Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1656

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, 860

Length: 1434
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36


Found at i:148 original size:85 final size:85

Alignment explanation


    Indices: 17--219  Score: 336
    Period size: 85  Copynumber: 2.4  Consensus size: 85

          7 GATATATTTG

                                                    *                        
         17 CGCCGTTTGTGTCAAAACTATTTTTGT-CGGCGCGCCGCTTCAAATCTGTTCCGCGCGCGGAATT
          1 CGCCGTTTGTGTCAAAACTATTTTT-TCCGGCGCGCCGCTCCAAATCTGTTCCGCGCGCGGAATT

                                 
         81 TTCGATATATCGATTCCTGCT
         65 TTCGATATATCGATTCCTGCT

                                              *                              
        102 CGCCGTTTGTGTCAAAACTATTTTTTCCGGCGCGGCGCTCCAAATCTGTTCCGCGCGCGGAATTT
          1 CGCCGTTTGTGTCAAAACTATTTTTTCCGGCGCGCCGCTCCAAATCTGTTCCGCGCGCGGAATTT

                                
        167 TCGATATATCGATTCCTGCT
         66 TCGATATATCGATTCCTGCT

                 * *         * *             
        187 CGCCGATCGTGTCAAAAATGTTTTTTCCGGCGC
          1 CGCCGTTTGTGTCAAAACTATTTTTTCCGGCGC

        220 TGCACCAGAA


Statistics
Matches: 111,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  84    1  0.01
  85  110  0.99

ACGTcount: A:0.17, C:0.28, G:0.23, T:0.33


Consensus pattern (85 bp):   
CGCCGTTTGTGTCAAAACTATTTTTTCCGGCGCGCCGCTCCAAATCTGTTCCGCGCGCGGAATTT
TCGATATATCGATTCCTGCT

Found at i:239 original size:85 final size:85

Alignment explanation


    Indices: 25--265  Score: 258
    Period size: 85  Copynumber: 2.8  Consensus size: 85

         15 TGCGCCGTTT

                     *                 * *          **                       
         25 GTGTCAAAACTATTTTTGT-CGGCGCGCCGCTTC-AAATCTGTTCCGCGCGCGGAATTTTCGATA
          1 GTGTCAAAAATATTTTT-TCCGGCGCGGCAC-TCAAAATCAATTCCGCGCGCGGAATTTTCGATA

                               * *
         88 TATCGATTCCTGCTCGCCGTTT
         64 TATCGATTCCTGCTCGCCGATC

                     *                  *   *     **                         
        110 GTGTCAAAACTATTTTTTCCGGCGCGGCGCTCCAAATCTGTTCCGCGCGCGGAATTTTCGATATA
          1 GTGTCAAAAATATTTTTTCCGGCGCGGCACTCAAAATCAATTCCGCGCGCGGAATTTTCGATATA

                                
        175 TCGATTCCTGCTCGCCGATC
         66 TCGATTCCTGCTCGCCGATC

                       *             *                           *  *        
        195 GTGTCAAAAATGTTTTTTCCGGCGCTGCAC-CAGAAAAT-AATTCCGCGCGC-CACTTTTTCGAT
          1 GTGTCAAAAATATTTTTTCCGGCGCGGCACTC--AAAATCAATTCCGCGCGCGGA-ATTTTCGAT

                     
        257 ATATCGATT
         63 ATATCGATT

        266 TTTCTGCGCG


Statistics
Matches: 139,  Mismatches: 12, Indels: 10
        0.86            0.07        0.06

Matches are distributed among these distances:
  84    5  0.04
  85  130  0.94
  86    4  0.03

ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32


Consensus pattern (85 bp):   
GTGTCAAAAATATTTTTTCCGGCGCGGCACTCAAAATCAATTCCGCGCGCGGAATTTTCGATATA
TCGATTCCTGCTCGCCGATC
Done.