Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013981.1 Corchorus olitorius cultivar O-4 contig14014, 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: 20538
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:3564 original size:12 final size:11

Alignment explanation


    Indices: 3536--3564  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

       3526 AAAATTTTTT

                       
       3536 TATTTTTGAAA
          1 TATTTTTGAAA

                       
       3547 TATTTTTGAAA
          1 TATTTTTGAAA

                   
       3558 TATTTTT
          1 TATTTTT

       3565 CAATTAAACT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62


Consensus pattern (11 bp):   
TATTTTTGAAA

Found at i:6748 original size:30 final size:33

Alignment explanation


    Indices: 6678--6763  Score: 97
    Period size: 36  Copynumber: 2.6  Consensus size: 33

       6668 TAAGTAAACT

                                       *       *
       6678 CCAAAAGAAGGTTTTGGAAAATAAGTTTGGATAATT
          1 CCAAAAGAAGGTTTTGGAAAATAA--TAGGAT-ATC

                                             
       6714 CCAAAAGAAGGTTTTGGAAAATAA-AGG-T-TC
          1 CCAAAAGAAGGTTTTGGAAAATAATAGGATATC

                      *         
       6744 CCAAAAGAAGATTTTGGAAA
          1 CCAAAAGAAGGTTTTGGAAA

       6764 CAAATAAAAT


Statistics
Matches: 47,  Mismatches: 3, Indels: 6
        0.84            0.05        0.11

Matches are distributed among these distances:
  30   20  0.43
  32    1  0.02
  33    2  0.04
  36   24  0.51

ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26


Consensus pattern (33 bp):   
CCAAAAGAAGGTTTTGGAAAATAATAGGATATC

Found at i:6791 original size:38 final size:37

Alignment explanation


    Indices: 6749--6827  Score: 113
    Period size: 38  Copynumber: 2.1  Consensus size: 37

       6739 GGTTCCCAAA

                                          *       
       6749 AGAAGATTTTGGAAACAAATAAAATTGGTCGAGTTTTT
          1 AGAAGATTTTGGAAACAAATAAAATTGGT-AAGTTTTT

                           ** *                  
       6787 AGAAGATTTTGGAAATTAGTAAAATTGGTAAGTTTTT
          1 AGAAGATTTTGGAAACAAATAAAATTGGTAAGTTTTT

                
       6824 AGAA
          1 AGAA

       6828 AAATCAAATG


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  37   11  0.30
  38   26  0.70

ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35


Consensus pattern (37 bp):   
AGAAGATTTTGGAAACAAATAAAATTGGTAAGTTTTT

Found at i:19922 original size:27 final size:27

Alignment explanation


    Indices: 19892--19992  Score: 184
    Period size: 27  Copynumber: 3.7  Consensus size: 27

      19882 TAGGGTCACC

                                   *   
      19892 CAGGGGCATTTTGGTCATTTGCACGTA
          1 CAGGGGCATTTTGGTCATTTGCATGTA

                                       
      19919 CAGGGGCATTTTGGTCATTTGCATGTA
          1 CAGGGGCATTTTGGTCATTTGCATGTA

                                      *
      19946 CAGGGGCATTTTGGTCATTTGCATGTC
          1 CAGGGGCATTTTGGTCATTTGCATGTA

                                
      19973 CAGGGGCATTTTGGTCATTT
          1 CAGGGGCATTTTGGTCATTT

      19993 CAAGTGCACT


Statistics
Matches: 72,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   72  1.00

ACGTcount: A:0.17, C:0.17, G:0.30, T:0.37


Consensus pattern (27 bp):   
CAGGGGCATTTTGGTCATTTGCATGTA
Done.