Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012071.1 Corchorus olitorius cultivar O-4 contig12104, 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: 34656
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:6928 original size:21 final size:21

Alignment explanation


    Indices: 6902--6964  Score: 83
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       6892 GGGGCTACAG

                                 
       6902 AAGAGATAGATACATAAATGA
          1 AAGAGATAGATACATAAATGA

                           *      
       6923 AAGAGATAGA-ATCAGAAATGA
          1 AAGAGATAGATA-CATAAATGA

            *     *              
       6944 CAGAGAAAGATACATAAATGA
          1 AAGAGATAGATACATAAATGA

       6965 TGATTACCGA


Statistics
Matches: 36,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  20    1  0.03
  21   34  0.94
  22    1  0.03

ACGTcount: A:0.57, C:0.06, G:0.21, T:0.16


Consensus pattern (21 bp):   
AAGAGATAGATACATAAATGA

Found at i:8017 original size:16 final size:16

Alignment explanation


    Indices: 7967--8030  Score: 51
    Period size: 16  Copynumber: 4.0  Consensus size: 16

       7957 GATTTTAGAA

                          *  
       7967 TTTTCGGGTTCTA-ATT
          1 TTTTCGGGTTC-AGGTT

                       *   * 
       7983 TTTTCGGGTT-TGAGCT
          1 TTTTCGGGTTCAG-GTT

                            
       7999 TTTTCGGGTTCAGGTT
          1 TTTTCGGGTTCAGGTT

                *      *    
       8015 TTTTGGGGTTCGGGTT
          1 TTTTCGGGTTCAGGTT

       8031 CGAGCGGGTT


Statistics
Matches: 38,  Mismatches: 7, Indels: 6
        0.75            0.14        0.12

Matches are distributed among these distances:
  16   37  0.97
  17    1  0.03

ACGTcount: A:0.06, C:0.11, G:0.31, T:0.52


Consensus pattern (16 bp):   
TTTTCGGGTTCAGGTT

Found at i:11622 original size:2 final size:2

Alignment explanation


    Indices: 11617--11651  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      11607 CTGAAACGTA

                                                                
      11617 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

      11652 CATATTTTCA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49


Consensus pattern (2 bp):   
CT

Found at i:16034 original size:11 final size:11

Alignment explanation


    Indices: 16010--16044  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      16000 TTGACAGCGC

                       
      16010 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
      16021 AACGAAAACGA
          1 AACAAAAACAA

                       
      16032 AACAAAAACAA
          1 AACAAAAACAA

              
      16043 AA
          1 AA

      16045 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:27343 original size:18 final size:18

Alignment explanation


    Indices: 27320--27355  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      27310 GATATCTCCT

                              
      27320 AATTACACTTGAAAGCTG
          1 AATTACACTTGAAAGCTG

                              
      27338 AATTACACTTGAAAGCTG
          1 AATTACACTTGAAAGCTG

      27356 GTAGTGCCCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28


Consensus pattern (18 bp):   
AATTACACTTGAAAGCTG
Done.