Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013401.1 Corchorus capsularis cultivar CVL-1 contig13422, 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: 5594
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:3141 original size:51 final size:51

Alignment explanation


    Indices: 3081--3277  Score: 286
    Period size: 51  Copynumber: 3.9  Consensus size: 51

       3071 CCCTAAACGG

                             *             *                   
       3081 TGCTGCAGTACTCGGAGAAGGACTTGGAGGATGGGAAATGCCAGGGAGGCT
          1 TGCTGCAGTACTCGGAGCAGGACTTGGAGGACGGGAAATGCCAGGGAGGCT

                         *                 * *               * 
       3132 TGCTGCAGTACTCAGAGCAGGACTTGGAGGATGAGAAATGCCAGGGAGGGT
          1 TGCTGCAGTACTCGGAGCAGGACTTGGAGGACGGGAAATGCCAGGGAGGCT

                           *      *  *                         
       3183 TGCTGCAGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGGGAGGCT
          1 TGCTGCAGTACTCGGAGCAGGACTTGGAGGACGGGAAATGCCAGGGAGGCT

                           *      *  *                  
       3234 TGCTGCAGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAG
          1 TGCTGCAGTACTCGGAGCAGGACTTGGAGGACGGGAAATGCCAG

       3278 CATCATTTGG


Statistics
Matches: 135,  Mismatches: 11, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  51  135  1.00

ACGTcount: A:0.24, C:0.17, G:0.41, T:0.18


Consensus pattern (51 bp):   
TGCTGCAGTACTCGGAGCAGGACTTGGAGGACGGGAAATGCCAGGGAGGCT

Found at i:3296 original size:51 final size:51

Alignment explanation


    Indices: 3189--3361  Score: 224
    Period size: 51  Copynumber: 3.4  Consensus size: 51

       3179 GGGTTGCTGC

                                                   *         *  *
       3189 AGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGGGAGGC--TTGCTGC
          1 AGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCA-GCA-GCATTTGGTGT

                                                    *          
       3240 AGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGCATCATTTGGTGT
          1 AGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGCAGCATTTGGTGT

            *      *                  *      * *               
       3291 TGTACTCAGGGCAGGAGTTTGAGGACTGGAAATTCTAGCAGCATTTGGTGT
          1 AGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGCAGCATTTGGTGT

                *               
       3342 AGTAATCGGGGCAGGAGTTT
          1 AGTACTCGGGGCAGGAGTTT

       3362 TATTCTGTGA


Statistics
Matches: 107,  Mismatches: 13, Indels: 4
        0.86            0.10        0.03

Matches are distributed among these distances:
  49    1  0.01
  50    2  0.02
  51  104  0.97

ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24


Consensus pattern (51 bp):   
AGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGCAGCATTTGGTGT

Found at i:3296 original size:102 final size:102

Alignment explanation


    Indices: 3081--3323  Score: 290
    Period size: 102  Copynumber: 2.4  Consensus size: 102

       3071 CCCTAAACGG

                           * *    *  *     *                                 
       3081 TGCTGCAGTACTCGGAGAAGGACTTGGAGGATGGGAAATGCCAGGGAGGCTTGCTGCAGTACTCA
          1 TGCTGCAGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGGGAGGCTTGCTGCAGTACTCA

                             *             * **  
       3146 GAGCAGGACTTGGAGGATGAGAAATGCCAGGGAGGGT
         66 GAGCAGGACTTGGAGGACGAGAAATGCCAGGCACAGT

                                                                            *
       3183 TGCTGCAGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGGGAGGCTTGCTGCAGTACTCG
          1 TGCTGCAGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGGGAGGCTTGCTGCAGTACTCA

             *      *  *       *                * 
       3248 GGGCAGGAGTTTGAGGACGGGAAATGCCA-GCATCATT
         66 GAGCAGGACTTGGAGGACGAGAAATGCCAGGCA-CAGT

              *  **      *                  *      
       3285 TGGTGTTGTACTCAGGGCAGGAGTTTGAGGACTGGAAAT
          1 TGCTGCAGTACTCGGGGCAGGAGTTTGAGGACGGGAAAT

       3324 TCTAGCAGCA


Statistics
Matches: 120,  Mismatches: 20, Indels: 2
        0.85            0.14        0.01

Matches are distributed among these distances:
 101    2  0.02
 102  118  0.98

ACGTcount: A:0.24, C:0.16, G:0.40, T:0.20


Consensus pattern (102 bp):   
TGCTGCAGTACTCGGGGCAGGAGTTTGAGGACGGGAAATGCCAGGGAGGCTTGCTGCAGTACTCA
GAGCAGGACTTGGAGGACGAGAAATGCCAGGCACAGT

Found at i:3753 original size:27 final size:29

Alignment explanation


    Indices: 3683--3763  Score: 87
    Period size: 27  Copynumber: 2.8  Consensus size: 29

       3673 ATTAGTTTAG

                *         *                
       3683 AAATTCAGCAAACATAGTGGAAACATATATA
          1 AAATGCAGCAAACAAAGTGGAAAC--ATATA

                                          
       3714 AAATGCA-CTAAACAAAGTGGAAAC-T-TA
          1 AAATGCAGC-AAACAAAGTGGAAACATATA

                            *      
       3741 AAATGCAGCAAACAAAATGGAAA
          1 AAATGCAGCAAACAAAGTGGAAA

       3764 GAAAACCTTT


Statistics
Matches: 45,  Mismatches: 3, Indels: 8
        0.80            0.05        0.14

Matches are distributed among these distances:
  27   22  0.49
  28    2  0.04
  30    1  0.02
  31   20  0.44

ACGTcount: A:0.54, C:0.14, G:0.15, T:0.17


Consensus pattern (29 bp):   
AAATGCAGCAAACAAAGTGGAAACATATA
Done.