Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1896

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: 235474
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


File 2 of 2

Found at i:221037 original size:12 final size:12

Alignment explanation


    Indices: 221022--221071  Score: 52
    Period size: 11  Copynumber: 4.3  Consensus size: 12

     221012 AATAAAATTG

                        
     221022 AAATGAAAATAA
          1 AAATGAAAATAA

                *     * 
     221034 AAATAAAAATCA
          1 AAATGAAAATAA

                         
     221046 AAA-GAAAA-ATA
          1 AAATGAAAATA-A

                        
     221057 AAAT-AAAATAA
          1 AAATGAAAATAA

                
     221068 AAAT
          1 AAAT

     221072 AAGACTAAAT


Statistics
Matches: 31,  Mismatches: 4, Indels: 7
        0.74            0.10        0.17

Matches are distributed among these distances:
  11   17  0.55
  12   14  0.45

ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16


Consensus pattern (12 bp):   
AAATGAAAATAA

Found at i:221048 original size:7 final size:6

Alignment explanation


    Indices: 221022--221073  Score: 63
    Period size: 6  Copynumber: 9.0  Consensus size: 6

     221012 AATAAAATTG

                *                    *     *                       
     221022 AAATGA AAATAA AAATAA AAATCA AAAGAA AAAT-A AAAT-A AAATAA
          1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA

                  
     221068 AAATAA
          1 AAATAA

     221074 GACTAAATAA


Statistics
Matches: 40,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
   5   10  0.25
   6   30  0.75

ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15


Consensus pattern (6 bp):   
AAATAA

Found at i:221052 original size:23 final size:23

Alignment explanation


    Indices: 221002--221064  Score: 65
    Period size: 23  Copynumber: 2.7  Consensus size: 23

     220992 TATGTCTTGC

                             * *   * 
     221002 AAAATAAAATAATAAAATTGAAATG
          1 AAAAT-AAA-AATAAAAATCAAAAG

                                   
     221027 AAAATAAAAATAAAAATCAAAAG
          1 AAAATAAAAATAAAAATCAAAAG

                            
     221050 AAAA-ATAAAATAAAA
          1 AAAATA-AAAATAAAA

     221065 TAAAAATAAG


Statistics
Matches: 34,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  22    1  0.03
  23   25  0.74
  24    3  0.09
  25    5  0.15

ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17


Consensus pattern (23 bp):   
AAAATAAAAATAAAAATCAAAAG

Found at i:221966 original size:14 final size:14

Alignment explanation


    Indices: 221947--221980  Score: 68
    Period size: 14  Copynumber: 2.4  Consensus size: 14

     221937 CTAATATACC

                          
     221947 ATTTCACCATAAAA
          1 ATTTCACCATAAAA

                          
     221961 ATTTCACCATAAAA
          1 ATTTCACCATAAAA

                  
     221975 ATTTCA
          1 ATTTCA

     221981 GAATTTTTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32


Consensus pattern (14 bp):   
ATTTCACCATAAAA

Found at i:222733 original size:66 final size:66

Alignment explanation


    Indices: 222629--222756  Score: 195
    Period size: 66  Copynumber: 1.9  Consensus size: 66

     222619 AGCAACCCTC

                                         *         *                         
     222629 GGGGAATCAGCACATAGCAACGCCCCTTTTCATTTCAAATATACAATGGATATCGCACTTAGAAC
          1 GGGGAATCAGCACATAGCAACGCCCCTTTACATTTCAAAGATACAATGGATATCGCACTTAGAAC

             
     222694 G
         66 G

                                                        ***                
     222695 GGGGAATCAGCACATAGCAAC-CCCCTTTCACATTTCAAAGATATGGTGGATATCGCACTTAG
          1 GGGGAATCAGCACATAGCAACGCCCCTTT-ACATTTCAAAGATACAATGGATATCGCACTTAG

     222757 CACCACCAAT


Statistics
Matches: 56,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  65    7  0.12
  66   49  0.88

ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24


Consensus pattern (66 bp):   
GGGGAATCAGCACATAGCAACGCCCCTTTACATTTCAAAGATACAATGGATATCGCACTTAGAAC
G

Done.