Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019165.1 Corchorus olitorius cultivar O-4 contig19198, 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: 13603
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:5011 original size:26 final size:27

Alignment explanation


    Indices: 4982--5037  Score: 71
    Period size: 26  Copynumber: 2.1  Consensus size: 27

       4972 CTTTTTTCAC

                                        
       4982 AAAT-ATATTTCTAAATAAT-CATTATT
          1 AAATAATA-TTCTAAATAATCCATTATT

                          *  *         
       5008 AAATAATATTCTAATTATTCCATTATT
          1 AAATAATATTCTAAATAATCCATTATT

               
       5035 AAA
          1 AAA

       5038 ATAAAGGAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  26   13  0.50
  27   13  0.50

ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45


Consensus pattern (27 bp):   
AAATAATATTCTAAATAATCCATTATT

Found at i:7622 original size:29 final size:29

Alignment explanation


    Indices: 7584--7643  Score: 77
    Period size: 31  Copynumber: 2.0  Consensus size: 29

       7574 TGTGAAAGCA

                        **               
       7584 TTTATTGACC-ATCAAATCATGTTTTATT
          1 TTTATTGACCAAAAAAATCATGTTTTATT

                                           
       7612 TTTATTCGACCAAAAAAAATCATGTTTTATT
          1 TTTATT-GACC-AAAAAAATCATGTTTTATT

             
       7643 T
          1 T

       7644 ATTCATTAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  28    6  0.22
  29    4  0.15
  31   17  0.63

ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47


Consensus pattern (29 bp):   
TTTATTGACCAAAAAAATCATGTTTTATT

Found at i:8128 original size:31 final size:31

Alignment explanation


    Indices: 8087--8163  Score: 100
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       8077 TGTTTCTGTT

                 *          *      *     * 
       8087 TTTAGGCTCAAATTGATCAACTTTTGAAAGG
          1 TTTAGACTCAAATTGAGCAACTTCTGAAAAG

                                           
       8118 TTTAGACTCAAATTGAGCAACTTCTGAAAAG
          1 TTTAGACTCAAATTGAGCAACTTCTGAAAAG

                 *  *      
       8149 TTTAGCCTTAAATTG
          1 TTTAGACTCAAATTG

       8164 GTGGCTAAAA


Statistics
Matches: 40,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   40  1.00

ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35


Consensus pattern (31 bp):   
TTTAGACTCAAATTGAGCAACTTCTGAAAAG
Done.