Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016567.1 Corchorus olitorius cultivar O-4 contig16600, 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: 14641
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:1234 original size:14 final size:14

Alignment explanation


    Indices: 1215--1241  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       1205 AAGAAGGAGC

                          
       1215 CCAAGAAAATAAGG
          1 CCAAGAAAATAAGG

                         
       1229 CCAAGAAAATAAG
          1 CCAAGAAAATAAG

       1242 TCTTGAAGAC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.59, C:0.15, G:0.19, T:0.07


Consensus pattern (14 bp):   
CCAAGAAAATAAGG

Found at i:5333 original size:25 final size:24

Alignment explanation


    Indices: 5305--5366  Score: 81
    Period size: 25  Copynumber: 2.6  Consensus size: 24

       5295 GTGGATTGTA

                        *            
       5305 AAATAAATTGAATAATTAAGACATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
       5330 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     *    
       5354 AAA-AAATTCAAGA
          1 AAATAAATTGAAGA

       5367 CTGACCCAAT


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  23    9  0.26
  24    8  0.24
  25   17  0.50

ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT

Found at i:12598 original size:17 final size:17

Alignment explanation


    Indices: 12576--12611  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      12566 AGAAAACCCA

                             
      12576 AAACCAACTAAAGATCC
          1 AAACCAACTAAAGATCC

                         *   
      12593 AAACCAACTAAAGGTCC
          1 AAACCAACTAAAGATCC

              
      12610 AA
          1 AA

      12612 GGCTTCACCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.53, C:0.28, G:0.08, T:0.11


Consensus pattern (17 bp):   
AAACCAACTAAAGATCC

Found at i:12910 original size:13 final size:14

Alignment explanation


    Indices: 12889--12918  Score: 53
    Period size: 13  Copynumber: 2.2  Consensus size: 14

      12879 TAAGAAAATG

                          
      12889 CATTAAAAAACGAT
          1 CATTAAAAAACGAT

                          
      12903 CATT-AAAAACGAT
          1 CATTAAAAAACGAT

               
      12916 CAT
          1 CAT

      12919 GTATGTAGTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   12  0.75
  14    4  0.25

ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23


Consensus pattern (14 bp):   
CATTAAAAAACGAT
Done.