Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023461.1 Corchorus olitorius cultivar O-4 contig23494, 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: 18930
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:3947 original size:17 final size:18

Alignment explanation


    Indices: 3925--3966  Score: 52
    Period size: 17  Copynumber: 2.4  Consensus size: 18

       3915 CAAACCCATT

                              
       3925 TTCTTTTTATT-CTTGAA
          1 TTCTTTTTATTACTTGAA

                        *     
       3942 TTC-TTTTATTATTTGAA
          1 TTCTTTTTATTACTTGAA

            *       
       3959 ATCTTTTT
          1 TTCTTTTT

       3967 CAATTTTCTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 3
        0.81            0.08        0.12

Matches are distributed among these distances:
  16    7  0.33
  17   10  0.48
  18    4  0.19

ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67


Consensus pattern (18 bp):   
TTCTTTTTATTACTTGAA

Found at i:4280 original size:16 final size:17

Alignment explanation


    Indices: 4241--4289  Score: 71
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       4231 CATTGCTTTT

                              
       4241 GAAAATACATTTTTGAAA
          1 GAAAA-ACATTTTTGAAA

                             
       4259 GAAAAACATTTTTGAAA
          1 GAAAAACATTTTTGAAA

            *    *        
       4276 TAAAACCATTTTTG
          1 GAAAAACATTTTTG

       4290 TATTTTCTTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  17   24  0.83
  18    5  0.17

ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35


Consensus pattern (17 bp):   
GAAAAACATTTTTGAAA

Found at i:5106 original size:18 final size:21

Alignment explanation


    Indices: 5083--5124  Score: 63
    Period size: 18  Copynumber: 2.1  Consensus size: 21

       5073 AGCTGGTCTT

                                 
       5083 CCTCTTCTT-TTC-TC-AAAC
          1 CCTCTTCTTCTTCTTCGAAAC

                                 
       5101 CCTCTTCTTCTTCTTCGAAAC
          1 CCTCTTCTTCTTCTTCGAAAC

               
       5122 CCT
          1 CCT

       5125 AGCCACCTTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  18    9  0.43
  19    3  0.14
  20    2  0.10
  21    7  0.33

ACGTcount: A:0.14, C:0.40, G:0.02, T:0.43


Consensus pattern (21 bp):   
CCTCTTCTTCTTCTTCGAAAC

Found at i:8247 original size:15 final size:15

Alignment explanation


    Indices: 8229--8259  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       8219 TTTAAGTTTC

                           
       8229 AGGGACTTAATTGAA
          1 AGGGACTTAATTGAA

                     *     
       8244 AGGGACTTATTTGAA
          1 AGGGACTTAATTGAA

             
       8259 A
          1 A

       8260 TGAAAAGAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29


Consensus pattern (15 bp):   
AGGGACTTAATTGAA
Done.