Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015999.1 Corchorus olitorius cultivar O-4 contig16032, 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: 13758
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33


Found at i:5531 original size:15 final size:16

Alignment explanation


    Indices: 5501--5540  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       5491 TTACTTTGTT

                            
       5501 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
       5517 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

               *     
       5532 TTGCTTTCT
          1 TTGTTTTCT

       5541 TTCAACCTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:8839 original size:21 final size:21

Alignment explanation


    Indices: 8815--8897  Score: 55
    Period size: 21  Copynumber: 4.0  Consensus size: 21

       8805 CGCTACCACT

                                 
       8815 CGCGCCACCTGCCCGGCCATC
          1 CGCGCCACCTGCCCGGCCATC

                          *  *    
       8836 CGCG-CACCATGCCTGGTCATC
          1 CGCGCCACC-TGCCCGGCCATC

              *    *               
       8857 CGTGCCTTCCT-CCAC-GCCATC
          1 CGCGCC-ACCTGCC-CGGCCATC

              *    **           
       8878 CGAGCCAAGTGCCCGGCCAT
          1 CGCGCCACCTGCCCGGCCAT

       8898 GACCGGTACC


Statistics
Matches: 46,  Mismatches: 10, Indels: 12
        0.68            0.15        0.18

Matches are distributed among these distances:
  20    6  0.13
  21   36  0.78
  22    2  0.04
  23    2  0.04

ACGTcount: A:0.13, C:0.48, G:0.23, T:0.16


Consensus pattern (21 bp):   
CGCGCCACCTGCCCGGCCATC

Found at i:9110 original size:21 final size:21

Alignment explanation


    Indices: 9050--9111  Score: 70
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       9040 AAGCCATTAT

                   *          *   
       9050 CGGCCATTCACCGTGCCACCAC
          1 CGGCCATGC-CCGTGCCATCAC

               ** *              
       9072 CGGTTAAGCCCGTGCCATCAC
          1 CGGCCATGCCCGTGCCATCAC

                               
       9093 CGGCCATGCCCGTGCCATC
          1 CGGCCATGCCCGTGCCATC

       9112 GCCATTTCTA


Statistics
Matches: 32,  Mismatches: 8, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  21   27  0.84
  22    5  0.16

ACGTcount: A:0.16, C:0.45, G:0.23, T:0.16


Consensus pattern (21 bp):   
CGGCCATGCCCGTGCCATCAC

Found at i:12391 original size:15 final size:16

Alignment explanation


    Indices: 12361--12400  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      12351 TTACTTTGTT

                            
      12361 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
      12377 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

               *     
      12392 TTGCTTTCT
          1 TTGTTTTCT

      12401 TTCAACCTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA
Done.