Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_43 ID=scaffold_43-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: 43637
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.19

Warning! 18318 characters in sequence are not A, C, G, or T


Found at i:6307 original size:27 final size:27

Alignment explanation


    Indices: 6272--6326  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       6262 TGATAATGAC

                                       
       6272 AATATATCGCAAAGAAAAAATAGAAAT
          1 AATATATCGCAAAGAAAAAATAGAAAT

                                       
       6299 AATATATCGCAAAGAAAAAATAGAAAT
          1 AATATATCGCAAAGAAAAAATAGAAAT

             
       6326 A
          1 A

       6327 GAAAAAAATA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.64, C:0.07, G:0.11, T:0.18


Consensus pattern (27 bp):   
AATATATCGCAAAGAAAAAATAGAAAT

Found at i:6479 original size:23 final size:23

Alignment explanation


    Indices: 6453--6523  Score: 67
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       6443 ATGCCTATTT

                    *              
       6453 ATAGGCTTGTAAACCTTATTCTA
          1 ATAGGCTTCTAAACCTTATTCTA

                 ***   **          
       6476 ATAGGAGACTATGCC-TATT-T-
          1 ATAGGCTTCTAAACCTTATTCTA

                                   
       6496 ATAGGCTTCTAAACCTTATTCTA
          1 ATAGGCTTCTAAACCTTATTCTA

                 
       6519 ATAGG
          1 ATAGG

       6524 AGTGAAACTC


Statistics
Matches: 34,  Mismatches: 11, Indels: 6
        0.67            0.22        0.12

Matches are distributed among these distances:
  20   10  0.29
  21    5  0.15
  22    5  0.15
  23   14  0.41

ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37


Consensus pattern (23 bp):   
ATAGGCTTCTAAACCTTATTCTA

Found at i:6496 original size:43 final size:43

Alignment explanation


    Indices: 6438--6525  Score: 167
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       6428 CAAGAGGAGT

                                   *                   
       6438 AGACTATGCCTATTTATAGGCTTGTAAACCTTATTCTAATAGG
          1 AGACTATGCCTATTTATAGGCTTCTAAACCTTATTCTAATAGG

                                                       
       6481 AGACTATGCCTATTTATAGGCTTCTAAACCTTATTCTAATAGG
          1 AGACTATGCCTATTTATAGGCTTCTAAACCTTATTCTAATAGG

              
       6524 AG
          1 AG

       6526 TGAAACTCCT


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   44  1.00

ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Consensus pattern (43 bp):   
AGACTATGCCTATTTATAGGCTTCTAAACCTTATTCTAATAGG
Done.