Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005990.1 Corchorus capsularis cultivar CVL-1 contig06008, 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: 13110
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:2492 original size:20 final size:21

Alignment explanation


    Indices: 2474--2535  Score: 115
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       2464 TTAAAAACCA

                                 
       2474 TCTTCTTCCCCACAAAACCTT
          1 TCTTCTTCCCCACAAAACCTT

                                 
       2495 TCTTCTTCCCCACAAAACCTT
          1 TCTTCTTCCCCACAAAACCTT

                     *          
       2516 TCTTCTTCCACACAAAACCT
          1 TCTTCTTCCCCACAAAACCT

       2536 GTAACTCCAC


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  21   40  1.00

ACGTcount: A:0.26, C:0.42, G:0.00, T:0.32


Consensus pattern (21 bp):   
TCTTCTTCCCCACAAAACCTT

Found at i:9143 original size:19 final size:19

Alignment explanation


    Indices: 9121--9210  Score: 103
    Period size: 19  Copynumber: 4.7  Consensus size: 19

       9111 TTGGAGAATA

                 *     *       
       9121 ACTTTAAGTTTAGGGTTTG
          1 ACTTTCAGTTTGGGGTTTG

                   *           
       9140 ACTTTCATTTTGGGGTTTG
          1 ACTTTCAGTTTGGGGTTTG

                                 
       9159 ACTTT-ATGTTTGGGGGTTT-
          1 ACTTTCA-GTTT-GGGGTTTG

                   *       *   
       9178 ACTTTCATTTTGGGGATTG
          1 ACTTTCAGTTTGGGGTTTG

                          
       9197 ACTTTCAGTTTGGG
          1 ACTTTCAGTTTGGG

       9211 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:9152 original size:38 final size:38

Alignment explanation


    Indices: 9110--9208  Score: 92
    Period size: 38  Copynumber: 2.6  Consensus size: 38

       9100 TTACAATCGG

                                                   
       9110 TTTGGAGAATAACTTTAAGTTT-AGGGTTTGACTTTCAT
          1 TTTGGAGAATAACTTTAAGTTTGAGGGTTT-ACTTTCAT

                 * ** *      *     *              
       9148 TTTGGGGTTTGACTTTATGTTTGGGGGTTTACTTTCAT
          1 TTTGGAGAATAACTTTAAGTTTGAGGGTTTACTTTCAT

                 *  * *     *      
       9186 TTTGGGGATTGACTTTCAGTTTG
          1 TTTGGAGAATAACTTTAAGTTTG

       9209 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:9209 original size:38 final size:39

Alignment explanation


    Indices: 9133--9210  Score: 124
    Period size: 38  Copynumber: 2.0  Consensus size: 39

       9123 TTTAAGTTTA

                                  *                
       9133 GGGTTTGACTTTCATTTTGGGGTTTGACTTTATGTTTGG
          1 GGGTTTGACTTTCATTTTGGGGATTGACTTTATGTTTGG

                                                    
       9172 GGGTTT-ACTTTCATTTTGGGGATTGACTTTCA-GTTTGG
          1 GGGTTTGACTTTCATTTTGGGGATTGACTTT-ATGTTTGG

             
       9210 G
          1 G

       9211 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
Done.