Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018606.1 Corchorus olitorius cultivar O-4 contig18639, 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: 6838
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32


Found at i:2228 original size:173 final size:173

Alignment explanation


    Indices: 1933--2278  Score: 593
    Period size: 173  Copynumber: 2.0  Consensus size: 173

       1923 CTAGTAATAG

                 *                 *        *  *               *             
       1933 TTGAACATAATTATAAATCAAATGAAATAATTTCAGTTTACGATCTTCTTTTATTTTAAAAACTT
          1 TTGAAAATAATTATAAATCAAATAAAATAATTGCACTTTACGATCTTCTTTAATTTTAAAAACTT

                                                                             
       1998 TAAATTCTTGTTAGAGGGAAAGAATAAATTTTAATCACGATAGATTAAACTACCAAATAGAACCA
         66 TAAATTCTTGTTAGAGGGAAAGAATAAATTTTAATCACGATAGATTAAACTACCAAATAGAACCA

                                              *   *    
       2063 GACCAATCACAATACCTTTTTAAATTAAAATGGTTAAAGTAAA
        131 GACCAATCACAATACCTTTTTAAATTAAAATGGTAAAAATAAA

                               *                                         *   
       2106 TTGAAAATAATTATAAATCTAATAAAATAATTGCACTTTACGATCTTCTTTAATTTTAAAAGCTT
          1 TTGAAAATAATTATAAATCAAATAAAATAATTGCACTTTACGATCTTCTTTAATTTTAAAAACTT

                                      *                                   *  
       2171 TAAATTCTTGTTAGAGGGAAAGAATAGATTTTAATCACGATAGATTAAACTACCAAATAGAATCA
         66 TAAATTCTTGTTAGAGGGAAAGAATAAATTTTAATCACGATAGATTAAACTACCAAATAGAACCA

                                                       
       2236 GACCAATCACAATACCTTTTTAAATTAAAATGGTAAAAATAAA
        131 GACCAATCACAATACCTTTTTAAATTAAAATGGTAAAAATAAA

       2279 AATAGTTATA


Statistics
Matches: 162,  Mismatches: 11, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 173  162  1.00

ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34


Consensus pattern (173 bp):   
TTGAAAATAATTATAAATCAAATAAAATAATTGCACTTTACGATCTTCTTTAATTTTAAAAACTT
TAAATTCTTGTTAGAGGGAAAGAATAAATTTTAATCACGATAGATTAAACTACCAAATAGAACCA
GACCAATCACAATACCTTTTTAAATTAAAATGGTAAAAATAAA

Found at i:2431 original size:128 final size:129

Alignment explanation


    Indices: 2261--2512  Score: 391
    Period size: 128  Copynumber: 2.0  Consensus size: 129

       2251 CTTTTTAAAT

                                  *                                          
       2261 TAAAATGGTAAAAATAAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTC
          1 TAAAATGGTAAAAAT-AAAATAATTATAAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTC

                    *                            *                           
       2326 AGTAGAATGAAACTATAATAGTTTAAACAATGACATTTAAGAAATATATTCAAAAATAAAAATAG
         65 AGTAGAATAAAACTATAATAGTTTAAACAATGACATTAAAGAAATATATTCAAAAATAAAAATAG

                                         *                                  *
       2391 TAAAATGGTAAAAAT-AAATAATTATAAAGATATT-AGATTTAATTAAATAAAAATAGAGTTTTT
          1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGA-ATTTAATTAAATAAAAATAGAGTTTTC

                  *             *                             **       
       2454 AGTAGAGTAAAACTATAATATTTTAAACAATGACATTAAAGAAATATATTTGAAAATAA
         65 AGTAGAATAAAACTATAATAGTTTAAACAATGACATTAAAGAAATATATTCAAAAATAA

       2513 GGGTATAATG


Statistics
Matches: 112,  Mismatches: 9, Indels: 4
        0.90            0.07        0.03

Matches are distributed among these distances:
 127    1  0.01
 128   96  0.86
 130   15  0.13

ACGTcount: A:0.55, C:0.03, G:0.10, T:0.32


Consensus pattern (129 bp):   
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTCA
GTAGAATAAAACTATAATAGTTTAAACAATGACATTAAAGAAATATATTCAAAAATAAAAATAG

Found at i:3915 original size:2 final size:2

Alignment explanation


    Indices: 3910--3952  Score: 70
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       3900 TGTGTGTGTG

                                                                      *   
       3910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TC TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

              
       3951 TA
          1 TA

       3953 GTGTGTGGCT


Statistics
Matches: 38,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   37  0.97

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:4809 original size:21 final size:22

Alignment explanation


    Indices: 4751--4962  Score: 133
    Period size: 22  Copynumber: 9.7  Consensus size: 22

       4741 CATACTATAG

                    *  *        * 
       4751 TATCAAAAAATTATAGGGAGAT
          1 TATCAAAATATCATAGGGAGGT

              *      *            
       4773 TAACAAAATCTCATAGGGAGGT
          1 TATCAAAATATCATAGGGAGGT

                             *    
       4795 TATCAAAA-ATCATAGGAAGGT
          1 TATCAAAATATCATAGGGAGGT

                     *       *     
       4816 TAT-AAAATTTCATAGGAAGGTT
          1 TATCAAAATATCATAGGGAGG-T

               *     *      **    
       4838 TATTAAAATTTCATAGTTAGGT
          1 TATCAAAATATCATAGGGAGGT

                   *       *    * 
       4860 TATCAAAGTATCATATGGAGTT
          1 TATCAAAATATCATAGGGAGGT

                 *   * *     * ** 
       4882 TATCACAATTTTATAGGTAAAT
          1 TATCAAAATATCATAGGGAGGT

                     *        *  *
       4904 TATCAAAATTTCATAGGGTGGC
          1 TATCAAAATATCATAGGGAGGT

                     * *        *  
       4926 TATCAAAATTTAATA-GGATAGT
          1 TATCAAAATATCATAGGGA-GGT

                     *     
       4948 TATCAAAATTTCATA
          1 TATCAAAATATCATA

       4963 AAAATATTCA


Statistics
Matches: 148,  Mismatches: 38, Indels: 8
        0.76            0.20        0.04

Matches are distributed among these distances:
  20    4  0.03
  21   27  0.18
  22  102  0.69
  23   15  0.10

ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34


Consensus pattern (22 bp):   
TATCAAAATATCATAGGGAGGT

Done.