Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2071

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: 143672
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28


Found at i:2871 original size:24 final size:24

Alignment explanation


    Indices: 2839--2887  Score: 62
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2829 CAACGGATTC

                       *     *      
       2839 CTCACCCTCAGGAGCCCGAAGTAA
          1 CTCACCCTCAGCAGCCCCAAGTAA

                *     *             
       2863 CTCATCCTCATCAGCCCCAAGTAA
          1 CTCACCCTCAGCAGCCCCAAGTAA

             
       2887 C
          1 C

       2888 GAATCCGAAT


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.29, C:0.41, G:0.14, T:0.16


Consensus pattern (24 bp):   
CTCACCCTCAGCAGCCCCAAGTAA

Found at i:16749 original size:9 final size:9

Alignment explanation


    Indices: 16735--16759  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

      16725 ATGGGAACTA

                     
      16735 AAATAAAAT
          1 AAATAAAAT

                     
      16744 AAATAAAAT
          1 AAATAAAAT

                   
      16753 AAATAAA
          1 AAATAAA

      16760 TTGTATCGAA


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

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (9 bp):   
AAATAAAAT

Found at i:24421 original size:18 final size:17

Alignment explanation


    Indices: 24388--24421  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

      24378 TGAGTGAATC

                     *       
      24388 TCGTAGGCTTTTTTCTT
          1 TCGTAGGCTATTTTCTT

                             
      24405 TCGTAGGCCTATTTTCT
          1 TCGTAGG-CTATTTTCT

      24422 GTAAGCGGAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    7  0.47
  18    8  0.53

ACGTcount: A:0.09, C:0.21, G:0.18, T:0.53


Consensus pattern (17 bp):   
TCGTAGGCTATTTTCTT

Found at i:92704 original size:15 final size:15

Alignment explanation


    Indices: 92684--92740  Score: 80
    Period size: 15  Copynumber: 3.8  Consensus size: 15

      92674 TTGGCCAAAA

                           
      92684 ACCGCTGGTTCTGCT
          1 ACCGCTGGTTCTGCT

                      *    
      92699 ACCGCTGGTTTTGCT
          1 ACCGCTGGTTCTGCT

             *              
      92714 ATCGCTGGTT-TAGCT
          1 ACCGCTGGTTCT-GCT

                        
      92729 ACCGCTGGTTCT
          1 ACCGCTGGTTCT

      92741 TCTAATGACC


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  14    1  0.03
  15   35  0.95
  16    1  0.03

ACGTcount: A:0.09, C:0.28, G:0.26, T:0.37


Consensus pattern (15 bp):   
ACCGCTGGTTCTGCT
Done.