Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012145.1 Corchorus olitorius cultivar O-4 contig12178, 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: 25652
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:6737 original size:16 final size:15

Alignment explanation


    Indices: 6699--6740  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6689 ACAGAGGTTG

                           
       6699 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       6714 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6729 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6741 AGCAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:18139 original size:29 final size:30

Alignment explanation


    Indices: 18069--18145  Score: 86
    Period size: 29  Copynumber: 2.6  Consensus size: 30

      18059 TTAATGTCCT

                 *                        *
      18069 TTTTGTCCCTTAAACTTGTATGATTTTGACG
          1 TTTTGCCCCTTAAACTTGTA-GATTTTGACA

                                         * 
      18100 TTTTGCCCCTTAAACTT-TA-ATTTTGGATA
          1 TTTTGCCCCTTAAACTTGTAGATTTT-GACA

                       *     
      18129 TTTTGCCCCTTGAACTT
          1 TTTTGCCCCTTAAACTT

      18146 CCAATTTGAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  28    5  0.12
  29   18  0.44
  30    2  0.05
  31   16  0.39

ACGTcount: A:0.19, C:0.19, G:0.13, T:0.48


Consensus pattern (30 bp):   
TTTTGCCCCTTAAACTTGTAGATTTTGACA

Found at i:21381 original size:72 final size:72

Alignment explanation


    Indices: 21295--21430  Score: 254
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      21285 TTGTCCATTT

                               *                                *            
      21295 TGTACAAGTTAAAGTAATTGGCAATTTTGAAAGTTCAAGAGCTAATTGTCCTTTTTTACAGGTTT
          1 TGTACAAGTTAAAGTAATTAGCAATTTTGAAAGTTCAAGAGCTAATTGTCCTCTTTTACAGGTTT

                   
      21360 AGAGGAC
         66 AGAGGAC

                                                                            
      21367 TGTACAAGTTAAAGTAATTAGCAATTTTGAAAGTTCAAGAGCTAATTGTCCTCTTTTACAGGTT
          1 TGTACAAGTTAAAGTAATTAGCAATTTTGAAAGTTCAAGAGCTAATTGTCCTCTTTTACAGGTT

      21431 AAAAGGACAA


Statistics
Matches: 62,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  72   62  1.00

ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37


Consensus pattern (72 bp):   
TGTACAAGTTAAAGTAATTAGCAATTTTGAAAGTTCAAGAGCTAATTGTCCTCTTTTACAGGTTT
AGAGGAC

Found at i:22326 original size:14 final size:14

Alignment explanation


    Indices: 22307--22353  Score: 53
    Period size: 14  Copynumber: 3.5  Consensus size: 14

      22297 TTTCACCTCC

                          
      22307 TATGCACTTGCACA
          1 TATGCACTTGCACA

                      *  *
      22321 TATGCA-TT-AACC
          1 TATGCACTTGCACA

               *          
      22333 TATTCACTTGCACA
          1 TATGCACTTGCACA

                   
      22347 TATGCAC
          1 TATGCAC

      22354 ATATACTATG


Statistics
Matches: 25,  Mismatches: 6, Indels: 4
        0.71            0.17        0.11

Matches are distributed among these distances:
  12    7  0.28
  13    4  0.16
  14   14  0.56

ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32


Consensus pattern (14 bp):   
TATGCACTTGCACA
Done.