Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g02514.F1

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: 2469
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26


Found at i:1641 original size:330 final size:327

Alignment explanation


    Indices: 729--1666  Score: 1087
    Period size: 330  Copynumber: 2.8  Consensus size: 327

        719 TGAGAATTCC

                       *         **                                   *      
        729 GATGAATCAAACATCTTTACCTGCATGGAGATGAGTTTGTTTCTTGGGGTTGACGATGGAGTTAA
          1 GATGAATCAAATATCTTTACCAACATGGAGATGAGTTTGTTTCTTGGGGTTGA-GATGAAGTTAA

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

                                            *  *     *         *             
        857 CAATTCAAGTGACTTTGAAGAGGGTGATTATGATATGAGAAGAGATGTTGATGACACAAATTTCT
        127 CAATTCAAGTGACTTTGAAGAGGGTGATTATGTTACGAGAACAGATGTTGAGGACACAAATTTCT

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

                     **        *                        *                    
        987 CAGGATGCAATAATTGCAGCTAAATCTCCCCTTTCAAAGAATTCGGAAATTAGCAGAGAAAGTAA
        247 CAGGATGCAGCAATTGCAGATAAATCTCCCCTTTCAAAGAATTCAGAAATTAGCAGAGAAAGTAA

             *              
       1052 ATACCTAGCGAATCCT
        312 AGACCTAGCGAATCCT

                  * *               *                           * *          
       1068 GATGAACCGAATATCTTTACCAACGTGGAGATGAGTTTGTTTCTTGGGGTTCAATATGAAGTTAA
          1 GATGAATCAAATATCTTTACCAACATGGAGATGAGTTTGTTTCTTGGGGTT-GAGATGAAGTT-A

                           *         *           *    *            * *       
       1133 AAAATCAGATGCAAATGCCGGTGACGGTAATGATGTTGCTTTAGACAAGGCCATCACGGAATGCA
         64 AAAATCAGATGCAAAGGCCGGTGACAGTAATGATGTTACTTTGGACAAGGCCATCCCAGAATGCA

                       ** *            *    *                                
       1198 ATTCAAGTGACACTAAAGAGGGTGATTTTGTTGCGAGAACAGATGTTGAGGACACAAATTTCTCA
        129 ATTCAAGTGACTTTGAAGAGGGTGATTATGTTACGAGAACAGATGTTGAGGACACAAATTTCTCA

               *    **  *          *            **   *  *       **           
       1263 GTAAAAAATTATAGTCCTGAAGATACTGAA-GGA--ACAGTCAAAGACTTCTCGGGGCAGGATGC
        194 GT-GAAAAGGATGGTCCTGAAGAAAC--AATGGAGTTGAG-GAACGACTTCTATGGGCAGGATGC

                  *            *           *                    *  *         
       1325 AGCAATGGCAGATAAATCTTCCCTTTCAAAGCATTCAGAAATTAGCAGAGAATGTGAAGACCTAG
        255 AGCAATTGCAGATAAATCTCCCCTTTCAAAGAATTCAGAAATTAGCAGAGAAAGTAAAGACCTAG

                    
       1390 CGAATCCT
        320 CGAATCCT

                                         *                                   
       1398 GATGAATCAAATATCTTTACCAACATGGAAATGAGTTTGTTTCTTGGGGTTGGAGATGAAGTTAA
          1 GATGAATCAAATATCTTTACCAACATGGAGATGAGTTTGTTTCTTGGGGTT-GAGATGAAGTTAA

                  *           *                                              
       1463 AAATTCGGATGCAAAGGCTGGTGACAGTAATGATGTTACTTTGGACAAGGCCATCCCAGAATGCA
         65 AAA-TCAGATGCAAAGGCCGGTGACAGTAATGATGTTACTTTGGACAAGGCCATCCCAGAATGCA

                                      *                              *       
       1528 ATTCAAGTGACTTTGAAGAGGGTGATCATGTTACGAGAACAGATGTTGAGGACACAACTTT-TGC
        129 ATTCAAGTGACTTTGAAGAGGGTGATTATGTTACGAGAACAGATGTTGAGGACACAAATTTCT-C

            *                                                        *       
       1592 GGTGAAAGAGGATGGTCCTGAAGAAACAATGGAGTTGAGGAACGACTTCTATGGGCAAGATGCAG
        193 AGTGAAA-AGGATGGTCCTGAAGAAACAATGGAGTTGAGGAACGACTTCTATGGGCAGGATGCAG

             *        
       1657 CCATTGCAGA
        257 CAATTGCAGA

       1667 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.