Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_555 ID=scaffold_555-JGI_221_v2.0

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: 5864
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.32

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:250 original size:132 final size:132

Alignment explanation


    Indices: 8--316  Score: 501
    Period size: 132  Copynumber: 2.3  Consensus size: 132

          1 AGATAGG

                *           *                        *                   *   
          8 ATCTACAACCTACTCCACTGCTGCTTAGGGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCTACT
          1 ATCTTCAACCTACTCCGCTGCTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACT

                                        **                     *          *  
         73 ATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA
         66 ATCTTGGAAAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATATA

              
        138 CA
        131 CA

                                  *  *          *                            
        140 ATCTTCAACCTACTCCGCTGCTACTCAGGGAGACAATGCTTGGTGGCTTAAATCTGCTTCCCACT
          1 ATCTTCAACCTACTCCGCTGCTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACT

                                                  *                          
        205 ATCTTGGAAAGATAAGATTTGCCGTCTTCAATCTGCTCTACTACTGCTTAGAGAGATAAGATATA
         66 ATCTTGGAAAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATATA

              
        270 CA
        131 CA

                       *                                 
        272 ATCTTCAACCTTCTCCGCTGCTGCTTAGGGAGACAAGGCTTGGTG
          1 ATCTTCAACCTACTCCGCTGCTGCTTAGGGAGACAAGGCTTGGTG

        317 TTTCACCGGT


Statistics
Matches: 161,  Mismatches: 16, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 132  161  1.00

ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30


Consensus pattern (132 bp):   
ATCTTCAACCTACTCCGCTGCTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACT
ATCTTGGAAAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATATA
CA

Found at i:1569 original size:15 final size:15

Alignment explanation


    Indices: 1551--1584  Score: 59
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1541 TTCTTTTCCT

                           
       1551 TTTTCTTTCTTTCTA
          1 TTTTCTTTCTTTCTA

                          *
       1566 TTTTCTTTCTTTCTC
          1 TTTTCTTTCTTTCTA

                
       1581 TTTT
          1 TTTT

       1585 TTTTTTTAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76


Consensus pattern (15 bp):   
TTTTCTTTCTTTCTA

Found at i:1918 original size:36 final size:36

Alignment explanation


    Indices: 1878--1951  Score: 148
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       1868 AACTCAGAGA

                                                
       1878 GAAAGAATCTTGTCTTTAATAGGCAATACCGCAATG
          1 GAAAGAATCTTGTCTTTAATAGGCAATACCGCAATG

                                                
       1914 GAAAGAATCTTGTCTTTAATAGGCAATACCGCAATG
          1 GAAAGAATCTTGTCTTTAATAGGCAATACCGCAATG

              
       1950 GA
          1 GA

       1952 CCTAGGAGAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   38  1.00

ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27


Consensus pattern (36 bp):   
GAAAGAATCTTGTCTTTAATAGGCAATACCGCAATG
Done.