Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006963.1 Kokia drynarioides strain JFW-HI SEQ_121568, 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: 6291
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:1012 original size:36 final size:36

Alignment explanation


    Indices: 952--1035  Score: 123
    Period size: 36  Copynumber: 2.3  Consensus size: 36

        942 TATCAATCGC

                        * *                     
        952 CAAGACAAGAATCTGCTTTCGCAAGCAGTGGATTGG
          1 CAAGACAAGAATATACTTTCGCAAGCAGTGGATTGG

                      *        *     *          
        988 CAAGACAAGATTATACTTTTGCAAGTAGTGGATTGG
          1 CAAGACAAGAATATACTTTCGCAAGCAGTGGATTGG

                        
       1024 CAAGACAAGAAT
          1 CAAGACAAGAAT

       1036 CTATTTTCTC


Statistics
Matches: 42,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   42  1.00

ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24


Consensus pattern (36 bp):   
CAAGACAAGAATATACTTTCGCAAGCAGTGGATTGG

Found at i:1319 original size:18 final size:18

Alignment explanation


    Indices: 1298--1340  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1288 TTTCATCAAT

                      *       
       1298 ATTTATTTTATTTTTTAA
          1 ATTTATTTTAATTTTTAA

                *  *          
       1316 ATTTCTTATAATTTTTAA
          1 ATTTATTTTAATTTTTAA

                    
       1334 A-TTATTT
          1 ATTTATTT

       1341 GTTGTTGTGA


Statistics
Matches: 20,  Mismatches: 5, Indels: 1
        0.77            0.19        0.04

Matches are distributed among these distances:
  17    4  0.20
  18   16  0.80

ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67


Consensus pattern (18 bp):   
ATTTATTTTAATTTTTAA

Found at i:4338 original size:39 final size:39

Alignment explanation


    Indices: 4222--4601  Score: 300
    Period size: 39  Copynumber: 9.6  Consensus size: 39

       4212 ATAGTTTTAG

                        *     *  *   *  *        **
       4222 GGGTAAAAGATTAGATTGTTTTAATTTGTCCCATGGTCG
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA

                  *    * *  *                        
       4261 GGGTAAGAGATCGAATGGTCTTCAATCTGCCCTC-TGGTTA
          1 GGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTTA

               *                                  *
       4301 GGGAAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTG
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA

                  *     *  *    *        *       *    
       4340 GGGTAAGAGA-TCGAATGATATTCAATCTACCCTC-TTGTTA
          1 GGGTAAAAGATTGGATTG--CTTCAATCTGCCC-CATGGTTA

                   *                             * 
       4380 GGGTAAATGATTGGATTGCTTCAATCTGCCCCATGGTCA
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA

            *     *     *  *                  *      
       4419 AGGTAAGAGA-TCGAATGATCTTCAATCTGCCCCTTGGTTA
          1 GGGTAAAAGATTGGATTG--CTTCAATCTGCCCCATGGTTA

                            *    *     *         * 
       4459 GGGTAAAAGATTGGATCGCTTTAATCTACCCCATGGTCA
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA

                * *         *           *   **      
       4498 GGGTGAGAGATTGGATGGTCTTCAATCTTCCCTTTGGTTA
          1 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTTA

                         *               *       * 
       4538 GGGTAAAAGATTGAATTGCTTCAATCTGCTCCATGGTCA
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA

                        *            
       4577 GGGTAAAAGATTAGATTGCTTCAAT
          1 GGGTAAAAGATTGGATTGCTTCAAT

       4602 TTGTCTCATG


Statistics
Matches: 261,  Mismatches: 68, Indels: 24
        0.74            0.19        0.07

Matches are distributed among these distances:
  38   12  0.05
  39  132  0.51
  40  106  0.41
  41   11  0.04

ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32


Consensus pattern (39 bp):   
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA

Found at i:4588 original size:79 final size:79

Alignment explanation


    Indices: 4222--4587  Score: 473
    Period size: 79  Copynumber: 4.6  Consensus size: 79

       4212 ATAGTTTTAG

                        *     *  *   *  *         *                          
       4222 GGGTAAAAGATTAGATTGTTTTAATTTGTCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGAATGGTCTTCAAT

                   *      
       4287 CTGCCCTCTGGTTA
         66 CTGCCCTTTGGTTA

               *                                 **                 * *      
       4301 GGGAAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTGGGGTAAGAGATCGAATGATATTCAAT
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGAATGGTCTTCAAT

              *            
       4366 CTACCCTCTT-GTTA
         66 CTGCCCT-TTGGTTA

                   *                               *                *        
       4380 GGGTAAATGATTGGATTGCTTCAATCTGCCCCATGGTCAAGGTAAGAGATCGAATGATCTTCAAT
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGAATGGTCTTCAAT

                  *       
       4445 CTGCCCCTTGGTTA
         66 CTGCCCTTTGGTTA

                            *    *     *               *      * *            
       4459 GGGTAAAAGATTGGATCGCTTTAATCTACCCCATGGTCAGGGTGAGAGATTGGATGGTCTTCAAT
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGAATGGTCTTCAAT

              *           
       4524 CTTCCCTTTGGTTA
         66 CTGCCCTTTGGTTA

                         *               *               *    
       4538 GGGTAAAAGATTGAATTGCTTCAATCTGCTCCATGGTCAGGGTAAAAGAT
          1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGAT

       4588 TAGATTGCTT


Statistics
Matches: 248,  Mismatches: 37, Indels: 4
        0.86            0.13        0.01

Matches are distributed among these distances:
  78    2  0.01
  79  245  0.99
  80    1  0.00

ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31


Consensus pattern (79 bp):   
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGAATGGTCTTCAAT
CTGCCCTTTGGTTA

Found at i:6262 original size:63 final size:63

Alignment explanation


    Indices: 6172--6291  Score: 188
    Period size: 63  Copynumber: 1.9  Consensus size: 63

       6162 TTATTTATTT

                                                                            
       6172 ATTTATATATCTATATTAATAAAATAATAAA-AAATAAATAAAACAAAATTAATATTATTTTAC
          1 ATTTATATATCTATATTAATAAAATAATAAATAAAT-AATAAAACAAAATTAATATTATTTTAC

                  *   *      *   *                                   
       6235 ATTTATTTATTTATATTCATACAATAATAAATAAATAATAAAACAAAATTAATATTA
          1 ATTTATATATCTATATTAATAAAATAATAAATAAATAATAAAACAAAATTAATATTA


Statistics
Matches: 52,  Mismatches: 4, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  63   48  0.92
  64    4  0.08

ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39


Consensus pattern (63 bp):   
ATTTATATATCTATATTAATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
Done.