Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1304

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: 2081
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33


Found at i:16 original size:10 final size:10

Alignment explanation


    Indices: 2--40  Score: 51
    Period size: 10  Copynumber: 3.6  Consensus size: 10

          1 G

                      
          2 ATAAAATTTT
          1 ATAAAATTTT

                      
         12 ATAAAATTTT
          1 ATAAAATTTT

                         
         22 ATACAATTATTTT
          1 ATA-AA--ATTTT

                  
         35 ATAAAA
          1 ATAAAA

         41 ATCAATTTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  10   14  0.54
  11    2  0.08
  12    2  0.08
  13    8  0.31

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (10 bp):   
ATAAAATTTT

Found at i:352 original size:101 final size:103

Alignment explanation


    Indices: 155--360  Score: 299
    Period size: 103  Copynumber: 2.0  Consensus size: 103

        145 AGATAAGAAT

                *        *         *       *             *                   
        155 TAGCGGCGTTTTCTATAAAAACGTCACAAAATATAAATAAAATTATAAAAAATAAAAAAATTTAT
          1 TAGCAGCGTTTTCCATAAAAACGCCACAAAAAATAAATAAAATTAAAAAAAATAAAAAAATTTAT

            *       *                             
        220 TTGCATAGCAAAACGACGTCATTTTGTTCAAAATGAAA
         66 GTGCATAGAAAAACGACGTCATTTTGTTCAAAATGAAA

                                     *            *  *                       
        258 TAGCAGCGTTTTCCATAAAAACGCCGCAAAAAATAAATTAATTTAAAAAAAAT-AAAAAATTT-T
          1 TAGCAGCGTTTTCCATAAAAACGCCACAAAAAATAAATAAAATTAAAAAAAATAAAAAAATTTAT

                           *                      
        321 GTGCATAGAAAAACGGCGTCATTTTGTTCAAAATGAAA
         66 GTGCATAGAAAAACGACGTCATTTTGTTCAAAATGAAA

              
        359 TA
          1 TA

        361 ATATTTTGCG


Statistics
Matches: 92,  Mismatches: 11, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
 101   38  0.41
 102    9  0.10
 103   45  0.49

ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28


Consensus pattern (103 bp):   
TAGCAGCGTTTTCCATAAAAACGCCACAAAAAATAAATAAAATTAAAAAAAATAAAAAAATTTAT
GTGCATAGAAAAACGACGTCATTTTGTTCAAAATGAAA
Done.