Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009554.1 Corchorus olitorius cultivar O-4 contig09586, 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: 6949
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:24 original size:1 final size:1

Alignment explanation


    Indices: 18--44  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

          8 TTCTTCTTTC

                                       
         18 TTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTT

         45 CCGCCTCCAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:4300 original size:18 final size:18

Alignment explanation


    Indices: 4279--4317  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       4269 TCTTCCTCTT

                              
       4279 CTTCTTCCCCCATCCGAG
          1 CTTCTTCCCCCATCCGAG

                  ** *        
       4297 CTTCTTTTCTCATCCGAG
          1 CTTCTTCCCCCATCCGAG

               
       4315 CTT
          1 CTT

       4318 GGTTCCTCAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.10, C:0.41, G:0.10, T:0.38


Consensus pattern (18 bp):   
CTTCTTCCCCCATCCGAG

Found at i:5773 original size:2 final size:2

Alignment explanation


    Indices: 5722--5756  Score: 54
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       5712 AAATATATTT

                                                                 
       5722 TA TA TA GTA TA -A TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5757 TTGTAATGTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.90
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:5945 original size:22 final size:22

Alignment explanation


    Indices: 5832--6003  Score: 138
    Period size: 22  Copynumber: 7.9  Consensus size: 22

       5822 TGAATATTTT

                                   
       5832 TATGAAATTTTGATAA-CTACCC
          1 TATGAAATTTTGATAACCTA-CC

               *            *      
       5854 TATTAAATTTTGATAATC-ACAC
          1 TATGAAATTTTGATAACCTAC-C

                          * **    
       5876 TATGAAATTTTGATGATTTACC
          1 TATGAAATTTTGATAACCTACC

                     *      *     
       5898 TATGAAATTGTGATAAACT-CC
          1 TATGAAATTTTGATAACCTACC

                                 * 
       5919 ATATGAAATTTTGATAACCTAAC
          1 -TATGAAATTTTGATAACCTACC

                  *    *        *  
       5942 TATGAAGTTTTAATAAACCTTCC
          1 TATGAAATTTTGAT-AACCTACC

               *   *           *  
       5965 TATTAAAATTTG-TAACCTTCC
          1 TATGAAATTTTGATAACCTACC

                  *            
       5986 TATG-ATTTTTGATAACCT
          1 TATGAAATTTTGATAACCT

       6004 CTGTCTAAGA


Statistics
Matches: 121,  Mismatches: 22, Indels: 15
        0.77            0.14        0.09

Matches are distributed among these distances:
  20    5  0.04
  21   20  0.17
  22   78  0.64
  23   18  0.15

ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTACC

Done.