Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018453.1 Corchorus olitorius cultivar O-4 contig18486, 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: 8376
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38


Found at i:1870 original size:21 final size:21

Alignment explanation


    Indices: 1831--1872  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1821 CTTATAATAC

                          *      
       1831 TATAACATTTTTTATAACCTT
          1 TATAACATTTTTTACAACCTT

                                  
       1852 TATAAC-TTTTTTAGCAACCTT
          1 TATAACATTTTTTA-CAACCTT

       1873 AAAGAAGAAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20    7  0.37
  21   12  0.63

ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50


Consensus pattern (21 bp):   
TATAACATTTTTTACAACCTT

Found at i:7264 original size:11 final size:11

Alignment explanation


    Indices: 7240--7296  Score: 51
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       7230 GAACTTTCTG

                        
       7240 TTGATTTCTGAT
          1 TTGATTT-TGAT

               *       
       7252 TTGCTTTTGAT
          1 TTGATTTTGAT

                       
       7263 TTGATTTTGAT
          1 TTGATTTTGAT

                *         
       7274 CTTGGTTTCTGAAT
          1 -TTGATTT-TG-AT

                     
       7288 TCTGATTTT
          1 T-TGATTTT

       7297 TTATTACTGA


Statistics
Matches: 37,  Mismatches: 4, Indels: 7
        0.77            0.08        0.15

Matches are distributed among these distances:
  11   14  0.38
  12   12  0.32
  13    4  0.11
  14    7  0.19

ACGTcount: A:0.14, C:0.09, G:0.18, T:0.60


Consensus pattern (11 bp):   
TTGATTTTGAT

Found at i:8207 original size:2 final size:2

Alignment explanation


    Indices: 8196--8225  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       8186 CACAAAATCT

                                                          
       8196 TA TA -A TA 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 T

       8226 CTTATCTTAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.