Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022712.1 Corchorus olitorius cultivar O-4 contig22745, 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: 35183
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:250 original size:4 final size:4

Alignment explanation


    Indices: 241--267  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

        231 CTCTTTAAAA

                                             
        241 AATT AATT AATT AATT AATT AATT AAT
          1 AATT AATT AATT AATT AATT AATT AAT

        268 AAAAAGAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (4 bp):   
AATT

Found at i:9757 original size:25 final size:26

Alignment explanation


    Indices: 9729--9780  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       9719 CATTTTTAGG

                        *    *        
       9729 TCCACTTTTA-GTTTAGGTTAGCTAA
          1 TCCACTTTTAGGCTTAGATTAGCTAA

                *                     
       9754 TCCATTTTTAGGCTTAGATTAGCTAA
          1 TCCACTTTTAGGCTTAGATTAGCTAA

             
       9780 T
          1 T

       9781 TCATCTTTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25    9  0.39
  26   14  0.61

ACGTcount: A:0.25, C:0.15, G:0.15, T:0.44


Consensus pattern (26 bp):   
TCCACTTTTAGGCTTAGATTAGCTAA

Found at i:9917 original size:25 final size:25

Alignment explanation


    Indices: 9888--9941  Score: 99
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       9878 AGTATTTTGC

                   *                 
       9888 ATTTCATTCATGTAGCTCAAATCTA
          1 ATTTCATACATGTAGCTCAAATCTA

                                     
       9913 ATTTCATACATGTAGCTCAAATCTA
          1 ATTTCATACATGTAGCTCAAATCTA

                
       9938 ATTT
          1 ATTT

       9942 AGTTCATAGC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  25   28  1.00

ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41


Consensus pattern (25 bp):   
ATTTCATACATGTAGCTCAAATCTA

Found at i:11683 original size:24 final size:24

Alignment explanation


    Indices: 11655--11701  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11645 CTTTGTCTAC

                                     
      11655 AAGCACAAAG-AGGAGTTTAAATGG
          1 AAGCACAAAGAAGGA-TTTAAATGG

                    *              
      11679 AAGCACAATGAAGGATTTAAATG
          1 AAGCACAAAGAAGGATTTAAATG

      11702 CAAATAAAGG


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   17  0.81
  25    4  0.19

ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19


Consensus pattern (24 bp):   
AAGCACAAAGAAGGATTTAAATGG

Found at i:35002 original size:5 final size:5

Alignment explanation


    Indices: 34992--35018  Score: 54
    Period size: 5  Copynumber: 5.4  Consensus size: 5

      34982 TAATTAATCC

                                            
      34992 AATTA AATTA AATTA AATTA AATTA AA
          1 AATTA AATTA AATTA AATTA AATTA AA

      35019 GGGCATAATT


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

Matches are distributed among these distances:
   5   22  1.00

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (5 bp):   
AATTA

Found at i:35042 original size:13 final size:13

Alignment explanation


    Indices: 35026--35067  Score: 57
    Period size: 13  Copynumber: 3.2  Consensus size: 13

      35016 AAAGGGCATA

                         
      35026 ATTTTTTTATTAT
          1 ATTTTTTTATTAT

                       *  
      35039 ATTTTTTTATCAAT
          1 ATTTTTTTAT-TAT

             *           
      35053 AATTTTTTATTAT
          1 ATTTTTTTATTAT

              
      35066 AT
          1 AT

      35068 AATCTATATA


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  13   13  0.54
  14   11  0.46

ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69


Consensus pattern (13 bp):   
ATTTTTTTATTAT
Done.