Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018094.1 Corchorus olitorius cultivar O-4 contig18127, 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: 14492
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:3789 original size:16 final size:16

Alignment explanation


    Indices: 3768--3798  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       3758 AGGCCTAAAA

                            
       3768 TTCCATATGTAATGAG
          1 TTCCATATGTAATGAG

                           
       3784 TTCCATATGTAATGA
          1 TTCCATATGTAATGA

       3799 AGTATAAAAT


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:0.32, C:0.13, G:0.16, T:0.39


Consensus pattern (16 bp):   
TTCCATATGTAATGAG

Found at i:7778 original size:129 final size:131

Alignment explanation


    Indices: 7609--7871  Score: 390
    Period size: 130  Copynumber: 2.0  Consensus size: 131

       7599 GTCATTTAAG

                      *                                  *                   
       7609 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGGT-AAAAAT
          1 AAATATATTTAAAAAATTCTAATATA-CTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAAT

                                      *         *                 *       *  
       7673 AAAATAGGTATAAAGATATTAGATTTTA-TATAATAGAAATAGAGTTTTTAGTTGAGTAAAATTA
         65 AAAATAGGTATAAAGATATTAGATTTAATTA-AATAAAAATAGAGTTTTTAGTTAAGTAAAACTA

               
       7737 TAA
        129 TAA

                                                               *             
       7740 AAATATA-TTAAAAAATTCTAATATA-TAAGTTTTTTTAATTAAAATAGTACAATGGTAAAAAAT
          1 AAATATATTTAAAAAATTCTAATATACTAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAAT

                   *     *                                                   
       7803 AAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTAT
         65 AAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTAT

              
       7868 AA
        130 AA

              
       7870 AA
          1 AA

       7872 GTTTAAATAA


Statistics
Matches: 120,  Mismatches: 9, Indels: 7
        0.88            0.07        0.05

Matches are distributed among these distances:
 128    4  0.03
 129   24  0.20
 130   83  0.69
 131    9  0.08

ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38


Consensus pattern (131 bp):   
AAATATATTTAAAAAATTCTAATATACTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAATA
AAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATA
A

Found at i:13798 original size:2 final size:2

Alignment explanation


    Indices: 13791--13817  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      13781 ATCCCAATCA

                                                    
      13791 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      13818 GTGTATACAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:14442 original size:29 final size:28

Alignment explanation


    Indices: 14398--14453  Score: 85
    Period size: 29  Copynumber: 2.0  Consensus size: 28

      14388 TTCTTCAAAC

                            *   *       
      14398 TTTCTAATTTCAAGAATGCTCAAGAACA
          1 TTTCTAATTTCAAGAACGCTAAAGAACA

                                        
      14426 TTTCTAATCTTCAAGAACGCTAAAGAAC
          1 TTTCTAAT-TTCAAGAACGCTAAAGAAC

      14454 GTGGAATAAC


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  28    8  0.32
  29   17  0.68

ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30


Consensus pattern (28 bp):   
TTTCTAATTTCAAGAACGCTAAAGAACA
Done.