Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021450.1 Corchorus olitorius cultivar O-4 contig21483, 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: 2053
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29


Found at i:1443 original size:20 final size:20

Alignment explanation


    Indices: 1418--1470  Score: 72
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       1408 CTACAAAATT

                                 
       1418 AACAAAAACACAAAAAC-AAA
          1 AACAAAAACA-AAAAACGAAA

                         *      
       1438 AACAAAAACAAAATACGAAA
          1 AACAAAAACAAAAAACGAAA

              *          
       1458 AATAAAAACAAAA
          1 AACAAAAACAAAA

       1471 CTAAAGGAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  19    5  0.17
  20   25  0.83

ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04


Consensus pattern (20 bp):   
AACAAAAACAAAAAACGAAA

Found at i:1444 original size:5 final size:6

Alignment explanation


    Indices: 1422--1470  Score: 62
    Period size: 6  Copynumber: 7.7  Consensus size: 6

       1412 AAAATTAACA

                                                       *            
       1422 AAAACAC AAAAAC AAAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
          1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA

       1471 CTAAAGGAAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 5
        0.84            0.04        0.11

Matches are distributed among these distances:
   6   27  0.71
   7    7  0.18
   8    4  0.11

ACGTcount: A:0.80, C:0.14, G:0.02, T:0.04


Consensus pattern (6 bp):   
AAAAAC

Found at i:1449 original size:26 final size:26

Alignment explanation


    Indices: 1418--1470  Score: 72
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1408 CTACAAAATT

                                       
       1418 AACAAAA-ACACAAAAACAAAAACAAA
          1 AACAAAATAC-CAAAAACAAAAACAAA

                      *     *         
       1444 AACAAAATACGAAAAATAAAAACAAA
          1 AACAAAATACCAAAAACAAAAACAAA

             
       1470 A
          1 A

       1471 CTAAAGGAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  26   22  0.92
  27    2  0.08

ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04


Consensus pattern (26 bp):   
AACAAAATACCAAAAACAAAAACAAA

Done.