Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_10573

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, 250

Length: 417
ACGTcount: A:0.19, C:0.07, G:0.45, T:0.29


Found at i:225 original size:24 final size:24

Alignment explanation


    Indices: 198--284  Score: 60
    Period size: 24  Copynumber: 3.9  Consensus size: 24

        188 GAGGAGGGAT

                                    
        198 TAGTGGTGGTGGTGGTGCTAGTGC
          1 TAGTGGTGGTGGTGGTGCTAGTGC

                 * * *              
        222 TAGTGCTCGAGGT-G-G--A--GC
          1 TAGTGGTGGTGGTGGTGCTAGTGC

                * *    *       *   *
        240 TAGTAGAGGTGCTGGTGCTGGTGG
          1 TAGTGGTGGTGGTGGTGCTAGTGC

                                 
        264 TAGTGGTGGTGGTGGTGCTAG
          1 TAGTGGTGGTGGTGGTGCTAG

        285 AGGAGGCGTA


Statistics
Matches: 42,  Mismatches: 15, Indels: 12
        0.61            0.22        0.17

Matches are distributed among these distances:
  18    9  0.21
  19    1  0.02
  20    2  0.05
  22    1  0.02
  23    1  0.02
  24   28  0.67

ACGTcount: A:0.11, C:0.09, G:0.49, T:0.30


Consensus pattern (24 bp):   
TAGTGGTGGTGGTGGTGCTAGTGC

Found at i:298 original size:24 final size:24

Alignment explanation


    Indices: 271--332  Score: 70
    Period size: 24  Copynumber: 2.6  Consensus size: 24

        261 TGGTAGTGGT

                 *  *             * 
        271 GGTGGTGGTGCTAGAGGAGGCGTA
          1 GGTGGAGGAGCTAGAGGAGGCGCA

                        *       *   
        295 GGTGGAGGAGCTGGAGGAGGTGCA
          1 GGTGGAGGAGCTAGAGGAGGCGCA

                  *       
        319 GGTGGAAGAGCTAG
          1 GGTGGAGGAGCTAG

        333 TGCTGGTGGA


Statistics
Matches: 31,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.21, C:0.08, G:0.55, T:0.16


Consensus pattern (24 bp):   
GGTGGAGGAGCTAGAGGAGGCGCA
Done.