Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_20590

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: 3897
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:536 original size:20 final size:21

Alignment explanation


    Indices: 470--538  Score: 95
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        460 TCACTTCGTT

                                 
        470 TCTTTTTGTCCAAGTTACTTC
          1 TCTTTTTGTCCAAGTTACTTC

                            *    
        491 TCTTTTTGTCCAAGTTGCTTC
          1 TCTTTTTGTCCAAGTTACTTC

                      *  * *     
        512 TCTTTTTGTCTAACTCACTTC
          1 TCTTTTTGTCCAAGTTACTTC

                   
        533 -CTTTTT
          1 TCTTTTT

        539 TCTTTGTGAG


Statistics
Matches: 43,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  20    6  0.14
  21   37  0.86

ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55


Consensus pattern (21 bp):   
TCTTTTTGTCCAAGTTACTTC

Found at i:2937 original size:18 final size:18

Alignment explanation


    Indices: 2904--2997  Score: 131
    Period size: 18  Copynumber: 5.4  Consensus size: 18

       2894 AAGGTTTTCT

                              
       2904 TATTGATGATA-T--CGA
          1 TATTGATGATAGTGACGA

                              
       2919 TATTGATGATAGTGACGA
          1 TATTGATGATAGTGACGA

                    *         
       2937 TATTGATGCTAGTGACGA
          1 TATTGATGATAGTGACGA

                    *        *
       2955 TATTGATGCTAGTGACGC
          1 TATTGATGATAGTGACGA

                             *
       2973 TATTGATGATAGTGACGC
          1 TATTGATGATAGTGACGA

                   
       2991 TATTGAT
          1 TATTGAT

       2998 CGTGACCTTG


Statistics
Matches: 73,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   11  0.15
  16    1  0.01
  18   61  0.84

ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36


Consensus pattern (18 bp):   
TATTGATGATAGTGACGA

Done.