Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00221.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: 3564
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34


Found at i:910 original size:144 final size:144

Alignment explanation


    Indices: 710--1011  Score: 496
    Period size: 144  Copynumber: 2.1  Consensus size: 144

        700 CTCAAGCAAC

                             *                                              *
        710 ATGCTTGTTGGTCCAATCCCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTC
          1 ATGCTTGTTGGTCCAATACCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA

               *        *                                *               *   
        775 TACCAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
         66 TACAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                   *      
        840 ATCTATCTTCTAAT
        131 ATCTATCGTCTAAT

                                 *                                           
        854 ATGCTTGTTGGTCCAATACCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
          1 ATGCTTGTTGGTCCAATACCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA

             *                                        *     *               *
        919 TGCAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGGCTAACCAATTTGATTACACTGT
         66 TACAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                          
        984 ATCTATCGTCTAAT
        131 ATCTATCGTCTAAT

                          
        998 ATGCTTGTTGGTCC
          1 ATGCTTGTTGGTCC

       1012 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:1086 original size:144 final size:144

Alignment explanation


    Indices: 710--1098  Score: 386
    Period size: 144  Copynumber: 2.7  Consensus size: 144

        700 CTCAAGCAAC

                             *   * *                       *        *       *
        710 ATGCTTGTTGGTCCAATCCCAACTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTC
          1 ATGCTTGTTGGTCCAATACCATCCTCTGTCAACAACTTAACCAATCTGGCATCGTTCGTTCTTTA

             * *   *  * *  *                             *               *   
        775 TACCAACCAACTTAATGGATCCATTCCGCAAGAAATTGGGAGACTGACAAATTTGATTACATTGG
         66 TGCAAACAAAATAAACGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                   *      
        840 ATCTATCTTCTAAT
        131 ATCTATCGTCTAAT

                                   *                       *        *        
        854 ATGCTTGTTGGTCCAATACCATCTTCTGTCAACAACTTAACCAATCTTGCATCGTTGGTTCTTTA
          1 ATGCTTGTTGGTCCAATACCATCCTCTGTCAACAACTTAACCAATCTGGCATCGTTCGTTCTTTA

                   *  * *  *                          *     *               *
        919 TGCAAACCAACTCAATGGATCCATTCCGCAAGAAATTGGGAGGCTAACCAATTTGATTACACTGT
         66 TGCAAACAAAATAAACGGATCCATTCCGCAAGAAATTGGGAGACTAACAAATTTGATTACACTGG

                          
        984 ATCTATCGTCTAAT
        131 ATCTATCGTCTAAT

                          *  *  *      * ****  *   *          *       *      
        998 ATGCTTGTTGGTCCCATCCCTTCCTCTTTGGGTAATTTATCCAGA-CTGGTATCGTTCTTTCTTT
          1 ATGCTTGTTGGTCCAATACCATCCTCTGTCAACAACTTAACCA-ATCTGGCATCGTTCGTTCTTT

                    *           *        *        
       1062 AT-CAAAATAAAATAAACGGTTCCATTCCACAAGAAAT
         65 ATGC-AAACAAAATAAACGGATCCATTCCGCAAGAAAT

       1099 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.