Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_02246

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, 462

Length: 771
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29


Found at i:271 original size:75 final size:75

Alignment explanation


    Indices: 148--290  Score: 189
    Period size: 75  Copynumber: 1.9  Consensus size: 75

        138 TCCAAAACCA

                               *   * *    *         *             *  *       
        148 TCATCTCAAGTTCCTTCTTGGTTTCGAATGTCGCCACCTCGAAACGTCGCG-TCGTCGTCATCAT
          1 TCATCTCAAGTTCCTTCTTCGTTACAAATGCCGCCACCTCCAAACGTCG-GATCATCATCATCAT

                       
        212 CATCGTCGTCG
         65 CATCGTCGTCG

                        *                   *                                
        223 TCATCTCAAGTTTCTTCTTCGTTACAAATGCCTCCACCTCCAAACGTCGGATCATCATCATCATC
          1 TCATCTCAAGTTCCTTCTTCGTTACAAATGCCGCCACCTCCAAACGTCGGATCATCATCATCATC

               
        288 ATC
         66 ATC

        291 TAAAGTTCCT


Statistics
Matches: 58,  Mismatches: 9, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  74    1  0.02
  75   57  0.98

ACGTcount: A:0.20, C:0.33, G:0.15, T:0.32


Consensus pattern (75 bp):   
TCATCTCAAGTTCCTTCTTCGTTACAAATGCCGCCACCTCCAAACGTCGGATCATCATCATCATC
ATCGTCGTCG

Found at i:277 original size:63 final size:63

Alignment explanation


    Indices: 223--484  Score: 383
    Period size: 63  Copynumber: 4.3  Consensus size: 63

        213 ATCGTCGTCG

                        *      *        *                                  
        223 TCATCTCAAGTTTCTTCTTCGTTACAAATGCCTCCACCTCCAAACGTCGGATCATCATCATCA
          1 TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATCA

                  *                   *    *                               
        286 TCATCTAAAGTTCCTTCTTGGTTACAGACGCGTCCACCTCCAAACGTCGGATCATCATCATCA
          1 TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATCA

                           *         **                                    
        349 TCATCTCAAGTTCCTACTTGGTTACGGACGCCTCCACCTCCAAACGTCGG---ATCATCATCA
          1 TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATCA

                                     *                        *            
        409 TCATCTCAAGTTCCTTCTTGGTTACGAACGCCTCCACCTCCAAACGTCGGCTCATCATCATC-
          1 TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATCA

                            
        471 TC--CTCAAGTTCCTT
          1 TCATCTCAAGTTCCTT

        485 TTTCGCAGCC


Statistics
Matches: 184,  Mismatches: 12, Indels: 9
        0.90            0.06        0.04

Matches are distributed among these distances:
  60   70  0.38
  62    2  0.01
  63  112  0.61

ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30


Consensus pattern (63 bp):   
TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCATCA

Found at i:403 original size:60 final size:60

Alignment explanation


    Indices: 223--484  Score: 364
    Period size: 60  Copynumber: 4.3  Consensus size: 60

        213 ATCGTCGTCG

                        *      *        *                               
        223 TCATCTCAAGTTTCTTCTTCGTTACAAATGCCTCCACCTCCAAACGTCGGATCATCATCA
          1 TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCA

                                         *    *                              
        283 TCATCATCTAAAGTTCCTTCTTGGTTACAGACGCGTCCACCTCCAAACGTCGGATCATCATCATC
          1 TCATC-TC--AAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGG---ATCATCATC

             
        348 A
         60 A

                           *         **                                 
        349 TCATCTCAAGTTCCTACTTGGTTACGGACGCCTCCACCTCCAAACGTCGGATCATCATCA
          1 TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCA

                                     *                        *         
        409 TCATCTCAAGTTCCTTCTTGGTTACGAACGCCTCCACCTCCAAACGTCGGCTCATCATCA
          1 TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCA

                             
        469 TC-TCCTCAAGTTCCTT
          1 TCAT-CTCAAGTTCCTT

        485 TTTCGCAGCC


Statistics
Matches: 184,  Mismatches: 11, Indels: 14
        0.88            0.05        0.07

Matches are distributed among these distances:
  59    1  0.01
  60   86  0.47
  61    2  0.01
  63   78  0.42
  65    2  0.01
  66   15  0.08

ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30


Consensus pattern (60 bp):   
TCATCTCAAGTTCCTTCTTGGTTACAAACGCCTCCACCTCCAAACGTCGGATCATCATCA
Done.