Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018109.1 Corchorus olitorius cultivar O-4 contig18142, 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: 5706
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26


Found at i:12 original size:2 final size:2

Alignment explanation


    Indices: 1--40  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

                  *                                                    
          1 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         41 TTGTTGCTTT


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4560 original size:50 final size:50

Alignment explanation


    Indices: 4506--4682  Score: 336
    Period size: 50  Copynumber: 3.5  Consensus size: 50

       4496 ACCAGATATC

                                                              
       4506 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
          1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT

                                                              
       4556 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
          1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT

                          *                                   
       4606 AAGATTGAATTGGATGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
          1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT

                               *       
       4656 AAGATTGAATTGGAAGACAATTCGAAG
          1 AAGATTGAATTGGAAGACAGTTCGAAG

       4683 AAGTTGATCG


Statistics
Matches: 124,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  50  124  1.00

ACGTcount: A:0.35, C:0.11, G:0.29, T:0.24


Consensus pattern (50 bp):   
AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT

Found at i:4943 original size:28 final size:28

Alignment explanation


    Indices: 4896--5050  Score: 197
    Period size: 28  Copynumber: 5.5  Consensus size: 28

       4886 CTTTACTTCT

                *                       
       4896 CATTGTGGTCATTTTTCATGTCTAGGGG
          1 CATTTTGGTCATTTTTCATGTCTAGGGG

            *              *            
       4924 GATTTTGGTCATTTTCCATGTCTAGGGG
          1 CATTTTGGTCATTTTTCATGTCTAGGGG

                *                       
       4952 CATTATGGTCATTTTTCATGTCTAGGGG
          1 CATTTTGGTCATTTTTCATGTCTAGGGG

                              **  *     
       4980 CATTTTGGTCATTTTTCAAATCCAGGGG
          1 CATTTTGGTCATTTTTCATGTCTAGGGG

                           **            
       5008 CATTTTGGTCATTTGCACAT-TC-AGGGG
          1 CATTTTGGTCATTT-TTCATGTCTAGGGG

                            
       5035 TCATTTTGGTCATTTT
          1 -CATTTTGGTCATTTT

       5051 AAGTTCACTT


Statistics
Matches: 111,  Mismatches: 14, Indels: 5
        0.85            0.11        0.04

Matches are distributed among these distances:
  27    5  0.05
  28  104  0.94
  29    2  0.02

ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43


Consensus pattern (28 bp):   
CATTTTGGTCATTTTTCATGTCTAGGGG

Done.