Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006193.1 Corchorus capsularis cultivar CVL-1 contig06211, 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: 18713
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:15 original size:1 final size:1

Alignment explanation


    Indices: 11--38  Score: 56
    Period size: 1  Copynumber: 28.0  Consensus size: 1

          1 ATTTTTTGCC

                                        
         11 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT

         39 CCCTAAAGAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   27  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:14323 original size:2 final size:2

Alignment explanation


    Indices: 14316--14357  Score: 52
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      14306 AATAATAGTA

                           *     *                                        
      14316 AT AT AT AT -T TT AT GT AT A- 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 AT AT AT AT AT

              
      14356 AT
          1 AT

      14358 TTAGAAAAAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
   1    2  0.06
   2   33  0.94

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52


Consensus pattern (2 bp):   
AT

Found at i:14991 original size:2 final size:2

Alignment explanation


    Indices: 14984--15009  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      14974 AAGTCATGAT

                                                  
      14984 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

      15010 GATTCTTAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:15185 original size:12 final size:12

Alignment explanation


    Indices: 15168--15192  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      15158 AGATTATCTC

                        
      15168 AGGTTATTGGTG
          1 AGGTTATTGGTG

                        
      15180 AGGTTATTGGTG
          1 AGGTTATTGGTG

             
      15192 A
          1 A

      15193 AAACCAATTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40


Consensus pattern (12 bp):   
AGGTTATTGGTG

Found at i:18661 original size:15 final size:14

Alignment explanation


    Indices: 18633--18660  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      18623 TTTTTAATGT

                          
      18633 TTTTTTTTCAAAAA
          1 TTTTTTTTCAAAAA

                          
      18647 TTTTTTTTCAAAAA
          1 TTTTTTTTCAAAAA

      18661 AATGATTTTG


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57


Consensus pattern (14 bp):   
TTTTTTTTCAAAAA
Done.