Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006903.1 Corchorus capsularis cultivar CVL-1 contig06924, 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: 11151
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28


Found at i:6069 original size:24 final size:24

Alignment explanation


    Indices: 6042--6108  Score: 125
    Period size: 24  Copynumber: 2.8  Consensus size: 24

       6032 CTATCTGGAA

                          *         
       6042 AAAAATTGAGCATTTATAACAATG
          1 AAAAATTGAGCATTCATAACAATG

                                    
       6066 AAAAATTGAGCATTCATAACAATG
          1 AAAAATTGAGCATTCATAACAATG

                               
       6090 AAAAATTGAGCATTCATAA
          1 AAAAATTGAGCATTCATAA

       6109 ATTGCGCATT


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  24   42  1.00

ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27


Consensus pattern (24 bp):   
AAAAATTGAGCATTCATAACAATG

Found at i:8351 original size:74 final size:74

Alignment explanation


    Indices: 8245--8390  Score: 265
    Period size: 74  Copynumber: 2.0  Consensus size: 74

       8235 TATCCATTTC

                                      *        *              *              
       8245 ACTTACATAATTTTGATTCTGAATGTTCAATTGAATTGATTCAAATGTCTTTCAAAATATAATTT
          1 ACTTACATAATTTTGATTCTGAATGTCCAATTGAACTGATTCAAATGTCTATCAAAATATAATTT

                     
       8310 CATGATCTA
         66 CATGATCTA

                                                                             
       8319 ACTTACATAATTTTGATTCTGAATGTCCAATTGAACTGATTCAAATGTCTATCAAAATATAATTT
          1 ACTTACATAATTTTGATTCTGAATGTCCAATTGAACTGATTCAAATGTCTATCAAAATATAATTT

                   
       8384 CATGATC
         66 CATGATC

       8391 CACCACTTGT


Statistics
Matches: 69,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  74   69  1.00

ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41


Consensus pattern (74 bp):   
ACTTACATAATTTTGATTCTGAATGTCCAATTGAACTGATTCAAATGTCTATCAAAATATAATTT
CATGATCTA

Found at i:9178 original size:14 final size:15

Alignment explanation


    Indices: 9159--9187  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       9149 AAATAAAATG

                           
       9159 CTTA-CCTTTTATTT
          1 CTTACCCTTTTATTT

                           
       9173 CTTACCCTTTTATTT
          1 CTTACCCTTTTATTT

       9188 TCTCTTCAGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    4  0.29
  15   10  0.71

ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62


Consensus pattern (15 bp):   
CTTACCCTTTTATTT

Found at i:10314 original size:15 final size:15

Alignment explanation


    Indices: 10294--10323  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      10284 AGGGAGAAGA

                           
      10294 AAAAAGCAAAAAAAG
          1 AAAAAGCAAAAAAAG

                  *        
      10309 AAAAAGGAAAAAAAG
          1 AAAAAGCAAAAAAAG

      10324 GTTTCAGAGA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00


Consensus pattern (15 bp):   
AAAAAGCAAAAAAAG
Done.