Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold757

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: 20812
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31


Found at i:1486 original size:28 final size:28

Alignment explanation


    Indices: 1421--1571  Score: 223
    Period size: 28  Copynumber: 5.4  Consensus size: 28

       1411 GAGATTGGCG

                       *     *   *  *    
       1421 CTAAGTGTGCGGGTTTAAATTGTACAGCA
          1 CTAAGTGTGCGAGTTT-GATTATATAGCA

                                  *     
       1450 CTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                  *     
       1478 CTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
       1506 CTAAGTGTGCGAGTTTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
       1534 CTAAGTGTGCGAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

              *        
       1561 CTGAGTGTGCG
          1 CTAAGTGTGCG

       1572 GACTTAATAT


Statistics
Matches: 115,  Mismatches: 7, Indels: 2
        0.93            0.06        0.02

Matches are distributed among these distances:
  27   24  0.21
  28   76  0.66
  29   15  0.13

ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34


Consensus pattern (28 bp):   
CTAAGTGTGCGAGTTTGATTATATAGCA

Found at i:9531 original size:28 final size:28

Alignment explanation


    Indices: 9466--9616  Score: 214
    Period size: 28  Copynumber: 5.4  Consensus size: 28

       9456 GAGATTGGCG

                       *     *   *  *    
       9466 CTAAGTGTGCGGGTTTAAATTGTACAGCA
          1 CTAAGTGTGCGAGTTT-GATTATATAGCA

                                  *     
       9495 CTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                  *     
       9523 CTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
       9551 CTAAGTGTGCGAGTTTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                      *                 
       9579 CTAAGTGTGCAAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

              *        
       9606 CTGAGTGTGCG
          1 CTAAGTGTGCG

       9617 GACTTAATAT


Statistics
Matches: 113,  Mismatches: 9, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  27   23  0.20
  28   75  0.66
  29   15  0.13

ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34


Consensus pattern (28 bp):   
CTAAGTGTGCGAGTTTGATTATATAGCA

Found at i:15632 original size:16 final size:17

Alignment explanation


    Indices: 15603--15636  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

      15593 AGTTCAGTAT

                   *         
      15603 ACATGCTTATATATATA
          1 ACATGCTCATATATATA

                             
      15620 ACATGCTCA-ATATATA
          1 ACATGCTCATATATATA

             
      15636 A
          1 A

      15637 TTCACTTAAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    8  0.50
  17    8  0.50

ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35


Consensus pattern (17 bp):   
ACATGCTCATATATATA

Found at i:18154 original size:49 final size:49

Alignment explanation


    Indices: 18082--18536  Score: 718
    Period size: 49  Copynumber: 9.5  Consensus size: 49

      18072 GTGTGTATAC

                                            *                
      18082 GTGAAAGTGTATATATATGTGATAAGGCCTAACGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

                                                             
      18131 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

             *                                               
      18180 GCGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

                 *   *                                       
      18229 GTGAAGGTGCATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

                                                             
      18278 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

                                                             
      18327 GTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

                                                             
      18374 GTG-AAGTG--TATATATGTG-TAAGGCCTAATGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

             *                                               
      18419 GCGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

                                  * *    * *     * *      *  
      18466 GTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGAT
          1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

                                      
      18513 GTGAAAGTGTATA-A-ATGTGATAAG
          1 GTGAAAGTGTATATATATGTGATAAG

      18537 TCCCGAAGGG


Statistics
Matches: 384,  Mismatches: 18, Indels: 10
        0.93            0.04        0.02

Matches are distributed among these distances:
  45   29  0.08
  46   30  0.08
  47  124  0.32
  48    1  0.00
  49  200  0.52

ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29


Consensus pattern (49 bp):   
GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT

Found at i:18724 original size:37 final size:37

Alignment explanation


    Indices: 18655--18733  Score: 95
    Period size: 37  Copynumber: 2.1  Consensus size: 37

      18645 CCGAGCTCTA

                *     *           *    *         
      18655 AAGAACCGATGACTACGCGTGGGGATTTTGTCCAGGT
          1 AAGACCCGATAACTACGCGTGGAGATTATGTCCAGGT

                          *  *               *   
      18692 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
          1 AAGACCCGATAACTACGCGTGGAGATTATGTCCAGGT

                 
      18729 AAGAC
          1 AAGAC

      18734 TTCGTAATAA


Statistics
Matches: 35,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  37   35  1.00

ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24


Consensus pattern (37 bp):   
AAGACCCGATAACTACGCGTGGAGATTATGTCCAGGT
Done.