Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016817.1 Corchorus olitorius cultivar O-4 contig16850, 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: 10859
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:5603 original size:7 final size:7

Alignment explanation


    Indices: 5591--5620  Score: 51
    Period size: 7  Copynumber: 4.3  Consensus size: 7

       5581 TTAGAATCTA

                   
       5591 ATTATTT
          1 ATTATTT

                   
       5598 ATTATTT
          1 ATTATTT

                *  
       5605 ATTACTT
          1 ATTATTT

                   
       5612 ATTATTT
          1 ATTATTT

              
       5619 AT
          1 AT

       5621 AATTGATTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67


Consensus pattern (7 bp):   
ATTATTT

Found at i:9850 original size:24 final size:23

Alignment explanation


    Indices: 9809--9874  Score: 78
    Period size: 24  Copynumber: 2.7  Consensus size: 23

       9799 CTTTGGTCGG

                       * *          
       9809 TGTTAGTTAGTTCGTTTTGACTTT
          1 TGTTAGTTAGTCCATTTTG-CTTT

                                    
       9833 TGTTAGTTAGTCCATTTTTGCTTT
          1 TGTTAGTTAGTCCA-TTTTGCTTT

                *             
       9857 TGTCAAGTTAGTCCATTT
          1 TGT-TAGTTAGTCCATTT

       9875 AGCAAATTAG


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  24   22  0.59
  25   15  0.41

ACGTcount: A:0.15, C:0.12, G:0.18, T:0.55


Consensus pattern (23 bp):   
TGTTAGTTAGTCCATTTTGCTTT

Found at i:9865 original size:25 final size:25

Alignment explanation


    Indices: 9823--9874  Score: 79
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       9813 AGTTAGTTCG

                         *           
       9823 TTTTGACTTTTGTTAGTTAGTCCAT
          1 TTTTGACTTTTGTAAGTTAGTCCAT

                                      
       9848 TTTTG-CTTTTGTCAAGTTAGTCCAT
          1 TTTTGACTTTTGT-AAGTTAGTCCAT

              
       9873 TT
          1 TT

       9875 AGCAAATTAG


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  24    7  0.28
  25   18  0.72

ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56


Consensus pattern (25 bp):   
TTTTGACTTTTGTAAGTTAGTCCAT
Done.