Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12428

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: 1749
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31


Found at i:1153 original size:600 final size:607

Alignment explanation


    Indices: 1--1213  Score: 1992
    Period size: 600  Copynumber: 2.0  Consensus size: 607

                      *      *                                      *        
          1 GATTGGGCAGGACTACCTAATGAGCTTGTTGATTTGATATTACAAAGGTTGGCTTCGGTGTCGAA
          1 GATTGGGCAGAACTACCAAATGAGCTTGTTGATTTGATATTACAAAGGTTGGCTTCAGTGTCGAA

                        *                        *                           
         66 CTATTTCCGATTTGGTGCAACATGCACGGCGTGGCACGATGTTGCGACAGAGAACATAAACTACT
         66 CTATTTCCGATTCGGTGCAACATGCACGGCGTGGCACAATGTTGCGACAGAGAACATAAACTACT

                                                                             
        131 TGTTGTCCCTAAAGCACCCCATGCTCATTGTCCCTCTCAATGCCCAAGATGTTTGGAACCTATAT
        131 TGTTGTCCCTAAAGCACCCCATGCTCATTGTCCCTCTCAATGCCCAAGATGTTTGGAACCTATAT

                                                                             
        196 AGCATCAAAGACAACAAGCTTCTTCCCTTGCCATTTCAAGTACCATATGTCGACCGATTTGTCGA
        196 AGCATCAAAGACAACAAGCTTCTTCCCTTGCCATTT--A-TA-CATATGTC-ACCGATTTGTCGA

                                             **                          *   
        261 CTCTTCCAACGGATGGTTGGTCACCATGGACGATTATTTAGTTGTTCGTTTACTCAACCCATTGT
        256 CTCTTCCAACGGATGGTTGGTCACCATGGACGACGATTTAGTTGTTCGTTTACTCAACCCACTGT

                                                                      *      
        326 GTTTGGTCCCCGAGAAACAAATTGGTTGTGATCCAAATACTTACATTACTCTTCCACCGTTGGAT
        321 GTTTGGTCCCCGAGAAACAAATTGGTTGTGATCCAAATACTTACATTACTCTTCCACCATTGGAT

                                                                   *         
        391 CCACCATACAGTAATTTTGATCACATTCGCAAGGTTGTACTTTCTACTAATCCGATATCAAGCCC
        386 CCACCATACAGTAATTTTGATCACATTCGCAAGGTTGTACTTTCTACTAATCCGACATCAAGCCC

                                 *                               *           
        456 CGACGATTACATGATCATGGCTATATTTGGTGCCGATCATCACGTAGCATATATTAAACCAAGCA
        451 CGACGATTACATGATCATGGCCATATTTGGTGCCGATCATCACGTAGCATATACTAAACCAAGCA

                                                 *  *                   *    
        521 AAGACAAAAAATGGACTTACATTAACCATAATTGGGGTGTGCTTCATGATCTTATATACTTCCAA
        516 AAGACAAAAAATGGACTTACATTAACCATAATTGGGGCGTACTTCATGATCTTATATACTACCAA

            *                          
        586 TATCACTTTTGTGCAGTTGATCATAAG
        581 GATCACTTTTGTGCAGTTGATCATAAG

                                                                             
        613 GATTGGGCAGAACTACCAAATGAGCTTGTTGATTTGATATTACAAAGGTTGGCTTCAGTGTC-AG
          1 GATTGGGCAGAACTACCAAATGAGCTTGTTGATTTGATATTACAAAGGTTGGCTTCAGTGTCGA-

                                                             *        *      
        677 ACTATTTCCGATTCGGTGCAACATGCACGGCGTGGCACAATGTTGCGACGGAGAACATCAACTAC
         65 ACTATTTCCGATTCGGTGCAACATGCACGGCGTGGCACAATGTTGCGACAGAGAACATAAACTAC

                     *                                                       
        742 TTGTTGTCCTTAAAGCACCCCATGCTCATTGTCCCTCTCAATGCCCAAGATGTTTGGAACCTATA
        130 TTGTTGTCCCTAAAGCACCCCATGCTCATTGTCCCTCTCAATGCCCAAGATGTTTGGAACCTATA

                                     *                                  *    
        807 TAGCATCAAAGACAACAAGCTTCTTTCCTTGCCA-TT-T-CA-A-GT-ACC-ATTTGTCGGCTCT
        195 TAGCATCAAAGACAACAAGCTTCTTCCCTTGCCATTTATACATATGTCACCGATTTGTCGACTCT

                                 *    *                     *                
        865 TCCAACGGATGGTTGGTCACCGTGGATGACGATTTAGTTGTTCGTTTATTCAACCCACTGTGTTT
        260 TCCAACGGATGGTTGGTCACCATGGACGACGATTTAGTTGTTCGTTTACTCAACCCACTGTGTTT

                    *                                                        
        930 GGTCCCCGGGAAACAAATTGGTTGTGATCCAAATACTTACATTACTCTTCCACCATTGGATCCAC
        325 GGTCCCCGAGAAACAAATTGGTTGTGATCCAAATACTTACATTACTCTTCCACCATTGGATCCAC

               **                                    **                  *   
        995 CATGTAGTAATTTTGATCACATTCGCAAGGTTGTACTTTCTGGTAATCCGACATCAAGCCCTGAC
        390 CATACAGTAATTTTGATCACATTCGCAAGGTTGTACTTTCTACTAATCCGACATCAAGCCCCGAC

                     *                                           *     *     
       1060 GATTACATGGTCATGGCCATATTTGGTGCCGATCATCACGTAGCATATACTAAGCCAAGTAAAGA
        455 GATTACATGATCATGGCCATATTTGGTGCCGATCATCACGTAGCATATACTAAACCAAGCAAAGA

                           **                    *                           
       1125 CAAAAAATGGACTTATGTTAACCATAATTGGGGCGTATTTCATGATCTTATATACTACCAAGATC
        520 CAAAAAATGGACTTACATTAACCATAATTGGGGCGTACTTCATGATCTTATATACTACCAAGATC

                                   
       1190 ACTTTTGTGCAGTTGATCATAAG
        585 ACTTTTGTGCAGTTGATCATAAG

             
       1213 G
          1 G

       1214 GTGAAGTTAT


Statistics
Matches: 564,  Mismatches: 36, Indels: 14
        0.92            0.06        0.02

Matches are distributed among these distances:
 600  335  0.59
 601    3  0.01
 603    2  0.00
 604    1  0.00
 605    2  0.00
 607    1  0.00
 611    3  0.01
 612  217  0.38

ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31


Consensus pattern (607 bp):   
GATTGGGCAGAACTACCAAATGAGCTTGTTGATTTGATATTACAAAGGTTGGCTTCAGTGTCGAA
CTATTTCCGATTCGGTGCAACATGCACGGCGTGGCACAATGTTGCGACAGAGAACATAAACTACT
TGTTGTCCCTAAAGCACCCCATGCTCATTGTCCCTCTCAATGCCCAAGATGTTTGGAACCTATAT
AGCATCAAAGACAACAAGCTTCTTCCCTTGCCATTTATACATATGTCACCGATTTGTCGACTCTT
CCAACGGATGGTTGGTCACCATGGACGACGATTTAGTTGTTCGTTTACTCAACCCACTGTGTTTG
GTCCCCGAGAAACAAATTGGTTGTGATCCAAATACTTACATTACTCTTCCACCATTGGATCCACC
ATACAGTAATTTTGATCACATTCGCAAGGTTGTACTTTCTACTAATCCGACATCAAGCCCCGACG
ATTACATGATCATGGCCATATTTGGTGCCGATCATCACGTAGCATATACTAAACCAAGCAAAGAC
AAAAAATGGACTTACATTAACCATAATTGGGGCGTACTTCATGATCTTATATACTACCAAGATCA
CTTTTGTGCAGTTGATCATAAG
Done.