Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012725.1 Corchorus capsularis cultivar CVL-1 contig12746, 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: 6585
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Found at i:1628 original size:16 final size:16

Alignment explanation


    Indices: 1590--1634  Score: 56
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       1580 CATTGCATTT

                       * *  
       1590 TAAAAAA-AATGATAA
          1 TAAAAAATAATAACAA

               *            
       1605 TAATAAATAATAACAA
          1 TAAAAAATAATAACAA

                          
       1621 TAAAAAATAATAAC
          1 TAAAAAATAATAAC

       1635 GATTTTTGAC


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  15    6  0.24
  16   19  0.76

ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22


Consensus pattern (16 bp):   
TAAAAAATAATAACAA

Found at i:4221 original size:20 final size:20

Alignment explanation


    Indices: 4192--4235  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       4182 CCCAAACCCT

                 *    *  *      
       4192 CCAAATATAAGCATCAAAGC
          1 CCAAACATAAACAACAAAGC

                       *        
       4212 CCAAACATAAATAACAAAGC
          1 CCAAACATAAACAACAAAGC

                
       4232 CCAA
          1 CCAA

       4236 GAGAAAGTCT


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.55, C:0.27, G:0.07, T:0.11


Consensus pattern (20 bp):   
CCAAACATAAACAACAAAGC

Found at i:5028 original size:27 final size:28

Alignment explanation


    Indices: 4991--5062  Score: 101
    Period size: 27  Copynumber: 2.6  Consensus size: 28

       4981 GGTCATCTAG

                *                       
       4991 GGGGCATTTTGGTCATTTTCACA-TTCA
          1 GGGGTATTTTGGTCATTTTCACATTTCA

                               **     * 
       5018 GGGGTATTTTGGTCATTTTTGCATTTTA
          1 GGGGTATTTTGGTCATTTTCACATTTCA

                             
       5046 GGGGTATTTTGGTCATT
          1 GGGGTATTTTGGTCATT

       5063 CTTAATCTAC


Statistics
Matches: 40,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  27   20  0.50
  28   20  0.50

ACGTcount: A:0.15, C:0.11, G:0.26, T:0.47


Consensus pattern (28 bp):   
GGGGTATTTTGGTCATTTTCACATTTCA

Found at i:5655 original size:20 final size:20

Alignment explanation


    Indices: 5616--5656  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5606 ATGAATACAA

                          **    
       5616 GGCATTTGATTTACGGATTG
          1 GGCATTTGATTTACAAATTG

                        *       
       5636 GGCATTTGATTTGCAAATTG
          1 GGCATTTGATTTACAAATTG

             
       5656 G
          1 G

       5657 CGTTTTTCTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39


Consensus pattern (20 bp):   
GGCATTTGATTTACAAATTG
Done.