Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024805.1 Corchorus olitorius cultivar O-4 contig24838, 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: 7651
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:4037 original size:80 final size:80

Alignment explanation


    Indices: 3904--4053  Score: 214
    Period size: 80  Copynumber: 1.9  Consensus size: 80

       3894 CTAAAGATCT

                   *                        *                          *     
       3904 ATGTTCCTATATTGTGTTTATTCCTACAAAATTCGGGATGCATTTATTTAGAAAGCTTTGATTTT
          1 ATGTTCCAATATTGTGTTTATTCCTACAAAATCCGGGATGCATTTATTTAGAAAGCTTTAATTTT

                           
       3969 GGTCTCCTAAGAACC
         66 GGTCTCCTAAGAACC

                         *                    *            *                 
       3984 ATGTTCCAATATTTTGTTTATTCCTACAAAA-CCTGG-TGCACATTTGTTTAGAAAGCTTTAATT
          1 ATGTTCCAATATTGTGTTTATTCCTACAAAATCCGGGATG--CATTTATTTAGAAAGCTTTAATT

                   
       4047 TTGGTCT
         64 TTGGTCT

       4054 TTTGATATTA


Statistics
Matches: 62,  Mismatches: 6, Indels: 4
        0.86            0.08        0.06

Matches are distributed among these distances:
  78    2  0.03
  79    3  0.05
  80   57  0.92

ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43


Consensus pattern (80 bp):   
ATGTTCCAATATTGTGTTTATTCCTACAAAATCCGGGATGCATTTATTTAGAAAGCTTTAATTTT
GGTCTCCTAAGAACC

Found at i:4208 original size:48 final size:48

Alignment explanation


    Indices: 4153--4248  Score: 192
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       4143 AATATTGTCT

                                                            
       4153 GCTTATTTCAAACAAGTTGTATTTGGGATACAACAATACCACTTAAGA
          1 GCTTATTTCAAACAAGTTGTATTTGGGATACAACAATACCACTTAAGA

                                                            
       4201 GCTTATTTCAAACAAGTTGTATTTGGGATACAACAATACCACTTAAGA
          1 GCTTATTTCAAACAAGTTGTATTTGGGATACAACAATACCACTTAAGA

       4249 ACAGTTAGAG


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   48  1.00

ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31


Consensus pattern (48 bp):   
GCTTATTTCAAACAAGTTGTATTTGGGATACAACAATACCACTTAAGA

Found at i:5463 original size:43 final size:43

Alignment explanation


    Indices: 5416--5650  Score: 335
    Period size: 43  Copynumber: 5.5  Consensus size: 43

       5406 ACAACATTGT

                   *                              *    
       5416 AGATCGGTAGAAGTGTCAGAACATAGGAGAACAGAAACCTCGA
          1 AGATCGGCAGAAGTGTCAGAACATAGGAGAACAGAAACATCGA

                    *        *          *              
       5459 AGATCGGCTGAAGTGTCTGAACATAGGAAAACAGAAACATCGA
          1 AGATCGGCAGAAGTGTCAGAACATAGGAGAACAGAAACATCGA

                              *       *      *    *  * 
       5502 AGATCGGCAGAAGTGTCAAAACATAGTAGAACAAAAACCTCAA
          1 AGATCGGCAGAAGTGTCAGAACATAGGAGAACAGAAACATCGA

                 *               *                     
       5545 AGATCAGCAGAAGTGTCAGAATATAGGAGAACAGAAACATCGA
          1 AGATCGGCAGAAGTGTCAGAACATAGGAGAACAGAAACATCGA

                                  *     *              
       5588 AGATCGGCAGAAGTGTCAGAACGTAGGACAACAGAAACATCGA
          1 AGATCGGCAGAAGTGTCAGAACATAGGAGAACAGAAACATCGA

                  *             
       5631 AGATCGACAGAAGTGTCAGA
          1 AGATCGGCAGAAGTGTCAGA

       5651 TATGTAGACC


Statistics
Matches: 167,  Mismatches: 25, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  43  167  1.00

ACGTcount: A:0.44, C:0.17, G:0.26, T:0.14


Consensus pattern (43 bp):   
AGATCGGCAGAAGTGTCAGAACATAGGAGAACAGAAACATCGA

Done.