Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013113.1 Corchorus olitorius cultivar O-4 contig13146, 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: 10268
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:1817 original size:18 final size:18

Alignment explanation


    Indices: 1783--1817  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1773 AGACAACTGA

                        *     
       1783 GATGTTTTAAGTTGTTTG
          1 GATGTTTTAAGTAGTTTG

                     *       
       1801 GATGTTTTATGTAGTTT
          1 GATGTTTTAAGTAGTTT

       1818 AAATCTTCTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57


Consensus pattern (18 bp):   
GATGTTTTAAGTAGTTTG

Found at i:3107 original size:35 final size:37

Alignment explanation


    Indices: 3046--3115  Score: 92
    Period size: 35  Copynumber: 1.9  Consensus size: 37

       3036 AAATTATCTA

                                                 
       3046 AGAAAGCAATGAAGAAAATTAAAGAAAACAATTAATT
          1 AGAAAGCAATGAAGAAAATTAAAGAAAACAATTAATT

                                  *      *      
       3083 AGAAAGC-A-GAAGATAAATT-GAGAAAATAATTAA
          1 AGAAAGCAATGAAGA-AAATTAAAGAAAACAATTAA

       3116 GAAAACCCTC


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  35   17  0.57
  36    6  0.20
  37    7  0.23

ACGTcount: A:0.61, C:0.04, G:0.16, T:0.19


Consensus pattern (37 bp):   
AGAAAGCAATGAAGAAAATTAAAGAAAACAATTAATT

Found at i:4403 original size:22 final size:21

Alignment explanation


    Indices: 4351--4404  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

       4341 GCTCCTTGGA

                                  
       4351 AATAATTCTTC-AATGATCTTC
          1 AATAA-TCTTCAAATGATCTTC

                          *      
       4372 -A-AATCTTCAAATTATCTTC
          1 AATAATCTTCAAATGATCTTC

                          
       4391 AATAAGTCTTCAAA
          1 AATAA-TCTTCAAA

       4405 CACGAACTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    5  0.18
  19   11  0.39
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39


Consensus pattern (21 bp):   
AATAATCTTCAAATGATCTTC
Done.