Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006364.1 Corchorus olitorius cultivar O-4 contig06389, 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, 633

Length: 1056
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40


Found at i:86 original size:22 final size:23

Alignment explanation


    Indices: 54--103  Score: 59
    Period size: 22  Copynumber: 2.2  Consensus size: 23

         44 CTCTCTATGT

                                    
         54 ATTTTCGATAAAATCTCC-ATAAA
          1 ATTTTCGATAAAATC-CCTATAAA

                       **          
         77 ATTTTC-ATAACCTCCCTATAAA
          1 ATTTTCGATAAAATCCCTATAAA

                 
         99 ATTTT
          1 ATTTT

        104 GTTAACCTCT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  21    2  0.08
  22   16  0.67
  23    6  0.25

ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40


Consensus pattern (23 bp):   
ATTTTCGATAAAATCCCTATAAA

Found at i:109 original size:22 final size:22

Alignment explanation


    Indices: 72--130  Score: 73
    Period size: 22  Copynumber: 2.7  Consensus size: 22

         62 TAAAATCTCC

                      *           
         72 ATAAAATTTTCATAACCTCCCT
          1 ATAAAATTTTGATAACCTCCCT

                       *       *  
         94 ATAAAATTTTGTTAACCTCTCT
          1 ATAAAATTTTGATAACCTCCCT

             **            
        116 AGGAAATTTTGATAA
          1 ATAAAATTTTGATAA

        131 ACACAAATTT


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  22   31  1.00

ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39


Consensus pattern (22 bp):   
ATAAAATTTTGATAACCTCCCT

Found at i:182 original size:22 final size:22

Alignment explanation


    Indices: 157--260  Score: 97
    Period size: 22  Copynumber: 4.7  Consensus size: 22

        147 CCTCCCTCCC

                        *        *
        157 TATGAAATTTTGGTAACCTCTG
          1 TATGAAATTTTGATAACCTCTA

                                   
        179 TATGAAATTTTGATAA-CTAC-A
          1 TATGAAATTTTGATAACCT-CTA

                   *         *     
        200 CTATGAAGTTTTGATAATCTCTA
          1 -TATGAAATTTTGATAACCTCTA

                        *     *   
        223 TATGAAATTTTGGTAACCAC-A
          1 TATGAAATTTTGATAACCTCTA

               *             
        244 CTACGAAATTTTGATAA
          1 -TATGAAATTTTGATAA

        261 TCTTTCTATA


Statistics
Matches: 68,  Mismatches: 9, Indels: 10
        0.78            0.10        0.11

Matches are distributed among these distances:
  21    3  0.04
  22   62  0.91
  23    3  0.04

ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTCTA

Found at i:261 original size:44 final size:44

Alignment explanation


    Indices: 160--280  Score: 147
    Period size: 44  Copynumber: 2.8  Consensus size: 44

        150 CCCTCCCTAT

                     *   *    *            *    *      *
        160 GAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACACTAT
          1 GAAATTTTGATAATCTCTATATGAAATTTTGGTAACCACACTAC

               *                                        
        204 GAAGTTTTGATAATCTCTATATGAAATTTTGGTAACCACACTAC
          1 GAAATTTTGATAATCTCTATATGAAATTTTGGTAACCACACTAC

                                               
        248 GAAATTTTGATAATCTTTCTATAT--AATTTTGGT
          1 GAAATTTTGATAATC--TCTATATGAAATTTTGGT

        281 TTGATTGTCA


Statistics
Matches: 67,  Mismatches: 8, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  44   60  0.90
  46    7  0.10

ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41


Consensus pattern (44 bp):   
GAAATTTTGATAATCTCTATATGAAATTTTGGTAACCACACTAC
Done.