Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008176.1 Corchorus capsularis cultivar CVL-1 contig08197, 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: 9134
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:5333 original size:31 final size:31

Alignment explanation


    Indices: 5292--5460  Score: 185
    Period size: 31  Copynumber: 5.5  Consensus size: 31

       5282 TTTTGTGCAC

                 *     *   *               
       5292 GTGGCATGCCATGTGCCACTTTTTGAAACAT
          1 GTGGCGTGCCACGTGTCACTTTTTGAAACAT

                *                          
       5323 GTGGTGTGCCACGTGTCACTTTTTGAAACAT
          1 GTGGCGTGCCACGTGTCACTTTTTGAAACAT

                *                    **   *
       5354 GTGGTGTGCCACGTGTCACTTTTTGGTACAC
          1 GTGGCGTGCCACGTGTCACTTTTTGAAACAT

                    *  *             **    
       5385 GTGGCGTGACATGTGTCACTTTTTGGTACAT
          1 GTGGCGTGCCACGTGTCACTTTTTGAAACAT

                        *            **   *
       5416 GTGGCGTGCCACATGTCACTTTTTGGTACAC
          1 GTGGCGTGCCACGTGTCACTTTTTGAAACAT

                 *        
       5447 GTGGCATGCCACGT
          1 GTGGCGTGCCACGT

       5461 CGGACACCGT


Statistics
Matches: 121,  Mismatches: 17, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31  121  1.00

ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34


Consensus pattern (31 bp):   
GTGGCGTGCCACGTGTCACTTTTTGAAACAT

Found at i:5457 original size:93 final size:93

Alignment explanation


    Indices: 5289--5460  Score: 236
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       5279 TCCTTTTGTG

                       *                          *       *                 *
       5289 CACGTGGCATGCCATGTGCCACTTTTTGAAACATGTGGTGTGCCACGTGTCACTTTTTGAAACAT
          1 CACGTGGCATGACATGTGCCACTTTTTGAAACATGTGGCGTGCCACATGTCACTTTTTGAAACAC

                **                      
       5354 GTGGTGTGCCACGTGTCACTTTTTGGTA
         66 GTGGCATGCCACGTGTCACTTTTTGGTA

                    *         *         **                             **    
       5382 CACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACAC
          1 CACGTGGCATGACATGTGCCACTTTTTGAAACATGTGGCGTGCCACATGTCACTTTTTGAAACAC

                          
       5447 GTGGCATGCCACGT
         66 GTGGCATGCCACGT

       5461 CGGACACCGT


Statistics
Matches: 67,  Mismatches: 12, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  93   67  1.00

ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33


Consensus pattern (93 bp):   
CACGTGGCATGACATGTGCCACTTTTTGAAACATGTGGCGTGCCACATGTCACTTTTTGAAACAC
GTGGCATGCCACGTGTCACTTTTTGGTA

Found at i:8259 original size:31 final size:31

Alignment explanation


    Indices: 8224--8295  Score: 83
    Period size: 32  Copynumber: 2.3  Consensus size: 31

       8214 AATTCGGGAA

                                        *  
       8224 TTTTCGGGTTCGATTTCCTTCAGGTCAGTTT
          1 TTTTCGGGTTCGATTTCCTTCAGGTCAGATT

                    *  * *             *    
       8255 TTTTCAGGTTTGGTTTTCCTTCAGGTCGGATT
          1 TTTTC-GGGTTCGATTTCCTTCAGGTCAGATT

                      
       8287 TTTT-GGGTT
          1 TTTTCGGGTT

       8296 TAAGTTTTTC


Statistics
Matches: 34,  Mismatches: 6, Indels: 3
        0.79            0.14        0.07

Matches are distributed among these distances:
  30    4  0.12
  31    5  0.15
  32   25  0.74

ACGTcount: A:0.08, C:0.15, G:0.25, T:0.51


Consensus pattern (31 bp):   
TTTTCGGGTTCGATTTCCTTCAGGTCAGATT

Found at i:8288 original size:17 final size:16

Alignment explanation


    Indices: 8237--8288  Score: 52
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       8227 TCGGGTTCGA

                         *  
       8237 TTTCCTTCAGGTCAGT
          1 TTTCCTTCAGGTCGGT

                *        *   
       8253 TTT-TTTCAGGTTTGGT
          1 TTTCCTTCAGG-TCGGT

                             
       8269 TTTCCTTCAGGTCGGAT
          1 TTTCCTTCAGGTCGG-T

               
       8286 TTT
          1 TTT

       8289 TTGGGTTTAA


Statistics
Matches: 28,  Mismatches: 5, Indels: 5
        0.74            0.13        0.13

Matches are distributed among these distances:
  15    6  0.21
  16   12  0.43
  17   10  0.36

ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52


Consensus pattern (16 bp):   
TTTCCTTCAGGTCGGT

Found at i:8303 original size:32 final size:32

Alignment explanation


    Indices: 8237--8303  Score: 82
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       8227 TCGGGTTCGA

                           *             *  
       8237 TTTCCTTCAGGTCAGTTTTTTTCAGGTTTGGT
          1 TTTCCTTCAGGTCAGATTTTTTCAGGTTTAGT

                         *         *         
       8269 TTTCCTTCAGGTCGGATTTTTT-GGGTTTAAGT
          1 TTTCCTTCAGGTCAGATTTTTTCAGGTTT-AGT

               
       8301 TTT
          1 TTT

       8304 TCTGAGTTCG


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  31    5  0.17
  32   25  0.83

ACGTcount: A:0.10, C:0.13, G:0.22, T:0.54


Consensus pattern (32 bp):   
TTTCCTTCAGGTCAGATTTTTTCAGGTTTAGT
Done.