Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2317

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: 16711
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29


Found at i:3213 original size:40 final size:40

Alignment explanation


    Indices: 3169--3324  Score: 235
    Period size: 40  Copynumber: 3.9  Consensus size: 40

       3159 GGATATAGCT

                  *                *                
       3169 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

                    *                            *   
       3209 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA

                                             *       
       3249 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA

                                                
       3289 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT

       3325 CATCCGAATA


Statistics
Matches: 104,  Mismatches: 8, Indels: 8
        0.87            0.07        0.07

Matches are distributed among these distances:
  40  101  0.97
  41    3  0.03

ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24


Consensus pattern (40 bp):   
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

Found at i:11144 original size:40 final size:40

Alignment explanation


    Indices: 11100--11255  Score: 235
    Period size: 40  Copynumber: 3.9  Consensus size: 40

      11090 GGATATAGCT

                  *                *                
      11100 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

                    *                            *   
      11140 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA

                                             *       
      11180 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA

                                                
      11220 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT

      11256 CATCCGAATA


Statistics
Matches: 104,  Mismatches: 8, Indels: 8
        0.87            0.07        0.07

Matches are distributed among these distances:
  40  101  0.97
  41    3  0.03

ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24


Consensus pattern (40 bp):   
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

Done.