Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_624 ID=scaffold_624-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: 5163
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37


Found at i:474 original size:13 final size:14

Alignment explanation


    Indices: 452--488  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 14

        442 AAAAGATTCA

                 *        
        452 TTAATCGTTAACT-
          1 TTAATAGTTAACTG

                          
        465 TTAATAGTTAACTG
          1 TTAATAGTTAACTG

                       
        479 TTAA-AGTTAA
          1 TTAATAGTTAA

        489 TTACCCCTAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  13   18  0.82
  14    4  0.18

ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43


Consensus pattern (14 bp):   
TTAATAGTTAACTG

Found at i:610 original size:26 final size:26

Alignment explanation


    Indices: 581--661  Score: 76
    Period size: 26  Copynumber: 3.0  Consensus size: 26

        571 CAATAAATTT

                                      
        581 TATTAAATTTTAATAAAAATATAAAA
          1 TATTAAATTTTAATAAAAATATAAAA

                   **                * 
        607 TATTAAAAATTAGA-AAAAATATAATA
          1 TATTAAATTTTA-ATAAAAATATAAAA

                                          
        633 TATTGTAACATTTT-ATAAAAATAATAAAA
          1 TA-T-TAA-ATTTTAATAAAAAT-ATAAAA

        662 ATAGAAAGGC


Statistics
Matches: 43,  Mismatches: 6, Indels: 9
        0.74            0.10        0.16

Matches are distributed among these distances:
  26   23  0.53
  27    3  0.07
  28    9  0.21
  29    8  0.19

ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36


Consensus pattern (26 bp):   
TATTAAATTTTAATAAAAATATAAAA

Done.