Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024347.1 Corchorus olitorius cultivar O-4 contig24380, 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: 6714
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37


Found at i:163 original size:22 final size:21

Alignment explanation


    Indices: 121--175  Score: 58
    Period size: 22  Copynumber: 2.5  Consensus size: 21

        111 ATCACCTCAT

                         *  *     
        121 TTAAGATTTTTAGTGATCTTA-
          1 TTAA-ATTTTTAGAGACCTTAC

                                   
        142 TTAACATATTTTAGAGACCTTAC
          1 TTAA-AT-TTTTAGAGACCTTAC

                       
        165 TTAAATTTTTA
          1 TTAAATTTTTA

        176 TTCAGTAACC


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  21   11  0.38
  22   14  0.48
  23    4  0.14

ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49


Consensus pattern (21 bp):   
TTAAATTTTTAGAGACCTTAC

Found at i:251 original size:23 final size:20

Alignment explanation


    Indices: 205--273  Score: 59
    Period size: 21  Copynumber: 3.2  Consensus size: 20

        195 TTATCGTTAA

                   *            *
        205 CTTATGAAT-TTTATAGTAAC
          1 CTTATGAGTGTTT-TAGTAAT

                                   
        225 CTTATGAAGGTTGTTTTAGTAAT
          1 CTTATG-A-G-TGTTTTAGTAAT

                             *   
        248 CTTATTGAGTGTTTTAGAAAT
          1 CTTA-TGAGTGTTTTAGTAAT

                 
        269 CTTAT
          1 CTTAT

        274 AAAGTAACTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 10
        0.76            0.06        0.19

Matches are distributed among these distances:
  20    7  0.17
  21   16  0.39
  22    1  0.02
  23   12  0.29
  24    5  0.12

ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48


Consensus pattern (20 bp):   
CTTATGAGTGTTTTAGTAAT

Found at i:930 original size:21 final size:22

Alignment explanation


    Indices: 906--957  Score: 70
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        896 TTACTAAAGG

                          *   *   
        906 TTTTAGTAACCCTTGTTACAAT
          1 TTTTAGTAACCCTTATTAAAAT

                       *          
        928 TTTTAGTAACCTTTATTAAAA-
          1 TTTTAGTAACCCTTATTAAAAT

                     
        949 TTTTAGTAA
          1 TTTTAGTAA

        958 TCTTGTAAGC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  21    9  0.33
  22   18  0.67

ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48


Consensus pattern (22 bp):   
TTTTAGTAACCCTTATTAAAAT

Done.