Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2122

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: 141392
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


File 2 of 2

Found at i:139661 original size:19 final size:18

Alignment explanation


    Indices: 139636--139693  Score: 89
    Period size: 19  Copynumber: 3.1  Consensus size: 18

     139626 TTGTATCGAT

                              
     139636 ACATTGTATCGATACATG
          1 ACATTGTATCGATACATG

                                
     139654 ATCATTGTATCGATACATGG
          1 A-CATTGTATCGATACAT-G

                               
     139674 ACAATTGTATCGATACATG
          1 AC-ATTGTATCGATACATG

             
     139693 A
          1 A

     139694 AACTGGTAGT


Statistics
Matches: 37,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
  18    1  0.03
  19   19  0.51
  20   17  0.46

ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Consensus pattern (18 bp):   
ACATTGTATCGATACATG

Found at i:139665 original size:32 final size:31

Alignment explanation


    Indices: 139609--139671  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 31

     139599 ACACCCCAGA

                         *  *              
     139609 TGTACCGATACATTACTTTGTATCGATACAT
          1 TGTACCGATACATGACATTGTATCGATACAT

                *                           
     139640 TGTATCGATACATGATCATTGTATCGATACAT
          1 TGTACCGATACATGA-CATTGTATCGATACAT

     139672 GGACAATTGT


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  31   13  0.46
  32   15  0.54

ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38


Consensus pattern (31 bp):   
TGTACCGATACATGACATTGTATCGATACAT

Found at i:139682 original size:20 final size:20

Alignment explanation


    Indices: 139637--139692  Score: 89
    Period size: 20  Copynumber: 2.9  Consensus size: 20

     139627 TGTATCGATA

                                
     139637 CATTGTATCGATACAT-GAT
          1 CATTGTATCGATACATGGAT

                                
     139656 CATTGTATCGATACATGGA-
          1 CATTGTATCGATACATGGAT

                              
     139675 CAATTGTATCGATACATG
          1 C-ATTGTATCGATACATG

     139693 AAACTGGTAG


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  19   17  0.49
  20   18  0.51

ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Consensus pattern (20 bp):   
CATTGTATCGATACATGGAT

Found at i:139749 original size:20 final size:20

Alignment explanation


    Indices: 139724--139774  Score: 68
    Period size: 20  Copynumber: 2.5  Consensus size: 20

     139714 CCACTGTATG

                        *        
     139724 TATCGATACATGGT-ACATTA
          1 TATCGATACATGATGA-ATTA

                               *
     139744 TATCGATACATGATGAATTG
          1 TATCGATACATGATGAATTA

                       
     139764 TATCGATACAT
          1 TATCGATACAT

     139775 TGCTTGTAAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  20   27  0.96
  21    1  0.04

ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Consensus pattern (20 bp):   
TATCGATACATGATGAATTA

Done.