Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold812

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: 10358
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:8946 original size:13 final size:13

Alignment explanation


    Indices: 8928--8975  Score: 51
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       8918 CATAAAGTGT

                         
       8928 TGTATCGATACAA
          1 TGTATCGATACAA

                           
       8941 TGTATCGATACATAA
          1 TGTATCGATAC--AA

                            
       8956 GTTTGTATCGATACAA
          1 ---TGTATCGATACAA

                
       8972 TGTA
          1 TGTA

       8976 AGCTACTGCC


Statistics
Matches: 30,  Mismatches: 0, Indels: 10
        0.75            0.00        0.25

Matches are distributed among these distances:
  13   15  0.50
  15    2  0.07
  16    2  0.07
  18   11  0.37

ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:8964 original size:18 final size:18

Alignment explanation


    Indices: 8906--8970  Score: 77
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       8896 TTTCAACGAT

                               
       8906 TTTGTATCGATACATAAAG
          1 TTTGTATCGATACAT-AAG

                               
       8925 TGTTGTATCGATAC--AA-
          1 T-TTGTATCGATACATAAG

                              
       8941 --TGTATCGATACATAAG
          1 TTTGTATCGATACATAAG

                          
       8957 TTTGTATCGATACA
          1 TTTGTATCGATACA

       8971 ATGTAAGCTA


Statistics
Matches: 40,  Mismatches: 0, Indels: 13
        0.75            0.00        0.25

Matches are distributed among these distances:
  13   11  0.28
  15    2  0.05
  17    2  0.05
  18   12  0.30
  19    1  0.03
  20   12  0.30

ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37


Consensus pattern (18 bp):   
TTTGTATCGATACATAAG

Found at i:8965 original size:31 final size:33

Alignment explanation


    Indices: 8908--8975  Score: 122
    Period size: 31  Copynumber: 2.1  Consensus size: 33

       8898 TCAACGATTT

                                             
       8908 TGTATCGATACATAAAGTGTTGTATCGATACAA
          1 TGTATCGATACATAAAGTGTTGTATCGATACAA

                                             
       8941 TGTATCGATACAT-AAGT-TTGTATCGATACAA
          1 TGTATCGATACATAAAGTGTTGTATCGATACAA

                
       8972 TGTA
          1 TGTA

       8976 AGCTACTGCC


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  31   18  0.51
  32    4  0.11
  33   13  0.37

ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35


Consensus pattern (33 bp):   
TGTATCGATACATAAAGTGTTGTATCGATACAA

Found at i:9074 original size:52 final size:52

Alignment explanation


    Indices: 9032--9212  Score: 308
    Period size: 52  Copynumber: 3.5  Consensus size: 52

       9022 CACTGATCTT

                                 *                              
       9032 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
          1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA

                 *                                       *      
       9084 TGTATTGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACAATAAAA
          1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA

                                        *             *     *   
       9136 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATATACTATGAAA
          1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA

                                     
       9188 TGTATCGATACATGCAGGCAAATTT
          1 TGTATCGATACATGCAGGCAAATTT

       9213 TCATATTTCG


Statistics
Matches: 121,  Mismatches: 8, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  52  121  1.00

ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29


Consensus pattern (52 bp):   
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.