Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_219 ID=scaffold_219-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: 9570
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.30

Warning! 347 characters in sequence are not A, C, G, or T


Found at i:2137 original size:44 final size:42

Alignment explanation


    Indices: 2049--2156  Score: 139
    Period size: 44  Copynumber: 2.5  Consensus size: 42

       2039 CTACTATCCC

                                             *   *     
       2049 AGACAGGGTCTTACACGAAAT-TATATACGATGTCAATGTCCT
          1 AGACA-GGTCTTACACGAAATCTATATACGATGCCAACGTCCT

                                                         
       2091 AGACATGGTCTTACACGTAAATCTA-ATATCGATGCCAACGTCCT
          1 AGACA-GGTCTTACACG-AAATCTATATA-CGATGCCAACGTCCT

                                  
       2135 AGACGAGGTCTTACACGAAATC
          1 AGAC-AGGTCTTACACGAAATC

       2157 ACATATTAGA


Statistics
Matches: 59,  Mismatches: 3, Indels: 7
        0.86            0.04        0.10

Matches are distributed among these distances:
  42   16  0.27
  43   12  0.20
  44   30  0.51
  45    1  0.02

ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26


Consensus pattern (42 bp):   
AGACAGGTCTTACACGAAATCTATATACGATGCCAACGTCCT

Found at i:8189 original size:27 final size:27

Alignment explanation


    Indices: 8159--8213  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       8149 ACTATTACAC

                                       
       8159 ATTGTACCAAATTACCACACAAGACCA
          1 ATTGTACCAAATTACCACACAAGACCA

                                       
       8186 ATTGTACCAAATTACCACACAAGACCA
          1 ATTGTACCAAATTACCACACAAGACCA

             
       8213 A
          1 A

       8214 CTTACTTTTT


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:0.45, C:0.29, G:0.07, T:0.18


Consensus pattern (27 bp):   
ATTGTACCAAATTACCACACAAGACCA
Done.