Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019438.1 Corchorus olitorius cultivar O-4 contig19471, 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: 27903
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35


Found at i:6543 original size:20 final size:20

Alignment explanation


    Indices: 6518--6557  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       6508 AAAAGTACTC

                                
       6518 TGTACCAAATAAATGAAGTG
          1 TGTACCAAATAAATGAAGTG

                                
       6538 TGTACCAAATAAATGAAGTG
          1 TGTACCAAATAAATGAAGTG

       6558 AGCTGAATTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25


Consensus pattern (20 bp):   
TGTACCAAATAAATGAAGTG

Found at i:10441 original size:56 final size:57

Alignment explanation


    Indices: 10355--10465  Score: 197
    Period size: 56  Copynumber: 2.0  Consensus size: 57

      10345 TTTTTCCTTT

                                                  *         *        
      10355 CACACAATAAATGTTATAATAAATCATAT-CCCCCTATTTCTACTTAATTATTCTTC
          1 CACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAACTATTCTTC

                                                                   
      10411 CACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAACTATTCT
          1 CACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAACTATTCT

      10466 ACAAAATAAA


Statistics
Matches: 52,  Mismatches: 2, Indels: 1
        0.95            0.04        0.02

Matches are distributed among these distances:
  56   29  0.56
  57   23  0.44

ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37


Consensus pattern (57 bp):   
CACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAACTATTCTTC

Found at i:11040 original size:7 final size:7

Alignment explanation


    Indices: 11028--11053  Score: 52
    Period size: 7  Copynumber: 3.7  Consensus size: 7

      11018 CGTGATATAA

                   
      11028 AATAAAT
          1 AATAAAT

                   
      11035 AATAAAT
          1 AATAAAT

                   
      11042 AATAAAT
          1 AATAAAT

                 
      11049 AATAA
          1 AATAA

      11054 GGATTAGGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   19  1.00

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (7 bp):   
AATAAAT

Found at i:17772 original size:24 final size:24

Alignment explanation


    Indices: 17743--17791  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      17733 TTTTTCTTTT

                                    
      17743 ACTTAATTTTATCCAATTTTCTAC
          1 ACTTAATTTTATCCAATTTTCTAC

                         *          
      17767 ACTTAATTTTATCTAATTTTCTAC
          1 ACTTAATTTTATCCAATTTTCTAC

             
      17791 A
          1 A

      17792 GGAAGATGTA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51


Consensus pattern (24 bp):   
ACTTAATTTTATCCAATTTTCTAC

Found at i:24842 original size:26 final size:26

Alignment explanation


    Indices: 24812--24863  Score: 86
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      24802 TGAACGTGTT

                  *              *    
      24812 AGCACATTATTTTGGCCTTATTTACA
          1 AGCACACTATTTTGGCCTTATGTACA

                                      
      24838 AGCACACTATTTTGGCCTTATGTACA
          1 AGCACACTATTTTGGCCTTATGTACA

      24864 TTTATATAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38


Consensus pattern (26 bp):   
AGCACACTATTTTGGCCTTATGTACA

Found at i:27865 original size:2 final size:2

Alignment explanation


    Indices: 27858--27900  Score: 77
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      27848 TGAGCATTGA

                                                          *               
      27858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
      27900 A
          1 A

      27901 CTA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.