Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022774.1 Corchorus olitorius cultivar O-4 contig22807, 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: 4501
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27


Found at i:2624 original size:11 final size:12

Alignment explanation


    Indices: 2608--2636  Score: 51
    Period size: 11  Copynumber: 2.5  Consensus size: 12

       2598 GTTAACTGGT

                        
       2608 CCACGTAGG-TG
          1 CCACGTAGGATG

                        
       2619 CCACGTAGGATG
          1 CCACGTAGGATG

                  
       2631 CCACGT
          1 CCACGT

       2637 GTATTTTAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  11    9  0.53
  12    8  0.47

ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17


Consensus pattern (12 bp):   
CCACGTAGGATG

Found at i:2769 original size:31 final size:31

Alignment explanation


    Indices: 2710--2779  Score: 79
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2700 TTATAACATT

                                   *       
       2710 ATATCCTGAATTGCTTGTTCAGGTAAACCTC
          1 ATATCCTGAATTGCTTGTTCAGGCAAACCTC

                 *              *          *
       2741 ATATCGTGAATTGCATT-TTTAGGCAAACCTT
          1 ATATCCTGAATTGC-TTGTTCAGGCAAACCTC

               *    
       2772 ATACCCTG
          1 ATATCCTG

       2780 TATTATTTAT


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  31   30  0.94
  32    2  0.06

ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36


Consensus pattern (31 bp):   
ATATCCTGAATTGCTTGTTCAGGCAAACCTC

Found at i:3418 original size:18 final size:18

Alignment explanation


    Indices: 3397--3442  Score: 92
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       3387 GCGCAGAGGC

                              
       3397 AGAGGCAGGGCCAGATGT
          1 AGAGGCAGGGCCAGATGT

                              
       3415 AGAGGCAGGGCCAGATGT
          1 AGAGGCAGGGCCAGATGT

                      
       3433 AGAGGCAGGG
          1 AGAGGCAGGG

       3443 GCTGGTGGTG


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

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.28, C:0.15, G:0.48, T:0.09


Consensus pattern (18 bp):   
AGAGGCAGGGCCAGATGT

Found at i:3792 original size:66 final size:67

Alignment explanation


    Indices: 3685--3817  Score: 234
    Period size: 66  Copynumber: 2.0  Consensus size: 67

       3675 CCTGTCAAAA

                                 *                                           
       3685 AATGCAAAAAGGGAGATAAACCAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATA
          1 AATGCAAAAAGGGAGATAAACAAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATA

              
       3750 TG
         66 TG

                                                                             
       3752 AATGCAAAAAGGGAGA-AAGA-AAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGAT
          1 AATGCAAAAAGGGAGATAA-ACAAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGAT

               
       3815 ATG
         65 ATG

       3818 GAAAAGTGAC


Statistics
Matches: 64,  Mismatches: 1, Indels: 3
        0.94            0.01        0.04

Matches are distributed among these distances:
  66   47  0.73
  67   17  0.27

ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16


Consensus pattern (67 bp):   
AATGCAAAAAGGGAGATAAACAAGTCTTCAATACAGAAATTCAGAAATGGAGAAAGAGAAAGATA
TG
Done.