Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021050.1 Corchorus olitorius cultivar O-4 contig21083, 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: 6972
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30


Found at i:71 original size:47 final size:47

Alignment explanation


    Indices: 1--314  Score: 419
    Period size: 47  Copynumber: 6.8  Consensus size: 47

                                                           
          1 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAA-A
          1 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA

                                                            
         47 ATTTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA
          1 A-TTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA

                                              *             
         95 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGAAAAAG-GAGAAGA
          1 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAG-GAAGA

             *                                             
        142 AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA
          1 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA

                                     *               *     
        189 ATTTAG-----TT-TAGGTAATTAAGCTAAGTAGTAAAAGAAGAAGA
          1 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA

             *    *                       *          * *   
        230 AATTAGCTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGTAGA
          1 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA

            ***  *      *       *                 
        277 CCCTATTTTAATCCTAGGTAGTTAAACTAAGTAGTAAA
          1 ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA

        315 GAGTAGTCAA


Statistics
Matches: 240,  Mismatches: 18, Indels: 19
        0.87            0.06        0.07

Matches are distributed among these distances:
  41   36  0.15
  42    2  0.01
  46    4  0.02
  47  195  0.81
  48    3  0.01

ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31


Consensus pattern (47 bp):   
ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGA

Found at i:3142 original size:26 final size:25

Alignment explanation


    Indices: 3113--3172  Score: 72
    Period size: 23  Copynumber: 2.4  Consensus size: 25

       3103 TTTCTTCAAA

                                       
       3113 GACGCAGAAACAAATTTTTTTTT-TAT
          1 GACGCA-AAACAAATTTTTTTTTCT-T

                        *            
       3139 GACGC-AAA-AACTTTTTTTTTCTT
          1 GACGCAAAACAAATTTTTTTTTCTT

                       
       3162 GACGCAAAACA
          1 GACGCAAAACA

       3173 CAAAACAAAT


Statistics
Matches: 30,  Mismatches: 1, Indels: 7
        0.79            0.03        0.18

Matches are distributed among these distances:
  23   17  0.57
  24    7  0.23
  25    1  0.03
  26    5  0.17

ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37


Consensus pattern (25 bp):   
GACGCAAAACAAATTTTTTTTTCTT

Found at i:3535 original size:15 final size:15

Alignment explanation


    Indices: 3515--3556  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3505 GCAGAGGTTG

                           
       3515 AAAGAAAACAATTAA
          1 AAAGAAAACAATTAA

                   *       
       3530 AAAGAAAGCAATTAA
          1 AAAGAAAACAATTAA

              *         
       3545 ACTAGAAAACAA
          1 A-AAGAAAACAA

       3557 AGCAAAGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.69, C:0.10, G:0.10, T:0.12


Consensus pattern (15 bp):   
AAAGAAAACAATTAA
Done.