Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33936

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: 6819
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25


Found at i:2481 original size:18 final size:18

Alignment explanation


    Indices: 2458--2494  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2448 TGTATTGGAG

                              
       2458 ACACAAGAACTTTCTGAA
          1 ACACAAGAACTTTCTGAA

                              
       2476 ACACAAGAACTTTCTGAA
          1 ACACAAGAACTTTCTGAA

             
       2494 A
          1 A

       2495 ACATGAATAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22


Consensus pattern (18 bp):   
ACACAAGAACTTTCTGAA

Found at i:6196 original size:330 final size:327

Alignment explanation


    Indices: 5284--6221  Score: 1087
    Period size: 330  Copynumber: 2.8  Consensus size: 327

       5274 TGAGAATTCC

                       *         **                                   *      
       5284 GATGAATCAAACATCTTTACCTGCATGGAGATGAGTTTGTTTCTTGGGGTTGACGATGGAGTTAA
          1 GATGAATCAAATATCTTTACCAACATGGAGATGAGTTTGTTTCTTGGGGTTGA-GATGAAGTTAA

                *          *       *             *  *                        
       5349 AACACCAG-TCGCAATGGCCGGTCACAGTAAAT-ATGATAATTTGGACAAGGCCATCCCAGAATG
         65 AA-ATCAGAT-GCAAAGGCCGGTGACAGT-AATGATGTTACTTTGGACAAGGCCATCCCAGAATG

                                            *  *     *         *             
       5412 CAATTCAAGTGACTTTGAAGAGGGTGATTATGATATGAGAAGAGATGTTGATGACACAAATTTCT
        127 CAATTCAAGTGACTTTGAAGAGGGTGATTATGTTACGAGAACAGATGTTGAGGACACAAATTTCT

                                                 *                           
       5477 CAGTGGAAAAGGATGGTCCTGAAGATACTGAGGAAACGATGGAGTTGAGGAACGACTTCTATGGG
        192 CAGT-GAAAAGGATGGTCCT---G--A---A-GAAACAATGGAGTTGAGGAACGACTTCTATGGG

                     **        *                        *                    
       5542 CAGGATGCAATAATTGCAGCTAAATCTCCCCTTTCAAAGAATTCGGAAATTAGCAGAGAAAGTAA
        247 CAGGATGCAGCAATTGCAGATAAATCTCCCCTTTCAAAGAATTCAGAAATTAGCAGAGAAAGTAA

             *              
       5607 ATACCTAGCGAATCCT
        312 AGACCTAGCGAATCCT

                  * *               *                           * *          
       5623 GATGAACCGAATATCTTTACCAACGTGGAGATGAGTTTGTTTCTTGGGGTTCAATATGAAGTTAA
          1 GATGAATCAAATATCTTTACCAACATGGAGATGAGTTTGTTTCTTGGGGTT-GAGATGAAGTT-A

                           *         *           *    *            * *       
       5688 AAAATCAGATGCAAATGCCGGTGACGGTAATGATGTTGCTTTAGACAAGGCCATCACGGAATGCA
         64 AAAATCAGATGCAAAGGCCGGTGACAGTAATGATGTTACTTTGGACAAGGCCATCCCAGAATGCA

                       ** *            *    *                                
       5753 ATTCAAGTGACACTAAAGAGGGTGATTTTGTTGCGAGAACAGATGTTGAGGACACAAATTTCTCA
        129 ATTCAAGTGACTTTGAAGAGGGTGATTATGTTACGAGAACAGATGTTGAGGACACAAATTTCTCA

               *    **  *          *            **   *  *       **           
       5818 GTAAAAAATTATAGTCCTGAAGATACTGAA-GGA--ACAGTCAAAGACTTCTCGGGGCAGGATGC
        194 GT-GAAAAGGATGGTCCTGAAGAAAC--AATGGAGTTGAG-GAACGACTTCTATGGGCAGGATGC

                  *            *           *                    *  *         
       5880 AGCAATGGCAGATAAATCTTCCCTTTCAAAGCATTCAGAAATTAGCAGAGAATGTGAAGACCTAG
        255 AGCAATTGCAGATAAATCTCCCCTTTCAAAGAATTCAGAAATTAGCAGAGAAAGTAAAGACCTAG

                    
       5945 CGAATCCT
        320 CGAATCCT

                                         *                                   
       5953 GATGAATCAAATATCTTTACCAACATGGAAATGAGTTTGTTTCTTGGGGTTGGAGATGAAGTTAA
          1 GATGAATCAAATATCTTTACCAACATGGAGATGAGTTTGTTTCTTGGGGTT-GAGATGAAGTTAA

                  *           *                                              
       6018 AAATTCGGATGCAAAGGCTGGTGACAGTAATGATGTTACTTTGGACAAGGCCATCCCAGAATGCA
         65 AAA-TCAGATGCAAAGGCCGGTGACAGTAATGATGTTACTTTGGACAAGGCCATCCCAGAATGCA

                                      *                              *       
       6083 ATTCAAGTGACTTTGAAGAGGGTGATCATGTTACGAGAACAGATGTTGAGGACACAACTTT-TGC
        129 ATTCAAGTGACTTTGAAGAGGGTGATTATGTTACGAGAACAGATGTTGAGGACACAAATTTCT-C

            *                                                        *       
       6147 GGTGAAAGAGGATGGTCCTGAAGAAACAATGGAGTTGAGGAACGACTTCTATGGGCAAGATGCAG
        193 AGTGAAA-AGGATGGTCCTGAAGAAACAATGGAGTTGAGGAACGACTTCTATGGGCAGGATGCAG

             *        
       6212 CCATTGCAGA
        257 CAATTGCAGA

       6222 ACGTAAAGAC


Statistics
Matches: 497,  Mismatches: 89, Indels: 35
        0.80            0.14        0.06

Matches are distributed among these distances:
 328    2  0.00
 329   14  0.03
 330  297  0.60
 331    6  0.01
 332    1  0.00
 334    1  0.00
 336    1  0.00
 338    3  0.01
 339  166  0.33
 340    6  0.01

ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25


Consensus pattern (327 bp):   
GATGAATCAAATATCTTTACCAACATGGAGATGAGTTTGTTTCTTGGGGTTGAGATGAAGTTAAA
AATCAGATGCAAAGGCCGGTGACAGTAATGATGTTACTTTGGACAAGGCCATCCCAGAATGCAAT
TCAAGTGACTTTGAAGAGGGTGATTATGTTACGAGAACAGATGTTGAGGACACAAATTTCTCAGT
GAAAAGGATGGTCCTGAAGAAACAATGGAGTTGAGGAACGACTTCTATGGGCAGGATGCAGCAAT
TGCAGATAAATCTCCCCTTTCAAAGAATTCAGAAATTAGCAGAGAAAGTAAAGACCTAGCGAATC
CT
Done.