Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009294.1 Corchorus capsularis cultivar CVL-1 contig09315, 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: 5687
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34


Found at i:2903 original size:36 final size:36

Alignment explanation


    Indices: 2856--2928  Score: 146
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       2846 TGCGGTAAAA

                                                
       2856 TTGTGGTTGGCTTCTGCCGCGGAATGGTGTTTGACT
          1 TTGTGGTTGGCTTCTGCCGCGGAATGGTGTTTGACT

                                                
       2892 TTGTGGTTGGCTTCTGCCGCGGAATGGTGTTTGACT
          1 TTGTGGTTGGCTTCTGCCGCGGAATGGTGTTTGACT

             
       2928 T
          1 T

       2929 CTGCAGTAGA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   37  1.00

ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40


Consensus pattern (36 bp):   
TTGTGGTTGGCTTCTGCCGCGGAATGGTGTTTGACT

Found at i:2929 original size:24 final size:24

Alignment explanation


    Indices: 2902--3016  Score: 97
    Period size: 24  Copynumber: 4.8  Consensus size: 24

       2892 TTGTGGTTGG

                      *        *    
       2902 CTTCTGCCGCGGAATGGTGTTTGA
          1 CTTCTGCCGCAGAATGGTGATTGA

                   * *     *        
       2926 CTTCTGCAGTAGAATTGTGATTGA
          1 CTTCTGCCGCAGAATGGTGATTGA

                       *       *    
       2950 CTTCTGCCGCAAAATGGTGCTTGA
          1 CTTCTGCCGCAGAATGGTGATTGA

                      *     *      * 
       2974 CTTCTG-CGATAGAATTGTGATTAA
          1 CTTCTGCCG-CAGAATGGTGATTGA

                 * *   *       
       2998 CTTCTACAGCAAAATGGTG
          1 CTTCTGCCGCAGAATGGTG

       3017 CTTAAGATTG


Statistics
Matches: 69,  Mismatches: 20, Indels: 4
        0.74            0.22        0.04

Matches are distributed among these distances:
  23    2  0.03
  24   66  0.96
  25    1  0.01

ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33


Consensus pattern (24 bp):   
CTTCTGCCGCAGAATGGTGATTGA

Found at i:2966 original size:48 final size:48

Alignment explanation


    Indices: 2892--3019  Score: 168
    Period size: 48  Copynumber: 2.7  Consensus size: 48

       2882 GTGTTTGACT

                 *   *          **       *                   
       2892 TTGTGGTTGGCTTCTGCCGCGGAATGGTGTTTGACTTCTGC-AGTAGAA
          1 TTGTGATTGACTTCTGCCGCAAAATGGTGCTTGACTTCTGCGA-TAGAA

                                                            
       2940 TTGTGATTGACTTCTGCCGCAAAATGGTGCTTGACTTCTGCGATAGAA
          1 TTGTGATTGACTTCTGCCGCAAAATGGTGCTTGACTTCTGCGATAGAA

                    *      * *              
       2988 TTGTGATTAACTTCTACAGCAAAATGGTGCTT
          1 TTGTGATTGACTTCTGCCGCAAAATGGTGCTT

       3020 AAGATTGGTG


Statistics
Matches: 71,  Mismatches: 8, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  48   70  0.99
  49    1  0.01

ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35


Consensus pattern (48 bp):   
TTGTGATTGACTTCTGCCGCAAAATGGTGCTTGACTTCTGCGATAGAA

Found at i:3464 original size:28 final size:28

Alignment explanation


    Indices: 3424--3479  Score: 85
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       3414 AGTTACGGGG

                  *           *         
       3424 TTTTTGTAATTTTGGCTATTTGCGGCAA
          1 TTTTTGGAATTTTGGCTACTTGCGGCAA

                           *            
       3452 TTTTTGGAATTTTGGGTACTTGCGGCAA
          1 TTTTTGGAATTTTGGCTACTTGCGGCAA

       3480 ATTTGCAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.18, C:0.11, G:0.25, T:0.46


Consensus pattern (28 bp):   
TTTTTGGAATTTTGGCTACTTGCGGCAA

Found at i:3492 original size:28 final size:28

Alignment explanation


    Indices: 3426--3496  Score: 81
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       3416 TTACGGGGTT

                *        *  *          *
       3426 TTTGTAATTTTGGCTATTTGCGGCAATT
          1 TTTGCAATTTTGGGTACTTGCGGCAATA

                *                       
       3454 TTTGGAATTTTGGGTACTTGCGGCAA-A
          1 TTTGCAATTTTGGGTACTTGCGGCAATA

                            
       3481 TTTGCAATTTTTGGGT
          1 TTTGCAA-TTTTGGGT

       3497 TGCTGCGGCA


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  27    6  0.16
  28   31  0.84

ACGTcount: A:0.18, C:0.10, G:0.25, T:0.46


Consensus pattern (28 bp):   
TTTGCAATTTTGGGTACTTGCGGCAATA
Done.