Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001164.1 Corchorus olitorius cultivar O-4 contig01164, 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: 4971
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37


Found at i:2176 original size:78 final size:81

Alignment explanation


    Indices: 2039--2200  Score: 249
    Period size: 78  Copynumber: 2.0  Consensus size: 81

       2029 ACTACTATCA

                                                            *                
       2039 ATCATTATTGATTTCTTCATAGGATTATGGTTTGACTATCCTTTATTGTATCACATGGATGAGAA
          1 ATCATTATTGATTTCTTCATA-GATTATGGTTTGACTATCCTTTATTGCATCACATGGATGAGAA

                             
       2104 GAATATGTATTTATTGC
         65 GAATATGTATTTATTGC

                                 *            *                 *          * 
       2121 ATCATTATTGATTTCTTC-T-TATTATGG-TTGATTATCCTTTATTGCATCATATGGATGAGATG
          1 ATCATTATTGATTTCTTCATAGATTATGGTTTGACTATCCTTTATTGCATCACATGGATGAGAAG

                            
       2183 AATATGTATTTATTGC
         66 AATATGTATTTATTGC

              
       2199 AT
          1 AT

       2201 GTAACCCTTT


Statistics
Matches: 75,  Mismatches: 5, Indels: 4
        0.89            0.06        0.05

Matches are distributed among these distances:
  78   49  0.65
  79    7  0.09
  81    1  0.01
  82   18  0.24

ACGTcount: A:0.27, C:0.10, G:0.16, T:0.46


Consensus pattern (81 bp):   
ATCATTATTGATTTCTTCATAGATTATGGTTTGACTATCCTTTATTGCATCACATGGATGAGAAG
AATATGTATTTATTGC

Found at i:3880 original size:10 final size:10

Alignment explanation


    Indices: 3865--3895  Score: 53
    Period size: 10  Copynumber: 3.1  Consensus size: 10

       3855 CATTTATCAC

                      
       3865 ATATACTCTG
          1 ATATACTCTG

                      
       3875 ATATACTCTG
          1 ATATACTCTG

             *        
       3885 AGATACTCTG
          1 ATATACTCTG

             
       3895 A
          1 A

       3896 AACTCTAGAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35


Consensus pattern (10 bp):   
ATATACTCTG

Found at i:4845 original size:23 final size:23

Alignment explanation


    Indices: 4818--4861  Score: 79
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       4808 GATCAAAACT

                      *            
       4818 ATCATTTTCCTAAGAACTCAAAG
          1 ATCATTTTCCAAAGAACTCAAAG

                                 
       4841 ATCATTTTCCAAAGAACTCAA
          1 ATCATTTTCCAAAGAACTCAA

       4862 GAACACAAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30


Consensus pattern (23 bp):   
ATCATTTTCCAAAGAACTCAAAG
Done.