Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016437.1 Corchorus olitorius cultivar O-4 contig16470, 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: 80186
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:9741 original size:16 final size:15

Alignment explanation


    Indices: 9716--9746  Score: 53
    Period size: 16  Copynumber: 2.0  Consensus size: 15

       9706 TGATATGCAT

                           
       9716 GCAGAGTATCTGTGG
          1 GCAGAGTATCTGTGG

                            
       9731 GCAGAAGTATCTGTGG
          1 GCAG-AGTATCTGTGG

       9747 AGTATCAGTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    4  0.27
  16   11  0.73

ACGTcount: A:0.23, C:0.13, G:0.39, T:0.26


Consensus pattern (15 bp):   
GCAGAGTATCTGTGG

Found at i:14930 original size:7 final size:7

Alignment explanation


    Indices: 14918--14949  Score: 64
    Period size: 7  Copynumber: 4.6  Consensus size: 7

      14908 GGAAGGGCTT

                   
      14918 CCAAGTC
          1 CCAAGTC

                   
      14925 CCAAGTC
          1 CCAAGTC

                   
      14932 CCAAGTC
          1 CCAAGTC

                   
      14939 CCAAGTC
          1 CCAAGTC

                
      14946 CCAA
          1 CCAA

      14950 TATGCCAATG


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

Matches are distributed among these distances:
   7   25  1.00

ACGTcount: A:0.31, C:0.44, G:0.12, T:0.12


Consensus pattern (7 bp):   
CCAAGTC

Found at i:39769 original size:22 final size:21

Alignment explanation


    Indices: 39744--39787  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 21

      39734 AGCAACTTGG

                *                 
      39744 ATAATCATAACTAATAATAGTA
          1 ATAAGCATAACTAA-AATAGTA

                      *          
      39766 ATAAGCATAATTAAAATAGTA
          1 ATAAGCATAACTAAAATAGTA

             
      39787 A
          1 A

      39788 AAAGGGAATA


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

Matches are distributed among these distances:
  21    8  0.40
  22   12  0.60

ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30


Consensus pattern (21 bp):   
ATAAGCATAACTAAAATAGTA

Found at i:51768 original size:21 final size:21

Alignment explanation


    Indices: 51734--51790  Score: 80
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      51724 TAAGAAGATT

                                  
      51734 AAATCGTTATTTTTATTAAAGA
          1 AAATCGTTATTTTTATTAAA-A

                    *            
      51756 AAATC-TTTTTTTTATTAAAA
          1 AAATCGTTATTTTTATTAAAA

                           
      51776 AAATTCGTTATTTTT
          1 AAA-TCGTTATTTTT

      51791 TTTTGGTTGG


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  20    4  0.13
  21   15  0.48
  22   12  0.39

ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53


Consensus pattern (21 bp):   
AAATCGTTATTTTTATTAAAA

Found at i:61021 original size:6 final size:6

Alignment explanation


    Indices: 61010--61039  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      61000 AAAGCGAGAA

                                              
      61010 GCGAAG GCGAAG GCGAAG GCGAAG GCGAAG
          1 GCGAAG GCGAAG GCGAAG GCGAAG GCGAAG

      61040 CAGAGGAACC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00


Consensus pattern (6 bp):   
GCGAAG

Found at i:69066 original size:29 final size:29

Alignment explanation


    Indices: 69007--69069  Score: 72
    Period size: 29  Copynumber: 2.2  Consensus size: 29

      68997 GTAAAACGTC

                       *              *  
      69007 CCAAAATTGAAGTTCAGGGAACAAAATGT
          1 CCAAAATTGAAATTCAGGGAACAAAAGGT

                          *    ** *      
      69036 CCAAAATTGAAATTTAGGGGGCCAAAGGT
          1 CCAAAATTGAAATTCAGGGAACAAAAGGT

                 
      69065 CCAAA
          1 CCAAA

      69070 CGCTACAAGT


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19


Consensus pattern (29 bp):   
CCAAAATTGAAATTCAGGGAACAAAAGGT
Done.