Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2629

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: 22071
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30


Found at i:9210 original size:15 final size:15

Alignment explanation


    Indices: 9190--9220  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       9180 CATATATGAT

                           
       9190 GGTGTTTCGGTTATG
          1 GGTGTTTCGGTTATG

                           
       9205 GGTGTTTCGGTTATG
          1 GGTGTTTCGGTTATG

             
       9220 G
          1 G

       9221 AGTACATGAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.06, C:0.06, G:0.42, T:0.45


Consensus pattern (15 bp):   
GGTGTTTCGGTTATG

Found at i:9945 original size:40 final size:40

Alignment explanation


    Indices: 9851--9995  Score: 193
    Period size: 40  Copynumber: 3.6  Consensus size: 40

       9841 TACTCGAATG

                                    *                
       9851 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT

             *      *                                
       9892 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
          1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT

                                        *      *   *
       9932 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

                     *    *         
       9972 ATATCCGGGTTAAGACCCGAAGGC
          1 ATATCCGGGCTAAGTCCCGAAGGC

       9996 CTTGTGCGAG


Statistics
Matches: 92,  Mismatches: 10, Indels: 5
        0.86            0.09        0.05

Matches are distributed among these distances:
  39    1  0.01
  40   62  0.67
  41   28  0.30
  42    1  0.01

ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

Found at i:17960 original size:40 final size:40

Alignment explanation


    Indices: 17866--18010  Score: 193
    Period size: 40  Copynumber: 3.6  Consensus size: 40

      17856 TACTCGAATG

                                    *                
      17866 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT

             *      *                                
      17907 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
          1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT

                                        *      *   *
      17947 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

                     *    *         
      17987 ATATCCGGGTTAAGACCCGAAGGC
          1 ATATCCGGGCTAAGTCCCGAAGGC

      18011 CTTGTGCGAG


Statistics
Matches: 92,  Mismatches: 10, Indels: 5
        0.86            0.09        0.05

Matches are distributed among these distances:
  39    1  0.01
  40   62  0.67
  41   28  0.30
  42    1  0.01

ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Done.