Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014664.1 Corchorus capsularis cultivar CVL-1 contig14685, 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: 15440
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:180 original size:29 final size:28

Alignment explanation


    Indices: 134--206  Score: 130
    Period size: 27  Copynumber: 2.6  Consensus size: 28

        124 CAACTTTACT

                                        
        134 AAAAAAAACAAATCTTTTTTTGAGAT-A
          1 AAAAAAAACAAATCTTTTTTTGAGATAA

                                         
        161 AAAAAAAACAAATCTTTTTTTGAGATAAA
          1 AAAAAAAACAAATCTTTTTTTGAGAT-AA

                             
        190 AAAAAAAACAAATCTTT
          1 AAAAAAAACAAATCTTT

        207 CAACTTACAA


Statistics
Matches: 44,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  27   26  0.59
  29   18  0.41

ACGTcount: A:0.56, C:0.08, G:0.05, T:0.30


Consensus pattern (28 bp):   
AAAAAAAACAAATCTTTTTTTGAGATAA

Found at i:4171 original size:32 final size:31

Alignment explanation


    Indices: 4081--4200  Score: 132
    Period size: 31  Copynumber: 3.8  Consensus size: 31

       4071 GGCGTGCCAT

                        *      *    *      
       4081 CTTTTGGTACACATGGCGTACCACATGTCAC
          1 CTTTTGGTACACGTGGCGTGCCACGTGTCAC

                       *     *             
       4112 CTTTTGGTACATGTGGCATGCCACGTGTCAC
          1 CTTTTGGTACACGTGGCGTGCCACGTGTCAC

                                           *
       4143 CTTTTGGTACACGTGCGCGTGCCACGTGTCAT
          1 CTTTTGGTACACGTG-GCGTGCCACGTGTCAC

            *    *  *        **       
       4175 TTTTTTGTCCACGTGGCACGCCACGT
          1 CTTTTGGTACACGTGGCGTGCCACGT

       4201 CGAACTCCGT


Statistics
Matches: 75,  Mismatches: 13, Indels: 2
        0.83            0.14        0.02

Matches are distributed among these distances:
  31   49  0.65
  32   26  0.35

ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32


Consensus pattern (31 bp):   
CTTTTGGTACACGTGGCGTGCCACGTGTCAC

Found at i:4198 original size:63 final size:62

Alignment explanation


    Indices: 4081--4200  Score: 150
    Period size: 63  Copynumber: 1.9  Consensus size: 62

       4071 GGCGTGCCAT

                                                      *      *            
       4081 CTTTTGGTACACATGGCGTACCACATGTCACCTTTTGGTACATGTGGCATGCCACGTGTCAC
          1 CTTTTGGTACACATGGCGTACCACATGTCACCTTTTGGTACACGTGGCACGCCACGTGTCAC

                        *       *    *     **    *  *                 
       4143 CTTTTGGTACACGTGCGCGTGCCACGTGTCATTTTTTTGTCCACGTGGCACGCCACGT
          1 CTTTTGGTACACATG-GCGTACCACATGTCACCTTTTGGTACACGTGGCACGCCACGT

       4201 CGAACTCCGT


Statistics
Matches: 48,  Mismatches: 9, Indels: 1
        0.83            0.16        0.02

Matches are distributed among these distances:
  62   14  0.29
  63   34  0.71

ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32


Consensus pattern (62 bp):   
CTTTTGGTACACATGGCGTACCACATGTCACCTTTTGGTACACGTGGCACGCCACGTGTCAC

Found at i:9195 original size:12 final size:12

Alignment explanation


    Indices: 9178--9206  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       9168 TACTTAAGAA

                        
       9178 CAAGTGGGTGTT
          1 CAAGTGGGTGTT

                        
       9190 CAAGTGGGTGTT
          1 CAAGTGGGTGTT

                 
       9202 CAAGT
          1 CAAGT

       9207 AAAAAGAAAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.21, C:0.10, G:0.38, T:0.31


Consensus pattern (12 bp):   
CAAGTGGGTGTT
Done.