Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01942.F1

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, 766

Length: 1278
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24


Found at i:446 original size:45 final size:45

Alignment explanation


    Indices: 396--633  Score: 237
    Period size: 45  Copynumber: 5.3  Consensus size: 45

        386 GTATCATACT

                                *                         
        396 GAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTAT-GACGTC
          1 GAAGAGAAATGGAATAAGCCATCTAGCCCCGTTCAGTATCG-CGTC

            *                      *  *  *    *      *  *
        441 AAAGAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTT
          1 GAAGAGAAATGGAATAAGCCATCTAGCCCCGTTCAGTATCGCGTC

                                *                         
        486 GAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTAT-GACGTC
          1 GAAGAGAAATGGAATAAGCCATCTAGCCCCGTTCAGTATCG-CGTC

                                   *  *  *    *      *   
        531 GAAGAGAAATGGAATAAGCCATCGAGTCCTGTTCGGTATCGTGTC
          1 GAAGAGAAATGGAATAAGCCATCTAGCCCCGTTCAGTATCGCGTC

                            *   *     *  *    *   * ** * 
        576 GAAGAGAAATGGAATAGGCCCTCTAGTCCTGTTCGGTACCATGCC
          1 GAAGAGAAATGGAATAAGCCATCTAGCCCCGTTCAGTATCGCGTC

                         
        621 GAAGAGAAATGGA
          1 GAAGAGAAATGGA

        634 CGAACCGGCC


Statistics
Matches: 162,  Mismatches: 28, Indels: 6
        0.83            0.14        0.03

Matches are distributed among these distances:
  44    1  0.01
  45  159  0.98
  46    2  0.01

ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23


Consensus pattern (45 bp):   
GAAGAGAAATGGAATAAGCCATCTAGCCCCGTTCAGTATCGCGTC

Found at i:509 original size:90 final size:90

Alignment explanation


    Indices: 375--601  Score: 391
    Period size: 90  Copynumber: 2.5  Consensus size: 90

        365 GGAGAGTTCA

                            * **                                             
        375 AGTCCTGTTCGGTATCATACTGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT
          1 AGTCCTGTTCGGTATCGTGTTGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT

                                     
        440 CAAAGAGAAATGGAATAAGCCATCG
         66 CAAAGAGAAATGGAATAAGCCATCG

                                                                             
        465 AGTCCTGTTCGGTATCGTGTTGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT
          1 AGTCCTGTTCGGTATCGTGTTGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT

             *                       
        530 CGAAGAGAAATGGAATAAGCCATCG
         66 CAAAGAGAAATGGAATAAGCCATCG

                                *                *   *     
        555 AGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAGGCCCTCTAG
          1 AGTCCTGTTCGGTATCGTGTTGAAGAGAAATGGAATAAGCCTTCTAG

        602 TCCTGTTCGG


Statistics
Matches: 130,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  90  130  1.00

ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24


Consensus pattern (90 bp):   
AGTCCTGTTCGGTATCGTGTTGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT
CAAAGAGAAATGGAATAAGCCATCG

Found at i:624 original size:90 final size:90

Alignment explanation


    Indices: 375--633  Score: 385
    Period size: 90  Copynumber: 2.9  Consensus size: 90

        365 GGAGAGTTCA

                            *  *                                             
        375 AGTCCTGTTCGGTATCAT-ACTGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACG
          1 AGTCCTGTTCGGTATCGTGTC-GAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACG

              *                       
        439 TCAAAGAGAAATGGAATAAGCCATCG
         65 TCGAAGAGAAATGGAATAAGCCATCG

                                *                                            
        465 AGTCCTGTTCGGTATCGTGTTGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT
          1 AGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT

                                     
        530 CGAAGAGAAATGGAATAAGCCATCG
         66 CGAAGAGAAATGGAATAAGCCATCG

                                                 *   *     *  *    *   ** * *
        555 AGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAGGCCCTCTAGTCCTGTTCGGTACCATGC
          1 AGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT

                          
        620 CGAAGAGAAATGGA
         66 CGAAGAGAAATGGA

        634 CGAACCGGCC


Statistics
Matches: 154,  Mismatches: 14, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
  90  154  1.00

ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24


Consensus pattern (90 bp):   
AGTCCTGTTCGGTATCGTGTCGAAGAGAAATGGAATAAGCCTTCTAGCCCCGTTCAGTATGACGT
CGAAGAGAAATGGAATAAGCCATCG
Done.