Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015062.1 Corchorus olitorius cultivar O-4 contig15095, 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: 12266
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:1472 original size:17 final size:18

Alignment explanation


    Indices: 1436--1472  Score: 67
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1426 TGATTTATAT

                              
       1436 CATTTAAAAAAAACTAGC
          1 CATTTAAAAAAAACTAGC

                              
       1454 CATTTAAAAAAAACT-GC
          1 CATTTAAAAAAAACTAGC

              
       1471 CA
          1 CA

       1473 CCAACTACTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    4  0.21
  18   15  0.79

ACGTcount: A:0.54, C:0.19, G:0.05, T:0.22


Consensus pattern (18 bp):   
CATTTAAAAAAAACTAGC

Found at i:8540 original size:13 final size:15

Alignment explanation


    Indices: 8512--8543  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       8502 CATTAATTAT

                           
       8512 AAATAAATTATATAA
          1 AAATAAATTATATAA

                           
       8527 AAATAAATT-T-TAA
          1 AAATAAATTATATAA

                
       8540 AAAT
          1 AAAT

       8544 TATGTTTTGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  13    7  0.41
  14    1  0.06
  15    9  0.53

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (15 bp):   
AAATAAATTATATAA

Found at i:9047 original size:29 final size:29

Alignment explanation


    Indices: 9010--9071  Score: 81
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       9000 ATTTATAGCG

                *                 *   *   
       9010 TTTGGACATTTTG-CTCCATGAGCTTTAAT
          1 TTTGAACATTTTGTC-CCATGAACTTCAAT

                                         
       9039 TTTGAACATTTTGTCCCATGAACTTCAAT
          1 TTTGAACATTTTGTCCCATGAACTTCAAT

                
       9068 TTTG
          1 TTTG

       9072 GGACGTTTTG


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  29   28  0.97
  30    1  0.03

ACGTcount: A:0.23, C:0.18, G:0.15, T:0.45


Consensus pattern (29 bp):   
TTTGAACATTTTGTCCCATGAACTTCAAT

Found at i:9302 original size:29 final size:28

Alignment explanation


    Indices: 9231--9304  Score: 85
    Period size: 29  Copynumber: 2.5  Consensus size: 28

       9221 AGTATGAGGA

                               *         
       9231 GGCAAAACGTCCCAAAATTGAAGTTCAGG
          1 GGCAAAACGT-CCAAAATTAAAGTTCAGG

                    *                   * 
       9260 GGACAAAATGTCCAAAATTAAAGTTCAATG
          1 GG-CAAAACGTCCAAAATTAAAGTTC-AGG

                    *      
       9290 GGCAAAACATCCAAA
          1 GGCAAAACGTCCAAA

       9305 CGCTACAAAT


Statistics
Matches: 38,  Mismatches: 5, Indels: 4
        0.81            0.11        0.09

Matches are distributed among these distances:
  29   27  0.71
  30   11  0.29

ACGTcount: A:0.45, C:0.19, G:0.19, T:0.18


Consensus pattern (28 bp):   
GGCAAAACGTCCAAAATTAAAGTTCAGG
Done.