Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17149

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: 4092
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30


Found at i:3050 original size:210 final size:210

Alignment explanation


    Indices: 2660--3257  Score: 803
    Period size: 210  Copynumber: 2.8  Consensus size: 210

       2650 TTGAAAAATG

                 *    *    *                       *                  **     
       2660 TTCCACTAACGGGACAATGTT-ATTCTCTTGAAAAGCTTCGCATTTCATCATGTGAAAGTTTAAG
          1 TTCCAATAACCGGACGATGTTCA-TCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAG

                            *                             *       *  *    *  
       2724 CAAGATCGGAGACGGACTATCTACCTCCACTTGTCTCAAAGAATTATATCTATATGAGTGT-TTT
         65 CAAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTATAAGATTGTCCTT

                                                         *            *    * 
       2788 AATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAATATCTGTCAATTCTAA-GTT
        130 -ATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT-AAATGGT

              *               
       2852 GCTACGAATTGGAAGTAC
        193 GCAACGAATTGGAAGTAC

                                                          ****  *            
       2870 TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGC
          1 TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAGC

                 *     *        *                                            
       2935 AAGATTGGAGATGGATTATCAACCTCCACTTGTCTCAAAGAATTAGATCT-TGAAGATTGTCCTT
         66 AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTAT-AAGATTGTCCTT

                         *  *                                                
       2999 ATTTAAGTTCGATTCCTAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAAATGGTGC
        130 ATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAAATGGTGC

                            
       3064 AACGAATTGGAAGTAC
        195 AACGAATTGGAAGTAC

                          *       * *         *                       *      
       3080 TTCCAATAACCGGAGGATGTTCTTTTCTTGAAAATCTTAGCATTTCATCATGTGAAAAGTTAAGC
          1 TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAGC

                                                           *                 
       3145 AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATT-GTGTCTA-AAGAATTGTCCT
         66 AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAG-ATCTATAAG-ATTGTCCT

            *                                  *              
       3208 AATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCATCTCTTCAAAATCT
        129 TATTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCT

       3258 ATCAGTTGAT


Statistics
Matches: 338,  Mismatches: 43, Indels: 14
        0.86            0.11        0.04

Matches are distributed among these distances:
 209    7  0.02
 210  328  0.97
 211    3  0.01

ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34


Consensus pattern (210 bp):   
TTCCAATAACCGGACGATGTTCATCTCTTGAAAAGCTTAGCATTTCATCATGTGAAAAATTAAGC
AAGATCGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTATAAGATTGTCCTTA
TTTAAGTTCGATCCCAAATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAAATGGTGCA
ACGAATTGGAAGTAC

Found at i:3200 original size:14 final size:15

Alignment explanation


    Indices: 3175--3204  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       3165 TACCTCCACT

                           
       3175 TGTCTCAAAGAATTG
          1 TGTCTCAAAGAATTG

                           
       3190 TGTCT-AAAGAATTG
          1 TGTCTCAAAGAATTG

             
       3204 T
          1 T

       3205 CCTAATTTAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   10  0.67
  15    5  0.33

ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37


Consensus pattern (15 bp):   
TGTCTCAAAGAATTG

Found at i:3908 original size:144 final size:144

Alignment explanation


    Indices: 3651--3913  Score: 332
    Period size: 144  Copynumber: 1.8  Consensus size: 144

       3641 TTGGTTGGGA

                                          **  **      *              *       
       3651 AAAGCTAAAGAGTCTTCCTCACCAACTTCAGTTCTTCACTGCTCTCGAAGAATTGACGATGGAAG
          1 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTCGAAGAATTGACAATGGAAG

                     *            *     * *    **      *     *               
       3716 GGTTTCAAGGAATAGAAGCCTTTCCAGAGTGGTTGGGAAAACTTTCTTCTCTAAAGCGTCTAAGT
         66 GGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGCAAAAACTCTCTTCCCTAAAGCGTCTAAGT

                          
       3781 TTGAGTGGTTTTGG
        131 TTGAGTGGTTTTGG

                                                         *     *            *
       3795 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTTGAAGAGTTGACAATGTG-C
          1 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTCGAAGAATTGACAATG-GAA

                    *                                               
       3859 GGGTTTCATGAAATAGAAGCCTTGCCAGACTCGTT-CAAAAATCTCTCTTCCCTAA
         65 GGGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGCAAAAA-CTCTCTTCCCTAA

       3914 GGTGTCTGCG


Statistics
Matches: 99,  Mismatches: 18, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
 143    4  0.04
 144   94  0.95
 145    1  0.01

ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29


Consensus pattern (144 bp):   
AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTCGAAGAATTGACAATGGAAG
GGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGCAAAAACTCTCTTCCCTAAAGCGTCTAAGT
TTGAGTGGTTTTGG
Done.