Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021675.1 Corchorus olitorius cultivar O-4 contig21708, 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: 15921
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:4650 original size:19 final size:18

Alignment explanation


    Indices: 4617--4652  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4607 TGAAAATAAT

                              
       4617 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       4635 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       4653 TAAGTCTTCA


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:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:9821 original size:16 final size:15

Alignment explanation


    Indices: 9783--9824  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       9773 GCAAAGGTTG

                           
       9783 AAAGAAAACAATTAA
          1 AAAGAAAACAATTAA

                           
       9798 AAAGAAAACAATTAA
          1 AAAGAAAACAATTAA

              *         
       9813 ACTAGAAAACAA
          1 A-AAGAAAACAA

       9825 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.71, C:0.10, G:0.07, T:0.12


Consensus pattern (15 bp):   
AAAGAAAACAATTAA

Found at i:12842 original size:27 final size:26

Alignment explanation


    Indices: 12811--12882  Score: 81
    Period size: 27  Copynumber: 2.7  Consensus size: 26

      12801 GGGTCATCTA

                              ** *  * 
      12811 AGGGCATTTTGGTCATTTTTATATTC
          1 AGGGCATTTTGGTCATTTGAACATCC

                       *           *   
      12837 AGGGGCATTTTAGTCATTTGAACGTCC
          1 A-GGGCATTTTGGTCATTTGAACATCC

                               
      12864 AGGGCATTTTGGTCATTTG
          1 AGGGCATTTTGGTCATTTG

      12883 CGCACTCAAG


Statistics
Matches: 38,  Mismatches: 7, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  26   18  0.47
  27   20  0.53

ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42


Consensus pattern (26 bp):   
AGGGCATTTTGGTCATTTGAACATCC

Found at i:13467 original size:19 final size:19

Alignment explanation


    Indices: 13445--13482  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      13435 GTACAAATAT

                      *        
      13445 TCACCAAGTATACAAGACC
          1 TCACCAAGTACACAAGACC

                               
      13464 TCACCAAGTACACAAGACC
          1 TCACCAAGTACACAAGACC

      13483 AAAATGAGTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.42, C:0.34, G:0.11, T:0.13


Consensus pattern (19 bp):   
TCACCAAGTACACAAGACC

Found at i:14816 original size:26 final size:26

Alignment explanation


    Indices: 14776--14867  Score: 139
    Period size: 26  Copynumber: 3.5  Consensus size: 26

      14766 TTTTTTTTTT

                            * *   *   
      14776 CACATTAGTAATTAGGTAATAGTATC
          1 CACATTAGTAATTAGGCATTAGCATC

                      *               
      14802 CACATTAGTAGTTAGGCATTAGCATC
          1 CACATTAGTAATTAGGCATTAGCATC

                                     *
      14828 CACATTAGTAATTAGGCATTAGCATT
          1 CACATTAGTAATTAGGCATTAGCATC

                          
      14854 CACATTAGTAATTA
          1 CACATTAGTAATTA

      14868 CTTGTAGTTA


Statistics
Matches: 60,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  26   60  1.00

ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Consensus pattern (26 bp):   
CACATTAGTAATTAGGCATTAGCATC
Done.