Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007547.1 Corchorus capsularis cultivar CVL-1 contig07568, 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: 10556
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:227 original size:10 final size:9

Alignment explanation


    Indices: 199--239  Score: 57
    Period size: 9  Copynumber: 4.6  Consensus size: 9

        189 TTCTTCTTTC

                 *   
        199 TTTTCTTTT
          1 TTTTCATTT

                      
        208 CTTTTC-TTT
          1 -TTTTCATTT

                     
        217 TTTTCATTT
          1 TTTTCATTT

                     
        226 TTTTCATTT
          1 TTTTCATTT

                 
        235 TTTTC
          1 TTTTC

        240 CAAGAACAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
   8    5  0.17
   9   20  0.67
  10    5  0.17

ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80


Consensus pattern (9 bp):   
TTTTCATTT

Found at i:229 original size:22 final size:22

Alignment explanation


    Indices: 185--235  Score: 59
    Period size: 23  Copynumber: 2.3  Consensus size: 22

        175 CAGGTTTCTC

                          *       
        185 TCTTTTCTTCTTTCTTTTCTTT
          1 TCTTTTCTTCTTTCATTTCTTT

                      *            
        207 TCTTTTCTTTTTTTCATTT-TTT
          1 TCTTTTC-TTCTTTCATTTCTTT

                   
        229 TCATTTT
          1 TC-TTTT

        236 TTTCCAAGAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  22   12  0.48
  23   13  0.52

ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78


Consensus pattern (22 bp):   
TCTTTTCTTCTTTCATTTCTTT

Found at i:235 original size:18 final size:18

Alignment explanation


    Indices: 192--239  Score: 62
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        182 CTCTCTTTTC

                        *      
        192 TTCTTTCTTTTCTTTTCTT
          1 TTCTTT-TTTTCATTTCTT

                              
        211 TTCTTTTTTTCATTT-TT
          1 TTCTTTTTTTCATTTCTT

                        
        228 TTCATTTTTTTC
          1 TTC-TTTTTTTC

        240 CAAGAACAAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  17    5  0.19
  18   16  0.59
  19    6  0.22

ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79


Consensus pattern (18 bp):   
TTCTTTTTTTCATTTCTT

Found at i:3894 original size:14 final size:14

Alignment explanation


    Indices: 3875--3904  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       3865 AAAAACAGAT

                          
       3875 AAAGAAACAGAGAG
          1 AAAGAAACAGAGAG

                   *      
       3889 AAAGAAAGAGAGAG
          1 AAAGAAACAGAGAG

              
       3903 AA
          1 AA

       3905 TTTGGAAGAG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

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


Consensus pattern (14 bp):   
AAAGAAACAGAGAG

Found at i:6920 original size:22 final size:22

Alignment explanation


    Indices: 6892--6935  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6882 CTAATCAAAG

                                  
       6892 ATTAAAGTATAAAGGTAAGATT
          1 ATTAAAGTATAAAGGTAAGATT

                        *         
       6914 ATTAAAGTATAAGGGTAAGATT
          1 ATTAAAGTATAAAGGTAAGATT

       6936 CTGAGATGCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32


Consensus pattern (22 bp):   
ATTAAAGTATAAAGGTAAGATT
Done.