Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018190.1 Corchorus olitorius cultivar O-4 contig18223, 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: 40629
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:13710 original size:20 final size:20

Alignment explanation


    Indices: 13681--13718  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      13671 CACCTAACCG

                 *              
      13681 CGGGATCAATGTAAAAAGCT
          1 CGGGACCAATGTAAAAAGCT

                              
      13701 CGGGACCAATGTAAAAAG
          1 CGGGACCAATGTAAAAAG

      13719 ACTGCATTGG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16


Consensus pattern (20 bp):   
CGGGACCAATGTAAAAAGCT

Found at i:20185 original size:13 final size:13

Alignment explanation


    Indices: 20167--20194  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      20157 CACGAGCGCA

                         
      20167 AAGAGAGAGAAAG
          1 AAGAGAGAGAAAG

                         
      20180 AAGAGAGAGAAAG
          1 AAGAGAGAGAAAG

              
      20193 AA
          1 AA

      20195 AGGAGGCGTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (13 bp):   
AAGAGAGAGAAAG

Found at i:27713 original size:2 final size:2

Alignment explanation


    Indices: 27706--27732  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      27696 CGGTAAATAC

                                                    
      27706 AT 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 AT A

      27733 ATTCATTCAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:29175 original size:12 final size:12

Alignment explanation


    Indices: 29158--29183  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      29148 AGATTCTTAG

                        
      29158 ATTAAAGTTTAA
          1 ATTAAAGTTTAA

                        
      29170 ATTAAAGTTTAA
          1 ATTAAAGTTTAA

              
      29182 AT
          1 AT

      29184 AATCAAACAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42


Consensus pattern (12 bp):   
ATTAAAGTTTAA

Found at i:39455 original size:24 final size:25

Alignment explanation


    Indices: 39422--39478  Score: 82
    Period size: 25  Copynumber: 2.4  Consensus size: 25

      39412 TCAGCCTTGT

                                 *   
      39422 AATTT-TTTAATGT-TTAATTCTTA
          1 AATTTATTTAATGTCTTAATTATTA

                                    *
      39445 AATTTATTTAATGTCTTAATTATTC
          1 AATTTATTTAATGTCTTAATTATTA

                     
      39470 AATTTATTT
          1 AATTTATTT

      39479 TACAATCAAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60


Consensus pattern (25 bp):   
AATTTATTTAATGTCTTAATTATTA

Done.