Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017239.1 Corchorus olitorius cultivar O-4 contig17272, 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: 12470
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:809 original size:2 final size:2

Alignment explanation


    Indices: 802--833  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        792 CTTCTACCGC

                                                           
        802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        834 TCATAAATGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:9257 original size:28 final size:29

Alignment explanation


    Indices: 9220--9327  Score: 114
    Period size: 29  Copynumber: 3.8  Consensus size: 29

       9210 AACGTGAACT

                            *            
       9220 CAAAAATGACCAAAATACCCCTGAATGTG
          1 CAAAAATGACCAAAATGCCCCTGAATGTG

                 *      *        *  *    
       9249 C-AAAGTGACCATAATGCCCCCGAGTGTG
          1 CAAAAATGACCAAAATGCCCCTGAATGTG

                                      * *  
       9277 CAAAAATGACCAAAATGCCCCTAGATTTTTG
          1 CAAAAATGACCAAAATGCCCCT-GA-ATGTG

                                  
       9308 --AAAATGACCAAAATGCCCCT
          1 CAAAAATGACCAAAATGCCCCT

       9328 AGGTGATCTT


Statistics
Matches: 66,  Mismatches: 10, Indels: 6
        0.80            0.12        0.07

Matches are distributed among these distances:
  28   23  0.35
  29   38  0.58
  30    2  0.03
  31    3  0.05

ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19


Consensus pattern (29 bp):   
CAAAAATGACCAAAATGCCCCTGAATGTG

Found at i:10987 original size:13 final size:13

Alignment explanation


    Indices: 10969--10998  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      10959 AACCGTTAAT

                         
      10969 ATCAAAATCATAA
          1 ATCAAAATCATAA

                  *      
      10982 ATCAAAGTCATAA
          1 ATCAAAATCATAA

                
      10995 ATCA
          1 ATCA

      10999 GAGTAAAACC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23


Consensus pattern (13 bp):   
ATCAAAATCATAA
Done.