Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009612.1 Corchorus olitorius cultivar O-4 contig09644, 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: 11277
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32


Found at i:10 original size:2 final size:2

Alignment explanation


    Indices: 4--46  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

          1 TAC

                                                                          
          4 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
         46 T
          1 T

         47 TGAAGTCCAA


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2125 original size:85 final size:84

Alignment explanation


    Indices: 2021--2185  Score: 201
    Period size: 85  Copynumber: 1.9  Consensus size: 84

       2011 TGAAAATCAT

                     *                                                       
       2021 CCAAACAATCCAATCTGTAATGCTTT-AAAACGTTGAAAAA-CAACCAACCAATACAATCTATAA
          1 CCAAACAATACAATCTGTAATG-TTTGAAAACGTT-AAAAATC-ACCAACCAATACAATCTATAA

                                   
       2084 TAG-TTGAAAATGATAGACTCAG
         63 -AGCTTGAAAATGATAGACTCAG

                          *               *           *       *            * 
       2106 CCAAACAATACAATTTGTAATGTTTGAAAATGTTAAAAATTCGCCAACCAGTACAATCTATAACG
          1 CCAAACAATACAATCTGTAATGTTTGAAAACGTTAAAAA-TCACCAACCAATACAATCTATAAAG

                      *    
       2171 CTTGAAAATGTTAGA
         65 CTTGAAAATGATAGA

       2186 ATATTAGAAA


Statistics
Matches: 69,  Mismatches: 7, Indels: 8
        0.82            0.08        0.10

Matches are distributed among these distances:
  84    9  0.13
  85   59  0.86
  86    1  0.01

ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26


Consensus pattern (84 bp):   
CCAAACAATACAATCTGTAATGTTTGAAAACGTTAAAAATCACCAACCAATACAATCTATAAAGC
TTGAAAATGATAGACTCAG

Found at i:4628 original size:25 final size:25

Alignment explanation


    Indices: 4594--4645  Score: 77
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       4584 ATGCAATCTC

                 *        *       *  
       4594 TCATAGAAAGACACCTTTTCATGTT
          1 TCATAAAAAGACACATTTTCATATT

                                     
       4619 TCATAAAAAGACACATTTTCATATT
          1 TCATAAAAAGACACATTTTCATATT

              
       4644 TC
          1 TC

       4646 TGCAGAGTTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37


Consensus pattern (25 bp):   
TCATAAAAAGACACATTTTCATATT

Found at i:10675 original size:21 final size:21

Alignment explanation


    Indices: 10649--10698  Score: 84
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      10639 TGCTAGGAGA

                                  
      10649 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
      10670 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
      10691 TCATTGGA
          1 TCATTGGA

      10699 ATTGCCTAAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  20    2  0.07
  21   26  0.93

ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC
Done.