Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008371.1 Corchorus olitorius cultivar O-4 contig08398, 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: 1681
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33


Found at i:486 original size:35 final size:35

Alignment explanation


    Indices: 438--608  Score: 193
    Period size: 35  Copynumber: 4.9  Consensus size: 35

        428 TCCAGTGCGG

                 *             *               
        438 TCATTCCAAGAAGTTTTCGGTGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *     *        **                
        473 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                        *      *   *            
        508 TCATTTTCAAGATGTTTT-TATGGTCAGAGTTGATC
          1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                                      *        
        543 TCATTTCAAGAAGTTTTCGATGATCAAAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *               * *           
        578 TCGTTTCAA-AGAGTTTTTGTTGATCAGAGTT
          1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTT

        609 TTTGTTGATC


Statistics
Matches: 115,  Mismatches: 18, Indels: 6
        0.83            0.13        0.04

Matches are distributed among these distances:
  34   14  0.12
  35   89  0.77
  36   12  0.10

ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41


Consensus pattern (35 bp):   
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

Found at i:608 original size:16 final size:16

Alignment explanation


    Indices: 587--624  Score: 76
    Period size: 16  Copynumber: 2.4  Consensus size: 16

        577 CTCGTTTCAA

                            
        587 AGAGTTTTTGTTGATC
          1 AGAGTTTTTGTTGATC

                            
        603 AGAGTTTTTGTTGATC
          1 AGAGTTTTTGTTGATC

                  
        619 AGAGTT
          1 AGAGTT

        625 GATCTCATTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47


Consensus pattern (16 bp):   
AGAGTTTTTGTTGATC

Found at i:693 original size:38 final size:37

Alignment explanation


    Indices: 617--758  Score: 239
    Period size: 38  Copynumber: 3.8  Consensus size: 37

        607 TTTTTGTTGA

                                                 
        617 TCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGG
          1 TCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGG

                                                  
        654 TCAGAGTTGATCTCATTTCAAGAAGTTTTTTCATATGG
          1 TCAGAGTTGATCTCATTTCAAGAAGTTTTTT-ATATGG

                          *                 *    *
        692 TCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTTATGA
          1 TCAGAGTTGATCTCATTTCAAGAAG-TTTTTTATATGG

                                         
        730 TCAGAGTTGATCTCATTTCAAGAAGTTTT
          1 TCAGAGTTGATCTCATTTCAAGAAGTTTT

        759 CGATGATCAG


Statistics
Matches: 99,  Mismatches: 4, Indels: 4
        0.93            0.04        0.04

Matches are distributed among these distances:
  37   35  0.35
  38   58  0.59
  39    6  0.06

ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44


Consensus pattern (37 bp):   
TCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGG

Found at i:739 original size:123 final size:120

Alignment explanation


    Indices: 493--741  Score: 299
    Period size: 123  Copynumber: 2.0  Consensus size: 120

        483 AAGTTTTTTA

                                                                             
        493 TGATCAGAGTTGATCTCATTTTCAAGATGTTTTTATGGTCAGAGTTGATCTCATTTCAAGAAGTT
          1 TGATCAGAGTTGATCTCATTTTCAAGATGTTTTTATGGTCAGAGTTGATCTCATTTCAAGAAGTT

                                  *                           ****  
        558 TTCGATGATCAAAGTTGATCTCGTTTCAAAGAGTTTTTGTTGATCAGAGTTTTTGT
         66 TTCGATGATCAAAGTTGATCTCCTTTCAAAGAGTTTTTGTTGAT-AGAGTCAGAGT

                                          *                                  
        614 TGATCAGAGTTGATCTCA-TTTCAAGAAGTTTTTTATATGGTCAGAGTTGATCTCATTTCAAGAA
          1 TGATCAGAGTTGATCTCATTTTCAAG-A-TGTTTT-TATGGTCAGAGTTGATCTCATTTCAAGAA

                     *   *   *                           *  *             
        678 GTTTTTTCATATGGTCAGAGTTGATCTCCTTTC-AAGAAGTTTTTTTTTAT-GA-TCAGAGT
         63 G--TTTTC-GATGATCAAAGTTGATCTCCTTTCAAAG-AGTTTTTGTTGATAGAGTCAGAGT

                 
        737 TGATC
          1 TGATC

        742 TCATTTCAAG


Statistics
Matches: 110,  Mismatches: 11, Indels: 12
        0.83            0.08        0.09

Matches are distributed among these distances:
 120    7  0.06
 121   19  0.17
 122    5  0.05
 123   38  0.35
 124    2  0.02
 125    8  0.07
 126   31  0.28

ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43


Consensus pattern (120 bp):   
TGATCAGAGTTGATCTCATTTTCAAGATGTTTTTATGGTCAGAGTTGATCTCATTTCAAGAAGTT
TTCGATGATCAAAGTTGATCTCCTTTCAAAGAGTTTTTGTTGATAGAGTCAGAGT

Done.