Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021935.1 Corchorus olitorius cultivar O-4 contig21968, 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: 4032
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29


Found at i:1842 original size:11 final size:11

Alignment explanation


    Indices: 1826--1851  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       1816 CTAGCCCTAA

                       
       1826 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       1837 AAAACTAGAAG
          1 AAAACTAGAAG

                
       1848 AAAA
          1 AAAA

       1852 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:2497 original size:29 final size:29

Alignment explanation


    Indices: 2441--2498  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2431 TTGGAAATAA

                               * *       
       2441 ATCTTCAATGGTCTTCAAGTCTCCAATTT
          1 ATCTTCAATGGTCTTCAAGACACCAATTT

                                    *     
       2470 ATCTTCAAATGGTCTTCAA-ACACGAATTT
          1 ATCTTC-AATGGTCTTCAAGACACCAATTT

       2499 CGAATCTCCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29   13  0.52
  30   12  0.48

ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38


Consensus pattern (29 bp):   
ATCTTCAATGGTCTTCAAGACACCAATTT

Found at i:2747 original size:27 final size:26

Alignment explanation


    Indices: 2716--2801  Score: 100
    Period size: 27  Copynumber: 3.2  Consensus size: 26

       2706 AGCTCAATCA

                                   *   
       2716 GTGGTCCAAGTGGGGCTGAAAATCTTG
          1 GTGGTCCAAG-GGGGCTGAAAATGTTG

                          *    *       
       2743 GTGGTCCAAGGGTGTCTGACAATGTTG
          1 GTGGTCCAAGGG-GGCTGAAAATGTTG

                *       *              
       2770 GTGGGCCAAGAGTGGCTGAAAATGTTG
          1 GTGGTCCAAG-GGGGCTGAAAATGTTG

                 
       2797 GTGGT
          1 GTGGT

       2802 GGGGCAAGTG


Statistics
Matches: 49,  Mismatches: 8, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  26    2  0.04
  27   46  0.94
  28    1  0.02

ACGTcount: A:0.21, C:0.13, G:0.40, T:0.27


Consensus pattern (26 bp):   
GTGGTCCAAGGGGGCTGAAAATGTTG

Done.