Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014230.1 Corchorus olitorius cultivar O-4 contig14263, 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: 42718
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:23248 original size:6 final size:6

Alignment explanation


    Indices: 23239--23264  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      23229 GCATATGTAT

                                          
      23239 ATTTTA ATTTTA ATTTTA ATTTTA AT
          1 ATTTTA ATTTTA ATTTTA ATTTTA AT

      23265 ATATAACCAT


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

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (6 bp):   
ATTTTA

Found at i:24499 original size:2 final size:2

Alignment explanation


    Indices: 24492--24516  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      24482 ATAATAACAC

                                                 
      24492 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      24517 ATTGATATAA


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

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:39035 original size:74 final size:72

Alignment explanation


    Indices: 38902--39046  Score: 202
    Period size: 74  Copynumber: 2.0  Consensus size: 72

      38892 ACACCACCTA

                *                           *                                
      38902 TAAAGTAAATTGTTTGGTTCAATGGCACGTATGCTCCATGAAACCATTAGGTTTAAGATTCAAAT
          1 TAAAATAAATTGTTTGGTTCAATGGCACGTATACTCCATGAAACCATTAGGTTTAAGATTCAAAT

                   
      38967 GCCACTC
         66 GCCACTC

                                     *                    *          *       
      38974 TAAAATAAATTGTTTGGTTCAATGGTATCGTGCATACTCC-TGAAATCATTAGGTTTCAGATTCA
          1 TAAAATAAATTGTTTGGTTCAATGGCA-CGT--ATACTCCATGAAACCATTAGGTTTAAGATTCA

             *       
      39038 AGTGCCACT
         63 AATGCCACT

      39047 GCATGTGGGT


Statistics
Matches: 64,  Mismatches: 6, Indels: 4
        0.86            0.08        0.05

Matches are distributed among these distances:
  72   25  0.39
  73    3  0.05
  74   30  0.47
  75    6  0.09

ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Consensus pattern (72 bp):   
TAAAATAAATTGTTTGGTTCAATGGCACGTATACTCCATGAAACCATTAGGTTTAAGATTCAAAT
GCCACTC

Found at i:42652 original size:48 final size:48

Alignment explanation


    Indices: 42573--42714  Score: 196
    Period size: 48  Copynumber: 3.0  Consensus size: 48

      42563 TGCACCACCA

                          *        **  *                     
      42573 CCACCACCACCAGGGCCATCA-GGGCCGCCTCCACCCACATTTTCTCCC
          1 CCACCACCACCAGGACCA-CATGCTCCACCTCCACCCACATTTTCTCCC

                     *                                      
      42621 CCACCACCATCAGGACCACATGCTCCACCTCCACCCACATTTTCTCCC
          1 CCACCACCACCAGGACCACATGCTCCACCTCCACCCACATTTTCTCCC

                               *             *  *         
      42669 CCACCACCACCAGGACCACCTGCTCCACCTCCATCCGCATTTTCTC
          1 CCACCACCACCAGGACCACATGCTCCACCTCCACCCACATTTTCTC

      42715 ACCC


Statistics
Matches: 84,  Mismatches: 9, Indels: 2
        0.88            0.09        0.02

Matches are distributed among these distances:
  47    2  0.02
  48   82  0.98

ACGTcount: A:0.20, C:0.52, G:0.10, T:0.18


Consensus pattern (48 bp):   
CCACCACCACCAGGACCACATGCTCCACCTCCACCCACATTTTCTCCC
Done.