Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006947.1 Corchorus capsularis cultivar CVL-1 contig06968, 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: 13791
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32


Found at i:2817 original size:32 final size:33

Alignment explanation


    Indices: 2776--2848  Score: 121
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       2766 ACAAAGTTTA

                *               *            
       2776 TTTAACATGCATAATCT-CTTCTTCTACCTTTC
          1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC

                                             
       2808 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
          1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC

                    
       2841 TTTATCAT
          1 TTTATCAT

       2849 TAAAAATTAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  32   16  0.42
  33   22  0.58

ACGTcount: A:0.21, C:0.29, G:0.03, T:0.48


Consensus pattern (33 bp):   
TTTATCATGCATAATCTCCTCCTTCTACCTTTC

Found at i:2923 original size:33 final size:33

Alignment explanation


    Indices: 2879--3010  Score: 210
    Period size: 33  Copynumber: 4.0  Consensus size: 33

       2869 ATACTACCTT

                                          *  
       2879 GTATATTAGTGGCACCTGAAGTTGTCACATTAA
          1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA

                  *                          
       2912 GTATATAAGTGGCACCTGAAGTTGTCACATCAA
          1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA

                                *            
       2945 GTATATTAGTGGCACCTGAACTTGTCACATCAA
          1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA

                 *     *           *         
       2978 GTATAGTAGTGACACCTGAAGTTATCACATCAA
          1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA

       3011 AAATATAATA


Statistics
Matches: 91,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  33   91  1.00

ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30


Consensus pattern (33 bp):   
GTATATTAGTGGCACCTGAAGTTGTCACATCAA

Found at i:3998 original size:42 final size:42

Alignment explanation


    Indices: 3937--4020  Score: 141
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       3927 ATGGTCGCGG

                          *                    *      
       3937 TCGTGATCGTAGCTCTGGATATAATGGTGATCATTTGAAAAA
          1 TCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAAA

                 *                                    
       3979 TCGTGGTCGTAGCTATGGATATAATGGTGATCATTCGAAAAA
          1 TCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAAA

       4021 CATATCCTTC


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32


Consensus pattern (42 bp):   
TCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAAA

Found at i:13388 original size:2 final size:2

Alignment explanation


    Indices: 13381--13426  Score: 65
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      13371 TTAATTAGTA

                                                   *        *              
      13381 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT ACT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT

                
      13424 AT A
          1 AT A

      13427 AGTCTAAACT


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
   2   37  0.95
   3    2  0.05

ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:13721 original size:42 final size:38

Alignment explanation


    Indices: 13666--13744  Score: 113
    Period size: 42  Copynumber: 2.0  Consensus size: 38

      13656 AATTCCTATG

                                                    
      13666 TAATATATATAATAACTAAAATACTTACATTAATTAAATA
          1 TAATATATATAATAACTAAAATACTTAC-TT-ATTAAATA

                               *                   
      13706 TAATAATACTATAATAACTGAAATACTTACTTATTAAAT
          1 TAAT-ATA-TATAATAACTAAAATACTTACTTATTAAAT

      13745 TCTTAAGGTG


Statistics
Matches: 36,  Mismatches: 1, Indels: 4
        0.88            0.02        0.10

Matches are distributed among these distances:
  40   11  0.31
  41    5  0.14
  42   20  0.56

ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38


Consensus pattern (38 bp):   
TAATATATATAATAACTAAAATACTTACTTATTAAATA
Done.