Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010737.1 Kokia drynarioides strain JFW-HI SEQ_125690, 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: 4290
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2135 original size:45 final size:45

Alignment explanation


    Indices: 2056--2182  Score: 137
    Period size: 45  Copynumber: 2.8  Consensus size: 45

       2046 GGGAGGAATA

                  *   *  *     *     *  *        *       
       2056 GAGTATCGCGATGGCTCGTTAAACTCAGCCTGATATCTTTCCCTT
          1 GAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATCATTCCCTT

                         *         *     *      *   **   
       2101 GAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATAATTGGCTT
          1 GAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATCATTCCCTT

                                                 
       2146 GAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATC
          1 GAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATC

       2183 CCTAGCTTGA


Statistics
Matches: 67,  Mismatches: 15, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  45   67  1.00

ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32


Consensus pattern (45 bp):   
GAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATCATTCCCTT

Found at i:2191 original size:45 final size:45

Alignment explanation


    Indices: 2098--2192  Score: 127
    Period size: 45  Copynumber: 2.1  Consensus size: 45

       2088 ATATCTTTCC

                            *         *     *        * * 
       2098 CTTGAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATAATTGG
          1 CTTGAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATAACTAG

                                                   **    
       2143 CTTGAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATCCCTAG
          1 CTTGAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATAACTAG

                 
       2188 CTTGA
          1 CTTGA

       2193 TGACCTATGC


Statistics
Matches: 43,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  45   43  1.00

ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33


Consensus pattern (45 bp):   
CTTGAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATAACTAG

Found at i:4143 original size:16 final size:16

Alignment explanation


    Indices: 4122--4170  Score: 50
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       4112 TGATGGGGAT

                            
       4122 ATTATTTTGATAAATA
          1 ATTATTTTGATAAATA

                        *  *
       4138 ATTATTTT--TATATT
          1 ATTATTTTGATAAATA

                         *  
       4152 A-TATTTTGATAATTA
          1 ATTATTTTGATAAATA

                
       4167 ATTA
          1 ATTA

       4171 GTTAGGTTTA


Statistics
Matches: 25,  Mismatches: 5, Indels: 6
        0.69            0.14        0.17

Matches are distributed among these distances:
  13    6  0.24
  14    5  0.20
  15    4  0.16
  16   10  0.40

ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57


Consensus pattern (16 bp):   
ATTATTTTGATAAATA
Done.