Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015734.1 Corchorus olitorius cultivar O-4 contig15767, 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: 33072
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:8890 original size:22 final size:22

Alignment explanation


    Indices: 8865--8939  Score: 82
    Period size: 21  Copynumber: 3.5  Consensus size: 22

       8855 TCAAAAAATT

                    *             
       8865 ATAGGGAGATTAACAAAATCTC
          1 ATAGGGAGGTTAACAAAATCTC

                *       *         
       8887 ATAGTGAGGTTATCAAAA-CTC
          1 ATAGGGAGGTTAACAAAATCTC

              *                *  
       8908 ATTGGGAGGTT-ACAAAATTTC
          1 ATAGGGAGGTTAACAAAATCTC

                 *     
       8929 ATAGGAAGGTT
          1 ATAGGGAGGTT

       8940 TATTAAAATT


Statistics
Matches: 43,  Mismatches: 9, Indels: 3
        0.78            0.16        0.05

Matches are distributed among these distances:
  20    5  0.12
  21   23  0.53
  22   15  0.35

ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28


Consensus pattern (22 bp):   
ATAGGGAGGTTAACAAAATCTC

Found at i:9032 original size:22 final size:21

Alignment explanation


    Indices: 8983--9064  Score: 94
    Period size: 22  Copynumber: 3.8  Consensus size: 21

       8973 AGTATGAAGT

                  *               
       8983 TTATCACAATTTCAT-AGGTTA
          1 TTATCAAAATTTCATAAGG-TA

                             *   
       9004 TTATCAAAATTTCATAACGTA
          1 TTATCAAAATTTCATAAGGTA

                         *   *     
       9025 GTTATCAAAATTTAATAGGGTAA
          1 -TTATCAAAATTTCATAAGGT-A

                             
       9048 TTATCAAAATTTCATAA
          1 TTATCAAAATTTCATAA

       9065 AAATATTCAA


Statistics
Matches: 51,  Mismatches: 7, Indels: 5
        0.81            0.11        0.08

Matches are distributed among these distances:
  21   16  0.31
  22   34  0.67
  23    1  0.02

ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39


Consensus pattern (21 bp):   
TTATCAAAATTTCATAAGGTA

Found at i:13805 original size:18 final size:19

Alignment explanation


    Indices: 13771--13806  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      13761 GGCCATCGCC

                  *            
      13771 TCAAGACTCGCCTCCGATT
          1 TCAAGAATCGCCTCCGATT

                              
      13790 TCAAGAATCG-CTCCGAT
          1 TCAAGAATCGCCTCCGAT

      13807 CAATGATCTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25


Consensus pattern (19 bp):   
TCAAGAATCGCCTCCGATT

Found at i:21246 original size:21 final size:21

Alignment explanation


    Indices: 21222--21263  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      21212 TTATATATGC

                                 
      21222 TTTATTATTTGCTGATATTGG
          1 TTTATTATTTGCTGATATTGG

                                 
      21243 TTTATTATTTGCTGATATTGG
          1 TTTATTATTTGCTGATATTGG

      21264 CTTCCTAGCA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57


Consensus pattern (21 bp):   
TTTATTATTTGCTGATATTGG
Done.