Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003377.1 Kokia drynarioides strain JFW-HI SEQ_116105, 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: 2327
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34


Found at i:130 original size:8 final size:8

Alignment explanation


    Indices: 113--144  Score: 57
    Period size: 8  Copynumber: 4.1  Consensus size: 8

        103 GACTTAATTT

                    
        113 AAAAAA-A
          1 AAAAAAGA

                    
        120 AAAAAAGA
          1 AAAAAAGA

                    
        128 AAAAAAGA
          1 AAAAAAGA

                    
        136 AAAAAAGA
          1 AAAAAAGA

             
        144 A
          1 A

        145 GGAACAAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   7    6  0.25
   8   18  0.75

ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00


Consensus pattern (8 bp):   
AAAAAAGA

Found at i:400 original size:60 final size:58

Alignment explanation


    Indices: 336--487  Score: 153
    Period size: 59  Copynumber: 2.6  Consensus size: 58

        326 CGTAAATTTG

                       *        *                             * *       
        336 GAAAGTTTAGGAGTCAAAATGTAATTTTTAGAAAGTGCAAGGGTAAAAATGTGATTTTTA
          1 GAAAGTTTAGGGGTCAAAATATAATTTTT-GAAAGTGCAA-GGTAAAAATATAATTTTTA

                    *       *             *      * *    *               
        396 GAAAGTTTGGGGGTCACAATCA-AAGTTTTGGAAAGTTCGAGGTCAAAATATAATTTTTA
          1 GAAAGTTTAGGGGTCAAAAT-ATAA-TTTTTGAAAGTGCAAGGTAAAAATATAATTTTTA

            *   *                            
        455 AAAAATTTAGGGGTCAAAATATAATTTTTGAAA
          1 GAAAGTTTAGGGGTCAAAATATAATTTTTGAAA

        488 AATTCGAGTG


Statistics
Matches: 74,  Mismatches: 15, Indels: 8
        0.76            0.15        0.08

Matches are distributed among these distances:
  58    9  0.12
  59   34  0.46
  60   27  0.36
  61    4  0.05

ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33


Consensus pattern (58 bp):   
GAAAGTTTAGGGGTCAAAATATAATTTTTGAAAGTGCAAGGTAAAAATATAATTTTTA

Found at i:468 original size:59 final size:60

Alignment explanation


    Indices: 389--505  Score: 139
    Period size: 59  Copynumber: 2.0  Consensus size: 60

        379 TAAAAATGTG

                   *   *   *       *              *   *                  
        389 ATTTTTAGAAAGTTTGGGGGTCACAATCA-AAGTTTTGGAAAGTTCGAG-GTCAAAATATA
          1 ATTTTTAAAAAATTTAGGGGTCAAAAT-ATAAGTTTTGAAAAATTCGAGTGTCAAAATATA

                                           *                    *     
        448 ATTTTTAAAAAATTTAGGGGTCAAAATATAATTTTTGAAAAATTCGAGTGTCGAAATA
          1 ATTTTTAAAAAATTTAGGGGTCAAAATATAAGTTTTGAAAAATTCGAGTGTCAAAATA

        506 GAAGTTCTGG


Statistics
Matches: 48,  Mismatches: 8, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  58    1  0.02
  59   39  0.81
  60    8  0.17

ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34


Consensus pattern (60 bp):   
ATTTTTAAAAAATTTAGGGGTCAAAATATAAGTTTTGAAAAATTCGAGTGTCAAAATATA

Found at i:505 original size:30 final size:29

Alignment explanation


    Indices: 421--505  Score: 98
    Period size: 30  Copynumber: 2.9  Consensus size: 29

        411 ACAATCAAAG

                 *   *                   
        421 TTTTGGAAAGTTCGAGGTCAAAATATAAT
          1 TTTTGAAAAATTCGAGGTCAAAATATAAT

                *        * *              
        450 TTTTAAAAAATTTAGGGGTCAAAATATAAT
          1 TTTTGAAAAA-TTCGAGGTCAAAATATAAT

                                *     
        480 TTTTGAAAAATTCGAGTGTCGAAATA
          1 TTTTGAAAAATTCGAG-GTCAAAATA

        506 GAAGTTCTGG


Statistics
Matches: 45,  Mismatches: 9, Indels: 3
        0.79            0.16        0.05

Matches are distributed among these distances:
  29   11  0.24
  30   34  0.76

ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35


Consensus pattern (29 bp):   
TTTTGAAAAATTCGAGGTCAAAATATAAT
Done.