Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold9838.1

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: 4194
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34


Found at i:1253 original size:53 final size:53

Alignment explanation


    Indices: 1097--1262  Score: 221
    Period size: 53  Copynumber: 3.1  Consensus size: 53

       1087 GACGAAAAAT

                                 *                             ** 
       1097 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
          1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA

                                                                 
       1149 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
          1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA

                          *                       *      *         
       1202 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
          1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A

                   
       1256 TATGTGA
          1 -ATGTGA

       1263 ACCGTGTAAG


Statistics
Matches: 103,  Mismatches: 6, Indels: 7
        0.89            0.05        0.06

Matches are distributed among these distances:
  51    4  0.04
  52   11  0.11
  53   81  0.79
  54    1  0.01
  55    6  0.06

ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30


Consensus pattern (53 bp):   
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA

Found at i:2609 original size:30 final size:30

Alignment explanation


    Indices: 2573--2631  Score: 109
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2563 AATGACAATG

                                          
       2573 TTTATATATAAGACCATAGCTGGGCTATGA
          1 TTTATATATAAGACCATAGCTGGGCTATGA

                   *                     
       2603 TTTATATGTAAGACCATAGCTGGGCTATG
          1 TTTATATATAAGACCATAGCTGGGCTATG

       2632 GCAATAATGT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34


Consensus pattern (30 bp):   
TTTATATATAAGACCATAGCTGGGCTATGA

Found at i:2701 original size:33 final size:33

Alignment explanation


    Indices: 2664--2850  Score: 130
    Period size: 33  Copynumber: 5.6  Consensus size: 33

       2654 GACGGATAAA

                   *    *                    
       2664 ACCATAATTGGGTTATGGCACTATGAATGTAAG
          1 ACCATAACTGGGCTATGGCACTATGAATGTAAG

                  **   * *      *  * *         
       2697 ACCAT-GGTGGACCATGGCAATGTTTATATGTAAG
          1 ACCATAACTGGGCTATGGCACT-ATGA-ATGTAAG

                            **    *           
       2731 ACCATAACTGGGCTATAACACTCTG-ATGATAAG
          1 ACCATAACTGGGCTATGGCACTATGAATG-TAAG

                        *                    
       2764 ACCATAACTGGGTTATGGCACTATGAATGTAAG
          1 ACCATAACTGGGCTATGGCACTATGAATGTAAG

               * *    *  *    *                
       2797 ACCTTGACTGAGCCATGGTA--ATGTATATGTAAG
          1 ACCATAACTGGGCTATGGCACTATG-A-ATGTAAG

                       *         
       2830 ACCATAACTGGACTATGGCAC
          1 ACCATAACTGGGCTATGGCAC

       2851 AAAGAAAACG


Statistics
Matches: 113,  Mismatches: 33, Indels: 15
        0.70            0.20        0.09

Matches are distributed among these distances:
  31    3  0.03
  32   14  0.12
  33   71  0.63
  34   16  0.14
  35    9  0.08

ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27


Consensus pattern (33 bp):   
ACCATAACTGGGCTATGGCACTATGAATGTAAG
Done.