Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2195_ERROPOS1964815+

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: 398699
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


File 2 of 2

Found at i:388927 original size:29 final size:29

Alignment explanation


    Indices: 388868--388926  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

     388858 TTTGAACAAA

                    *               *    
     388868 TGTGCAATGTTATACATAAAATTTGATTT
          1 TGTGCAATTTTATACATAAAATTTCATTT

                           *     *        
     388897 TGTGCAATTTTATACTTGAAATTTTCATTT
          1 TGTGCAATTTTATACAT-AAAATTTCATTT

     388927 GATTCAATTT


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  29   15  0.60
  30   10  0.40

ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49


Consensus pattern (29 bp):   
TGTGCAATTTTATACATAAAATTTCATTT

Found at i:394828 original size:50 final size:50

Alignment explanation


    Indices: 394698--394937  Score: 295
    Period size: 50  Copynumber: 4.7  Consensus size: 50

     394688 ATTTGGGTAA

                *                                *         *      
     394698 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATC-
          1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-CG

                      *                                        
     394751 ATGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
          1 A-GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG

                                               * *          * 
     394802 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
          1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG

                     * *                                   *   
     394852 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATTACG
          1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG

                **                              
     394902 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
          1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC

     394938 TTTGGCATGT


Statistics
Matches: 165,  Mismatches: 18, Indels: 10
        0.85            0.09        0.05

Matches are distributed among these distances:
  49    1  0.01
  50   90  0.55
  51   33  0.20
  53    3  0.02
  54   38  0.23

ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20


Consensus pattern (50 bp):   
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG

Found at i:394889 original size:100 final size:103

Alignment explanation


    Indices: 394698--394945  Score: 369
    Period size: 100  Copynumber: 2.4  Consensus size: 103

     394688 ATTTGGGTAA

                                                                             
     394698 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGGTCCCCT
          1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TAAGATCATGAGGTCCCCT

            *                                       
     394763 GTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
         65 ATAAGACCATGTCTGGGACATGGCATGGGCACC-ATGACG

                *                              *          *    *             
     394802 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAGATGA-GAGGTCCCCTA
          1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCATGAGGTCCCCTA

                                              *   
     394864 TAAGACCATGTCTGGGACATGGCATGGGCACCATTACG
         66 TAAGACCATGTCTGGGACATGGCATGGGCACCATGACG

                *                               *       
     394902 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
          1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT

     394946 GTTATTATCA


Statistics
Matches: 132,  Mismatches: 9, Indels: 8
        0.89            0.06        0.05

Matches are distributed among these distances:
  99    1  0.01
 100   47  0.36
 101   42  0.32
 103    2  0.02
 104   40  0.30

ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21


Consensus pattern (103 bp):   
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCATGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATGACG

Done.