Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022771.1 Corchorus olitorius cultivar O-4 contig22804, 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: 13857
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:3764 original size:13 final size:14

Alignment explanation


    Indices: 3748--3777  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       3738 CAATCAAAGC

                          
       3748 AATAAT-CAAGGAA
          1 AATAATGCAAGGAA

                          
       3761 AATAATGCAAGGAA
          1 AATAATGCAAGGAA

               
       3775 AAT
          1 AAT

       3778 TAAAAAGATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.38
  14   10  0.62

ACGTcount: A:0.60, C:0.07, G:0.17, T:0.17


Consensus pattern (14 bp):   
AATAATGCAAGGAA

Found at i:4153 original size:21 final size:21

Alignment explanation


    Indices: 4129--4182  Score: 72
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       4119 GACATGAAAT

                *            **  
       4129 GGTGATGGCACGGGCATGGCC
          1 GGTGGTGGCACGGGCATAACC

                           *     
       4150 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCATAACC

                        
       4171 GGTGGTGGCACG
          1 GGTGGTGGCACG

       4183 ATGAATGGGT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.13, C:0.22, G:0.48, T:0.17


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCATAACC

Found at i:9652 original size:2 final size:2

Alignment explanation


    Indices: 9647--9674  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       9637 GTTTTTTACA

                                                     
       9647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9675 CCACTAAGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:13076 original size:20 final size:21

Alignment explanation


    Indices: 13036--13076  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      13026 GATTTTTATG

                *        *       
      13036 TATTTATAATTTTTTTCTTAA
          1 TATTGATAATTTTCTTCTTAA

                                 
      13057 TATTGATAATTTTCTT-TTAA
          1 TATTGATAATTTTCTTCTTAA

      13077 AAGTCCCTTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  20    4  0.22
  21   14  0.78

ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63


Consensus pattern (21 bp):   
TATTGATAATTTTCTTCTTAA

Found at i:13835 original size:2 final size:2

Alignment explanation


    Indices: 13828--13857  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      13818 TGGATACTAG

                                                        
      13828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
TA

Done.