Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012986.1 Corchorus olitorius cultivar O-4 contig13019, 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: 48446
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35


Found at i:3547 original size:7 final size:7

Alignment explanation


    Indices: 3535--3583  Score: 71
    Period size: 7  Copynumber: 7.0  Consensus size: 7

       3525 TACATTTGTG

                   
       3535 CTTTGCA
          1 CTTTGCA

             *    *
       3542 CCTTGCG
          1 CTTTGCA

                   
       3549 CTTTGCA
          1 CTTTGCA

                   
       3556 CTTTGCA
          1 CTTTGCA

                 * 
       3563 CTTTGGA
          1 CTTTGCA

                   
       3570 CTTTGCA
          1 CTTTGCA

                   
       3577 CTTTGCA
          1 CTTTGCA

       3584 GTCACATACA


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   7   36  1.00

ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41


Consensus pattern (7 bp):   
CTTTGCA

Found at i:42933 original size:31 final size:31

Alignment explanation


    Indices: 42893--42969  Score: 100
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      42883 CTTAGTAAGC

                          *    *          *
      42893 GATCAATTTAGTCCCTGTATTCAAAAGATTG
          1 GATCAATTTAGTCCATGTACTCAAAAGATTA

             *                     *       
      42924 GGTCAATTTAGTCCATGTACTCACAAGATTA
          1 GATCAATTTAGTCCATGTACTCAAAAGATTA

                    *      
      42955 GATCAATTGAGTCCA
          1 GATCAATTTAGTCCA

      42970 ATCGGTAAAG


Statistics
Matches: 39,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   39  1.00

ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Consensus pattern (31 bp):   
GATCAATTTAGTCCATGTACTCAAAAGATTA

Found at i:43046 original size:31 final size:31

Alignment explanation


    Indices: 43011--43069  Score: 91
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      43001 CCTAATGGCT

                  *      *    *            
      43011 AATCTTGTAAGTATAGGGCCTAAATTGACTC
          1 AATCTTATAAGTACAGGGACTAAATTGACTC

                                        
      43042 AATCTTATAAGTACAGGGACTAAATTGA
          1 AATCTTATAAGTACAGGGACTAAATTGA

      43070 TCGCTTTTTG


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

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31


Consensus pattern (31 bp):   
AATCTTATAAGTACAGGGACTAAATTGACTC

Found at i:43821 original size:25 final size:25

Alignment explanation


    Indices: 43783--43834  Score: 95
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      43773 ATGCAATCTC

                                     
      43783 TCATAGAAAGACACCTTTTCATGTT
          1 TCATAGAAAGACACCTTTTCATGTT

                     *               
      43808 TCATAGAAATACACCTTTTCATGTT
          1 TCATAGAAAGACACCTTTTCATGTT

              
      43833 TC
          1 TC

      43835 TGCAGATTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38


Consensus pattern (25 bp):   
TCATAGAAAGACACCTTTTCATGTT

Found at i:47599 original size:27 final size:27

Alignment explanation


    Indices: 47568--47639  Score: 90
    Period size: 29  Copynumber: 2.6  Consensus size: 27

      47558 CCGTGTATTC

                                       
      47568 ATAAAGGCAGAGAATTTTTTCGTGAAA
          1 ATAAAGGCAGAGAATTTTTTCGTGAAA

                    *             *      
      47595 ATAAAGGCTGAGAATTTTTTTTGGTGAAA
          1 ATAAAGGCAGAGAA--TTTTTTCGTGAAA

             *     *        
      47624 ACAAAGGTAGAGAATT
          1 ATAAAGGCAGAGAATT

      47640 AGAGTGAGGT


Statistics
Matches: 38,  Mismatches: 5, Indels: 4
        0.81            0.11        0.09

Matches are distributed among these distances:
  27   15  0.39
  29   23  0.61

ACGTcount: A:0.40, C:0.06, G:0.24, T:0.31


Consensus pattern (27 bp):   
ATAAAGGCAGAGAATTTTTTCGTGAAA

Done.