Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024393.1 Corchorus olitorius cultivar O-4 contig24426, 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: 9401
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:1971 original size:27 final size:27

Alignment explanation


    Indices: 1941--2005  Score: 103
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       1931 AACAGTAAAC

                                   *  *
       1941 TGCAAATGACCAAAATGCCCCTGGACG
          1 TGCAAATGACCAAAATGCCCCTGAACA

                      *                
       1968 TGCAAATGACTAAAATGCCCCTGAACA
          1 TGCAAATGACCAAAATGCCCCTGAACA

                       
       1995 TGCAAATGACC
          1 TGCAAATGACC

       2006 CCAAGATCCC


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   34  1.00

ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17


Consensus pattern (27 bp):   
TGCAAATGACCAAAATGCCCCTGAACA

Found at i:3712 original size:19 final size:18

Alignment explanation


    Indices: 3679--3714  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3669 TTGAAATAAT

                              
       3679 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       3697 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       3715 TGAGCCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:4635 original size:71 final size:71

Alignment explanation


    Indices: 4519--4660  Score: 189
    Period size: 71  Copynumber: 2.0  Consensus size: 71

       4509 TGAACTTCGC

                          *                        *           *          *  
       4519 TCTGAATCATTCATGTAAAAGACTAAGTATCGATTCACTGTCAAAATAATTGGAATTTGATCTGA
          1 TCTGAATCATTCATATAAAAGACTAAGTATCGATTCACTATCAAAATAATTAGAATTTGATCAGA

                  
       4584 CATCTT
         66 CATCTT

                            *     *               *                          
       4590 TCTGAATCATTCATATCAAAG-TTAAAGTATC-AGTTCCCTATCAAAATAATTAGAATTTGATCA
          1 TCTGAATCATTCATATAAAAGACT-AAGTATCGA-TTCACTATCAAAATAATTAGAATTTGATCA

                    
       4653 GACATCTT
         64 GACATCTT

       4661 GCGAACAGAA


Statistics
Matches: 62,  Mismatches: 7, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  70    2  0.03
  71   60  0.97

ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35


Consensus pattern (71 bp):   
TCTGAATCATTCATATAAAAGACTAAGTATCGATTCACTATCAAAATAATTAGAATTTGATCAGA
CATCTT

Found at i:6649 original size:31 final size:30

Alignment explanation


    Indices: 6613--6674  Score: 81
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       6603 TAAAAACACT

                                            
       6613 AAAATTAAATAAAAACAATTAA-CTAGAAAGC
          1 AAAATTAAA-AAAAACAATTAATC-AGAAAGC

                     **                   
       6644 AAAATTAAAGGAAACAATTAATCAGAAAGC
          1 AAAATTAAAAAAAACAATTAATCAGAAAGC

             
       6674 A
          1 A

       6675 GTGAAGTAAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  30   18  0.64
  31   10  0.36

ACGTcount: A:0.63, C:0.10, G:0.10, T:0.18


Consensus pattern (30 bp):   
AAAATTAAAAAAAACAATTAATCAGAAAGC

Found at i:8598 original size:34 final size:34

Alignment explanation


    Indices: 8555--8621  Score: 107
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       8545 CTCTTACAAG

                       * *        *           
       8555 CAATGAAGTTACATGGGCCTTCGTCACGCCTTTC
          1 CAATGAAGTTAAACGGGCCTTCATCACGCCTTTC

                                             
       8589 CAATGAAGTTAAACGGGCCTTCATCACGCCTTT
          1 CAATGAAGTTAAACGGGCCTTCATCACGCCTTT

       8622 ACAAGTTGAG


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28


Consensus pattern (34 bp):   
CAATGAAGTTAAACGGGCCTTCATCACGCCTTTC

Found at i:8967 original size:16 final size:15

Alignment explanation


    Indices: 8928--8969  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       8918 ACAGAGGTTG

                           
       8928 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                *          
       8943 ACAGGAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       8958 ACTAGAAAACAA
          1 AC-AGAAAACAA

       8970 AACAAAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.