Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015126.1 Corchorus olitorius cultivar O-4 contig15159, 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: 1762
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:55 original size:39 final size:39

Alignment explanation


    Indices: 1--331  Score: 554
    Period size: 39  Copynumber: 8.5  Consensus size: 39

                                                   
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

                                *   *              
         40 AAACAGGCCATCTTTTCAGCGTTTGTCAAAGTTGGTTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

                                                   
         79 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

                                    *              
        118 AAACAGGCCATCTTTTCAGCATTTGTCAAAGTTGGTTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

                                    *              
        157 AAACAGGCCATCTTTTCAGCATTTCTCAAAGTTGGTTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

               *                   *               
        196 AAATAGGCCATCTTTTCAGCATTCATCAAAGTTGGTTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

                               *                   
        235 AAACAGGCCATCTTTTCAGTATTTATCAAAGTTGGTTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

                      *                       **   
        274 AAACAGGCCAACTTTTCAGCATTTATCAAAGTTGACTGG
          1 AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

                   *  *        
        313 AAACAGGTCAACTTTTCAG
          1 AAACAGGCCATCTTTTCAG

        332 TTTTATGTTG


Statistics
Matches: 275,  Mismatches: 17, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  39  275  1.00

ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33


Consensus pattern (39 bp):   
AAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGG

Found at i:648 original size:45 final size:44

Alignment explanation


    Indices: 532--649  Score: 123
    Period size: 45  Copynumber: 2.6  Consensus size: 44

        522 ATTTTAATAA

                        *                                 
        532 AGCCCATTTCCTCATTAGTTTCATTC-AAGTCCATTACCATTTTAG
          1 AGCCCATTTCCTTATTAGTTTC--TCAAAGTCCATTACCATTTTAG

                                **             *  **      
        577 AGCCCATTTCCTTATTTAGTAACTCAAAGTCCATTTCTTTTTTTA-
          1 AGCCCATTTCCTTA-TTAGTTTCTCAAAGTCCATTAC-CATTTTAG

                                        
        622 AGACCCATTTCCTTATTAGTTTCTCAAA
          1 AG-CCCATTTCCTTATTAGTTTCTCAAA

        650 ATGTTTTTGG


Statistics
Matches: 61,  Mismatches: 8, Indels: 8
        0.79            0.10        0.10

Matches are distributed among these distances:
  44    2  0.03
  45   36  0.59
  46   23  0.38

ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42


Consensus pattern (44 bp):   
AGCCCATTTCCTTATTAGTTTCTCAAAGTCCATTACCATTTTAG

Found at i:709 original size:13 final size:15

Alignment explanation


    Indices: 681--713  Score: 52
    Period size: 13  Copynumber: 2.3  Consensus size: 15

        671 TGGTCTTCTC

                           
        681 CTTTTTTCCTTCTTT
          1 CTTTTTTCCTTCTTT

                           
        696 CTTTTTT-CTT-TTT
          1 CTTTTTTCCTTCTTT

                 
        709 CTTTT
          1 CTTTT

        714 CTTTTGGGTC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  13    8  0.44
  14    3  0.17
  15    7  0.39

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (15 bp):   
CTTTTTTCCTTCTTT
Done.