Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_390 ID=scaffold_390-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: 7553
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.33


Found at i:322 original size:18 final size:17

Alignment explanation


    Indices: 296--334  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 17

        286 ATTTTCCTTC

                              
        296 CACATTC-AATATTAATT
          1 CACATTCAAATA-TAATT

                              
        313 CACATATCAAATATAATT
          1 CACAT-TCAAATATAATT

                
        331 CACA
          1 CACA

        335 ATTTGTAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  17    5  0.25
  18   11  0.55
  19    4  0.20

ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33


Consensus pattern (17 bp):   
CACATTCAAATATAATT

Found at i:5704 original size:35 final size:35

Alignment explanation


    Indices: 5658--5729  Score: 144
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       5648 CATCATATGA

                                               
       5658 AGAAAAGATTCTCGAGCCTCATCTCCTTGACCCTG
          1 AGAAAAGATTCTCGAGCCTCATCTCCTTGACCCTG

                                               
       5693 AGAAAAGATTCTCGAGCCTCATCTCCTTGACCCTG
          1 AGAAAAGATTCTCGAGCCTCATCTCCTTGACCCTG

              
       5728 AG
          1 AG

       5730 TCTCGGGTCG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   37  1.00

ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25


Consensus pattern (35 bp):   
AGAAAAGATTCTCGAGCCTCATCTCCTTGACCCTG

Found at i:7454 original size:18 final size:17

Alignment explanation


    Indices: 7428--7466  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       7418 ATTTTCCTTC

                              
       7428 CACATTC-AATATTAATT
          1 CACATTCAAATA-TAATT

                              
       7445 CACATATCAAATATAATT
          1 CACAT-TCAAATATAATT

                
       7463 CACA
          1 CACA

       7467 ATTTATAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  17    5  0.25
  18   11  0.55
  19    4  0.20

ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33


Consensus pattern (17 bp):   
CACATTCAAATATAATT
Done.