Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009061.1 Kokia drynarioides strain JFW-HI SEQ_123761, 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: 2319
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36


Found at i:604 original size:43 final size:43

Alignment explanation


    Indices: 550--724  Score: 181
    Period size: 43  Copynumber: 4.1  Consensus size: 43

        540 CTGTTAATGT

                 *       *                 *           
        550 TAGTGGCGTTTGTAGGAAAAGCGCCGCTAAAGATCATGTTCTA
          1 TAGTGACGTTTGTGGGAAAAGCGCCGCTAAAAATCATGTTCTA

                  *                 *        *      *  
        593 TAGTGATGTTTGTGGGAAAAGCGCTGCTAAAAACCATGTTTTA
          1 TAGTGACGTTTGTGGGAAAAGCGCCGCTAAAAATCATGTTCTA

                                 ***   *                
        636 TAGT-AGCGTTTGTGGGAAAAATACCGTTAAAAATCATGTTCTA
          1 TAGTGA-CGTTTGTGGGAAAAGCGCCGCTAAAAATCATGTTCTA

               * *                 * *     *     *     
        679 TAGCGGCGTTTGTGGGAAAAGCGTCTCTAAAGATCATATTCTA
          1 TAGTGACGTTTGTGGGAAAAGCGCCGCTAAAAATCATGTTCTA

               
        722 TAG
          1 TAG

        725 CAGCGTTTTC


Statistics
Matches: 105,  Mismatches: 25, Indels: 4
        0.78            0.19        0.03

Matches are distributed among these distances:
  42    1  0.01
  43  104  0.99

ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31


Consensus pattern (43 bp):   
TAGTGACGTTTGTGGGAAAAGCGCCGCTAAAAATCATGTTCTA

Found at i:679 original size:86 final size:86

Alignment explanation


    Indices: 550--732  Score: 215
    Period size: 86  Copynumber: 2.1  Consensus size: 86

        540 CTGTTAATGT

                *               * *        *              *  *               
        550 TAGTGGCGTTTGTAGGAAAAGCGCCGCTAAAGATCATGTTCTATAGTGATGTTTGTGGGAAAAGC
          1 TAGTAGCGTTTGTAGGAAAAACACCGCTAAAAATCATGTTCTATAGCGACGTTTGTGGGAAAAGC

                            *  *  
        615 G-CTGCTAAAAACCATGTTTTA
         66 GTCT-CTAAAAACCATATTCTA

                         *       *    *                     *                
        636 TAGTAGCGTTTGTGGGAAAAATACCGTTAAAAATCATGTTCTATAGCGGCGTTTGTGGGAAAAGC
          1 TAGTAGCGTTTGTAGGAAAAACACCGCTAAAAATCATGTTCTATAGCGACGTTTGTGGGAAAAGC

                     * *         
        701 GTCTCTAAAGATCATATTCTA
         66 GTCTCTAAAAACCATATTCTA

               *       
        722 TAGCAGCGTTT
          1 TAGTAGCGTTT

        733 TCTCACATAA


Statistics
Matches: 81,  Mismatches: 15, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  86   79  0.98
  87    2  0.02

ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31


Consensus pattern (86 bp):   
TAGTAGCGTTTGTAGGAAAAACACCGCTAAAAATCATGTTCTATAGCGACGTTTGTGGGAAAAGC
GTCTCTAAAAACCATATTCTA

Found at i:986 original size:101 final size:101

Alignment explanation


    Indices: 811--1007  Score: 367
    Period size: 101  Copynumber: 2.0  Consensus size: 101

        801 TTAGCAAGAA

                                                                             
        811 TAAATCTTCCAAAAATGATAAAAATGTGCAAGCACATTTGTATGATTAATAATAATGATAACAAT
          1 TAAATCTTCCAAAAATGATAAAAATGTGCAAGCACATTTGTATGATTAATAATAATGATAACAAT

              *               *                 
        876 GATAAGAAGTTGTTTCCTGCCAAGTGGAAATCTTGC
         66 GACAAGAAGTTGTTTCCTACCAAGTGGAAATCTTGC

                                                                             
        912 TAAATCTTCCAAAAATGATAAAAATGTGCAAGCACATTTGTATGATTAATAATAATGATAACAAT
          1 TAAATCTTCCAAAAATGATAAAAATGTGCAAGCACATTTGTATGATTAATAATAATGATAACAAT

                                  *        
        977 GACAAGAAGTTGTTTCCTACCACGTGGAAAT
         66 GACAAGAAGTTGTTTCCTACCAAGTGGAAAT

       1008 TTATGGAATC


Statistics
Matches: 93,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 101   93  1.00

ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30


Consensus pattern (101 bp):   
TAAATCTTCCAAAAATGATAAAAATGTGCAAGCACATTTGTATGATTAATAATAATGATAACAAT
GACAAGAAGTTGTTTCCTACCAAGTGGAAATCTTGC

Found at i:1243 original size:30 final size:30

Alignment explanation


    Indices: 1202--1260  Score: 82
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1192 ATTTAATTAT

                *                         
       1202 AAAATATTATAAAATAGTCATTCAACTATA
          1 AAAAAATTATAAAATAGTCATTCAACTATA

                           *   *  *      
       1232 AAAAAATTATAAAATGGTCTTTTAACTAT
          1 AAAAAATTATAAAATAGTCATTCAACTAT

       1261 TTAATTTTGT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36


Consensus pattern (30 bp):   
AAAAAATTATAAAATAGTCATTCAACTATA
Done.