Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001018.1 Corchorus capsularis cultivar CVL-1 contig01018, 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: 1709
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36


Found at i:1575 original size:15 final size:15

Alignment explanation


    Indices: 1543--1576  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1533 GGCGGGTTTC

                        ** 
       1543 GGGTTCGGGTCATCT
          1 GGGTTCGGGTCAAAT

                           
       1558 GGGTTCGGGTCAAAT
          1 GGGTTCGGGTCAAAT

                
       1573 GGGT
          1 GGGT

       1577 CATGCAGTTT


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

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.12, C:0.15, G:0.44, T:0.29


Consensus pattern (15 bp):   
GGGTTCGGGTCAAAT

Found at i:1646 original size:16 final size:16

Alignment explanation


    Indices: 1587--1709  Score: 142
    Period size: 16  Copynumber: 7.8  Consensus size: 16

       1577 CATGCAGTTT

                    *       
       1587 TTTCGGGTAATTCGGG
          1 TTTCGGGTCATTCGGG

              *              
       1603 TTACGGGTCA-TCTGGG
          1 TTTCGGGTCATTC-GGG

                    *       
       1619 -TTCGGGTTATTCGGG
          1 TTTCGGGTCATTCGGG

               *          * 
       1634 TTTTGGGTCATTCGAG
          1 TTTCGGGTCATTCGGG

             *         *    
       1650 TCTCGGGTCATACGGG
          1 TTTCGGGTCATTCGGG

                            
       1666 TTTCGGGTCATTCGGG
          1 TTTCGGGTCATTCGGG

             *              
       1682 TCTCGGGTCATTCGGG
          1 TTTCGGGTCATTCGGG

             *          
       1698 TCTCGGGTCATT
          1 TTTCGGGTCATT


Statistics
Matches: 90,  Mismatches: 14, Indels: 6
        0.82            0.13        0.05

Matches are distributed among these distances:
  15   12  0.13
  16   78  0.87

ACGTcount: A:0.10, C:0.19, G:0.36, T:0.36


Consensus pattern (16 bp):   
TTTCGGGTCATTCGGG

Found at i:1687 original size:7 final size:7

Alignment explanation


    Indices: 1649--1706  Score: 53
    Period size: 7  Copynumber: 7.4  Consensus size: 7

       1639 GGTCATTCGA

                   
       1649 GTCTCGG
          1 GTCTCGG

                     
       1656 GTCATACGG
          1 GTC-T-CGG

              *    
       1665 GTTTCGG
          1 GTCTCGG

                     
       1672 GTCATTCGG
          1 GTC--TCGG

                   
       1681 GTCTCGG
          1 GTCTCGG

                     
       1688 GTCATTCGG
          1 GTC--TCGG

                   
       1697 GTCTCGG
          1 GTCTCGG

               
       1704 GTC
          1 GTC

       1707 ATT


Statistics
Matches: 43,  Mismatches: 2, Indels: 12
        0.75            0.04        0.21

Matches are distributed among these distances:
   7   22  0.51
   8    2  0.05
   9   19  0.44

ACGTcount: A:0.07, C:0.24, G:0.38, T:0.31


Consensus pattern (7 bp):   
GTCTCGG

Done.