Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14778

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, 873

Length: 1455
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.25


Found at i:639 original size:39 final size:39

Alignment explanation


    Indices: 585--664  Score: 142
    Period size: 39  Copynumber: 2.1  Consensus size: 39

        575 CATATGCATC

                                     *             
        585 TGGTGATAAGATCATGAGTGAAGATTTTATGGCTAAGTT
          1 TGGTGATAAGATCATGAGTGAAGATGTTATGGCTAAGTT

                            *                      
        624 TGGTGATAAGATCATGGGTGAAGATGTTATGGCTAAGTT
          1 TGGTGATAAGATCATGAGTGAAGATGTTATGGCTAAGTT

              
        663 TG
          1 TG

        665 AGGCTTTGAC


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.29, C:0.05, G:0.31, T:0.35


Consensus pattern (39 bp):   
TGGTGATAAGATCATGAGTGAAGATGTTATGGCTAAGTT

Found at i:841 original size:180 final size:177

Alignment explanation


    Indices: 624--949  Score: 474
    Period size: 180  Copynumber: 1.8  Consensus size: 177

        614 TGGCTAAGTT

                          * *             *           *                      
        624 TGGTGATAAGATCATGGGTGAAGATGTTATGGCTAAGTTTGAGGCTTTGACAGAGAAGGCT-TCC
          1 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGAAGG-TGTCC

                        *   *             *      *                       *   
        688 CATATTATAGCTGATGGTGTAGCTAGGATCCTTAAAGGTAAGGCTGCAGAATCAATCTCGCGTGG
         65 CATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGG

                                                               
        753 AAGAAATGAAGTTTCCCATGTCTATAATGAGGTAGAGGAAACATATGTATC
        130 -AG--ATGAAGTTTCCCATGTCTATAATGAGGTAGAGGAAACATATGTATC

                                                                    *     *  
        804 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGACGGTGTGCC
          1 TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGAAGGTGTCCC

              *                         *                      *             
        869 ATGTTATAGCTAATGATGTAGCTAGGATTATTAAAGATAAGGCTGCAGAATTAATCTCGCATGGA
         66 ATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGGA

                       *    
        934 GATGAAGTTTCGCATG
        131 GATGAAGTTTCCCATG

        950 CCACATATGC


Statistics
Matches: 130,  Mismatches: 15, Indels: 5
        0.87            0.10        0.03

Matches are distributed among these distances:
 177   14  0.11
 179    3  0.02
 180  113  0.87

ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29


Consensus pattern (177 bp):   
TGGTGATAAGATCACGAGTGAAGATGTTATAGCTAAGTTTGAAGCTTTGACAGAGAAGGTGTCCC
ATATTATAGCTAATGATGTAGCTAGGATCATTAAAGATAAGGCTGCAGAATCAATCTCGCATGGA
GATGAAGTTTCCCATGTCTATAATGAGGTAGAGGAAACATATGTATC
Done.