Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014509.1 Corchorus olitorius cultivar O-4 contig14542, 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: 21822
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:554 original size:15 final size:15

Alignment explanation


    Indices: 534--562  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        524 CGCTTCTGTC

                           
        534 ACCGTCGTTTGCCAA
          1 ACCGTCGTTTGCCAA

                          
        549 ACCGTCGTTTGCCA
          1 ACCGTCGTTTGCCA

        563 TGGAATTGAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.17, C:0.34, G:0.21, T:0.28


Consensus pattern (15 bp):   
ACCGTCGTTTGCCAA

Found at i:6294 original size:14 final size:15

Alignment explanation


    Indices: 6275--6311  Score: 51
    Period size: 14  Copynumber: 2.6  Consensus size: 15

       6265 TATATAGGAT

                           
       6275 TATATTATTATA-TA
          1 TATATTATTATACTA

                           
       6289 TATATTA-TATACTA
          1 TATATTATTATACTA

            *        
       6303 AATATTATT
          1 TATATTATT

       6312 TGAAACACCC


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  13    4  0.20
  14   15  0.75
  15    1  0.05

ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54


Consensus pattern (15 bp):   
TATATTATTATACTA

Found at i:9370 original size:11 final size:11

Alignment explanation


    Indices: 9354--9380  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       9344 GATAAGCATT

                       
       9354 TACAATTTAAA
          1 TACAATTTAAA

                       
       9365 TACAATTTAAA
          1 TACAATTTAAA

                 
       9376 TACAA
          1 TACAA

       9381 ACAAATAACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33


Consensus pattern (11 bp):   
TACAATTTAAA

Found at i:16509 original size:25 final size:24

Alignment explanation


    Indices: 16481--16533  Score: 61
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      16471 AAAATCTGCA

                                     
      16481 GAAACATTAAAAGATGTATTTCTAT
          1 GAAACA-TAAAAGATGTATTTCTAT

                *  *    *   *       
      16506 GAAATATGAAAGGTGTCTTTCTAT
          1 GAAACATAAAAGATGTATTTCTAT

                
      16530 GAAA
          1 GAAA

      16534 GATTGCATCT


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  24   19  0.79
  25    5  0.21

ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34


Consensus pattern (24 bp):   
GAAACATAAAAGATGTATTTCTAT
Done.