Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010522.1 Corchorus olitorius cultivar O-4 contig10554, 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: 7413
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Found at i:6849 original size:12 final size:12

Alignment explanation


    Indices: 6834--6893  Score: 70
    Period size: 13  Copynumber: 5.0  Consensus size: 12

       6824 AAAAGGAGGA

                        
       6834 AAAAGGAAAAAG
          1 AAAAGGAAAAAG

                  *      
       6846 AAAATGCAAAAAG
          1 AAAA-GGAAAAAG

                  *     
       6859 AAAAGGGAAAAG
          1 AAAAGGAAAAAG

                        
       6871 AAAA-G-AAAAG
          1 AAAAGGAAAAAG

                         
       6881 AAAAAGGAAAAAG
          1 -AAAAGGAAAAAG

       6894 GGAAATAGGA


Statistics
Matches: 41,  Mismatches: 3, Indels: 7
        0.80            0.06        0.14

Matches are distributed among these distances:
  10    5  0.12
  11    5  0.12
  12   15  0.37
  13   16  0.39

ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02


Consensus pattern (12 bp):   
AAAAGGAAAAAG

Found at i:6864 original size:35 final size:32

Alignment explanation


    Indices: 6817--6915  Score: 89
    Period size: 30  Copynumber: 3.0  Consensus size: 32

       6807 GAGGCCAACA

                  *                           
       6817 GAAAAAAAAAAGGAGGAAAAAGGAAAAAGAAAAT
          1 GAAAAAGAAAA-G-GGAAAAAGGAAAAAGAAAAT

                                             
       6851 GCAAAAAGAAAAGGG-AAAA-G-AAAAGAAAA-
          1 G-AAAAAGAAAAGGGAAAAAGGAAAAAGAAAAT

                               *                
       6880 GAAAAAGGAAAAAGGGAAATAGGAAAATAAGAAAAT
          1 GAAAAA-G-AAAAGGGAAAAAGG-AAA-AAGAAAAT

       6916 TAAAGATTAA


Statistics
Matches: 54,  Mismatches: 2, Indels: 16
        0.75            0.03        0.22

Matches are distributed among these distances:
  28    5  0.09
  29    2  0.04
  30   16  0.30
  31    4  0.07
  32    5  0.09
  33    2  0.04
  34    4  0.07
  35   16  0.30

ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04


Consensus pattern (32 bp):   
GAAAAAGAAAAGGGAAAAAGGAAAAAGAAAAT

Found at i:6890 original size:17 final size:17

Alignment explanation


    Indices: 6854--6891  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       6844 AGAAAATGCA

                       *     
       6854 AAAAGAAAAGGGAAAAG
          1 AAAAGAAAAGGAAAAAG

                              
       6871 AAAAGAAAA-GAAAAAGG
          1 AAAAGAAAAGGAAAAA-G

                
       6888 AAAA
          1 AAAA

       6892 AGGGAAATAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  16    5  0.26
  17   14  0.74

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (17 bp):   
AAAAGAAAAGGAAAAAG

Found at i:6897 original size:8 final size:7

Alignment explanation


    Indices: 6830--6906  Score: 53
    Period size: 7  Copynumber: 12.0  Consensus size: 7

       6820 AAAAAAAAGG

                   
       6830 AGGAAAA
          1 AGGAAAA

                   
       6837 AGGAAAA
          1 AGGAAAA

                   
       6844 A-GAAAA
          1 AGGAAAA

            * *    
       6850 TGCAAAA
          1 AGGAAAA

                   
       6857 A-G-AAA
          1 AGGAAAA

               *   
       6862 AGGGAAA
          1 AGGAAAA

                   
       6869 A-G-AAA
          1 AGGAAAA

                   
       6874 A-G-AAA
          1 AGGAAAA

                   
       6879 A-GAAAA
          1 AGGAAAA

                   
       6885 AGGAAAA
          1 AGGAAAA

                   *
       6892 AGGGAAAT
          1 A-GGAAAA

                   
       6900 AGGAAAA
          1 AGGAAAA

       6907 TAAGAAAATT


Statistics
Matches: 58,  Mismatches: 6, Indels: 12
        0.76            0.08        0.16

Matches are distributed among these distances:
   5   14  0.24
   6   11  0.19
   7   27  0.47
   8    6  0.10

ACGTcount: A:0.70, C:0.01, G:0.26, T:0.03


Consensus pattern (7 bp):   
AGGAAAA
Done.