Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011235.1 Corchorus olitorius cultivar O-4 contig11268, 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: 6159
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:901 original size:26 final size:26

Alignment explanation


    Indices: 816--912  Score: 140
    Period size: 27  Copynumber: 3.7  Consensus size: 26

        806 GGTCATCTAT

                     *           *     
        816 GGGCATTTTAGTCATTTGCACCTCTAG
          1 GGGCATTTTGGTCATTTGCACTTC-AG

                    *                  
        843 GGGCATTTCGGTCATTTGCACATTCAG
          1 GGGCATTTTGGTCATTTGCAC-TTCAG

                              *       
        870 GGGCATTTTGGTCATTTGTACTTCAG
          1 GGGCATTTTGGTCATTTGCACTTCAG

                             
        896 GGGCATTTTGGTCATTT
          1 GGGCATTTTGGTCATTT

        913 TTCTTTCTTT


Statistics
Matches: 64,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  26   22  0.34
  27   40  0.62
  28    2  0.03

ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTGCACTTCAG

Found at i:1416 original size:16 final size:16

Alignment explanation


    Indices: 1395--1438  Score: 63
    Period size: 15  Copynumber: 2.8  Consensus size: 16

       1385 TATACATATT

                            
       1395 ATAATACAAGTATGGA
          1 ATAATACAAGTATGGA

                      *     
       1411 ATAATACAA-AATGGA
          1 ATAATACAAGTATGGA

               *         
       1426 ATAGTACAAGTAT
          1 ATAATACAAGTAT

       1439 AGGTTGCATG


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  15   13  0.54
  16   11  0.46

ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25


Consensus pattern (16 bp):   
ATAATACAAGTATGGA

Found at i:4617 original size:27 final size:27

Alignment explanation


    Indices: 4585--4661  Score: 109
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       4575 GCTTTAAGCT

                  *                    
       4585 CATTCAGGGGCATTTTAGTCATTTGCA
          1 CATTCAAGGGCATTTTAGTCATTTGCA

            **    *                    
       4612 TGTTCATGGGCATTTTAGTCATTTGCA
          1 CATTCAAGGGCATTTTAGTCATTTGCA

                            *      
       4639 CATTCAAGGGCATTTTGGTCATT
          1 CATTCAAGGGCATTTTAGTCATT

       4662 CGAACCCTTA


Statistics
Matches: 43,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   43  1.00

ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40


Consensus pattern (27 bp):   
CATTCAAGGGCATTTTAGTCATTTGCA
Done.