Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024525.1 Corchorus olitorius cultivar O-4 contig24558, 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: 11879
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:870 original size:16 final size:15

Alignment explanation


    Indices: 832--873  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        822 ATAGAGGTTG

                           
        832 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
        847 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        862 ACTAGAAAACAA
          1 AC-AGAAAACAA

        874 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:7891 original size:6 final size:6

Alignment explanation


    Indices: 7880--7972  Score: 150
    Period size: 6  Copynumber: 14.8  Consensus size: 6

       7870 AAATATTATA

                                                                      
       7880 TATATC TATATC TATATC TATATATC TATATC TATATAC TATATC TATATC
          1 TATATC TATATC TATATC --TATATC TATATC TATAT-C TATATC TATATC

                                                            
       7931 TATATC TATATAC TATATC TATATC TATATC TATATC TATAT
          1 TATATC TATAT-C TATATC TATATC TATATC TATATC TATAT

       7973 ATTATATAAG


Statistics
Matches: 83,  Mismatches: 0, Indels: 8
        0.91            0.00        0.09

Matches are distributed among these distances:
   6   65  0.78
   7   12  0.14
   8    6  0.07

ACGTcount: A:0.35, C:0.15, G:0.00, T:0.49


Consensus pattern (6 bp):   
TATATC

Found at i:7934 original size:25 final size:24

Alignment explanation


    Indices: 7880--7972  Score: 150
    Period size: 25  Copynumber: 3.7  Consensus size: 24

       7870 AAATATTATA

                                      
       7880 TATATCTATATCTATATCTATATATC
          1 TATATCTATATCTATATC--TATATC

                                     
       7906 TATATCTATATACTATATCTATATC
          1 TATATCTATAT-CTATATCTATATC

                                     
       7931 TATATCTATATACTATATCTATATC
          1 TATATCTATAT-CTATATCTATATC

                             
       7956 TATATCTATATCTATAT
          1 TATATCTATATCTATAT

       7973 ATTATATAAG


Statistics
Matches: 66,  Mismatches: 0, Indels: 4
        0.94            0.00        0.06

Matches are distributed among these distances:
  24    6  0.09
  25   42  0.64
  26   11  0.17
  27    7  0.11

ACGTcount: A:0.35, C:0.15, G:0.00, T:0.49


Consensus pattern (24 bp):   
TATATCTATATCTATATCTATATC

Found at i:7973 original size:31 final size:31

Alignment explanation


    Indices: 7876--7979  Score: 158
    Period size: 31  Copynumber: 3.3  Consensus size: 31

       7866 TATTAAATAT

                                             
       7876 TATA-TATATCTATATCTATATCTATATATCTA
          1 TATACTATATCTATATCTATATC--TATATCTA

                                            
       7908 TAT-CTATATACTATATCTATATCTATATCTA
          1 TATACTATAT-CTATATCTATATCTATATCTA

                                           
       7939 TATACTATATCTATATCTATATCTATATCTA
          1 TATACTATATCTATATCTATATCTATATCTA

                *     
       7970 TATATTATAT
          1 TATACTATAT

       7980 AAGTCTAAAC


Statistics
Matches: 68,  Mismatches: 1, Indels: 7
        0.89            0.01        0.09

Matches are distributed among these distances:
  31   41  0.60
  32   14  0.21
  33   13  0.19

ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50


Consensus pattern (31 bp):   
TATACTATATCTATATCTATATCTATATCTA

Found at i:8379 original size:21 final size:21

Alignment explanation


    Indices: 8334--8380  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       8324 TAAGTCCTTT

                                *
       8334 TTTTCATTTTATTTAATTTCT
          1 TTTTCATTTTATTTAATTTCC

                            *     
       8355 TTTTCATTTT-TCTTATTTTCC
          1 TTTTCATTTTAT-TTAATTTCC

                 
       8376 TTTTC
          1 TTTTC

       8381 TTATTTGAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  20    1  0.04
  21   22  0.96

ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72


Consensus pattern (21 bp):   
TTTTCATTTTATTTAATTTCC
Done.