Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021807.1 Corchorus olitorius cultivar O-4 contig21840, 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: 16702
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34


Found at i:168 original size:21 final size:21

Alignment explanation


    Indices: 16--212  Score: 87
    Period size: 22  Copynumber: 9.1  Consensus size: 21

          6 AGTTTCATTC

                  *               
         16 TCATAGGGAGGTTATCAAATTT
          1 TCATAGTGAGGTTATCAAA-TT

             *  *   *       *      
         38 TTATGGTGTGGTTATTAAAATTT
          1 TCATAGTGAGGTTA-TCAAA-TT

                             *    
         61 TCATAGTGCA-GTTA-CCAATT
          1 TCATAGTG-AGGTTATCAAATT

                     * *   *       
         81 AT-ATAGTGTGATTAACAAAATT
          1 -TCATAGTGAGGTTATC-AAATT

             *    *   *         * 
        103 TTATAGGGAGATTATCAAAACT
          1 TCATAGTGAGGTTATC-AAATT

               * * *              
        125 TCACACTAAGGTTATCGAAATT
          1 TCATAGTGAGGTTATC-AAATT

                *   *             
        147 TCATGGTGTGGTTATCAAATTT
          1 TCATAGTGAGGTTATCAAA-TT

                   *        *     
        169 TCATAG-AAGGTTATTGAAATT
          1 TCATAGTGAGGTTA-TCAAATT

                 *               
        190 TCATAATGAGGTTATCAAATT
          1 TCATAGTGAGGTTATCAAATT

              
        211 TC
          1 TC

        213 TACATTGGAG


Statistics
Matches: 128,  Mismatches: 37, Indels: 21
        0.69            0.20        0.11

Matches are distributed among these distances:
  20   11  0.09
  21   28  0.22
  22   72  0.56
  23   17  0.13

ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39


Consensus pattern (21 bp):   
TCATAGTGAGGTTATCAAATT

Found at i:4206 original size:22 final size:22

Alignment explanation


    Indices: 4178--4220  Score: 86
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4168 AGTATGTCAG

                                  
       4178 ATCTAAATTATCTAAATTAAAC
          1 ATCTAAATTATCTAAATTAAAC

                                 
       4200 ATCTAAATTATCTAAATTAAA
          1 ATCTAAATTATCTAAATTAAA

       4221 GTTGGTCAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37


Consensus pattern (22 bp):   
ATCTAAATTATCTAAATTAAAC

Found at i:8293 original size:21 final size:19

Alignment explanation


    Indices: 8259--8299  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

       8249 TTCTGTTTCA

                               
       8259 GTATTGGGGTTTGTATTTT
          1 GTATTGGGGTTTGTATTTT

                            *    
       8278 GTATATGGGGCTTTGTGTTTT
          1 GTAT-TGGGG-TTTGTATTTT

             
       8299 G
          1 G

       8300 CACCAAAGTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19    4  0.21
  20    5  0.26
  21   10  0.53

ACGTcount: A:0.10, C:0.02, G:0.34, T:0.54


Consensus pattern (19 bp):   
GTATTGGGGTTTGTATTTT
Done.