Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022375.1 Corchorus olitorius cultivar O-4 contig22408, 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: 3193
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2571 original size:51 final size:50

Alignment explanation


    Indices: 2470--2571  Score: 127
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       2460 GTTCTTCATA

                                                     * **     
       2470 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            *                    
       2520 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
       2571 T
          1 T

       2572 CTTTATTCAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   37  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:2976 original size:21 final size:23

Alignment explanation


    Indices: 2940--3021  Score: 98
    Period size: 23  Copynumber: 3.7  Consensus size: 23

       2930 CACAGAGAGG

                      *         *  
       2940 TTATCAAAA-ATCATAGGAATG-
          1 TTATCAAAATTTCATAGGAAGGT

                        *          
       2961 TTA-CAAAATTTGATAGGAAGGT
          1 TTATCAAAATTTCATAGGAAGGT

                *                  
       2983 TTATTAAAATTTCATAGGAAGGT
          1 TTATCAAAATTTCATAGGAAGGT

                *           
       3006 TTATTAAAATTTCATA
          1 TTATCAAAATTTCATA

       3022 CTTAGATTAT


Statistics
Matches: 53,  Mismatches: 5, Indels: 4
        0.85            0.08        0.06

Matches are distributed among these distances:
  20    5  0.09
  21   12  0.23
  22    3  0.06
  23   33  0.62

ACGTcount: A:0.43, C:0.06, G:0.15, T:0.37


Consensus pattern (23 bp):   
TTATCAAAATTTCATAGGAAGGT

Found at i:2994 original size:23 final size:23

Alignment explanation


    Indices: 2965--3021  Score: 105
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       2955 GGAATGTTAC

                   *               
       2965 AAAATTTGATAGGAAGGTTTATT
          1 AAAATTTCATAGGAAGGTTTATT

                                   
       2988 AAAATTTCATAGGAAGGTTTATT
          1 AAAATTTCATAGGAAGGTTTATT

                       
       3011 AAAATTTCATA
          1 AAAATTTCATA

       3022 CTTAGATTAT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   33  1.00

ACGTcount: A:0.42, C:0.04, G:0.16, T:0.39


Consensus pattern (23 bp):   
AAAATTTCATAGGAAGGTTTATT

Found at i:3082 original size:22 final size:22

Alignment explanation


    Indices: 3057--3117  Score: 77
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       3047 CATAGGTAAA

                       *        * 
       3057 TTATCAAAATTCCATAACGTGG
          1 TTATCAAAATTTCATAACGTAG

                  *     *    *    
       3079 TTATCAGAATTTAATAAGGTAG
          1 TTATCAAAATTTCATAACGTAG

                             
       3101 TTATCAAAATTTCATAA
          1 TTATCAAAATTTCATAA

       3118 AAATATTCAA


Statistics
Matches: 32,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  22   32  1.00

ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36


Consensus pattern (22 bp):   
TTATCAAAATTTCATAACGTAG
Done.