Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021693.1 Corchorus olitorius cultivar O-4 contig21726, 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: 7039
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:1172 original size:18 final size:18

Alignment explanation


    Indices: 1149--1185  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1139 CTCCTCTTGC

                     *        
       1149 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
       1167 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

             
       1185 A
          1 A

       1186 ACTACCCTTT


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:1782 original size:21 final size:21

Alignment explanation


    Indices: 1752--1801  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1742 AGGGGCTGAG

                 *        *       
       1752 CTGGGTGCTGA-GCCTTGTCGC
          1 CTGGGCGCTGAGGCATT-TCGC

                               * 
       1773 CTGGGCGCTGAGGCATTTCTC
          1 CTGGGCGCTGAGGCATTTCGC

                    
       1794 CTGGGCGC
          1 CTGGGCGC

       1802 CCAGCAACAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  21   21  0.84
  22    4  0.16

ACGTcount: A:0.06, C:0.30, G:0.38, T:0.26


Consensus pattern (21 bp):   
CTGGGCGCTGAGGCATTTCGC

Found at i:5233 original size:18 final size:18

Alignment explanation


    Indices: 5212--5260  Score: 71
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       5202 GTGGGATTTT

                      *    *  
       5212 TATGTGTATTGGGGTCTG
          1 TATGTGTATTAGGGTATG

                              
       5230 TATGTGTATTAGGGTATG
          1 TATGTGTATTAGGGTATG

                   *     
       5248 TATGTGTTTTAGG
          1 TATGTGTATTAGG

       5261 ATCTGTCTTT


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.16, C:0.02, G:0.35, T:0.47


Consensus pattern (18 bp):   
TATGTGTATTAGGGTATG
Done.