Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000067.1 Corchorus olitorius cultivar O-4 contig00067, whole genome shotgun sequence

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, 646

Length: 1078
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38


Found at i:173 original size:15 final size:15

Alignment explanation


    Indices: 153--183  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        143 ACAATACATT

                           
        153 AACTATCAAATAGAA
          1 AACTATCAAATAGAA

                           
        168 AACTATCAAATAGAA
          1 AACTATCAAATAGAA

             
        183 A
          1 A

        184 CAGGTTAATC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19


Consensus pattern (15 bp):   
AACTATCAAATAGAA

Found at i:230 original size:14 final size:14

Alignment explanation


    Indices: 211--245  Score: 52
    Period size: 14  Copynumber: 2.5  Consensus size: 14

        201 CCTTTTAAAT

                          
        211 TAAAATAGTAAAAA
          1 TAAAATAGTAAAAA

                  *       
        225 TAAAATGGTAAAAA
          1 TAAAATAGTAAAAA

              *    
        239 TATAATA
          1 TAAAATA

        246 ATTATAAAAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26


Consensus pattern (14 bp):   
TAAAATAGTAAAAA

Found at i:640 original size:27 final size:28

Alignment explanation


    Indices: 610--662  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

        600 TAATATGATT

                                         
        610 ATTTAT-TTT-GGTATTTTATGATTTCAG
          1 ATTTATCTTTAGGT-TTTTATGATTTCAG

                       *              
        637 ATTTATCTTTATGTTTTTATGATTTC
          1 ATTTATCTTTAGGTTTTTATGATTTC

        663 TAATTGATTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  27    6  0.26
  28   15  0.65
  29    2  0.09

ACGTcount: A:0.21, C:0.06, G:0.11, T:0.62


Consensus pattern (28 bp):   
ATTTATCTTTAGGTTTTTATGATTTCAG
Done.