Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020358.1 Corchorus olitorius cultivar O-4 contig20391, 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: 11676
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:893 original size:1 final size:1

Alignment explanation


    Indices: 887--921  Score: 70
    Period size: 1  Copynumber: 35.0  Consensus size: 1

        877 GTATTTTGAA

                                               
        887 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

        922 ACAAAATTAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   34  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:10010 original size:152 final size:150

Alignment explanation


    Indices: 9706--10014  Score: 530
    Period size: 152  Copynumber: 2.0  Consensus size: 150

       9696 ACTGCTCTGT

                    *                                              *         
       9706 AATTGCATTTAAGCAACAAGCTTTGCAATGAAAAGAACCTAAATTCAACCTTTTTGAAGCTCCTA
          1 AATTGCATGTAAGCAACAAGCTTTGCAATGAAAAGAACCTAAATTCAACCTTTTTAAAGCTCCTA

                                           *                     * *         
       9771 CTGTTTGTGCTAATTGCAACAGTTCCTAAAGGAAGTTTTTGTTTCCCTTGATATTGGGAATTAAT
         66 CTGTTTGTGCTAATTGCAACAGTTCCTAAAGAAAGTTTTTGTTTCCCTTGATACTAGGAATTAAT

                                
       9836 TAACTTTTAAACATGAATTA
        131 TAACTTTTAAACATGAATTA

                                           *                                 
       9856 AATTGCATGGTAAGCAACAAGCTTTGCAATGGAAAGAACCTAAATTCAACCTTTTTAAAGCTCCT
          1 AATTGCAT-GTAAGCAACAAGCTTTGCAATGAAAAGAACCTAAATTCAACCTTTTTAAAGCTCCT

                                                                             
       9921 ACTGTTTGTGCTAATTTGCAACAGTTCCTAAAGAAAGTTTTTGTTTCCCTTGATACTAGGAATTA
         65 ACTGTTTGTGCTAA-TTGCAACAGTTCCTAAAGAAAGTTTTTGTTTCCCTTGATACTAGGAATTA

                                   
       9986 ATTAACTTTTAAACATG-ATGTA
        129 ATTAACTTTTAAACATGAAT-TA

                   
      10008 AATTGCA
          1 AATTGCA

      10015 AAAAAATGCA


Statistics
Matches: 150,  Mismatches: 6, Indels: 4
        0.94            0.04        0.03

Matches are distributed among these distances:
 150    8  0.05
 151   69  0.46
 152   73  0.49

ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Consensus pattern (150 bp):   
AATTGCATGTAAGCAACAAGCTTTGCAATGAAAAGAACCTAAATTCAACCTTTTTAAAGCTCCTA
CTGTTTGTGCTAATTGCAACAGTTCCTAAAGAAAGTTTTTGTTTCCCTTGATACTAGGAATTAAT
TAACTTTTAAACATGAATTA

Found at i:10723 original size:56 final size:59

Alignment explanation


    Indices: 10663--10779  Score: 179
    Period size: 56  Copynumber: 2.0  Consensus size: 59

      10653 TAGCCTACTT

                                                                        
      10663 GCTTTTGTCCT-AATTTGCTAATCATTCATGTT-A-AT-ATCACAAGAACGAATAAGACC
          1 GCTTTTGT-CTAAATTTGCTAATCATTCATGTTAATATAATCACAAGAACGAATAAGACC

                                                                         
      10719 GCTTTTGTCTAAATTTGCTAATCATTCATGTTAATATAAAATCACAAGAACGAATAAGACC
          1 GCTTTTGTCTAAATTTGCTAATCATTCATGTTAATAT--AATCACAAGAACGAATAAGACC

      10780 ACTGAATGCA


Statistics
Matches: 55,  Mismatches: 0, Indels: 7
        0.89            0.00        0.11

Matches are distributed among these distances:
  55    2  0.04
  56   29  0.53
  57    1  0.02
  58    2  0.04
  61   21  0.38

ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33


Consensus pattern (59 bp):   
GCTTTTGTCTAAATTTGCTAATCATTCATGTTAATATAATCACAAGAACGAATAAGACC
Done.