Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018949.1 Corchorus olitorius cultivar O-4 contig18982, 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: 18458
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28


Found at i:7070 original size:19 final size:19

Alignment explanation


    Indices: 7046--7086  Score: 73
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       7036 TGCAGCAGCC

                               
       7046 CAATGCTTCACTGTAGAAT
          1 CAATGCTTCACTGTAGAAT

                      *        
       7065 CAATGCTTCAGTGTAGAAT
          1 CAATGCTTCACTGTAGAAT

               
       7084 CAA
          1 CAA

       7087 GCACCGGTTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29


Consensus pattern (19 bp):   
CAATGCTTCACTGTAGAAT

Found at i:8617 original size:12 final size:12

Alignment explanation


    Indices: 8600--8624  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       8590 ATCTTAGCAA

                        
       8600 CTCACGTATTTT
          1 CTCACGTATTTT

                        
       8612 CTCACGTATTTT
          1 CTCACGTATTTT

             
       8624 C
          1 C

       8625 CTTGCAGGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48


Consensus pattern (12 bp):   
CTCACGTATTTT

Found at i:8899 original size:87 final size:87

Alignment explanation


    Indices: 8753--8915  Score: 326
    Period size: 87  Copynumber: 1.9  Consensus size: 87

       8743 CATAGTGGGG

                                                                             
       8753 TTTGCTTGGTAAACTTTCTGTTATACCCCTATTCACATGAGTTGTTCTTAGCAGGTTGCTGACAT
          1 TTTGCTTGGTAAACTTTCTGTTATACCCCTATTCACATGAGTTGTTCTTAGCAGGTTGCTGACAT

                                  
       8818 GTCCAAGTGGGGTTTGCTAAGA
         66 GTCCAAGTGGGGTTTGCTAAGA

                                                                             
       8840 TTTGCTTGGTAAACTTTCTGTTATACCCCTATTCACATGAGTTGTTCTTAGCAGGTTGCTGACAT
          1 TTTGCTTGGTAAACTTTCTGTTATACCCCTATTCACATGAGTTGTTCTTAGCAGGTTGCTGACAT

                       
       8905 GTCCAAGTGGG
         66 GTCCAAGTGGG

       8916 ACATCCTGAA


Statistics
Matches: 76,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  87   76  1.00

ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38


Consensus pattern (87 bp):   
TTTGCTTGGTAAACTTTCTGTTATACCCCTATTCACATGAGTTGTTCTTAGCAGGTTGCTGACAT
GTCCAAGTGGGGTTTGCTAAGA

Found at i:10561 original size:2 final size:2

Alignment explanation


    Indices: 10549--10592  Score: 72
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      10539 TGGAAAATAA

                     *                                                    
      10549 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                
      10590 AT A
          1 AT A

      10593 ATGCCATCTG


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   38  0.97

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:14118 original size:39 final size:39

Alignment explanation


    Indices: 14067--14152  Score: 138
    Period size: 39  Copynumber: 2.2  Consensus size: 39

      14057 GTTGCATCTT

                   *            *                 *
      14067 TATTCTCTTATCTAACCATTGTGTGAAGTTTTCTTTCTG
          1 TATTCTCCTATCTAACCATTCTGTGAAGTTTTCTTTCTC

                                                   
      14106 TATTCTCCTATCTAACCATTCTGTGAAGTTTTCTTTCTC
          1 TATTCTCCTATCTAACCATTCTGTGAAGTTTTCTTTCTC

                     
      14145 T-TTCTCCT
          1 TATTCTCCT

      14153 GTGTCTCTAT


Statistics
Matches: 44,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  38    7  0.16
  39   37  0.84

ACGTcount: A:0.16, C:0.23, G:0.09, T:0.51


Consensus pattern (39 bp):   
TATTCTCCTATCTAACCATTCTGTGAAGTTTTCTTTCTC
Done.