Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019263.1 Corchorus olitorius cultivar O-4 contig19296, 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: 48292
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:1851 original size:4 final size:4

Alignment explanation


    Indices: 1844--1873  Score: 60
    Period size: 4  Copynumber: 7.5  Consensus size: 4

       1834 TTCCTTTCTT

                                                 
       1844 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
          1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT

       1874 GTAATCTTCC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   26  1.00

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTTC

Found at i:10672 original size:3 final size:3

Alignment explanation


    Indices: 10664--10721  Score: 71
    Period size: 3  Copynumber: 19.3  Consensus size: 3

      10654 GAAAATGGAG

                                                 **          *             
      10664 TAA TAA TAA TAA TAA TAA TAA TAA TAA TCC TAA TAA TCA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

            *   *        
      10712 CAA CAA TAA T
          1 TAA TAA TAA T

      10722 GGATAGCAGA


Statistics
Matches: 47,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   3   47  1.00

ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31


Consensus pattern (3 bp):   
TAA

Found at i:20757 original size:11 final size:11

Alignment explanation


    Indices: 20741--20778  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      20731 ACGAATTTAA

                       
      20741 AAAAGAAAAAG
          1 AAAAGAAAAAG

                        
      20752 AAAAGAGAAAA-
          1 AAAAGA-AAAAG

             *         
      20763 ATAAGAAAAAG
          1 AAAAGAAAAAG

                 
      20774 AAAAG
          1 AAAAG

      20779 CCTCTTCAAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  10    4  0.17
  11   15  0.65
  12    4  0.17

ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03


Consensus pattern (11 bp):   
AAAAGAAAAAG

Found at i:30391 original size:1 final size:1

Alignment explanation


    Indices: 30385--30418  Score: 68
    Period size: 1  Copynumber: 34.0  Consensus size: 1

      30375 GTGATTGAGA

                                              
      30385 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      30419 ATCTTCTACC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   33  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:32227 original size:19 final size:19

Alignment explanation


    Indices: 32203--32243  Score: 82
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      32193 AAGCAATTAC

                               
      32203 AATAGTTCAAGTCTAAGCT
          1 AATAGTTCAAGTCTAAGCT

                               
      32222 AATAGTTCAAGTCTAAGCT
          1 AATAGTTCAAGTCTAAGCT

               
      32241 AAT
          1 AAT

      32244 TGCCCAAAGC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32


Consensus pattern (19 bp):   
AATAGTTCAAGTCTAAGCT
Done.