Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12419

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: 1788
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23


Found at i:197 original size:81 final size:81

Alignment explanation


    Indices: 56--212  Score: 199
    Period size: 81  Copynumber: 1.9  Consensus size: 81

         46 TCTGAGAACC

                            *    *      *      *          *   *              
         56 CTCATATGGATACTACTCCTCCTCTTGATAACCCCCATGACATGGGTAGTTCACACATAGATATT
          1 CTCATATGGATACTACCCCTCATCTTGAAAACCCCAATGACATGGGCAGTCCACACATAGATATT

                            
        121 CAACAAGATCTCAACT
         66 CAACAAGATCTCAACT

                          *                    *     *              *        
        137 CTCATATGGATACTCCCCCTCATAC-TGAAAACCCTAATGATATGGGCAGTCCACATATAGATAT
          1 CTCATATGGATACTACCCCTCAT-CTTGAAAACCCCAATGACATGGGCAGTCCACACATAGATAT

               *        
        201 TCATCAAGATCT
         65 TCAACAAGATCT

        213 GTTTCCAGAT


Statistics
Matches: 64,  Mismatches: 11, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  81   63  0.98
  82    1  0.02

ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28


Consensus pattern (81 bp):   
CTCATATGGATACTACCCCTCATCTTGAAAACCCCAATGACATGGGCAGTCCACACATAGATATT
CAACAAGATCTCAACT

Found at i:908 original size:126 final size:126

Alignment explanation


    Indices: 679--919  Score: 347
    Period size: 126  Copynumber: 1.9  Consensus size: 126

        669 AGCAGCGCCT

                      *                     *         *        **  *         
        679 GCAGCACCAGCAGAAGGAACAGAAGATGATAAGCAAGAAAGTGACACAAAAGGTCTCCGTAGAAC
          1 GCAGCACCAGAAGAAGGAACAGAAGATGATAAACAAGAAAGTAACACAAAAACTCCCCGTAGAAC

                                 *         *            *                
        744 CCAAAGGAAGAGGGCTCCCCCTCCTCCCCCATTCAGTACTCCGAGTTCCATCGAAGCACCA
         66 CCAAAGGAAGAGGGCTCCCCCGCCTCCCCCAGTCAGTACTCCGAATTCCATCGAAGCACCA

                 *              *       *                *                   
        805 GCAGCGCCAGAAGAAGGAACGGAAGATGTTAAACAAGAAAGTAACTCAAAAACTCCCCGTAGAAC
          1 GCAGCACCAGAAGAAGGAACAGAAGATGATAAACAAGAAAGTAACACAAAAACTCCCCGTAGAAC

                                  *          *                
        870 CCAAAGGAAGAGGGCTCCCCCGGCTCCCCCAGTGAGTACTCCGAATTCCA
         66 CCAAAGGAAGAGGGCTCCCCCGCCTCCCCCAGTCAGTACTCCGAATTCCA

        920 GTGATGGTAA


Statistics
Matches: 100,  Mismatches: 15, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
 126  100  1.00

ACGTcount: A:0.35, C:0.29, G:0.23, T:0.12


Consensus pattern (126 bp):   
GCAGCACCAGAAGAAGGAACAGAAGATGATAAACAAGAAAGTAACACAAAAACTCCCCGTAGAAC
CCAAAGGAAGAGGGCTCCCCCGCCTCCCCCAGTCAGTACTCCGAATTCCATCGAAGCACCA
Done.