Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_24013

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, 624

Length: 1041
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.21


Found at i:264 original size:42 final size:42

Alignment explanation


    Indices: 205--335  Score: 201
    Period size: 42  Copynumber: 3.1  Consensus size: 42

        195 TCCTCCAAAG

                                                      
        205 CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA
          1 CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA

                 *     *        *  *     *            
        247 CCACCGAAGCCACCGGTGGTGAAGCCACCGTATCACCCTAAA
          1 CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA

                                                       
        289 CCACCTAAGCCTCCGGTGGTGAAACCC-CCATATCACCCTAAA
          1 CCACCTAAGCCTCCGGTGGT-AAACCCACCATATCACCCTAAA

                 
        331 CCACC
          1 CCACC

        336 AAAACATCCA


Statistics
Matches: 78,  Mismatches: 10, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  42   74  0.95
  43    4  0.05

ACGTcount: A:0.29, C:0.41, G:0.15, T:0.15


Consensus pattern (42 bp):   
CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA

Found at i:440 original size:69 final size:69

Alignment explanation


    Indices: 367--569  Score: 298
    Period size: 69  Copynumber: 2.9  Consensus size: 69

        357 CAAGCCACCT

                                      *     **    *        *  *              
        367 GTTGTGAAGCCTCCATATATACCCAAGCCACCTATTGTAAAGCCTCCACCGTATACACCCAAACC
          1 GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC

            *   
        432 TCCG
         66 GCCG

                                                                             
        436 GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC
          1 GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC

                
        501 GCCG
         66 GCCG

                                  *         *                                
        505 GTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAA
          1 GTTGTGAAGCCT---CCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAA

        570 GCCACCTTAC


Statistics
Matches: 122,  Mismatches: 9, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
  69   74  0.61
  72   48  0.39

ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20


Consensus pattern (69 bp):   
GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC
GCCG

Found at i:446 original size:36 final size:36

Alignment explanation


    Indices: 355--575  Score: 256
    Period size: 36  Copynumber: 6.3  Consensus size: 36

        345 ACCGCATCAT

                 *     *                      * 
        355 CCCAAGCCACCTGTTGTGAAGCCT---CCATATATA
          1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA

                 *     **    *           *      
        388 CCCAAGCCACCTATTGTAAAGCCTCCACCGTATACA
          1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA

                    *                         * 
        424 CCCAAACCTCCGGTTGTGAAGCCT---CCATATATA
          1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA

                                      *         
        457 CCCAAACCACCGGTTGTGAAGCCTCCGCCATATACA
          1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA

                    *                 *         
        493 CCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACA
          1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA

                    *                 *         
        529 CCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACA
          1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA

                 *     
        565 CCCAAGCCACC
          1 CCCAAACCACC

        576 TTACTATCCA


Statistics
Matches: 166,  Mismatches: 16, Indels: 9
        0.87            0.08        0.05

Matches are distributed among these distances:
  33   52  0.31
  36  114  0.69

ACGTcount: A:0.27, C:0.38, G:0.16, T:0.19


Consensus pattern (36 bp):   
CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA

Found at i:709 original size:24 final size:24

Alignment explanation


    Indices: 682--740  Score: 73
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        672 GATTCTACCA

                             *      
        682 CCACCATCACCACCTATTGTGAAG
          1 CCACCATCACCACCTATCGTGAAG

                  * *  *            
        706 CCACCAACGCCTCCTATCGTGAAG
          1 CCACCATCACCACCTATCGTGAAG

                 *     
        730 CCACCTTCACC
          1 CCACCATCACC

        741 GGAAACACCG


Statistics
Matches: 28,  Mismatches: 7, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  24   28  1.00

ACGTcount: A:0.25, C:0.44, G:0.12, T:0.19


Consensus pattern (24 bp):   
CCACCATCACCACCTATCGTGAAG
Done.