Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013804.1 Corchorus olitorius cultivar O-4 contig13837, 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: 14355
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:3567 original size:2 final size:2

Alignment explanation


    Indices: 3560--3591  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       3550 TAGTCCACGC

                                                           
       3560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3592 CTAGTGCATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:5121 original size:2 final size:2

Alignment explanation


    Indices: 5114--5138  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       5104 CCAACTTATC

                                                 
       5114 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 A

       5139 GTTGTAATAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:9145 original size:56 final size:57

Alignment explanation


    Indices: 9040--9152  Score: 183
    Period size: 56  Copynumber: 2.0  Consensus size: 57

       9030 ATTAATAAAA

                    *                                                
       9040 AAAGTTTAGTGACTAAAAAGAATATTAATTAAAAAATTATTATAATATAATACTAAG
          1 AAAGTTTAATGACTAAAAAGAATATTAATTAAAAAATTATTATAATATAATACTAAG

                                          *             *       *    
       9097 AAAGTTTAATGACTAAAAA-AATATTAATTTAAAAATTATTATACTATAATATTAAG
          1 AAAGTTTAATGACTAAAAAGAATATTAATTAAAAAATTATTATAATATAATACTAAG

       9153 GGTATTTTAG


Statistics
Matches: 52,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  56   34  0.65
  57   18  0.35

ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35


Consensus pattern (57 bp):   
AAAGTTTAATGACTAAAAAGAATATTAATTAAAAAATTATTATAATATAATACTAAG

Found at i:12618 original size:18 final size:18

Alignment explanation


    Indices: 12595--12631  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      12585 AAGCTGCTCT

                              
      12595 AGATCGATTCAAAAGGAA
          1 AGATCGATTCAAAAGGAA

                              
      12613 AGATCGATTCAAAAGGAA
          1 AGATCGATTCAAAAGGAA

             
      12631 A
          1 A

      12632 TTCCCGTTTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.51, C:0.11, G:0.22, T:0.16


Consensus pattern (18 bp):   
AGATCGATTCAAAAGGAA

Found at i:13395 original size:25 final size:24

Alignment explanation


    Indices: 13367--13430  Score: 85
    Period size: 25  Copynumber: 2.7  Consensus size: 24

      13357 GTGGATTGTA

                        *            
      13367 AAATAAATTGAATAATTAAGACATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
      13392 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     *      
      13416 AAA-AAATTCAAGAAT
          1 AAATAAATTGAAGAAT

      13431 GACCCAATTG


Statistics
Matches: 36,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  23   11  0.31
  24    8  0.22
  25   17  0.47

ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT
Done.