Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016070.1 Corchorus olitorius cultivar O-4 contig16103, 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: 9244
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32


Found at i:686 original size:51 final size:50

Alignment explanation


    Indices: 585--686  Score: 127
    Period size: 51  Copynumber: 2.0  Consensus size: 50

        575 GTTCTTCATA

                                                     * **     
        585 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            *                    
        635 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
        686 T
          1 T

        687 CTTCATTCAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   37  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:6370 original size:16 final size:15

Alignment explanation


    Indices: 6330--6371  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6320 ACAGAGATTG

                   *       
       6330 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

               *           
       6345 ACATAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6360 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6372 AGCAGAGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:7147 original size:11 final size:11

Alignment explanation


    Indices: 7131--7156  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       7121 CCTTTGCATA

                       
       7131 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       7142 AAAACTAGAAG
          1 AAAACTAGAAG

                
       7153 AAAA
          1 AAAA

       7157 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.