Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009548.1 Corchorus olitorius cultivar O-4 contig09580, 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: 4650
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34


Found at i:1766 original size:21 final size:22

Alignment explanation


    Indices: 1635--1779  Score: 104
    Period size: 22  Copynumber: 6.7  Consensus size: 22

       1625 GAATATTTTA

                              *    
       1635 ATGAAATTTTGATAACC-ACCAT
          1 ATGAAATTTTGATAACCTTCC-T

                                   
       1657 ATGAAATTTTGATAA--TTACCT
          1 ATGAAATTTTGATAACCTT-CCT

              *     *      *       
       1678 ATAAAATTGTGATAAAC-TCCAT
          1 ATGAAATTTTGATAACCTTCC-T

             *    *           *** 
       1700 AAGAAACTTTGATAACCTAATT
          1 ATGAAATTTTGATAACCTTCCT

                      *      *     
       1722 ATGAAATTTTAATAAACTTTCCT
          1 ATGAAATTTTGAT-AACCTTCCT

                                  
       1745 ATGAAATTTTG-TAACCTTCCT
          1 ATGAAATTTTGATAACCTTCCT

                 *         
       1766 ATG-ATTTTTGATAA
          1 ATGAAATTTTGATAA

       1780 TCTTTCTGTC


Statistics
Matches: 94,  Mismatches: 21, Indels: 17
        0.71            0.16        0.13

Matches are distributed among these distances:
  20    6  0.06
  21   30  0.32
  22   43  0.46
  23   15  0.16

ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39


Consensus pattern (22 bp):   
ATGAAATTTTGATAACCTTCCT

Found at i:4408 original size:18 final size:18

Alignment explanation


    Indices: 4354--4411  Score: 64
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       4344 ACTTGTCGAG

                   *           
       4354 TTAAAAATTACAACAAATA
          1 TTAAAAAAT-CAACAAATA

                          *     
       4373 TTCAAAAAAT-AATAAAATA
          1 TT-AAAAAATCAA-CAAATA

                              
       4392 TTAAAAAATCAACAAATA
          1 TTAAAAAATCAACAAATA

              
       4410 TT
          1 TT

       4412 TATTTCTCTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 7
        0.77            0.07        0.16

Matches are distributed among these distances:
  18   16  0.48
  19   11  0.33
  20    6  0.18

ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28


Consensus pattern (18 bp):   
TTAAAAAATCAACAAATA
Done.