Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024180.1 Corchorus olitorius cultivar O-4 contig24213, 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: 4728
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30


Found at i:308 original size:9 final size:9

Alignment explanation


    Indices: 294--319  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

        284 AAGTTCTCCT

                     
        294 ACAAAATTA
          1 ACAAAATTA

                     
        303 ACAAAATTA
          1 ACAAAATTA

                    
        312 ACAAAATT
          1 ACAAAATT

        320 GTTAGAATAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23


Consensus pattern (9 bp):   
ACAAAATTA

Found at i:391 original size:13 final size:13

Alignment explanation


    Indices: 373--397  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        363 TTTTTACCAC

                         
        373 CTTAAAATTATTG
          1 CTTAAAATTATTG

                        
        386 CTTAAAATTATT
          1 CTTAAAATTATT

        398 TTTTGGCAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48


Consensus pattern (13 bp):   
CTTAAAATTATTG

Found at i:3585 original size:51 final size:50

Alignment explanation


    Indices: 3484--3585  Score: 118
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       3474 GTTCTTCATA

                                                     * **     
       3484 TTTTTCTTGTTTAGATCTTGTCTCCAGACAAACAAACACTCTTTTAGTGT
          1 TTTTTCTTGTTTAGATCTTGTCTCCAGACAAACAAACACTCATACAGTGT

                                       *    *                    
       3534 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-ATACACGTGT
          1 TTTT-TCTTGTTT-AGATCTTGTCTCCAGACAAACAAACACTCATACA-GTGT

             
       3585 T
          1 T

       3586 CTTCATTCAG


Statistics
Matches: 44,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  50    6  0.14
  51   37  0.84
  52    1  0.02

ACGTcount: A:0.24, C:0.23, G:0.12, T:0.42


Consensus pattern (50 bp):   
TTTTTCTTGTTTAGATCTTGTCTCCAGACAAACAAACACTCATACAGTGT
Done.