Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011871.1 Corchorus olitorius cultivar O-4 contig11904, 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: 8190
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32


Found at i:32 original size:15 final size:16

Alignment explanation


    Indices: 8--46  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

          1 GGTTGAA

                 *          
          8 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
         23 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                    
         39 AGAAAACA
          1 AGAAAACA

         47 GAGCAAAGTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.62, C:0.13, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:7066 original size:22 final size:23

Alignment explanation


    Indices: 7035--7080  Score: 60
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       7025 TAATATCCAC

                                    
       7035 ACACAATTAAT-ATATAAT-TAAA
          1 ACACAATTAATCATA-AATATAAA

                 *                 
       7057 ACACACTTAATCATAAATATAAA
          1 ACACAATTAATCATAAATATAAA

             
       7080 A
          1 A

       7081 ATAGTAAATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  22   13  0.62
  23    8  0.38

ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28


Consensus pattern (23 bp):   
ACACAATTAATCATAAATATAAA

Found at i:7906 original size:19 final size:20

Alignment explanation


    Indices: 7884--7928  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 20

       7874 CTATTTAGTA

                          *     
       7884 TAATG-ATCACTATTAGGTG
          1 TAATGAATCACTATCAGGTG

                       *         
       7903 TAATGATATCATTATCAGGTG
          1 TAATGA-ATCACTATCAGGTG

                 
       7924 TAATG
          1 TAATG

       7929 GAAAATTAAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  19    5  0.23
  21   17  0.77

ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38


Consensus pattern (20 bp):   
TAATGAATCACTATCAGGTG

Found at i:7922 original size:21 final size:21

Alignment explanation


    Indices: 7889--7928  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       7879 TAGTATAATG

                    *            
       7889 ATCACTATTAGGTGTAATGAT
          1 ATCACTATCAGGTGTAATGAT

                *              
       7910 ATCATTATCAGGTGTAATG
          1 ATCACTATCAGGTGTAATG

       7929 GAAAATTAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38


Consensus pattern (21 bp):   
ATCACTATCAGGTGTAATGAT
Done.