Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000180.1 Corchorus capsularis cultivar CVL-1 contig00180, 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: 4358
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:2389 original size:46 final size:46

Alignment explanation


    Indices: 2322--2413  Score: 157
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       2312 TACGAATTCA

                          * *             *               
       2322 TTAAACTTTTGTTCGTGATTTTCCGAACTTCCATATCCTAAAAGCT
          1 TTAAACTTTTGTTCATAATTTTCCGAACTTACATATCCTAAAAGCT

                                                          
       2368 TTAAACTTTTGTTCATAATTTTCCGAACTTACATATCCTAAAAGCT
          1 TTAAACTTTTGTTCATAATTTTCCGAACTTACATATCCTAAAAGCT

       2414 AACTTAAGAT


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  46   43  1.00

ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41


Consensus pattern (46 bp):   
TTAAACTTTTGTTCATAATTTTCCGAACTTACATATCCTAAAAGCT

Found at i:3017 original size:31 final size:31

Alignment explanation


    Indices: 2958--3018  Score: 77
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2948 ATTTAGGAAC

                                 *         
       2958 TGATTTGAGCAAATTTTGCAATGCTAGGGAT
          1 TGATTTGAGCAAATTTTGCAACGCTAGGGAT

                      **      *    *      
       2989 TGATTTGAGCTGATTTTGGAACGTTAGGGA
          1 TGATTTGAGCAAATTTTGCAACGCTAGGGA

       3019 CTTAATTAAC


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.26, C:0.08, G:0.30, T:0.36


Consensus pattern (31 bp):   
TGATTTGAGCAAATTTTGCAACGCTAGGGAT

Found at i:3655 original size:21 final size:20

Alignment explanation


    Indices: 3631--3677  Score: 67
    Period size: 21  Copynumber: 2.3  Consensus size: 20

       3621 TGAGATTGTG

                                
       3631 AGATTAAATACTGTACAGAT
          1 AGATTAAATACTGTACAGAT

                   **            
       3651 CAGATTAGGTACTGTACAGAT
          1 -AGATTAAATACTGTACAGAT

                  
       3672 AGATTA
          1 AGATTA

       3678 TAATCAGCGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  20    6  0.25
  21   18  0.75

ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30


Consensus pattern (20 bp):   
AGATTAAATACTGTACAGAT
Done.