Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3813

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: 16478
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30


Found at i:441 original size:53 final size:53

Alignment explanation


    Indices: 285--450  Score: 221
    Period size: 53  Copynumber: 3.1  Consensus size: 53

        275 GACGAAAAAT

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

                                                                 
        337 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
          1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA

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

                   
        444 TATGTGA
          1 -ATGTGA

        451 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:7144 original size:53 final size:53

Alignment explanation


    Indices: 6988--7153  Score: 221
    Period size: 53  Copynumber: 3.1  Consensus size: 53

       6978 GACGAAAAAT

                                 *                             ** 
       6988 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
          1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA

                                                                 
       7040 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
          1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA

                          *                       *      *         
       7093 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
          1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A

                   
       7147 TATGTGA
          1 -ATGTGA

       7154 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:14101 original size:52 final size:53

Alignment explanation


    Indices: 14019--14173  Score: 210
    Period size: 52  Copynumber: 3.0  Consensus size: 53

      14009 GACGAAAAAT

                                 *                             *  
      14019 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
          1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA

                                                               * 
      14071 ATGTGATAATGTGACTCCGTATAAGA-CATAGCTGGGCTATGGCATCGGTATA
          1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA

                          *                       *      *      
      14123 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTA
          1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTA

      14174 TGATATGTGA


Statistics
Matches: 93,  Mismatches: 6, Indels: 7
        0.88            0.06        0.07

Matches are distributed among these distances:
  51    4  0.04
  52   60  0.65
  53   29  0.31

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


Consensus pattern (53 bp):   
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Done.