Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_632 ID=scaffold_632-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: 5098
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35


Found at i:1488 original size:44 final size:44

Alignment explanation


    Indices: 1440--1549  Score: 166
    Period size: 44  Copynumber: 2.5  Consensus size: 44

       1430 AACTCATCGG

                                     *                  
       1440 AATAATAACAGATACACGGTGGCCTGCACACAGTCCGTACCACC
          1 AATAATAACAGATACACGGTGGCCTACACACAGTCCGTACCACC

                    *     **              *       *     
       1484 AATAATAATAGATAGGCGGTGGCCTACACATAGTCCGTGCCACC
          1 AATAATAACAGATACACGGTGGCCTACACACAGTCCGTACCACC

                                  
       1528 AATAATAACAGATACACGGTGG
          1 AATAATAACAGATACACGGTGG

       1550 ATTAGCACAT


Statistics
Matches: 57,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  44   57  1.00

ACGTcount: A:0.35, C:0.25, G:0.21, T:0.18


Consensus pattern (44 bp):   
AATAATAACAGATACACGGTGGCCTACACACAGTCCGTACCACC

Found at i:1587 original size:43 final size:43

Alignment explanation


    Indices: 1538--1668  Score: 192
    Period size: 43  Copynumber: 3.0  Consensus size: 43

       1528 AATAATAACA

                          *                            
       1538 GATACACGGTGGATTAGCACATAGCACCACCCTTATAGTCAAT
          1 GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT

                   **              *        *    *     
       1581 GATACACAATGGATCAGCACATAACACCACCCGTATAATCAAT
          1 GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT

                                                        
       1624 GATAC-CTGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT
          1 GATACAC-GGTGGATCAGCACATAGCACCACCCTTATAGTCAAT

              
       1667 GA
          1 GA

       1669 CATCTGGTAC


Statistics
Matches: 76,  Mismatches: 11, Indels: 2
        0.85            0.12        0.02

Matches are distributed among these distances:
  42    1  0.01
  43   75  0.99

ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21


Consensus pattern (43 bp):   
GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT

Found at i:3413 original size:15 final size:15

Alignment explanation


    Indices: 3393--3422  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3383 TCAGAAGAAC

                           
       3393 TTCCAGTTAATACAT
          1 TTCCAGTTAATACAT

                           
       3408 TTCCAGTTAATACAT
          1 TTCCAGTTAATACAT

       3423 ACATTCTTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40


Consensus pattern (15 bp):   
TTCCAGTTAATACAT
Done.