Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005394.1 Kokia drynarioides strain JFW-HI SEQ_119399, 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, 768

Length: 1281
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25


Found at i:368 original size:206 final size:205

Alignment explanation


    Indices: 1--682  Score: 1034
    Period size: 206  Copynumber: 3.3  Consensus size: 205

                 *                              *                            
          1 AACCCTAGCTTCCTGAGAAGACACTGAGAAGCAGGTTGAAGCAATAAAAGGTTAGCTTCCTGATG
          1 AACCCCAGCTTCCTGAGAAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATG

                                           *          *         *            
         66 AGATACTGAGGAGTGAACCAAATTCGTCTTCATGATGAGATATAGAGAGACGGATTAAGATAAAC
         66 AGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAGA-GAATTAAGATAAAC

                                *                                            
        131 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAG
        130 GACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAG

                       
        196 CAAAATCTTCG
        195 CAAAATCTTCG

                        *                       *                        *   
        207 AACCCCAGCTTCTTGAGAAGACACTGAGAAGCAGGTTGAAGCAATAAAAGGTTAGCTTCCTTATG
          1 AACCCCAGCTTCCTGAGAAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATG

                                                                        *    
        272 AGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAGATGAATTAAGACAAAC
         66 AGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAGA-GAATTAAGATAAAC

                       *      *                                          *   
        337 GACGCGGTCATATTCCTGGTAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAG
        130 GACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAG

                       
        402 CAAAATCTTCG
        195 CAAAATCTTCG

              *                                                              
        413 AATCCCAGC-TCCTTGAGAAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGAT
          1 AACCCCAGCTTCC-TGAGAAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGAT

                                     *                                *      
        477 GAGATACTGAGGAGTGAACCAAATTTGTCTTCCTGATGAGATACAGAGA-AGCAGATTGAGATAA
         65 GAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAGAG-A-ATTAAGATAA

                *                                       *            *  *    
        541 ACGAGGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAGTCAAACCCACGCGC-GA-TG
        128 ACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTG

                 *  *     
        604 A--ATGAACCTTCG
        193 AGCA-AAATCTTCG

                            *    *                   *                       
        616 AACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGTTAGCTTCCTGAT
          1 AACCCCAGCTTCCTGAGAAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTAGCTTCCTGAT

              
        681 GA
         65 GA

        683 AATATGGGGA


Statistics
Matches: 438,  Mismatches: 32, Indels: 14
        0.90            0.07        0.03

Matches are distributed among these distances:
 202    1  0.00
 203   48  0.11
 204   23  0.05
 205    5  0.01
 206  361  0.82

ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21


Consensus pattern (205 bp):   
AACCCCAGCTTCCTGAGAAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATG
AGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAGAGAATTAAGATAAACG
ACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAGC
AAAATCTTCG

Found at i:1158 original size:6 final size:6

Alignment explanation


    Indices: 1149--1216  Score: 57
    Period size: 6  Copynumber: 11.2  Consensus size: 6

       1139 TTTAAATTGG

                       **                   *              *       **
       1149 TTTAAA TTTATT TTTAAA TTTAAA TTTATA -TTAAA TTTAAT TTTATCTT
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA

                                  
       1198 TTTAAA TTTAAA TTTAAA T
          1 TTTAAA TTTAAA TTTAAA T

       1217 GGATTTAAAA


Statistics
Matches: 49,  Mismatches: 10, Indels: 6
        0.75            0.15        0.09

Matches are distributed among these distances:
   5    4  0.08
   6   40  0.82
   8    5  0.10

ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59


Consensus pattern (6 bp):   
TTTAAA

Found at i:1255 original size:13 final size:13

Alignment explanation


    Indices: 1239--1272  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       1229 TTAATATTTA

                         
       1239 AAATTAAAAGCCC
          1 AAATTAAAAGCCC

                      *  
       1252 AAATTAAAAGTCC
          1 AAATTAAAAGCCC

               *    
       1265 AAAATAAA
          1 AAATTAAA

       1273 TACAAAGTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18


Consensus pattern (13 bp):   
AAATTAAAAGCCC
Done.