Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023257.1 Corchorus olitorius cultivar O-4 contig23290, 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: 44890
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:3765 original size:3 final size:3

Alignment explanation


    Indices: 3759--3786  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       3749 AAAATAATAA

                                                 
       3759 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A

       3787 CAATGTTGGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:19265 original size:18 final size:18

Alignment explanation


    Indices: 19233--19271  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      19223 CAAACCCTTC

                           *  
      19233 ATTCAAATCAACATTTCT
          1 ATTCAAATCAACATTCCT

                     **       
      19251 ATTCAAATCCCCATTCCT
          1 ATTCAAATCAACATTCCT

               
      19269 ATT
          1 ATT

      19272 ACTCTCTAGG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.33, C:0.28, G:0.00, T:0.38


Consensus pattern (18 bp):   
ATTCAAATCAACATTCCT

Found at i:30771 original size:120 final size:120

Alignment explanation


    Indices: 30556--30793  Score: 440
    Period size: 120  Copynumber: 2.0  Consensus size: 120

      30546 TGCTAAATTT

                                                                             
      30556 AGGCAAACACACAAAGAAGTTACTATTTCTACAATTGGATTACACTGATCTCAGTAAAAGCTTAA
          1 AGGCAAACACACAAAGAAGTTACTATTTCTACAATTGGATTACACTGATCTCAGTAAAAGCTTAA

                                               *                   
      30621 GACTTCACGTCCACGCCTATCCAGGGAAAATGCCCGCAATGCATAGTCCAAATCA
         66 GACTTCACGTCCACGCCTATCCAGGGAAAATGCCCACAATGCATAGTCCAAATCA

                         *                                                   
      30676 AGGCAAACACACACAGAAGTTACTATTTCTACAATTGGATTACACTGATCTCAGTAAAAGCTTAA
          1 AGGCAAACACACAAAGAAGTTACTATTTCTACAATTGGATTACACTGATCTCAGTAAAAGCTTAA

                                     *      *                    
      30741 GACTTCACGTCCACGCCTATCCAGGTAAAATGTCCACAATGCATAGTCCAAAT
         66 GACTTCACGTCCACGCCTATCCAGGGAAAATGCCCACAATGCATAGTCCAAAT

      30794 TTGTCAAAAC


Statistics
Matches: 114,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 120  114  1.00

ACGTcount: A:0.37, C:0.25, G:0.15, T:0.24


Consensus pattern (120 bp):   
AGGCAAACACACAAAGAAGTTACTATTTCTACAATTGGATTACACTGATCTCAGTAAAAGCTTAA
GACTTCACGTCCACGCCTATCCAGGGAAAATGCCCACAATGCATAGTCCAAATCA

Found at i:42334 original size:23 final size:23

Alignment explanation


    Indices: 42304--42349  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      42294 TAAGTTACAA

                                   
      42304 TTTACAAAGGAGTTAAAATATGG
          1 TTTACAAAGGAGTTAAAATATGG

                                   
      42327 TTTACAAAGGAGTTAAAATATGG
          1 TTTACAAAGGAGTTAAAATATGG

      42350 AGTAGCGCGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30


Consensus pattern (23 bp):   
TTTACAAAGGAGTTAAAATATGG
Done.