Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020308.1 Corchorus olitorius cultivar O-4 contig20341, 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: 17188
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:2406 original size:42 final size:42

Alignment explanation


    Indices: 2354--2436  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       2344 AACTTTTTTC

                             *                        
       2354 ATTAATTTTATTAATTTTCCAAAAAATCCTTTTTTAAACTTG
          1 ATTAATTTTATTAATTTGCCAAAAAATCCTTTTTTAAACTTG

                                                     
       2396 ATTAATTTTATTAATTTGCCAAAAAATCCTTTTTTAAACTT
          1 ATTAATTTTATTAATTTGCCAAAAAATCCTTTTTTAAACTT

       2437 AAAGAAAACC


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.36, C:0.12, G:0.02, T:0.49


Consensus pattern (42 bp):   
ATTAATTTTATTAATTTGCCAAAAAATCCTTTTTTAAACTTG

Found at i:6459 original size:13 final size:13

Alignment explanation


    Indices: 6418--6461  Score: 54
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       6408 GAAAAAATAA

                         
       6418 AGAG-ACAGAGGC
          1 AGAGCACAGAGGC

                    *   *
       6430 AGAGCACAAAGGT
          1 AGAGCACAGAGGC

                      *  
       6443 AGAGCACAGACGC
          1 AGAGCACAGAGGC

                  
       6456 AGAGCA
          1 AGAGCA

       6462 TTAAACAAAG


Statistics
Matches: 26,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  12    4  0.15
  13   22  0.85

ACGTcount: A:0.43, C:0.20, G:0.34, T:0.02


Consensus pattern (13 bp):   
AGAGCACAGAGGC

Found at i:7004 original size:28 final size:28

Alignment explanation


    Indices: 6951--7005  Score: 67
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       6941 TGAGAACGGA

                              * **      
       6951 GAAGACGAGAGAAGAAAATATCAGGAGG
          1 GAAGACGAGAGAAGAAAAAAAAAGGAGG

                                        
       6979 GAAGA-GAGAGAGAGAAAAAAAAAGGAG
          1 GAAGACGAGAGA-AGAAAAAAAAAGGAG

       7006 AGAAAAGGGG


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  27    6  0.26
  28   17  0.74

ACGTcount: A:0.56, C:0.04, G:0.36, T:0.04


Consensus pattern (28 bp):   
GAAGACGAGAGAAGAAAAAAAAAGGAGG

Found at i:10130 original size:8 final size:8

Alignment explanation


    Indices: 10119--10151  Score: 66
    Period size: 8  Copynumber: 4.1  Consensus size: 8

      10109 CTAAAATGAG

                    
      10119 AATGGCCC
          1 AATGGCCC

                    
      10127 AATGGCCC
          1 AATGGCCC

                    
      10135 AATGGCCC
          1 AATGGCCC

                    
      10143 AATGGCCC
          1 AATGGCCC

             
      10151 A
          1 A

      10152 GCCCTTGAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   25  1.00

ACGTcount: A:0.27, C:0.36, G:0.24, T:0.12


Consensus pattern (8 bp):   
AATGGCCC

Found at i:17180 original size:30 final size:31

Alignment explanation


    Indices: 17130--17188  Score: 102
    Period size: 30  Copynumber: 1.9  Consensus size: 31

      17120 ATCTTTTCTT

                         *                 
      17130 TTCCCTCCCCTTTTCTTTTCCTTTAAAAAAC
          1 TTCCCTCCCCTTTCCTTTTCCTTTAAAAAAC

                                         
      17161 TTCCCTCCCC-TTCCTTTTCCTTTAAAAA
          1 TTCCCTCCCCTTTCCTTTTCCTTTAAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  30   17  0.63
  31   10  0.37

ACGTcount: A:0.19, C:0.37, G:0.00, T:0.44


Consensus pattern (31 bp):   
TTCCCTCCCCTTTCCTTTTCCTTTAAAAAAC
Done.