Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001377.1 Kokia drynarioides strain JFW-HI SEQ_112847, 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: 5582
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:1382 original size:156 final size:156

Alignment explanation


    Indices: 1098--1404  Score: 470
    Period size: 156  Copynumber: 2.0  Consensus size: 156

       1088 GTTACAGCCC

                 *          *           *                        *         * 
       1098 CTTCTTCACCTCCACTGCCAACACCTACTGCACCTTCATGGCCACCGGCCCCGTCTTTGCCTATA
          1 CTTCTCCACCTCCACTACCAACACCTACAGCACCTTCATGGCCACCGGCCCCGGCTTTGCCTACA

                                         *                                   
       1163 ACACCAGCAACAACTCCTGAGCCTTGGGCGCCAACTACAGTTTCAGTGCCAGAAACAACAGTTAC
         66 ACACCAGCAACAACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTAC

              *             *         
       1228 TGGCCCTTGGGCACCATCTCCAATGT
        131 TGACCCTTGGGCACCAGCTCCAATGT

                       *        * *                *      *  *        *      
       1254 CTTCTCCACCTTCACTACCACCTCCTACAGCACCTTCATTGCCACCTGCTCCGGCTTTTCCTACA
          1 CTTCTCCACCTCCACTACCAACACCTACAGCACCTTCATGGCCACCGGCCCCGGCTTTGCCTACA

                     *                                                       
       1319 ACACCAGCACCAACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTAC
         66 ACACCAGCAACAACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTAC

                                 
       1384 TGACCCTTGGGCACCAGCTCC
        131 TGACCCTTGGGCACCAGCTCC

       1405 TGCACCTTCA


Statistics
Matches: 135,  Mismatches: 16, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
 156  135  1.00

ACGTcount: A:0.23, C:0.39, G:0.15, T:0.22


Consensus pattern (156 bp):   
CTTCTCCACCTCCACTACCAACACCTACAGCACCTTCATGGCCACCGGCCCCGGCTTTGCCTACA
ACACCAGCAACAACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTAC
TGACCCTTGGGCACCAGCTCCAATGT

Found at i:3779 original size:2 final size:2

Alignment explanation


    Indices: 3772--3799  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       3762 ATTCATAATA

                                                     
       3772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3800 GCATTTTTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4087 original size:22 final size:23

Alignment explanation


    Indices: 4042--4094  Score: 72
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       4032 AAATATTATA

                *                  
       4042 TTTAAATTTTAATTCACATAATT
          1 TTTATATTTTAATTCACATAATT

                          *        
       4065 TTTATATTTTAATTTA-ATAATT
          1 TTTATATTTTAATTCACATAATT

              *     
       4087 TTAATATT
          1 TTTATATT

       4095 ACTATTATAC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  22   13  0.48
  23   14  0.52

ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58


Consensus pattern (23 bp):   
TTTATATTTTAATTCACATAATT
Done.