Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_68 ID=scaffold_68-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: 17526
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:2635 original size:20 final size:21

Alignment explanation


    Indices: 2606--2645  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       2596 AAAGAGACCT

                 *       *       
       2606 CCTATTCTTT-CCGTCATGGG
          1 CCTATGCTTTACCATCATGGG

                                
       2626 CCTATGCTTTACCATCATGG
          1 CCTATGCTTTACCATCATGG

       2646 ATACTGAAGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    9  0.53
  21    8  0.47

ACGTcount: A:0.15, C:0.30, G:0.17, T:0.38


Consensus pattern (21 bp):   
CCTATGCTTTACCATCATGGG

Found at i:7220 original size:20 final size:21

Alignment explanation


    Indices: 7192--7233  Score: 59
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       7182 AATTATTATG

                *                
       7192 AAATTATATTTT-ATTTTAAA
          1 AAATAATATTTTGATTTTAAA

                         *       
       7212 AAATAATATTTTGGTTTTAAA
          1 AAATAATATTTTGATTTTAAA

             
       7233 A
          1 A

       7234 GAAAGATACT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20   11  0.58
  21    8  0.42

ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50


Consensus pattern (21 bp):   
AAATAATATTTTGATTTTAAA

Found at i:9650 original size:22 final size:20

Alignment explanation


    Indices: 9611--9650  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       9601 TTATTTTTCA

                         *      
       9611 ATAAAAATACATATATAATT
          1 ATAAAAATACATAAATAATT

                                
       9631 ATAAAAATATTCATAAATAA
          1 ATAAAAATA--CATAAATAA

       9651 ATGGATATCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    9  0.53
  22    8  0.47

ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33


Consensus pattern (20 bp):   
ATAAAAATACATAAATAATT
Done.