Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021063.1 Corchorus olitorius cultivar O-4 contig21096, 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: 7078
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:450 original size:15 final size:15

Alignment explanation


    Indices: 420--461  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        410 TTACTCTGTT

                            
        420 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        436 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        451 TTGCTTTCTGT
          1 TTGTTTTCTGT

        462 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:4013 original size:21 final size:21

Alignment explanation


    Indices: 3987--4038  Score: 68
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       3977 CCATTCACCA

                        **       
       3987 TGCCACCACCGGTTAAGCCCG
          1 TGCCACCACCGGCCAAGCCCG

                           *     
       4008 TGCCACCACCGGCCATGCCCG
          1 TGCCACCACCGGCCAAGCCCG

                 *    
       4029 TGCCATCACC
          1 TGCCACCACC

       4039 ATTCCAAGCC


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.17, C:0.48, G:0.21, T:0.13


Consensus pattern (21 bp):   
TGCCACCACCGGCCAAGCCCG

Found at i:4411 original size:15 final size:14

Alignment explanation


    Indices: 4391--4420  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       4381 ATCTTTTTAA

                           
       4391 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       4406 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       4420 T
          1 T

       4421 GCTTTGATTG


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

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT
Done.