Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016664.1 Corchorus olitorius cultivar O-4 contig16697, 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: 6761
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28


Found at i:2708 original size:32 final size:33

Alignment explanation


    Indices: 2667--2732  Score: 125
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2657 GAGAGAAGAT

                                             
       2667 TGGGAGGCTC-AAAAAAATGTCCTGGGGTAGTA
          1 TGGGAGGCTCAAAAAAAATGTCCTGGGGTAGTA

                                             
       2699 TGGGAGGCTCAAAAAAAATGTCCTGGGGTAGTA
          1 TGGGAGGCTCAAAAAAAATGTCCTGGGGTAGTA

             
       2732 T
          1 T

       2733 TGATTTTATA


Statistics
Matches: 33,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  32   10  0.30
  33   23  0.70

ACGTcount: A:0.32, C:0.12, G:0.33, T:0.23


Consensus pattern (33 bp):   
TGGGAGGCTCAAAAAAAATGTCCTGGGGTAGTA

Found at i:2985 original size:10 final size:10

Alignment explanation


    Indices: 2972--3014  Score: 50
    Period size: 10  Copynumber: 4.3  Consensus size: 10

       2962 ATAAGTATAT

                      
       2972 TCCATAAAAA
          1 TCCATAAAAA

                *     
       2982 TCCAAAAAAA
          1 TCCATAAAAA

            **      * 
       2992 GACATAAACA
          1 TCCATAAAAA

                      
       3002 TCCATAAAAA
          1 TCCATAAAAA

               
       3012 TCC
          1 TCC

       3015 CAAAATATAA


Statistics
Matches: 25,  Mismatches: 8, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  10   25  1.00

ACGTcount: A:0.58, C:0.23, G:0.02, T:0.16


Consensus pattern (10 bp):   
TCCATAAAAA

Found at i:5340 original size:26 final size:26

Alignment explanation


    Indices: 5292--5341  Score: 64
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       5282 AGCCTGAATA

                       *     **       
       5292 AAAAATAATAATTAATTTTAGTAAAT
          1 AAAAATAATAAGTAATTACAGTAAAT

                  *                 
       5318 AAAAATTATAAGTAATTACAGTAA
          1 AAAAATAATAAGTAATTACAGTAA

       5342 TATATAATTA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  26   20  1.00

ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34


Consensus pattern (26 bp):   
AAAAATAATAAGTAATTACAGTAAAT

Found at i:5634 original size:33 final size:33

Alignment explanation


    Indices: 5550--5635  Score: 88
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       5540 ATACTGGCGG

                                  *          
       5550 CGGCGCCCCCAGGAGGCGCCATCGACATGCCAC
          1 CGGCGCCCCCAGGAGGCGCCATAGACATGCCAC

                      *                    * *  
       5583 CGGCGCCTCGTC-GG-GGCGCCATAGACATATCGA-
          1 CGGCGCC-C-CCAGGAGGCGCCATAGACAT-GCCAC

                                
       5616 CGGCGCCCCCAGGAGGCGCC
          1 CGGCGCCCCCAGGAGGCGCC

       5636 GTCGATTTGC


Statistics
Matches: 43,  Mismatches: 5, Indels: 10
        0.74            0.09        0.17

Matches are distributed among these distances:
  31    1  0.02
  32    3  0.07
  33   33  0.77
  34    5  0.12
  35    1  0.02

ACGTcount: A:0.16, C:0.42, G:0.34, T:0.08


Consensus pattern (33 bp):   
CGGCGCCCCCAGGAGGCGCCATAGACATGCCAC
Done.