Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012801.1 Corchorus olitorius cultivar O-4 contig12834, 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: 19625
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:11341 original size:41 final size:41

Alignment explanation


    Indices: 11285--11389  Score: 174
    Period size: 41  Copynumber: 2.6  Consensus size: 41

      11275 CATAAATCCA

                    *                                
      11285 AAATAAAATCCTAAATCAGGGACAAAATTGAATCAATTAAC
          1 AAATAAAACCCTAAATCAGGGACAAAATTGAATCAATTAAC

                 **                                  
      11326 AAATATTACCCTAAATCAGGGACAAAATTGAATCAATTAAC
          1 AAATAAAACCCTAAATCAGGGACAAAATTGAATCAATTAAC

                     *             
      11367 AAATAAAACACTAAATCAGGGAC
          1 AAATAAAACCCTAAATCAGGGAC

      11390 TAAGTTGTAA


Statistics
Matches: 58,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  41   58  1.00

ACGTcount: A:0.52, C:0.16, G:0.10, T:0.21


Consensus pattern (41 bp):   
AAATAAAACCCTAAATCAGGGACAAAATTGAATCAATTAAC

Found at i:14426 original size:19 final size:20

Alignment explanation


    Indices: 14387--14427  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 20

      14377 GAAATTTATG

                            *   
      14387 AAATTAAAAATAAAATTACA
          1 AAATTAAAAATAAAATCACA

                    *           
      14407 AAATTAAATA-AAAATCACA
          1 AAATTAAAAATAAAATCACA

              
      14426 AA
          1 AA

      14428 CACACTTTAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  19   10  0.53
  20    9  0.47

ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22


Consensus pattern (20 bp):   
AAATTAAAAATAAAATCACA
Done.