Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010486.1 Kokia drynarioides strain JFW-HI SEQ_125391, 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: 2140
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:887 original size:96 final size:96

Alignment explanation


    Indices: 699--890  Score: 210
    Period size: 96  Copynumber: 2.0  Consensus size: 96

        689 CTTTTGCGAA

                                           **  *                             
        699 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
          1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA

               * *  *    *                 
        764 GAATCGAAGATAAGGAAACATTACCTCGATT
         66 GAACCCAAAATAAAGAAACATTACCTCGATT

                *           *                           *                *   
        795 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATTACACCTAGTGAGTTAAGGTGCA-AATTTTT
          1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAA-G-GCACAATATTT

            *                    *   *        
        859 GA-AACCCAAAATAAA-AGAATATTGCCTCGATT
         64 CAGAACCCAAAATAAAGA-AACATTACCTCGATT

        891 TTGAAGTTTA


Statistics
Matches: 79,  Mismatches: 14, Indels: 6
        0.80            0.14        0.06

Matches are distributed among these distances:
  95    1  0.01
  96   67  0.85
  97    8  0.10
  98    3  0.04

ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31


Consensus pattern (96 bp):   
AAGGATATTTGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
GAACCCAAAATAAAGAAACATTACCTCGATT

Found at i:1198 original size:59 final size:59

Alignment explanation


    Indices: 1128--1491  Score: 503
    Period size: 59  Copynumber: 6.2  Consensus size: 59

       1118 CAGATGCACT

                *               **   *  *      *         *           * 
       1128 GGGGAAAAATGGTAATTTTTTAAAGATTCGGGGTCGAAAATGGGACTTTTGGAAGTTTG
          1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG

                                         *                           **
       1187 GGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAGTTTA
          1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG

                                           *                           
       1246 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGTGTCAAAAATGGGATTTTTGGAAGTTCG
          1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG

            *                            *                    **       
       1305 AGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATGGGATTTTTATAAGTTCG
          1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG

            *          *                *             *              * 
       1364 AGGGTAAAATGATAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTTG
          1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG

                                            *                    *      
       1423 GGGGATAAAATGGTAATTTTTGGAAGGTTTGGAGTCAAAAATGGGATTTTTGGGAGTTCG
          1 GGGG-TAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG

               *     
       1483 GGGTTAAAA
          1 GGGGTAAAA

       1492 ATTAGATTTT


Statistics
Matches: 271,  Mismatches: 33, Indels: 2
        0.89            0.11        0.01

Matches are distributed among these distances:
  59  219  0.81
  60   52  0.19

ACGTcount: A:0.30, C:0.03, G:0.32, T:0.34


Consensus pattern (59 bp):   
GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG

Found at i:1491 original size:29 final size:29

Alignment explanation


    Indices: 1154--1520  Score: 268
    Period size: 29  Copynumber: 12.4  Consensus size: 29

       1144 TTTTTAAAGA

                     *         *         
       1154 TTCGGGGTCGAAAATGGGACTTTTGGAAG
          1 TTCGGGGTCAAAAATGGGATTTTTGGAAG

               *               *            
       1183 TTTGGGGGT--AAAATGGTAATTTTTGGAAGG
          1 -TTCGGGGTCAAAAATGG-GATTTTTGGAA-G

              **                         
       1213 TTTAGGGTCAAAAATGGGATTTTTGGAAG
          1 TTCGGGGTCAAAAATGGGATTTTTGGAAG

               *               *            
       1242 TTTAGGGGT--AAAATGGTAATTTTTGGAAGG
          1 -TTCGGGGTCAAAAATGG-GATTTTTGGAA-G

              *  *                       
       1272 TTTGGTGTCAAAAATGGGATTTTTGGAAG
          1 TTCGGGGTCAAAAATGGGATTTTTGGAAG

                               *            
       1301 TTCGAGGGT--AAAATGGTAATTTTTGGAAGG
          1 TTCG-GGGTCAAAAATGG-GATTTTTGGAA-G

              **                    **   
       1331 TTTAGGGTCAAAAATGGGATTTTTATAAG
          1 TTCGGGGTCAAAAATGGGATTTTTGGAAG

                              **            
       1360 TTCGAGGGT--AAAATGATAATTTTTGGAAGG
          1 TTCG-GGGTCAAAAATG-GGATTTTTGGAA-G

                            *            
       1390 TTCGGGGTCAAAAATGAGATTTTTGGAAG
          1 TTCGGGGTCAAAAATGGGATTTTTGGAAG

              *     *          *            
       1419 TTTGGGG-GATAAAATGGTAATTTTTGGAAGG
          1 TTCGGGGTCA-AAAATGG-GATTTTTGGAA-G

              *  *                    *  
       1450 TTTGGAGTCAAAAATGGGATTTTTGGGAG
          1 TTCGGGGTCAAAAATGGGATTTTTGGAAG

                    *      **         *  
       1479 TTCGGGGTTAAAAATTAGATTTTTGGGAG
          1 TTCGGGGTCAAAAATGGGATTTTTGGAAG

                          
       1508 TTCGAGGGT-AAAA
          1 TTCG-GGGTCAAAA

       1521 TGGTAATTTT


Statistics
Matches: 272,  Mismatches: 41, Indels: 49
        0.75            0.11        0.14

Matches are distributed among these distances:
  28   28  0.10
  29  111  0.41
  30   91  0.33
  31   41  0.15
  32    1  0.00

ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34


Consensus pattern (29 bp):   
TTCGGGGTCAAAAATGGGATTTTTGGAAG

Done.