Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7819.1

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: 6069
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:234 original size:29 final size:29

Alignment explanation


    Indices: 201--260  Score: 102
    Period size: 29  Copynumber: 2.1  Consensus size: 29

        191 ATAACCAAAC

                        *                
        201 CTACAAAAACTTTATATCCATAAACCCAT
          1 CTACAAAAACTTCATATCCATAAACCCAT

                 *                       
        230 CTACATAAACTTCATATCCATAAACCCAT
          1 CTACAAAAACTTCATATCCATAAACCCAT

              
        259 CT
          1 CT

        261 TTGAATCCTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28


Consensus pattern (29 bp):   
CTACAAAAACTTCATATCCATAAACCCAT

Found at i:253 original size:15 final size:15

Alignment explanation


    Indices: 207--254  Score: 53
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        197 AAACCTACAA

                  *        
        207 AAACTTTATATCCAT
          1 AAACTTCATATCCAT

                 *   * *   
        222 AAAC-CCATCTACAT
          1 AAACTTCATATCCAT

                           
        236 AAACTTCATATCCAT
          1 AAACTTCATATCCAT

                
        251 AAAC
          1 AAAC

        255 CCATCTTTGA


Statistics
Matches: 25,  Mismatches: 7, Indels: 2
        0.74            0.21        0.06

Matches are distributed among these distances:
  14   10  0.40
  15   15  0.60

ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29


Consensus pattern (15 bp):   
AAACTTCATATCCAT

Found at i:847 original size:24 final size:23

Alignment explanation


    Indices: 793--870  Score: 70
    Period size: 21  Copynumber: 3.4  Consensus size: 23

        783 GGATAATTAA

                          **       
        793 GAAATGGTATTTGGTTTTGGTAC
          1 GAAATGGTATTTGGAATTGGTAC

             ***                    
        816 GCTTTGGTATTTGGGAATTGGTAC
          1 GAAATGGTATTT-GGAATTGGTAC

                                  *
        840 GAAATGGTA--TGGAATTGGTAT
          1 GAAATGGTATTTGGAATTGGTAC

                 *    
        861 GAAATAGTAT
          1 GAAATGGTAT

        871 GGTATTTGGT


Statistics
Matches: 43,  Mismatches: 10, Indels: 5
        0.74            0.17        0.09

Matches are distributed among these distances:
  21   18  0.42
  22    1  0.02
  23    9  0.21
  24   15  0.35

ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38


Consensus pattern (23 bp):   
GAAATGGTATTTGGAATTGGTAC

Found at i:855 original size:21 final size:21

Alignment explanation


    Indices: 829--890  Score: 79
    Period size: 21  Copynumber: 2.9  Consensus size: 21

        819 TTGGTATTTG

                                 
        829 GGAATTGGTACGAAATGGTAT
          1 GGAATTGGTACGAAATGGTAT

                      *     *    
        850 GGAATTGGTATGAAATAGTAT
          1 GGAATTGGTACGAAATGGTAT

                *          *    
        871 GGTATTTGGTACGAATTGGT
          1 GG-AATTGGTACGAAATGGT

        891 TATGATTCAA


Statistics
Matches: 34,  Mismatches: 6, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  21   21  0.62
  22   13  0.38

ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34


Consensus pattern (21 bp):   
GGAATTGGTACGAAATGGTAT

Found at i:2439 original size:14 final size:14

Alignment explanation


    Indices: 2417--2464  Score: 60
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       2407 ACCTAAACCG

                *       * 
       2417 ACCAATTTGTTCAT
          1 ACCATTTTGTTCCT

                          
       2431 ACCATTTTGTTCCT
          1 ACCATTTTGTTCCT

               *   *      
       2445 ACCCTTTCGTTCCT
          1 ACCATTTTGTTCCT

                  
       2459 ACCATT
          1 ACCATT

       2465 CCATTCGTAC


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  14   29  1.00

ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44


Consensus pattern (14 bp):   
ACCATTTTGTTCCT

Found at i:2806 original size:21 final size:21

Alignment explanation


    Indices: 2780--2842  Score: 90
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       2770 TTGGTATTTG

                                 
       2780 GGAATTGGTACGAAATGGTAT
          1 GGAATTGGTACGAAATGGTAT

                      *          
       2801 GGAATTGGTATGAAATGGTAT
          1 GGAATTGGTACGAAATGGTAT

                *          *     
       2822 GGTATTTGGTACGAATTGGTA
          1 GG-AATTGGTACGAAATGGTA

       2843 ATGGTTCAAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  21   22  0.59
  22   15  0.41

ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33


Consensus pattern (21 bp):   
GGAATTGGTACGAAATGGTAT
Done.