Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005368.1 Kokia drynarioides strain JFW-HI SEQ_119351, 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: 3359
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:1695 original size:30 final size:29

Alignment explanation


    Indices: 1647--1764  Score: 96
    Period size: 30  Copynumber: 4.0  Consensus size: 29

       1637 AATAAAAATG

                      *  *             *  
       1647 AAAGTTTTAGGGTTAAAATGCAATTTTCAA
          1 AAAG-TTTAGAGTCAAAATGCAATTTTTAA

                                *          
       1677 AAAGTTTATGAGTCAAAATGAAATTTTTAGA
          1 AAAGTTTA-GAGTCAAAATGCAATTTTTA-A

                      *                  **
       1708 AAA-TTTGAGCGTCAAAAT-CGAATTTTTGG
          1 AAAGTTT-AGAGTCAAAATGC-AATTTTTAA

                   *           *        
       1737 AAAGTTTGGAGTCAAAATGGAATTTTTA
          1 AAAGTTTAGAGTCAAAATGCAATTTTTA

       1765 GGAAGTTCAA


Statistics
Matches: 70,  Mismatches: 12, Indels: 13
        0.74            0.13        0.14

Matches are distributed among these distances:
  29   23  0.33
  30   42  0.60
  31    5  0.07

ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36


Consensus pattern (29 bp):   
AAAGTTTAGAGTCAAAATGCAATTTTTAA

Found at i:1763 original size:59 final size:60

Alignment explanation


    Indices: 1677--1801  Score: 153
    Period size: 59  Copynumber: 2.1  Consensus size: 60

       1667 CAATTTTCAA

                    *                           **            *         
       1677 AAAGTTTATGAGTCAAAATGAAATTTTTAGAAAATTTGAGCGTCAAAATCGAATTTTTGG
          1 AAAGTTTAGGAGTCAAAATGAAATTTTTAGAAAATTCAAGCGTCAAAATCAAATTTTTGG

                                *         *  *      *      *            
       1737 AAAGTTT-GGAGTCAAAATGGAATTTTTAGGAAGTTCAAGGGTCAAATTCAAATTTTTGG
          1 AAAGTTTAGGAGTCAAAATGAAATTTTTAGAAAATTCAAGCGTCAAAATCAAATTTTTGG

            *     
       1796 GAAGTT
          1 AAAGTT

       1802 CGGGGGCCAA


Statistics
Matches: 55,  Mismatches: 10, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  59   48  0.87
  60    7  0.13

ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34


Consensus pattern (60 bp):   
AAAGTTTAGGAGTCAAAATGAAATTTTTAGAAAATTCAAGCGTCAAAATCAAATTTTTGG

Found at i:1770 original size:29 final size:30

Alignment explanation


    Indices: 1678--1771  Score: 104
    Period size: 30  Copynumber: 3.2  Consensus size: 30

       1668 AATTTTCAAA

                                *         *
       1678 AAGTTT-ATGAGTCAAAATGAAATTTTTAGA
          1 AAGTTTGA-GAGTCAAAATGGAATTTTTAGG

              *      *        *           
       1708 AAATTTGAGCGTCAAAATCGAATTTTT-GG
          1 AAGTTTGAGAGTCAAAATGGAATTTTTAGG

                                           
       1737 AAAGTTTG-GAGTCAAAATGGAATTTTTAGG
          1 -AAGTTTGAGAGTCAAAATGGAATTTTTAGG

                 
       1767 AAGTT
          1 AAGTT

       1772 CAAGGGTCAA


Statistics
Matches: 53,  Mismatches: 8, Indels: 7
        0.78            0.12        0.10

Matches are distributed among these distances:
  29   23  0.43
  30   29  0.55
  31    1  0.02

ACGTcount: A:0.38, C:0.05, G:0.21, T:0.35


Consensus pattern (30 bp):   
AAGTTTGAGAGTCAAAATGGAATTTTTAGG

Found at i:1791 original size:30 final size:30

Alignment explanation


    Indices: 1757--1822  Score: 87
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       1747 GTCAAAATGG

                                 *        
       1757 AATTTTTAGGAAGTTCAAGGGTCAAATTCA
          1 AATTTTTAGGAAGTTCAAGGGCCAAATTCA

                   *        **           *
       1787 AATTTTTGGGAAGTTCGGGGGCCAAATTCG
          1 AATTTTTAGGAAGTTCAAGGGCCAAATTCA

                  
       1817 AATTTT
          1 AATTTT

       1823 GTATAAAACA


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35


Consensus pattern (30 bp):   
AATTTTTAGGAAGTTCAAGGGCCAAATTCA

Found at i:2683 original size:14 final size:13

Alignment explanation


    Indices: 2645--2687  Score: 59
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       2635 TATTTTCAAA

                        *
       2645 ATAAAAAAGAAAA
          1 ATAAAAAAGAAAT

                   *     
       2658 ATAAAAATGAAAT
          1 ATAAAAAAGAAAT

                          
       2671 ATAAAACAAGAAAT
          1 ATAAAA-AAGAAAT

               
       2685 ATA
          1 ATA

       2688 TAGATCTATA


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  13   17  0.65
  14    9  0.35

ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16


Consensus pattern (13 bp):   
ATAAAAAAGAAAT
Done.