Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2130

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, 651

Length: 1086
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27


Found at i:480 original size:177 final size:176

Alignment explanation


    Indices: 184--807  Score: 980
    Period size: 177  Copynumber: 3.5  Consensus size: 176

        174 TGCATATGAG

                       *                                                     
        184 GAAAAACATTTAAGACAGGCGTAAAGAATGTAACAACGAAACACGTAGGAAAGGTGATTGACACG
          1 GAAAAACATTTTAGACAGGCGTAAA-AATGTAACAACGAAACACGTAGGAAAGGTGATTGACACG

                                                                             
        249 TTTTCGAAACGTTTCCTGTATGTGCTAATATCCATGCCGATGAGTCGTTCCCATGTGTCTGAAAC
         65 TTTTCGAAACGTTTCCTGTATGTGCTAATATCCATGCCGATGAGTCGTTCCCATGTGTCTGAAAC

                                                           
        314 GAGTCTGATGCGAATCTGATCTGTTGTCGAAGAAAGGTTGAACCGCA
        130 GAGTCTGATGCGAATCTGATCTGTTGTCGAAGAAAGGTTGAACCGCA

                                                                             
        361 GAAAAACATTTTAGACAGGCGTTAAAAATGTAACAACGAAACACGTAGGAAAGGTGATTGACACG
          1 GAAAAACATTTTAGACAGGCG-TAAAAATGTAACAACGAAACACGTAGGAAAGGTGATTGACACG

                                                                             
        426 TTTTCGAAACGTTTCCTGTATGTGCTAATATCCATGCCGATGAGTCGTTCCCATGTGTCTGAAAC
         65 TTTTCGAAACGTTTCCTGTATGTGCTAATATCCATGCCGATGAGTCGTTCCCATGTGTCTGAAAC

                                                           
        491 GAGTCTGATGCGAATCTGATCTGTTGTCGAAGAAAGGTTGAACCGCA
        130 GAGTCTGATGCGAATCTGATCTGTTGTCGAAGAAAGGTTGAACCGCA

                                                                             
        538 GAAAAACATTTTAGACAGGCGTTAAAAATGTAACAACGAAACACGTAGGAAAGGTGATTGACACG
          1 GAAAAACATTTTAGACAGGCG-TAAAAATGTAACAACGAAACACGTAGGAAAGGTGATTGACACG

                                                                             
        603 TTTTCGAAACGTTTCCTGTATGTGCTAATATCCATGCCGATGAGTCGTTCCCATGTGTCTGAAAC
         65 TTTTCGAAACGTTTCCTGTATGTGCTAATATCCATGCCGATGAGTCGTTCCCATGTGTCTGAAAC

             *                  *    *         *   *      *      *    
        668 GGGTCTGAAACGGGTCTAAAACGAAGCTGATCTGTGGTCCAA-AAATGTTGAAACGCA
        130 GAGTCTG--A------T---GCGAATCTGATCTGTTGTCGAAGAAAGGTTGAACCGCA

            *              *                              *  *      *        
        725 AAAAAACATTTTAGATAGGCGTAAGAAATGTAACAACGAAACACGTGGGGAAGGTGTTTGACACG
          1 GAAAAACATTTTAGACAGGCGTAA-AAATGTAACAACGAAACACGTAGGAAAGGTGATTGACACG

                *             
        790 TTTTTGAAACGTTTCCTG
         65 TTTTCGAAACGTTTCCTG

        808 CAACTCTCTA


Statistics
Matches: 420,  Mismatches: 14, Indels: 16
        0.93            0.03        0.04

Matches are distributed among these distances:
 177  307  0.73
 178    4  0.01
 179    1  0.00
 185    1  0.00
 186    3  0.01
 187   86  0.20
 188   18  0.04

ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26


Consensus pattern (176 bp):   
GAAAAACATTTTAGACAGGCGTAAAAATGTAACAACGAAACACGTAGGAAAGGTGATTGACACGT
TTTCGAAACGTTTCCTGTATGTGCTAATATCCATGCCGATGAGTCGTTCCCATGTGTCTGAAACG
AGTCTGATGCGAATCTGATCTGTTGTCGAAGAAAGGTTGAACCGCA

Found at i:675 original size:11 final size:11

Alignment explanation


    Indices: 659--690  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

        649 GTTCCCATGT

                       
        659 GTCTGAAACGG
          1 GTCTGAAACGG

                       
        670 GTCTGAAACGG
          1 GTCTGAAACGG

                *     
        681 GTCTAAAACG
          1 GTCTGAAACG

        691 AAGCTGATCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   20  1.00

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


Consensus pattern (11 bp):   
GTCTGAAACGG
Done.