Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008535.1 Corchorus olitorius cultivar O-4 contig08562, 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, 831

Length: 1385
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22


Found at i:931 original size:22 final size:21

Alignment explanation


    Indices: 905--969  Score: 80
    Period size: 22  Copynumber: 3.1  Consensus size: 21

        895 TATTATGCCT

                                  
        905 AATCAAAAAAATAAAAAAAATC
          1 AATCAAAAAAA-AAAAAAAATC

                                  
        927 AATCAAAAAAAATAAAAAAAT-
          1 AATCAAAAAAAA-AAAAAAATC

                  *  *           
        948 AAT-AATAATAAAAAAAAATC
          1 AATCAAAAAAAAAAAAAAATC

              
        968 AA
          1 AA

        970 AAAAACTCAG


Statistics
Matches: 39,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
  19    8  0.21
  20    8  0.21
  21    4  0.10
  22   19  0.49

ACGTcount: A:0.78, C:0.06, G:0.00, T:0.15


Consensus pattern (21 bp):   
AATCAAAAAAAAAAAAAAATC

Found at i:936 original size:14 final size:13

Alignment explanation


    Indices: 909--966  Score: 59
    Period size: 14  Copynumber: 4.5  Consensus size: 13

        899 ATGCCTAATC

                         
        909 AAAAA-AAT-AAA
          1 AAAAATAATAAAA

                      *   
        920 AAAAATCAATCAAA
          1 AAAAAT-AATAAAA

                         
        934 AAAAATAA-AAAA
          1 AAAAATAATAAAA

                           
        946 ATAATAATAATAAAA
          1 A-AA-AATAATAAAA

                  
        961 AAAAAT
          1 AAAAAT

        967 CAAAAAAACT


Statistics
Matches: 40,  Mismatches: 1, Indels: 10
        0.78            0.02        0.20

Matches are distributed among these distances:
  11    5  0.12
  12    4  0.10
  13   10  0.25
  14   16  0.40
  15    5  0.12

ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16


Consensus pattern (13 bp):   
AAAAATAATAAAA

Found at i:960 original size:23 final size:24

Alignment explanation


    Indices: 905--974  Score: 72
    Period size: 27  Copynumber: 2.9  Consensus size: 24

        895 TATTATGCCT

                                    
        905 AATC-AAAAAAAT-AAAAAAAATC
          1 AATCAAAAAAAATAAAAAAAAATC

                                      *
        927 AATCAAAAAAAATAAAAAAATAATAAT
          1 AATCAAAAAAAATAAAAAAA-AAT--C

               *         *       
        954 AATAAAAAAAAATCAAAAAAA
          1 AATCAAAAAAAATAAAAAAAA

        975 CTCAGCCTAA


Statistics
Matches: 40,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  22    4  0.10
  23    8  0.20
  24    6  0.15
  25    3  0.08
  26    1  0.03
  27   18  0.45

ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14


Consensus pattern (24 bp):   
AATCAAAAAAAATAAAAAAAAATC
Done.