Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005992.1 Corchorus capsularis cultivar CVL-1 contig06010, 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: 7129
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:2239 original size:19 final size:19

Alignment explanation


    Indices: 2217--2306  Score: 103
    Period size: 19  Copynumber: 4.7  Consensus size: 19

       2207 TTGGAGAATA

                 *     *       
       2217 ACTTTAAGTTTAGGGTTTG
          1 ACTTTCAGTTTGGGGTTTG

                   *           
       2236 ACTTTCATTTTGGGGTTTG
          1 ACTTTCAGTTTGGGGTTTG

                                 
       2255 ACTTT-ATGTTTGGGGGTTT-
          1 ACTTTCA-GTTT-GGGGTTTG

                   *       *   
       2274 ACTTTCATTTTGGGGATTG
          1 ACTTTCAGTTTGGGGTTTG

                          
       2293 ACTTTCAGTTTGGG
          1 ACTTTCAGTTTGGG

       2307 CTTTCAGTTT


Statistics
Matches: 60,  Mismatches: 7, Indels: 8
        0.80            0.09        0.11

Matches are distributed among these distances:
  18    7  0.12
  19   45  0.75
  20    8  0.13

ACGTcount: A:0.14, C:0.09, G:0.28, T:0.49


Consensus pattern (19 bp):   
ACTTTCAGTTTGGGGTTTG

Found at i:2248 original size:38 final size:38

Alignment explanation


    Indices: 2206--2304  Score: 92
    Period size: 38  Copynumber: 2.6  Consensus size: 38

       2196 TTACAATCGG

                                                   
       2206 TTTGGAGAATAACTTTAAGTTT-AGGGTTTGACTTTCAT
          1 TTTGGAGAATAACTTTAAGTTTGAGGGTTT-ACTTTCAT

                 * ** *      *     *              
       2244 TTTGGGGTTTGACTTTATGTTTGGGGGTTTACTTTCAT
          1 TTTGGAGAATAACTTTAAGTTTGAGGGTTTACTTTCAT

                 *  * *     *      
       2282 TTTGGGGATTGACTTTCAGTTTG
          1 TTTGGAGAATAACTTTAAGTTTG

       2305 GGCTTTCAGT


Statistics
Matches: 51,  Mismatches: 9, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  38   45  0.88
  39    6  0.12

ACGTcount: A:0.17, C:0.08, G:0.26, T:0.48


Consensus pattern (38 bp):   
TTTGGAGAATAACTTTAAGTTTGAGGGTTTACTTTCAT

Found at i:2305 original size:38 final size:39

Alignment explanation


    Indices: 2229--2306  Score: 124
    Period size: 38  Copynumber: 2.0  Consensus size: 39

       2219 TTTAAGTTTA

                                  *                
       2229 GGGTTTGACTTTCATTTTGGGGTTTGACTTTATGTTTGG
          1 GGGTTTGACTTTCATTTTGGGGATTGACTTTATGTTTGG

                                                    
       2268 GGGTTT-ACTTTCATTTTGGGGATTGACTTTCA-GTTTGG
          1 GGGTTTGACTTTCATTTTGGGGATTGACTTT-ATGTTTGG

             
       2306 G
          1 G

       2307 CTTTCAGTTT


Statistics
Matches: 37,  Mismatches: 1, Indels: 3
        0.90            0.02        0.07

Matches are distributed among these distances:
  38   30  0.81
  39    7  0.19

ACGTcount: A:0.12, C:0.09, G:0.31, T:0.49


Consensus pattern (39 bp):   
GGGTTTGACTTTCATTTTGGGGATTGACTTTATGTTTGG

Found at i:7021 original size:19 final size:19

Alignment explanation


    Indices: 6957--7026  Score: 63
    Period size: 19  Copynumber: 3.7  Consensus size: 19

       6947 AAAAAATTGC

                      *    *   
       6957 TTTGGGGTTTCACTTTC-A
          1 TTTGGGGTTTGACTTACAA

                           *    *
       6975 TGTTGGGGTTTGAC-AACCAG
          1 T-TTGGGGTTTGACTTA-CAA

               *               
       6995 TTTAGGGTTTGACTTACAA
          1 TTTGGGGTTTGACTTACAA

                         
       7014 TTTGGGGTTTGAC
          1 TTTGGGGTTTGAC

       7027 GACCATTACA


Statistics
Matches: 40,  Mismatches: 8, Indels: 7
        0.73            0.15        0.13

Matches are distributed among these distances:
  18    1  0.03
  19   37  0.93
  20    2  0.05

ACGTcount: A:0.17, C:0.13, G:0.29, T:0.41


Consensus pattern (19 bp):   
TTTGGGGTTTGACTTACAA
Done.