Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00221.F3

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: 3355
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Found at i:701 original size:144 final size:144

Alignment explanation


    Indices: 501--802  Score: 496
    Period size: 144  Copynumber: 2.1  Consensus size: 144

        491 CTCAAGCAAC

                             *                                              *
        501 ATGCTTGTTGGTCCAATCCCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTC
          1 ATGCTTGTTGGTCCAATACCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA

               *        *                                *               *   
        566 TACCAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
         66 TACAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                   *      
        631 ATCTATCTTCTAAT
        131 ATCTATCGTCTAAT

                                 *                                           
        645 ATGCTTGTTGGTCCAATACCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
          1 ATGCTTGTTGGTCCAATACCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA

             *                                        *     *               *
        710 TGCAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGGCTAACCAATTTGATTACACTGT
         66 TACAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                          
        775 ATCTATCGTCTAAT
        131 ATCTATCGTCTAAT

                          
        789 ATGCTTGTTGGTCC
          1 ATGCTTGTTGGTCC

        803 CATCCCTTCC


Statistics
Matches: 146,  Mismatches: 12, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 144  146  1.00

ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33


Consensus pattern (144 bp):   
ATGCTTGTTGGTCCAATACCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
TACAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG
ATCTATCGTCTAAT

Found at i:877 original size:144 final size:144

Alignment explanation


    Indices: 501--889  Score: 386
    Period size: 144  Copynumber: 2.7  Consensus size: 144

        491 CTCAAGCAAC

                             *   * *                       *        *       *
        501 ATGCTTGTTGGTCCAATCCCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTC
          1 ATGCTTGTTGGTCCAATACCATCCTCTGTCAACAACTTAACCAATCTGGCATCGTTCGTTCTTTA

             * *   *  * *  *                             *               *   
        566 TACCAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
         66 TGCAAACAAAATAAACGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                   *      
        631 ATCTATCTTCTAAT
        131 ATCTATCGTCTAAT

                                   *                       *        *        
        645 ATGCTTGTTGGTCCAATACCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
          1 ATGCTTGTTGGTCCAATACCATCCTCTGTCAACAACTTAACCAATCTGGCATCGTTCGTTCTTTA

                   *  * *  *                          *     *               *
        710 TGCAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGGCTAACCAATTTGATTACACTGT
         66 TGCAAACAAAATAAACGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                          
        775 ATCTATCGTCTAAT
        131 ATCTATCGTCTAAT

                          *  *  *      * ****  *   *          *       *      
        789 ATGCTTGTTGGTCCCATCCCTTCCTCTTTGGGTAATTTATCCAGA-CTGGTATCGTTCTTTCTTT
          1 ATGCTTGTTGGTCCAATACCATCCTCTGTCAACAACTTAACCA-ATCTGGCATCGTTCGTTCTTT

                    *           *        *        
        853 AT-CAAAATAAAATAAACGGTTCCATTCCACAAGAAAT
         65 ATGC-AAACAAAATAAACGGATCCATTCCGCAAGAAAT

        890 AAGACATCTT


Statistics
Matches: 209,  Mismatches: 34, Indels: 4
        0.85            0.14        0.02

Matches are distributed among these distances:
 143    1  0.00
 144  207  0.99
 145    1  0.00

ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34


Consensus pattern (144 bp):   
ATGCTTGTTGGTCCAATACCATCCTCTGTCAACAACTTAACCAATCTGGCATCGTTCGTTCTTTA
TGCAAACAAAATAAACGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG
ATCTATCGTCTAAT
Done.