Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold552

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: 29955
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:621 original size:14 final size:13

Alignment explanation


    Indices: 601--637  Score: 58
    Period size: 14  Copynumber: 2.8  Consensus size: 13

        591 AATATTTGAC

                         
        601 TTGTTCTTAATTA
          1 TTGTTCTTAATTA

                          
        614 TGTGTTCTTAATTA
          1 T-TGTTCTTAATTA

                       
        628 TTGTT-TTAAT
          1 TTGTTCTTAAT

        638 ATTCTAGGAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  12    5  0.22
  13    5  0.22
  14   13  0.57

ACGTcount: A:0.22, C:0.05, G:0.11, T:0.62


Consensus pattern (13 bp):   
TTGTTCTTAATTA

Found at i:2395 original size:29 final size:29

Alignment explanation


    Indices: 2353--2413  Score: 113
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       2343 TCTAATAAAA

                                         
       2353 AACATAATAAAATAATGCACCAGGTAGGT
          1 AACATAATAAAATAATGCACCAGGTAGGT

                                *        
       2382 AACATAATAAAATAATGCACTAGGTAGGT
          1 AACATAATAAAATAATGCACCAGGTAGGT

               
       2411 AAC
          1 AAC

       2414 TCTAAAAGAG


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.49, C:0.13, G:0.16, T:0.21


Consensus pattern (29 bp):   
AACATAATAAAATAATGCACCAGGTAGGT

Found at i:11788 original size:43 final size:41

Alignment explanation


    Indices: 11741--11899  Score: 133
    Period size: 43  Copynumber: 3.8  Consensus size: 41

      11731 TGTTCTCGAT

                              *                        
      11741 TAAGACCACGTCTGGGACGTTGGCATTGATATGTGGTTACGAG
          1 TAAGACCACGTCTGGGACATTGGCATTG-TATGTGGTTA-GAG

                    *           *     *    *  *  * * 
      11784 TAAGACCATGTCTGGGACATCGGCATCGTATTTGATTTGTG
          1 TAAGACCACGTCTGGGACATTGGCATTGTATGTGGTTAGAG

                                *              * *       
      11825 TAAGACC-CTGTCTGGGACAATGGCATTGATATG-AGATAGCATG
          1 TAAGACCAC-GTCTGGGACATTGGCATTG-TATGTGGTTAG-A-G

                         *    *             
      11868 TAAGACCACGTCTAGGACGTTGGCATTGTATG
          1 TAAGACCACGTCTGGGACATTGGCATTGTATG

      11900 GTATATGTGA


Statistics
Matches: 90,  Mismatches: 21, Indels: 11
        0.74            0.17        0.09

Matches are distributed among these distances:
  41   27  0.30
  42   14  0.16
  43   48  0.53
  44    1  0.01

ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29


Consensus pattern (41 bp):   
TAAGACCACGTCTGGGACATTGGCATTGTATGTGGTTAGAG

Found at i:23647 original size:13 final size:14

Alignment explanation


    Indices: 23629--23663  Score: 54
    Period size: 14  Copynumber: 2.6  Consensus size: 14

      23619 CTGGGATATC

                          
      23629 AGAACAAG-AATTA
          1 AGAACAAGAAATTA

                  *       
      23642 AGAACACGAAATTA
          1 AGAACAAGAAATTA

                    
      23656 AGAACAAG
          1 AGAACAAG

      23664 TTAAATATTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  13    7  0.37
  14   12  0.63

ACGTcount: A:0.60, C:0.11, G:0.17, T:0.11


Consensus pattern (14 bp):   
AGAACAAGAAATTA

Found at i:29266 original size:21 final size:21

Alignment explanation


    Indices: 29242--29297  Score: 67
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      29232 GAAACAGGGC

                  *              
      29242 ACACACTCGTGTGGAAAGGCA
          1 ACACACACGTGTGGAAAGGCA

                  *         *   *
      29263 ACACACCCGTGTGGAAGGGCT
          1 ACACACACGTGTGGAAAGGCA

                *         
      29284 ACACGCACGTGTGG
          1 ACACACACGTGTGG

      29298 TCATTATAAC


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14


Consensus pattern (21 bp):   
ACACACACGTGTGGAAAGGCA
Done.