Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4772

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: 13530
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:2208 original size:39 final size:39

Alignment explanation


    Indices: 2123--2225  Score: 131
    Period size: 39  Copynumber: 2.6  Consensus size: 39

       2113 TGGATGATAA

                                        *           
       2123 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
          1 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTGACTAATT

                                            *        
       2163 CC-GGCTAAGCTCCGAA-GCATTTGTGCGAGTTACT-ATAT
          1 CCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTGACTAAT-T

                                     
       2201 CCGGGCTAAGTCTCGAAGGCATTTG
          1 CCGGGCTAAGTC-CGAAGGCATTTG

       2226 AGCAAGTAGT


Statistics
Matches: 56,  Mismatches: 2, Indels: 10
        0.82            0.03        0.15

Matches are distributed among these distances:
  37    2  0.04
  38   21  0.38
  39   23  0.41
  40   10  0.18

ACGTcount: A:0.22, C:0.23, G:0.27, T:0.27


Consensus pattern (39 bp):   
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTGACTAATT

Found at i:7856 original size:47 final size:47

Alignment explanation


    Indices: 7792--8059  Score: 225
    Period size: 47  Copynumber: 5.7  Consensus size: 47

       7782 GTGGTAAGGT

                                                     **      
       7792 GCCGATGCCAATGTCCCAGACATGGTCTTACACTGGCCTCACACTCAA-
          1 GCCGATGCC-ATGTCCCAGACAT-GTCTTACACTGGCCTCAGTCTCAAG

             *                                * *         * 
       7840 GTCGATGCCATGTCCCAGACATAGTCTTACACTGACATCA-TCTC-GG
          1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCCTCAGTCTCAAG

                                                   *          
       7886 TAGCCGATG-CATGTCCCAGACATGTCTTACACT-GCCTTATGTCTCAAG
          1 --GCCGATGCCATGTCCCAGACATGTCTTACACTGGCCTCA-GTCTCAAG

                                    *       *              *
       7934 GCCGATG-CATGT-CCAGACATGTTTTACACTAGCTCTC-GTCTCAAT
          1 GCCGATGCCATGTCCCAGACATGTCTTACACTGGC-CTCAGTCTCAAG

                                                          *  ** 
       7979 GCCGGATGCCATGTCCCAGACATGGTCCTTACACTGGCTCTCA-TAAT-GTG
          1 GCC-GATGCCATGTCCCAGACAT-GT-CTTACACTGGC-CTCAGT-CTCAAG

                                       *    
       8029 GCCGATG-CATGTCCCAGACATGTCTTGCACT
          1 GCCGATGCCATGTCCCAGACATGTCTTACACT

       8060 AGCCAAAATA


Statistics
Matches: 184,  Mismatches: 21, Indels: 32
        0.78            0.09        0.14

Matches are distributed among these distances:
  45   30  0.16
  46   38  0.21
  47   55  0.30
  48   37  0.20
  49    6  0.03
  50   17  0.09
  51    1  0.01

ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26


Consensus pattern (47 bp):   
GCCGATGCCATGTCCCAGACATGTCTTACACTGGCCTCAGTCTCAAG

Found at i:7932 original size:93 final size:94

Alignment explanation


    Indices: 7792--8059  Score: 257
    Period size: 93  Copynumber: 2.8  Consensus size: 94

       7782 GTGGTAAGGT

                                                              *              
       7792 GCCGATGCCAATGTCCCAGACATGGTCTTACACTGGCCTCACACTCAA-GTCGATGCCATGTCCC
          1 GCCGATGCCAATGTCCCAGACATGGTCTTACACTGGCCTCACACTCAAGGCCGATG-CATGT-CC

                                            
       7856 AGACATAGTCTTACACTGACATCATCTCGGTA
         64 AGACAT-GTCTTACACTGACATCATCTCGGTA

                                                   *  **                     
       7888 GCCGATG-C-ATGTCCCAGACAT-GTCTTACACT-GCCTTATGTCTCAAGGCCGATGCATGTCCA
          1 GCCGATGCCAATGTCCCAGACATGGTCTTACACTGGCCTCA-CACTCAAGGCCGATGCATGTCCA

                   *            *  *    **  
       7949 GACATGTTTTACACT-AGCTCTCGTCTCAAT-
         65 GACATGTCTTACACTGA-C-ATCATCTCGGTA

                                                        * *  **              
       7979 GCCGGATGCC-ATGTCCCAGACATGGTCCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTC
          1 GCC-GATGCCAATGTCCCAGACATGGT-CTTACACTGGC-CTCACACTCAAGGCCGATGCATGT-

                         *    
       8042 CCAGACATGTCTTGCACT
         62 CCAGACATGTCTTACACT

       8060 AGCCAAAATA


Statistics
Matches: 144,  Mismatches: 17, Indels: 22
        0.79            0.09        0.12

Matches are distributed among these distances:
  90    1  0.01
  91   13  0.09
  92   24  0.17
  93   34  0.24
  94   21  0.15
  95   22  0.15
  96   26  0.18
  97    3  0.02

ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26


Consensus pattern (94 bp):   
GCCGATGCCAATGTCCCAGACATGGTCTTACACTGGCCTCACACTCAAGGCCGATGCATGTCCAG
ACATGTCTTACACTGACATCATCTCGGTA

Done.