGAGGTAAAAGATTTACATCTGC

Found at i:1370 original size:39 final size:39

Alignment explanation


    Indices: 1265--1374  Score: 121
    Period size: 40  Copynumber: 2.8  Consensus size: 39

       1255 GCTTTAGGTG

                        *  ***        *            
       1265 TAAAAGATTGGACTGCCACAATCTGCACCATGGTTGGGA
          1 TAAAAGATTGGATTGTTTCAATCTGCCCCATGGTTGGGA

               *    **   *                         *
       1304 TAAGAGATCAGATGGTCTTCAATCTGCCCCATGGTTGGGC
          1 TAAAAGATTGGATTGT-TTCAATCTGCCCCATGGTTGGGA

                                           
       1344 TAAAAGATTGGATTGTTTCAATCTGCCCCAT
          1 TAAAAGATTGGATTGTTTCAATCTGCCCCAT

       1375 TGATAAGTGA


Statistics
Matches: 56,  Mismatches: 14, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
  39   25  0.45
  40   31  0.55

ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28


Consensus pattern (39 bp):   
TAAAAGATTGGATTGTTTCAATCTGCCCCATGGTTGGGA
Done.