Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001087.1 Corchorus olitorius cultivar O-4 contig01087, 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: 29698
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Found at i:6954 original size:2 final size:2

Alignment explanation


    Indices: 6947--6985  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       6937 TATCTGTCAA

                                                                      
       6947 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A

       6986 TATAAATTTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:9820 original size:158 final size:158

Alignment explanation


    Indices: 9532--9852  Score: 633
    Period size: 158  Copynumber: 2.0  Consensus size: 158

       9522 TTTGGCGATG

                                                                             
       9532 CTAATTTGTTTAAAATAATAGTGTCTTTAGATTTTGTCTAAAGCTCATTTAGTTAACAGTAAATG
          1 CTAATTTGTTTAAAATAATAGTGTCTTTAGATTTTGTCTAAAGCTCATTTAGTTAACAGTAAATG

                                                                             
       9597 CTCTTCAATCCTTGTCAGAACTATACTGCACTTCAATGATTAATACTATGTTGGTTTTGGAATAT
         66 CTCTTCAATCCTTGTCAGAACTATACTGCACTTCAATGATTAATACTATGTTGGTTTTGGAATAT

                                        
       9662 AATTTTTGCAGCCTTCAATATACCTGCA
        131 AATTTTTGCAGCCTTCAATATACCTGCA

                                                                             
       9690 CTAATTTGTTTAAAATAATAGTGTCTTTAGATTTTGTCTAAAGCTCATTTAGTTAACAGTAAATG
          1 CTAATTTGTTTAAAATAATAGTGTCTTTAGATTTTGTCTAAAGCTCATTTAGTTAACAGTAAATG

                                                                             
       9755 CTCTTCAATCCTTGTCAGAACTATACTGCACTTCAATGATTAATACTATGTTGGTTTTGGAATAT
         66 CTCTTCAATCCTTGTCAGAACTATACTGCACTTCAATGATTAATACTATGTTGGTTTTGGAATAT

                                       *
       9820 AATTTTTGCAGCCTTCAATATACCTGCT
        131 AATTTTTGCAGCCTTCAATATACCTGCA

                 
       9848 CTAAT
          1 CTAAT

       9853 AATCTTTCTT


Statistics
Matches: 162,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 158  162  1.00

ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41


Consensus pattern (158 bp):   
CTAATTTGTTTAAAATAATAGTGTCTTTAGATTTTGTCTAAAGCTCATTTAGTTAACAGTAAATG
CTCTTCAATCCTTGTCAGAACTATACTGCACTTCAATGATTAATACTATGTTGGTTTTGGAATAT
AATTTTTGCAGCCTTCAATATACCTGCA

Found at i:17735 original size:2 final size:2

Alignment explanation


    Indices: 17728--17754  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      17718 TTGTTTATAA

                                                    
      17728 TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC T

      17755 TCATTTGTTG


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

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:29639 original size:2 final size:2

Alignment explanation


    Indices: 29632--29698  Score: 134
    Period size: 2  Copynumber: 33.5  Consensus size: 2

      29622 AAACTACCTT

                                                                          
      29632 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                                 
      29674 GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA G


Statistics
Matches: 65,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   65  1.00

ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00


Consensus pattern (2 bp):   
GA

Done.