Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023977.1 Corchorus olitorius cultivar O-4 contig24010, 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: 8375
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32


Found at i:7449 original size:19 final size:20

Alignment explanation


    Indices: 7415--7454  Score: 73
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       7405 AGGGGAGACA

                                
       7415 TTGCTAGGGTTTTTTTAGGT
          1 TTGCTAGGGTTTTTTTAGGT

                                
       7435 TTGCTAGGGTTTTTTT-GGT
          1 TTGCTAGGGTTTTTTTAGGT

             
       7454 T
          1 T

       7455 CTCAGTAAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    4  0.20
  20   16  0.80

ACGTcount: A:0.07, C:0.05, G:0.30, T:0.57


Consensus pattern (20 bp):   
TTGCTAGGGTTTTTTTAGGT

Found at i:7857 original size:19 final size:19

Alignment explanation


    Indices: 7829--7871  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       7819 TTTTGGTCAT

                 *          *  
       7829 TTTTGTACATCCAGGGGCA
          1 TTTTGCACATCCAGGGACA

                         *     
       7848 TTTTGCACATCCATGGACA
          1 TTTTGCACATCCAGGGACA

                 
       7867 TTTTG
          1 TTTTG

       7872 GTCATTTTTA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37


Consensus pattern (19 bp):   
TTTTGCACATCCAGGGACA

Found at i:7880 original size:29 final size:29

Alignment explanation


    Indices: 7848--7962  Score: 144
    Period size: 29  Copynumber: 4.0  Consensus size: 29

       7838 TCCAGGGGCA

                         *       *       
       7848 TTTTGCACATCCATGGACATTTTGGTCAT
          1 TTTTGCACATCCAGGGACATTATGGTCAT

                *           *    *  *    
       7877 TTTTACACATCCAGGGGCATTTTGATCAT
          1 TTTTGCACATCCAGGGACATTATGGTCAT

                                          
       7906 TTTTGCACATCCAGGGGA-ATTATGGTCAT
          1 TTTTGCACATCCA-GGGACATTATGGTCAT

                                         
       7935 TTTTGCACATCCA-GGAGCATTATGGTCA
          1 TTTTGCACATCCAGGGA-CATTATGGTCA

       7963 CTTACTAGTT


Statistics
Matches: 75,  Mismatches: 8, Indels: 6
        0.84            0.09        0.07

Matches are distributed among these distances:
  27    3  0.04
  29   69  0.92
  30    3  0.04

ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37


Consensus pattern (29 bp):   
TTTTGCACATCCAGGGACATTATGGTCAT
Done.