Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014761.1 Corchorus olitorius cultivar O-4 contig14794, 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, 1000

Length: 3602
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31


Found at i:2028 original size:57 final size:57

Alignment explanation


    Indices: 1910--2028  Score: 168
    Period size: 57  Copynumber: 2.1  Consensus size: 57

       1900 CCTTTCGCAC

                                                *             **  * *
       1910 AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCTTTAACAC
          1 AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCAACTTAATTATTCTACAAAAA

                       *                                              
       1967 AATAAATGTTATAATAAATCCTATC-CCCCTATCTCAACTTAATTATTCTACAAAATA
          1 AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCAACTTAATTATTCTACAAAA-A

                 
       2024 AATAA
          1 AATAA

       2029 TATTTTCTTT


Statistics
Matches: 55,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  56   26  0.47
  57   29  0.53

ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36


Consensus pattern (57 bp):   
AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCAACTTAATTATTCTACAAAAA

Found at i:2106 original size:21 final size:21

Alignment explanation


    Indices: 2082--2149  Score: 59
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       2072 AAGGATCAAG

                                 
       2082 ATTTAAGTTGAGTATTTCTTA
          1 ATTTAAGTTGAGTATTTCTTA

                    **  *         *
       2103 ATTTACA-AAGAAT-TTTCTATG
          1 ATTTA-AGTTGAGTATTTCT-TA

                *                
       2124 ATTTGAGTTGAGTATTTCTTA
          1 ATTTAAGTTGAGTATTTCTTA

                 
       2145 ATTTA
          1 ATTTA

       2150 CAAAGAATTT


Statistics
Matches: 33,  Mismatches: 10, Indels: 8
        0.65            0.20        0.16

Matches are distributed among these distances:
  20    6  0.18
  21   21  0.64
  22    6  0.18

ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50


Consensus pattern (21 bp):   
ATTTAAGTTGAGTATTTCTTA

Found at i:2133 original size:42 final size:42

Alignment explanation


    Indices: 2081--2161  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       2071 TAAGGATCAA

                                                      
       2081 GATTTAAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTAAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

                 *                                 
       2123 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
          1 GATTTAAGTTGAGTATTTCTTAATTTACAAAGAATTTTC

       2162 AAGACTTAGC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47


Consensus pattern (42 bp):   
GATTTAAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.