Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3060

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: 26526
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31


Found at i:7161 original size:105 final size:105

Alignment explanation


    Indices: 6979--7247  Score: 459
    Period size: 105  Copynumber: 2.6  Consensus size: 105

       6969 TAACCGTTAT

                    *                 **                                     
       6979 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
          1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG

                                                    
       7044 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
         66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA

                                            *                                
       7084 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
          1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG

                                                    
       7149 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
         66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA

                            *                               **          
       7189 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
          1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT

       7248 TTATATACAA


Statistics
Matches: 155,  Mismatches: 8, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
 105  154  0.99
 106    1  0.01

ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19


Consensus pattern (105 bp):   
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA

Found at i:14167 original size:104 final size:105

Alignment explanation


    Indices: 13987--14254  Score: 450
    Period size: 104  Copynumber: 2.6  Consensus size: 105

      13977 TAACCGTTAT

                    *                 **                                     
      13987 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
          1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG

                                                    
      14052 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
         66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA

                                            *                                
      14091 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
          1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG

                                                    
      14156 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
         66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA

                            *                               **          
      14196 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
          1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT

      14255 TTATATACAA


Statistics
Matches: 154,  Mismatches: 8, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
 104   82  0.53
 105   71  0.46
 106    1  0.01

ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19


Consensus pattern (105 bp):   
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA

Done.