Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_22419

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, 547

Length: 912
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21


Found at i:383 original size:45 final size:45

Alignment explanation


    Indices: 292--481  Score: 247
    Period size: 45  Copynumber: 4.2  Consensus size: 45

        282 CTATGGTGAG

                                                     *   
        292 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTTGAA
          1 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAA

                             *  *  *  *    *       *      
        337 GAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTAT-GACGTCGAA
          1 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCG-TGTCGAA

                                                         
        382 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAA
          1 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAA

                         *   *  *              * *  *    
        427 GAGAAATGGAATAGGCCCTCTAGTCCTGTTCGGTACCATGCCGAA
          1 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAA

                      
        472 GAGAAATGGA
          1 GAGAAATGGA

        482 CGAACCGGCC


Statistics
Matches: 124,  Mismatches: 19, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
  44    1  0.01
  45  122  0.98
  46    1  0.01

ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23


Consensus pattern (45 bp):   
GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAA

Found at i:449 original size:90 final size:90

Alignment explanation


    Indices: 292--481  Score: 290
    Period size: 90  Copynumber: 2.1  Consensus size: 90

        282 CTATGGTGAG

                                                     *                    *  
        292 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTTGAAGAGAAATGGAATAAGCCTTC
          1 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAAGCCCTC

                           **   *    
        357 TAGCCCCGTTCAGTATGACGTCGAA
         66 TAGCCCCGTTCAGTACCACGCCGAA

                                                                      *      
        382 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAGGCCCTC
          1 GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAAGCCCTC

               *  *    *      *      
        447 TAGTCCTGTTCGGTACCATGCCGAA
         66 TAGCCCCGTTCAGTACCACGCCGAA

                      
        472 GAGAAATGGA
          1 GAGAAATGGA

        482 CGAACCGGCC


Statistics
Matches: 90,  Mismatches: 10, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  90   90  1.00

ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23


Consensus pattern (90 bp):   
GAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAAGCCCTC
TAGCCCCGTTCAGTACCACGCCGAA
Done.