Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3622

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: 18681
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31


Found at i:2815 original size:20 final size:21

Alignment explanation


    Indices: 2773--2817  Score: 56
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       2763 TGAAATATGG

                                 
       2773 ATGTGTCATGATTATTGATAT
          1 ATGTGTCATGATTATTGATAT

                      *            
       2794 ATGTG-CATGGTTATTCGAATAT
          1 ATGTGTCATGATTATT-G-ATAT

              
       2816 AT
          1 AT

       2818 CCGAGCTAAG


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  20    9  0.43
  21    6  0.29
  22    6  0.29

ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44


Consensus pattern (21 bp):   
ATGTGTCATGATTATTGATAT

Found at i:2874 original size:40 final size:40

Alignment explanation


    Indices: 2813--2997  Score: 223
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       2803 GTTATTCGAA

                    *                 *              
       2813 TATATCCGAGCTAAG-TCCCGAAGGCTTTTATGCTAGTGAC
          1 TATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGAC

                     *                   *   *       
       2853 TATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-C
          1 TATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGAC

                            *            *      *  *
       2893 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGAT
          1 TATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGAC

                                                     
       2933 TATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGAC
          1 TATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGAC

            *               *        
       2973 CATATCCGGGCTAAGACCCGAAGGC
          1 TATATCCGGGCTAAGATCCGAAGGC

       2998 CTTGTGCGAG


Statistics
Matches: 124,  Mismatches: 16, Indels: 10
        0.83            0.11        0.07

Matches are distributed among these distances:
  39    1  0.01
  40  120  0.97
  41    3  0.02

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


Consensus pattern (40 bp):   
TATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGAC

Found at i:2947 original size:80 final size:79

Alignment explanation


    Indices: 2813--3028  Score: 260
    Period size: 80  Copynumber: 2.7  Consensus size: 79

       2803 GTTATTCGAA

                    *      *             *         *         *               
       2813 TATATCCGAGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGC
          1 TATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGATCCGAAGGC

                *           
       2878 ATTTGTGCGAGTTG-C
         65 ATTTATGCGAG-TGAC

                                                *                            
       2893 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAG-TCCCGAAGG
          1 TATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGAT-CCGAAGG

                     *      
       2957 CATTTATGCTAGTGAC
         64 CATTTATGCGAGTGAC

            *                        *      *    *                    
       2973 CATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAA-ATCC
          1 TATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCC

       3029 CAAAGATACT


Statistics
Matches: 119,  Mismatches: 14, Indels: 9
        0.84            0.10        0.06

Matches are distributed among these distances:
  77    2  0.02
  78    7  0.06
  79   20  0.17
  80   90  0.76

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


Consensus pattern (79 bp):   
TATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCCGAAGGCA
TTTATGCGAGTGAC

Found at i:10965 original size:40 final size:40

Alignment explanation


    Indices: 10906--11088  Score: 221
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      10896 TATTCGAATG

                                     *               
      10906 ATATCC-GGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
          1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT

                    *                   *   *        
      10945 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
          1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT

                           *            *      *  * 
      10985 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
          1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT

                                                    *
      11025 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
          1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT

                           *        
      11065 ATATCCGGGCTAAGACCCGAAGGC
          1 ATATCCGGGCTAAGATCCGAAGGC

      11089 CTTGTGCGAG


Statistics
Matches: 123,  Mismatches: 15, Indels: 11
        0.83            0.10        0.07

Matches are distributed among these distances:
  39    7  0.06
  40  113  0.92
  41    3  0.02

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


Consensus pattern (40 bp):   
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT

Found at i:11045 original size:80 final size:79

Alignment explanation


    Indices: 10906--11120  Score: 258
    Period size: 80  Copynumber: 2.7  Consensus size: 79

      10896 TATTCGAATG

                          *             *         *         *                
      10906 ATATCC-GGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
          1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAG-TCCCGAAGGC

                *           *
      10969 ATTTGTGCGAGTTG-CT
         64 ATTTATGCGAG-TGACC

                                               *                             
      10985 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAGTCCCGAAGGCA
          1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCA

                   *       
      11050 TTTATGCTAGTGACC
         65 TTTATGCGAGTGACC

                                    *      *    *               *    
      11065 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAAATCCC
          1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGTCCC

      11121 AAGATACTTG


Statistics
Matches: 119,  Mismatches: 14, Indels: 7
        0.85            0.10        0.05

Matches are distributed among these distances:
  78   10  0.08
  79   26  0.22
  80   83  0.70

ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26


Consensus pattern (79 bp):   
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCAT
TTATGCGAGTGACC
Done.