Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2263

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: 10736
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36


Found at i:4994 original size:18 final size:19

Alignment explanation


    Indices: 4959--4995  Score: 58
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       4949 TCTTCTGAAA

                         *     
       4959 ATTTCTTATGATTTCTATG
          1 ATTTCTTATGATTACTATG

                               
       4978 ATTTCTT-TGATTACTATG
          1 ATTTCTTATGATTACTATG

       4996 GGCCTTCCGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18   10  0.59
  19    7  0.41

ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57


Consensus pattern (19 bp):   
ATTTCTTATGATTACTATG

Found at i:5406 original size:157 final size:157

Alignment explanation


    Indices: 5204--5566  Score: 375
    Period size: 157  Copynumber: 2.3  Consensus size: 157

       5194 CTTTTAAGTA

                           * *      *           *   *                      * 
       5204 GAAGGTATACCTTAAAGATATTTTCGTAATTTTTTTGGAACCGAGTTC-TAAGTTATCA-CTGGG
          1 GAAGGTATACCTTAAGGGTATTTTTGTAATTTTTTTAGAATCGAGTTCTTAAGTTATCATCT-CG

                                                                 *           
       5267 TCCACTTTTATGTCGAAA-ATGGGTATTTAGGATAGGTTCATCCCATATACAGTA-ATTTTTAAG
         65 TCCACTTTTATGTC-AAATATGGGTATTTAGGATAGGTTCATCCCATATA-AGAATATTTTTAAG

                                 *      *   
       5330 TCCTTT-AGGGTTATCAAAATTCCTTAATGTC
        128 TCCTTTAAGGG-TATC-AAATACCTTAACGTC

                           *                                    *   * *      
       5361 GAAGGTATACCTATAGGGGTATTTTTGTAA-TTTTTTAGAATCGAG-TCTTAGGTTGTTATCTCG
          1 GAAGGTATACCT-TAAGGGTATTTTTGTAATTTTTTTAGAATCGAGTTCTTAAGTTATCATCTCG

              ***             *                           *  *               
       5424 TCTGTTTTTATGTCAAATGTGGGTATTTAGGATAGGTTCATCCCATCTATGAATATTTTTAAGTC
         65 TCCACTTTTATGTCAAATATGGGTATTTAGGATAGGTTCATCCCATATAAGAATATTTTTAAGTC

            *             **   *  *     
       5489 TTTTAAGGGTATCAGGTACTTTTACGTC
        130 CTTTAAGGGTATCAAATACCTTAACGTC

                           *                                    
       5517 GAAGGTACTA-CTTATGGGTATTTTTGTAATTTTTTTAGAATCGAG-TCTTA
          1 GAAGGTA-TACCTTAAGGGTATTTTTGTAATTTTTTTAGAATCGAGTTCTTA

       5567 GGTTGTCACT


Statistics
Matches: 173,  Mismatches: 25, Indels: 17
        0.80            0.12        0.08

Matches are distributed among these distances:
 155   16  0.09
 156   45  0.26
 157   93  0.54
 158   19  0.11

ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42


Consensus pattern (157 bp):   
GAAGGTATACCTTAAGGGTATTTTTGTAATTTTTTTAGAATCGAGTTCTTAAGTTATCATCTCGT
CCACTTTTATGTCAAATATGGGTATTTAGGATAGGTTCATCCCATATAAGAATATTTTTAAGTCC
TTTAAGGGTATCAAATACCTTAACGTC
Done.