Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007384.1 Kokia drynarioides strain JFW-HI SEQ_122002, 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: 8178
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35


Found at i:3463 original size:38 final size:38

Alignment explanation


    Indices: 3411--3497  Score: 95
    Period size: 39  Copynumber: 2.2  Consensus size: 38

       3401 TGGGACAAGT

                     *       *                      
       3411 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGGTTGTGA
          1 CTCTT-CAAAAGGTATCATCCAATATG-AAAGGGTTGTGA

                               *    *              
       3450 CTCTTCAAAAGGTATCCATTCAATTTGAAAGGGTTGTGA
          1 CTCTTCAAAAGGTAT-CATCCAATATGAAAGGGTTGTGA

             *       
       3489 CGCTTCAAA
          1 CTCTTCAAA

       3498 TGGTGTCCAT


Statistics
Matches: 41,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  38    9  0.22
  39   25  0.61
  40    7  0.17

ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Consensus pattern (38 bp):   
CTCTTCAAAAGGTATCATCCAATATGAAAGGGTTGTGA

Found at i:5366 original size:29 final size:29

Alignment explanation


    Indices: 5282--5487  Score: 231
    Period size: 28  Copynumber: 7.1  Consensus size: 29

       5272 AAGACTCACG

                    *                 *   
       5282 AACTTTCTTAAAATTATATTTTGACCTCTA
          1 AACTTT-TCAAAATTATATTTTGACCCCTA

             *             *              
       5312 AGCTTTTCCAAAATTTTATTTTGACCCCTA
          1 AACTTTT-CAAAATTATATTTTGACCCCTA

                                *        
       5342 AACTTTTCAAAATTATATTTCGA-CCCTA
          1 AACTTTTCAAAATTATATTTTGACCCCTA

                  *                      
       5370 AACTTTCCAAAATTATATTTTGACCCC-A
          1 AACTTTTCAAAATTATATTTTGACCCCTA

              *                        * 
       5398 AAATTTTCAAAATTATA-TTTGACCCCCA
          1 AACTTTTCAAAATTATATTTTGACCCCTA

                          **     *       
       5426 AACTTTTCAAAATTGCATTTTAACCCCTA
          1 AACTTTTCAAAATTATATTTTGACCCCTA

                          * *     *       
       5455 AACTTTTCTAAAATCACATTTTAACCCC-A
          1 AACTTTTC-AAAATTATATTTTGACCCCTA

                
       5484 AACT
          1 AACT

       5488 CTCCGAAACT


Statistics
Matches: 153,  Mismatches: 18, Indels: 11
        0.84            0.10        0.06

Matches are distributed among these distances:
  27    9  0.06
  28   57  0.37
  29   40  0.26
  30   47  0.31

ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39


Consensus pattern (29 bp):   
AACTTTTCAAAATTATATTTTGACCCCTA

Found at i:8144 original size:2 final size:2

Alignment explanation


    Indices: 8139--8178  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       8129 ACACACATAC

                                                                       
       8139 AT AT AT AT AT AT 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 AT AT AT AT AT AT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AT

Done.