Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017584.1 Corchorus olitorius cultivar O-4 contig17617, 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: 43239
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:4726 original size:83 final size:83

Alignment explanation


    Indices: 4582--4749  Score: 282
    Period size: 83  Copynumber: 2.0  Consensus size: 83

       4572 TTGAAGTCGA

                        *                        *                           
       4582 AACACAAACATTTAAATGGAAATTATATCAGCGTGTCGAGCTCACAAATGAATCAGCCCTTATTA
          1 AACACAAACATTCAAATGGAAATTATATCAGCGTGTCAAGCTCACAAATGAATCAGCCCTTATTA

                              
       4647 ATTTTCTAACGATAGCTT
         66 ATTTTCTAACGATAGCTT

                               *                               *    *        
       4665 AACACAAACATTCAAATGGGAATTATATCAGCGTGTCAAGCTCACAAATGAGTCAGTCCTTATTA
          1 AACACAAACATTCAAATGGAAATTATATCAGCGTGTCAAGCTCACAAATGAATCAGCCCTTATTA

                 *            
       4730 ATTTTTTAACGATAGCTT
         66 ATTTTCTAACGATAGCTT

              
       4748 AA
          1 AA

       4750 TTTTGTTTAT


Statistics
Matches: 79,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  83   79  1.00

ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30


Consensus pattern (83 bp):   
AACACAAACATTCAAATGGAAATTATATCAGCGTGTCAAGCTCACAAATGAATCAGCCCTTATTA
ATTTTCTAACGATAGCTT

Found at i:7764 original size:2 final size:2

Alignment explanation


    Indices: 7757--7812  Score: 69
    Period size: 2  Copynumber: 28.0  Consensus size: 2

       7747 TATTGGTATG

                                                       *    *     *        
       7757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA AA TA AA GTA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA

                                
       7800 TA TA -A TA TA TA TA
          1 TA TA TA TA TA TA TA

       7813 CTCAAAAGAT


Statistics
Matches: 46,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
   1    1  0.02
   2   44  0.96
   3    1  0.02

ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:24859 original size:13 final size:13

Alignment explanation


    Indices: 24835--24878  Score: 52
    Period size: 13  Copynumber: 3.3  Consensus size: 13

      24825 AATTCCAACT

                   *     
      24835 ATAATAACATATA
          1 ATAATAATATATA

              *          
      24848 ATCATAATATATA
          1 ATAATAATATATA

                    *     
      24861 ATAATAATGTAATA
          1 ATAATAATAT-ATA

                
      24875 ATAA
          1 ATAA

      24879 GAGTAACATA


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  13   19  0.73
  14    7  0.27

ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34


Consensus pattern (13 bp):   
ATAATAATATATA

Found at i:40174 original size:12 final size:12

Alignment explanation


    Indices: 40154--40197  Score: 70
    Period size: 12  Copynumber: 3.6  Consensus size: 12

      40144 TTAATGACAC

                *       
      40154 GTCAGGTGGAGG
          1 GTCAAGTGGAGG

                        
      40166 GTCAAGTGGAGG
          1 GTCAAGTGGAGG

                         
      40178 GTCAAAGTGGAGG
          1 GTC-AAGTGGAGG

                   
      40191 GTCAAGT
          1 GTCAAGT

      40198 AGCAAAACTC


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  12   18  0.60
  13   12  0.40

ACGTcount: A:0.25, C:0.09, G:0.48, T:0.18


Consensus pattern (12 bp):   
GTCAAGTGGAGG

Found at i:40187 original size:13 final size:13

Alignment explanation


    Indices: 40159--40195  Score: 67
    Period size: 13  Copynumber: 2.9  Consensus size: 13

      40149 GACACGTCAG

                         
      40159 GTGGAGGGTC-AA
          1 GTGGAGGGTCAAA

                         
      40171 GTGGAGGGTCAAA
          1 GTGGAGGGTCAAA

                        
      40184 GTGGAGGGTCAA
          1 GTGGAGGGTCAA

      40196 GTAGCAAAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  12   10  0.42
  13   14  0.58

ACGTcount: A:0.27, C:0.08, G:0.49, T:0.16


Consensus pattern (13 bp):   
GTGGAGGGTCAAA

Found at i:43199 original size:2 final size:2

Alignment explanation


    Indices: 43192--43233  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      43182 CTACTTAATC

                                                                          
      43192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      43234 CTGTAT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.