Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020214.1 Corchorus olitorius cultivar O-4 contig20247, 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: 24877
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:6502 original size:39 final size:39

Alignment explanation


    Indices: 6448--6552  Score: 185
    Period size: 39  Copynumber: 2.7  Consensus size: 39

       6438 GGCATCCAAA

                                                    
       6448 CATCAGAGTTCCAAACTAGAAGTAAAAAATATAAT-GCCT
          1 CATCAGAGTTCCAAACTAGAAGTAAAAAATATAATAG-CT

                                            *      
       6487 CATCAGAGTTCCAAACTAGAAGTAAAAAATATGATAGCT
          1 CATCAGAGTTCCAAACTAGAAGTAAAAAATATAATAGCT

                                       
       6526 CATCAGAGTTCCAAACTAGAAGTAAAA
          1 CATCAGAGTTCCAAACTAGAAGTAAAA

       6553 GTAAAAAATA


Statistics
Matches: 64,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  39   63  0.98
  40    1  0.02

ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22


Consensus pattern (39 bp):   
CATCAGAGTTCCAAACTAGAAGTAAAAAATATAATAGCT

Found at i:17244 original size:7 final size:7

Alignment explanation


    Indices: 17232--17273  Score: 59
    Period size: 7  Copynumber: 6.0  Consensus size: 7

      17222 TTTTGTTTTG

                  *
      17232 TTTTGTA
          1 TTTTGTT

                   
      17239 TTTTG-T
          1 TTTTGTT

                   
      17245 TTTTGTT
          1 TTTTGTT

                   
      17252 TTTTGTT
          1 TTTTGTT

                    
      17259 TTTTGTGT
          1 TTTTGT-T

                   
      17267 TTTTGTT
          1 TTTTGTT

      17274 AATTTTGCAG


Statistics
Matches: 32,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
   6    5  0.16
   7   20  0.62
   8    7  0.22

ACGTcount: A:0.02, C:0.00, G:0.17, T:0.81


Consensus pattern (7 bp):   
TTTTGTT

Found at i:17250 original size:13 final size:13

Alignment explanation


    Indices: 17227--17261  Score: 54
    Period size: 13  Copynumber: 2.8  Consensus size: 13

      17217 TTTAGTTTTG

                         
      17227 TTTTG-TTTTGTA
          1 TTTTGTTTTTGTA

                        *
      17239 TTTTGTTTTTGTT
          1 TTTTGTTTTTGTA

                      
      17252 TTTTGTTTTT
          1 TTTTGTTTTT

      17262 TGTGTTTTTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  12    5  0.24
  13   16  0.76

ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83


Consensus pattern (13 bp):   
TTTTGTTTTTGTA

Found at i:18838 original size:23 final size:23

Alignment explanation


    Indices: 18808--18854  Score: 85
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      18798 AATTAAATTG

                           *       
      18808 CATCAAAACAGTCACTACTAACC
          1 CATCAAAACAGTCACCACTAACC

                                   
      18831 CATCAAAACAGTCACCACTAACC
          1 CATCAAAACAGTCACCACTAACC

             
      18854 C
          1 C

      18855 TCTTCCTCCA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.43, C:0.38, G:0.04, T:0.15


Consensus pattern (23 bp):   
CATCAAAACAGTCACCACTAACC
Done.