Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013977.1 Kokia drynarioides strain JFW-HI SEQ_129008, 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: 7587
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:2667 original size:41 final size:41

Alignment explanation


    Indices: 2622--2932  Score: 374
    Period size: 41  Copynumber: 7.6  Consensus size: 41

       2612 ATAGGAAAAA

                                    *                 
       2622 CGCCGCTAAAGGTCAGAGCATTAGTGGCG-TTCATGAGGAAG
          1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTT-ATGAGGAAG

                       *       *        **           
       2663 CGCCGCTAAAGATCAGAGCGTTAGCGGCATTTATGAGGAAG
          1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGGAAG

                           * **                *  *   
       2704 CGCCGCTAAAGGTCACAATATTAGCGGCGCTTACTCA-TAAG
          1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTA-TGAGGAAG

               *   *         *                       
       2745 CGCTGCTGAAGGTCAGAACATTAGCGGCGCTTATGAGGAAG
          1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGGAAG

            *                  *   *                 
       2786 GGCCGCTAAAGGTCAGAGCGTTAACGGCGCTTATGAGGAAG
          1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGGAAG

             * *      *  *                           
       2827 CACTGCTAAAAGTGAGAGCATTAGCGGCGCTTATGAGGAAG
          1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGGAAG

              *                      *               
       2868 CGTCGCTAAAGGTCAGAGCATTAGCAGCGCTTATGAGGAAG
          1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGGAAG

               *           *        
       2909 CGCAGCTAAAGGTCAAAGCATTAG
          1 CGCCGCTAAAGGTCAGAGCATTAG

       2933 TTAATTTATA


Statistics
Matches: 226,  Mismatches: 41, Indels: 6
        0.83            0.15        0.02

Matches are distributed among these distances:
  40    2  0.01
  41  220  0.97
  42    4  0.02

ACGTcount: A:0.29, C:0.20, G:0.31, T:0.19


Consensus pattern (41 bp):   
CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGGAAG

Found at i:4363 original size:18 final size:21

Alignment explanation


    Indices: 4342--4383  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       4332 AATGATATTG

                                 
       4342 AATAAATT-TC-AAA-TATAA
          1 AATAAATTATCAAAATTATAA

                                 
       4360 AAT-AATTATCAAAATTATAA
          1 AATAAATTATCAAAATTATAA

                
       4380 AATA
          1 AATA

       4384 TTAATTAATA


Statistics
Matches: 20,  Mismatches: 0, Indels: 5
        0.80            0.00        0.20

Matches are distributed among these distances:
  17    4  0.20
  18    5  0.25
  19    3  0.15
  20    8  0.40

ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33


Consensus pattern (21 bp):   
AATAAATTATCAAAATTATAA

Found at i:6410 original size:43 final size:41

Alignment explanation


    Indices: 6362--6502  Score: 167
    Period size: 43  Copynumber: 3.3  Consensus size: 41

       6352 ATCTGTTAAT

                    *               *                  
       6362 TTTAGCGGTGTTTGTGGGCAAAGCACCATTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGTGGG-AAAGCGCC-TTAAAGACCATGTTC

                                                       
       6405 TTTAGCGGCGTTTGTGGGGAAAGCGCCTCTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGT-GGGAAAGCGCCT-TAAAGACCATGTTC

                   * *                  *              
       6448 TTTAGCGACATTTGTGAGG-AAGCGCCGCTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGTG-GGAAAGCGCC-TTAAAGACCATGTTC

             *           
       6490 TATAGCGGCGTTT
          1 TTTAGCGGCGTTT

       6503 TTCCTCATAA


Statistics
Matches: 86,  Mismatches: 8, Indels: 9
        0.83            0.08        0.09

Matches are distributed among these distances:
  42   33  0.38
  43   50  0.58
  44    3  0.03

ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29


Consensus pattern (41 bp):   
TTTAGCGGCGTTTGTGGGAAAGCGCCTTAAAGACCATGTTC

Done.