Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023266.1 Corchorus olitorius cultivar O-4 contig23299, 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: 8783
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34


Found at i:4944 original size:25 final size:24

Alignment explanation


    Indices: 4907--4953  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       4897 CTAGAAAATT

                                      
       4907 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       4933 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       4954 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:6028 original size:36 final size:35

Alignment explanation


    Indices: 5988--6090  Score: 118
    Period size: 36  Copynumber: 2.9  Consensus size: 35

       5978 TAAAAAAACT

                                               *
       5988 AAAACCTAATGGGAACTTTCCCAATTTGAAACTTTG
          1 AAAACCTAATGGGAACTTTCCCAATTTGAAAC-TTA

                                     *   *       
       6024 AAAA-CTGAATGGGAACTTTCCCGATTTTAAAACTTA
          1 AAAACCT-AATGGGAACTTTCCC-AATTTGAAACTTA

                 * **                      
       6060 AAAACTTGTTGGGAACTTTCCCAATTTGAAA
          1 AAAACCTAATGGGAACTTTCCCAATTTGAAA

       6091 AAAGTTGAAT


Statistics
Matches: 56,  Mismatches: 8, Indels: 7
        0.79            0.11        0.10

Matches are distributed among these distances:
  35    9  0.16
  36   38  0.68
  37    9  0.16

ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31


Consensus pattern (35 bp):   
AAAACCTAATGGGAACTTTCCCAATTTGAAACTTA

Found at i:6125 original size:52 final size:52

Alignment explanation


    Indices: 6057--6195  Score: 233
    Period size: 52  Copynumber: 2.7  Consensus size: 52

       6047 ATTTTAAAAC

                                                  *             
       6057 TTAAAAACTTGTTGGGAACTTTCCCAATTTGAAAAAAGTTGAATTGAATACT
          1 TTAAAAACTTGTTGGGAACTTTCCCAATTTGAAAAAAGCTGAATTGAATACT

              *        *                       *     *          
       6109 TTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTGGATTGAATACT
          1 TTAAAAACTTGTTGGGAACTTTCCCAATTTGAAAAAAGCTGAATTGAATACT

                                               
       6161 TTAAAAACTTGTTGGGAACTTTCCCAATTTGAAAA
          1 TTAAAAACTTGTTGGGAACTTTCCCAATTTGAAAA

       6196 CTATAATTGA


Statistics
Matches: 80,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  52   80  1.00

ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33


Consensus pattern (52 bp):   
TTAAAAACTTGTTGGGAACTTTCCCAATTTGAAAAAAGCTGAATTGAATACT

Found at i:6887 original size:22 final size:22

Alignment explanation


    Indices: 6807--6887  Score: 65
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       6797 AACTCTCAAC

                         *        
       6807 AAAGCCCAAATTATATAAAA-A
          1 AAAGCCCAAATTAAATAAAAGA

             *        *       *       
       6828 GGAAGCCCAACTGTAAAGGATAAAGA
          1 -AAAGCCCAAAT-TAAA-TA-AAAGA

                                    
       6854 AAAGGGCCCAAATTAAATAAAAGA
          1 AAA--GCCCAAATTAAATAAAAGA

                      
       6878 AAAGCCCAAA
          1 AAAGCCCAAA

       6888 GTCAGAAAAT


Statistics
Matches: 46,  Mismatches: 7, Indels: 12
        0.71            0.11        0.18

Matches are distributed among these distances:
  22   16  0.35
  23    3  0.07
  24    9  0.20
  25    6  0.13
  26    5  0.11
  27    7  0.15

ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12


Consensus pattern (22 bp):   
AAAGCCCAAATTAAATAAAAGA
Done.