Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019458.1 Corchorus olitorius cultivar O-4 contig19491, 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: 18999
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Found at i:2841 original size:9 final size:9

Alignment explanation


    Indices: 2827--2860  Score: 50
    Period size: 9  Copynumber: 3.6  Consensus size: 9

       2817 TATGCAGTGT

                     
       2827 TAAAAAAAA
          1 TAAAAAAAA

                     
       2836 TAAAAAAAA
          1 TAAAAAAAA

                       
       2845 TAATAAATAAA
          1 TAA-AAA-AAA

                 
       2856 TAAAA
          1 TAAAA

       2861 CCTTGAACAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
   9   12  0.52
  10    5  0.22
  11    6  0.26

ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18


Consensus pattern (9 bp):   
TAAAAAAAA

Found at i:4373 original size:69 final size:69

Alignment explanation


    Indices: 4292--4431  Score: 280
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       4282 CCTAGTAATA

                                                                             
       4292 ATACTAATAATAAGTAAATAGGTCAGGCCATGACTTGTATATAAGCAACAGTTGACCAATTAGAA
          1 ATACTAATAATAAGTAAATAGGTCAGGCCATGACTTGTATATAAGCAACAGTTGACCAATTAGAA

                
       4357 CAGC
         66 CAGC

                                                                             
       4361 ATACTAATAATAAGTAAATAGGTCAGGCCATGACTTGTATATAAGCAACAGTTGACCAATTAGAA
          1 ATACTAATAATAAGTAAATAGGTCAGGCCATGACTTGTATATAAGCAACAGTTGACCAATTAGAA

                
       4426 CAGC
         66 CAGC

              
       4430 AT
          1 AT

       4432 GAACAGGGAC


Statistics
Matches: 71,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  69   71  1.00

ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25


Consensus pattern (69 bp):   
ATACTAATAATAAGTAAATAGGTCAGGCCATGACTTGTATATAAGCAACAGTTGACCAATTAGAA
CAGC

Found at i:4553 original size:23 final size:21

Alignment explanation


    Indices: 4527--4570  Score: 61
    Period size: 23  Copynumber: 2.0  Consensus size: 21

       4517 AAAAAATATG

                                   
       4527 TTTTCAAAAATTTAAGTTTTAAA
          1 TTTTCAAAAATTT-A-TTTTAAA

                 *               
       4550 TTTTCCAAAATTTATTTTAAA
          1 TTTTCAAAAATTTATTTTAAA

       4571 AAAATTTTAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  21    7  0.35
  22    1  0.05
  23   12  0.60

ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50


Consensus pattern (21 bp):   
TTTTCAAAAATTTATTTTAAA

Found at i:10125 original size:2 final size:2

Alignment explanation


    Indices: 10118--10157  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      10108 GGCCGGGAGC

                                                                         
      10118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      10158 TTTGGCTAAA


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   36  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:16628 original size:15 final size:15

Alignment explanation


    Indices: 16608--16639  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      16598 ACAGAGGTTG

                           
      16608 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
      16623 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

              
      16638 AC
          1 AC

      16640 TGGAAAAACA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.