Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3218

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: 9536
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31


Found at i:1775 original size:102 final size:102

Alignment explanation


    Indices: 1592--1848  Score: 366
    Period size: 103  Copynumber: 2.5  Consensus size: 102

       1582 AACCGTTATT

                   *                                                         
       1592 GGTGGATCTCGCACTTAGCACCA-C-TGAAT--GGAATCAGCACTTAGCAACCCCTCGGGGGAAT
          1 GGTGGATATCGCACTTAGCACCACCATGAATCGGGAATCAGCACTTAGCAACCCCTCGGGGGAAT

                                  *              
       1653 CAGCACATAGCAACCCCCTTT-TCATTTCAAAGATAC
         66 CAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC

                                                                             
       1689 GGTGGATATCGCACTTAGCACCACCAATGAAATCGGGAATCAGCACTTAGCAACCCCTC-GGGGA
          1 GGTGGATATCGCACTTAGCACCACC-ATG-AATCGGGAATCAGCACTTAGCAACCCCTCGGGGGA

                                                  *
       1753 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
         64 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC

                           *               *              **          
       1792 GGTGGATCA-CGCACATAGCACCACCATGAACCGGGGAATCAGCACACAGCAACCCCT
          1 GGTGGAT-ATCGCACTTAGCACCACCATGAATC-GGGAATCAGCACTTAGCAACCCCT

       1849 TTTATATACA


Statistics
Matches: 144,  Mismatches: 7, Indels: 13
        0.88            0.04        0.08

Matches are distributed among these distances:
  97   22  0.15
  98    1  0.01
 100    2  0.01
 101    6  0.04
 102   53  0.37
 103   59  0.41
 104    1  0.01

ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19


Consensus pattern (102 bp):   
GGTGGATATCGCACTTAGCACCACCATGAATCGGGAATCAGCACTTAGCAACCCCTCGGGGGAAT
CAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC

Found at i:8727 original size:26 final size:26

Alignment explanation


    Indices: 8697--8747  Score: 93
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       8687 ACCAATGAAC

                          *           
       8697 CGGGGAATCAGCACTTAGCAACCCCT
          1 CGGGGAATCAGCACATAGCAACCCCT

                                     
       8723 CGGGGAATCAGCACATAGCAACCCC
          1 CGGGGAATCAGCACATAGCAACCCC

       8748 CTTTCACATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12


Consensus pattern (26 bp):   
CGGGGAATCAGCACATAGCAACCCCT

Found at i:8819 original size:102 final size:104

Alignment explanation


    Indices: 8561--8824  Score: 428
    Period size: 103  Copynumber: 2.6  Consensus size: 104

       8551 TAACCGTTAT

                     *                **                                     
       8561 TGGTGGATCTCGCACTTAGCACCACCGCTGAATC-GGGAATCAGCACTTAGCAACCCCTCGGGGG
          1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG

                                                   
       8625 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
         66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA

                                             *                               
       8664 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGG
          1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG

                                                    
       8727 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
         65 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA

                           *                               **          
       8767 T-GTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
          1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT

       8825 TTATATACAA


Statistics
Matches: 150,  Mismatches: 8, Indels: 7
        0.91            0.05        0.04

Matches are distributed among these distances:
 102   51  0.34
 103   74  0.49
 104   25  0.17

ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19


Consensus pattern (104 bp):   
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Done.