Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.011G146400.1-JGI_221_v2.1

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, 936

Length: 1560
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33


Found at i:843 original size:105 final size:105

Alignment explanation


    Indices: 672--878  Score: 292
    Period size: 105  Copynumber: 2.0  Consensus size: 105

        662 TCACGTATAA

                                                    *      *             *   
        672 TATATTGATAGATGCACATTGCAAGAAGAGGATGATTTCTGAAGCTGTAGATACTGTTGATGCAA
          1 TATATTGATAGATGCACATTGCAAGAAGAGGATGATTTCTAAAGCTGAAGATACTGTTGATACAA

                    *                               
        737 TGAGAAAGCAAGGCATTGAACCTAATGTTGTCACATACAG
         66 TGAGAAAGAAAGGCATTGAACCTAATGTTGTCACATACAG

                   * *                          *                  *         
        777 TATATTGGTTGATGCACATTGC-A-AAGAGGGAATGGTTTCTAAAGCTGAAGATATTGTTGATAC
          1 TATATTGATAGATGCACATTGCAAGAAGA-GG-ATGATTTCTAAAGCTGAAGATACTGTTGATAC

                                 *   *             
        840 AATGAGAAAGAAAGGCATTGAGCCTGATGTTGTCACATA
         64 AATGAGAAAGAAAGGCATTGAACCTAATGTTGTCACATA

        879 TAATGCATTA


Statistics
Matches: 90,  Mismatches: 10, Indels: 4
        0.87            0.10        0.04

Matches are distributed among these distances:
 103    4  0.04
 104    3  0.03
 105   83  0.92

ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29


Consensus pattern (105 bp):   
TATATTGATAGATGCACATTGCAAGAAGAGGATGATTTCTAAAGCTGAAGATACTGTTGATACAA
TGAGAAAGAAAGGCATTGAACCTAATGTTGTCACATACAG

Found at i:903 original size:105 final size:105

Alignment explanation


    Indices: 659--895  Score: 253
    Period size: 105  Copynumber: 2.3  Consensus size: 105

        649 TCTCTTGATA

                   *  *    *   *   *                         *     *      *  
        659 TTGTCACGTATAATATATTGATAGATGCACATTGC-AAGAAGAGG-ATGATTTCTGAAGCTGTAG
          1 TTGTCACATACAATACATTAATAAATGCACATTGCAAAG-AG-GGAATGGTTTCTAAAGCTGAAG

                       *           *                  
        722 ATACTGTTGATGCAATGAGAAAGCAAGGCATTGAACCTAATG
         64 ATACTGTTGATACAATGAGAAAGAAAGGCATTGAACCTAATG

                        *  *   ** **                                         
        764 TTGTCACATACAGTATATTGGTTGATGCACATTGCAAAGAGGGAATGGTTTCTAAAGCTGAAGAT
          1 TTGTCACATACAATACATTAATAAATGCACATTGCAAAGAGGGAATGGTTTCTAAAGCTGAAGAT

             *                              *   *   
        829 ATTGTTGATACAATGAGAAAGAAAGGCATTGAGCCTGATG
         66 ACTGTTGATACAATGAGAAAGAAAGGCATTGAACCTAATG

                      *   *            
        869 TTGTCACATATAATGCATTAATAAATG
          1 TTGTCACATACAATACATTAATAAATG

        896 GTCATTGCTT


Statistics
Matches: 109,  Mismatches: 21, Indels: 4
        0.81            0.16        0.03

Matches are distributed among these distances:
 104    2  0.02
 105  104  0.95
 106    3  0.03

ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30


Consensus pattern (105 bp):   
TTGTCACATACAATACATTAATAAATGCACATTGCAAAGAGGGAATGGTTTCTAAAGCTGAAGAT
ACTGTTGATACAATGAGAAAGAAAGGCATTGAACCTAATG
Done.