Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018604.1 Corchorus olitorius cultivar O-4 contig18637, 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: 11210
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:3915 original size:19 final size:20

Alignment explanation


    Indices: 3865--3915  Score: 63
    Period size: 19  Copynumber: 2.7  Consensus size: 20

       3855 TGTGAGATTT

                                
       3865 TTAATAA-TAATTATTTAAG
          1 TTAATAATTAATTATTTAAG

            **                  
       3884 AAAATAATT-ATTATTTAA-
          1 TTAATAATTAATTATTTAAG

                          
       3902 TTAATAATTAATTA
          1 TTAATAATTAATTA

       3916 ATTTCAGCCC


Statistics
Matches: 26,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  18    7  0.27
  19   18  0.69
  20    1  0.04

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47


Consensus pattern (20 bp):   
TTAATAATTAATTATTTAAG

Found at i:5904 original size:42 final size:44

Alignment explanation


    Indices: 5853--5946  Score: 106
    Period size: 45  Copynumber: 2.2  Consensus size: 44

       5843 AGAGCATTAC

                                    **     *             
       5853 CTAA-ATTCTA-T-TCCATCTCTAGGTAATTTATCAAAATAAAGT
          1 CTAATATTCTACTCTCCATCTCTAAATAATTCATCAAAATAAA-T

                                                   *     
       5895 -TAATATTCTACTCGTCCATCTCTAAATAATTCATCAAAGTAAAT
          1 CTAATATTCTACTC-TCCATCTCTAAATAATTCATCAAAATAAAT

                    
       5939 CTAATATT
          1 CTAATATT

       5947 AATTGTTGTT


Statistics
Matches: 43,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  41    3  0.07
  42    6  0.14
  43    1  0.02
  44    1  0.02
  45   32  0.74

ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38


Consensus pattern (44 bp):   
CTAATATTCTACTCTCCATCTCTAAATAATTCATCAAAATAAAT

Found at i:6952 original size:21 final size:21

Alignment explanation


    Indices: 6928--6995  Score: 50
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       6918 GTAATATATA

                                 
       6928 TAATAACTAAAATACTTACAT
          1 TAATAACTAAAATACTTACAT

                   *  *  *   *     
       6949 TAATTAAATGTAATTA-ATAC-T
          1 TAA-TAACT-AAAATACTTACAT

                     *            
       6970 ATAATAACTGAAATACTTACAT
          1 -TAATAACTAAAATACTTACAT

                
       6992 TAAT
          1 TAAT

       6996 TAAATTCTTA


Statistics
Matches: 34,  Mismatches: 8, Indels: 10
        0.65            0.15        0.19

Matches are distributed among these distances:
  20    4  0.12
  21   15  0.44
  22   11  0.32
  23    4  0.12

ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37


Consensus pattern (21 bp):   
TAATAACTAAAATACTTACAT

Found at i:10208 original size:23 final size:24

Alignment explanation


    Indices: 10182--10242  Score: 97
    Period size: 23  Copynumber: 2.6  Consensus size: 24

      10172 GGCTAGCCCG

                                    
      10182 CGCGCCAGGCCTGGGCGC-TGGCC
          1 CGCGCCAGGCCTGGGCGCTTGGCC

                  *               * 
      10205 CGCGCCTGGCCTGGGCGCTTGGGC
          1 CGCGCCAGGCCTGGGCGCTTGGCC

                          
      10229 CGCGCCAGGCCTGG
          1 CGCGCCAGGCCTGG

      10243 CCCAAGAGGC


Statistics
Matches: 34,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  23   17  0.50
  24   17  0.50

ACGTcount: A:0.03, C:0.41, G:0.44, T:0.11


Consensus pattern (24 bp):   
CGCGCCAGGCCTGGGCGCTTGGCC

Done.