Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09855

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, 289

Length: 483
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.21


Found at i:237 original size:58 final size:58

Alignment explanation


    Indices: 168--283  Score: 196
    Period size: 58  Copynumber: 2.0  Consensus size: 58

        158 GGGAGGGACA

                             *                                   *    
        168 GAGACGATTCATTCATTGTTGGGTACCGAACATGCAACGGTATCTGAATTCTAGCTTT
          1 GAGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTATCTGAATTCTACCTTT

                  *                           *                       
        226 GAGACGGTTCATTCATTATTGGGTACCGAACATGTAACGGTATCTGAATTCTACCTTT
          1 GAGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTATCTGAATTCTACCTTT

        284 TGGGATTGGG


Statistics
Matches: 54,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  58   54  1.00

ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34


Consensus pattern (58 bp):   
GAGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTATCTGAATTCTACCTTT

Found at i:364 original size:24 final size:23

Alignment explanation


    Indices: 320--364  Score: 54
    Period size: 24  Copynumber: 1.9  Consensus size: 23

        310 CGTTTTGTAT

                           *       
        320 ATCCCGGGATAGATCGCCGGATC
          1 ATCCCGGGATAGATCACCGGATC

                       *     *    
        343 ATCCCTGGGATGGATCATCGGA
          1 ATCCC-GGGATAGATCACCGGA

        365 GCACCGCCGG


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  23    5  0.28
  24   13  0.72

ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20


Consensus pattern (23 bp):   
ATCCCGGGATAGATCACCGGATC
Done.