Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000163.1 Corchorus olitorius cultivar O-4 contig00163, 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: 10910
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:467 original size:16 final size:16

Alignment explanation


    Indices: 446--476  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        436 TTACACTACA

                            
        446 TAAAATAAAATAGAAC
          1 TAAAATAAAATAGAAC

                           
        462 TAAAATAAAATAGAA
          1 TAAAATAAAATAGAA

        477 AATCAAAAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19


Consensus pattern (16 bp):   
TAAAATAAAATAGAAC

Found at i:5763 original size:15 final size:15

Alignment explanation


    Indices: 5743--5796  Score: 51
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       5733 CCAAAGAAAG

                           
       5743 AATTTGAAATTCATA
          1 AATTTGAAATTCATA

                            
       5758 AATTTGGAAA-TCATA
          1 AATTT-GAAATTCATA

            *    *          
       5773 CATTTCAAATGTC--A
          1 AATTTGAAAT-TCATA

                      
       5787 AATTTGAAAT
          1 AATTTGAAAT

       5797 CCAATTCCAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 7
        0.74            0.09        0.16

Matches are distributed among these distances:
  14   12  0.38
  15   14  0.44
  16    6  0.19

ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37


Consensus pattern (15 bp):   
AATTTGAAATTCATA

Found at i:7688 original size:29 final size:29

Alignment explanation


    Indices: 7651--7790  Score: 172
    Period size: 29  Copynumber: 4.8  Consensus size: 29

       7641 GCACGCCCAT

                                         
       7651 GGGCATTTTGGTCATTTTTGCATATCCAG
          1 GGGCATTTTGGTCATTTTTGCATATCCAG

               *                  *   *  
       7680 GGGAATTTTGGTCATTTTTGCACATCTAG
          1 GGGCATTTTGGTCATTTTTGCATATCCAG

            *                     *      
       7709 CGGCATTTTGGTCATTTTTGCACATCCAG
          1 GGGCATTTTGGTCATTTTTGCATATCCAG

                        **     *     *** 
       7738 GGGCATTTTGGTTGTTTTTCCATATTTTG
          1 GGGCATTTTGGTCATTTTTGCATATCCAG

                         *          
       7767 GGGCATTTTGGTCGTTTTTGCATA
          1 GGGCATTTTGGTCATTTTTGCATA

       7791 CTCTAGGTTC


Statistics
Matches: 95,  Mismatches: 16, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   95  1.00

ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44


Consensus pattern (29 bp):   
GGGCATTTTGGTCATTTTTGCATATCCAG

Done.