Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017100.1 Corchorus olitorius cultivar O-4 contig17133, 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: 18239
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:5885 original size:41 final size:41

Alignment explanation


    Indices: 5828--5906  Score: 124
    Period size: 41  Copynumber: 1.9  Consensus size: 41

       5818 TTTTTGTTCG

                                           *          
       5828 TTCAAGATCAAGTCATCAAAATCC-TTGAATTAAATTATAAA
          1 TTCAAGATCAAGTCATCAAAA-CCATTGAATCAAATTATAAA

                               *                  
       5869 TTCAAGATCAAGTCATCAAGACCATTGAATCAAATTAT
          1 TTCAAGATCAAGTCATCAAAACCATTGAATCAAATTAT

       5907 CAAACTCTGA


Statistics
Matches: 35,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  40    2  0.06
  41   33  0.94

ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30


Consensus pattern (41 bp):   
TTCAAGATCAAGTCATCAAAACCATTGAATCAAATTATAAA

Found at i:10365 original size:29 final size:31

Alignment explanation


    Indices: 10333--10397  Score: 98
    Period size: 31  Copynumber: 2.2  Consensus size: 31

      10323 GCAATTTGGG

                                           
      10333 ATATAACGTTAC-AAAA-CAAGCAATTAAGA
          1 ATATAACGTTACGAAAAGCAAGCAATTAAGA

                      *        *           
      10362 ATATAACGTTGCGAAAAGCGAGCAATTAAGA
          1 ATATAACGTTACGAAAAGCAAGCAATTAAGA

                 
      10393 ATATA
          1 ATATA

      10398 GTCTGTTAGT


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  29   11  0.34
  30    4  0.12
  31   17  0.53

ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22


Consensus pattern (31 bp):   
ATATAACGTTACGAAAAGCAAGCAATTAAGA

Found at i:10553 original size:31 final size:31

Alignment explanation


    Indices: 10518--10595  Score: 120
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      10508 CTAACTGATT

                                 **        
      10518 ATATCCTTAATTGCTTGAAATCGAAAACGTC
          1 ATATCCTTAATTGCTTGAAATAAAAAACGTC

                          *               *
      10549 ATATCCTTAATTGCGTGAAATAAAAAACGTT
          1 ATATCCTTAATTGCTTGAAATAAAAAACGTC

                            
      10580 ATATCCTTAATTGCTT
          1 ATATCCTTAATTGCTT

      10596 ATTTTGTAAC


Statistics
Matches: 42,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   42  1.00

ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36


Consensus pattern (31 bp):   
ATATCCTTAATTGCTTGAAATAAAAAACGTC

Found at i:11688 original size:31 final size:31

Alignment explanation


    Indices: 11653--11733  Score: 135
    Period size: 31  Copynumber: 2.6  Consensus size: 31

      11643 TTTGCTGCCA

                                     **    
      11653 CAAGCAATTAAGGATATAACGTTTTTTATTT
          1 CAAGCAATTAAGGATATAACGTTTTCGATTT

                             *             
      11684 CAAGCAATTAAGGATATGACGTTTTCGATTT
          1 CAAGCAATTAAGGATATAACGTTTTCGATTT

                               
      11715 CAAGCAATTAAGGATATAA
          1 CAAGCAATTAAGGATATAA

      11734 TCAGTTAGGG


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  31   46  1.00

ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35


Consensus pattern (31 bp):   
CAAGCAATTAAGGATATAACGTTTTCGATTT

Found at i:11887 original size:31 final size:29

Alignment explanation


    Indices: 11852--11918  Score: 82
    Period size: 31  Copynumber: 2.2  Consensus size: 29

      11842 TTTAACGGAC

                                            
      11852 TATATCTTTAATTG-TTCGCTTTTCGTAACGT
          1 TATATCTTTAATTGCTT-G-TTTT-GTAACGT

                  *                   *  
      11883 TATATCCTTAATTGCTTGTTTTGTAATGT
          1 TATATCTTTAATTGCTTGTTTTGTAACGT

                   
      11912 TATATCT
          1 TATATCT

      11919 CAAATTGCAT


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  29   12  0.38
  30    4  0.12
  31   14  0.44
  32    2  0.06

ACGTcount: A:0.21, C:0.13, G:0.12, T:0.54


Consensus pattern (29 bp):   
TATATCTTTAATTGCTTGTTTTGTAACGT

Found at i:18209 original size:18 final size:17

Alignment explanation


    Indices: 18155--18211  Score: 55
    Period size: 18  Copynumber: 3.4  Consensus size: 17

      18145 CCATGTCAGC

                              
      18155 TTTTTTATAAAAAA-ATA
          1 TTTTTTA-AAAAAATATA

             *              *
      18172 -ATTTTAAAAAAATATG
          1 TTTTTTAAAAAAATATA

                           *  
      18188 TTTTTTGAAAAAAATTTA
          1 TTTTTT-AAAAAAATATA

                  
      18206 TTTTTT
          1 TTTTTT

      18212 TTTGTTTTTT


Statistics
Matches: 32,  Mismatches: 5, Indels: 5
        0.76            0.12        0.12

Matches are distributed among these distances:
  15    6  0.19
  16    7  0.22
  17    4  0.12
  18   15  0.47

ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51


Consensus pattern (17 bp):   
TTTTTTAAAAAAATATA
Done.