Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016519.1 Corchorus olitorius cultivar O-4 contig16552, 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: 15151
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:12283 original size:12 final size:12

Alignment explanation


    Indices: 12262--12311  Score: 55
    Period size: 12  Copynumber: 4.2  Consensus size: 12

      12252 TGGCTGAAGC

                 *      
      12262 TCTTCCTCCTCT
          1 TCTTCATCCTCT

                       *
      12274 TCTTCATCCTCA
          1 TCTTCATCCTCT

              *     *   
      12286 TCCTCATCTTCT
          1 TCTTCATCCTCT

                 *      
      12298 TCTTCCTCCTCT
          1 TCTTCATCCTCT

              
      12310 TC
          1 TC

      12312 CTCTCCATCA


Statistics
Matches: 30,  Mismatches: 8, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  12   30  1.00

ACGTcount: A:0.06, C:0.46, G:0.00, T:0.48


Consensus pattern (12 bp):   
TCTTCATCCTCT

Found at i:12295 original size:18 final size:18

Alignment explanation


    Indices: 12268--12356  Score: 51
    Period size: 18  Copynumber: 5.1  Consensus size: 18

      12258 AAGCTCTTCC

                 *            
      12268 TCCTCTTCTTCATCCTCA
          1 TCCTCATCTTCATCCTCA

                             *
      12286 TCCTCATCTTC-T--TCT
          1 TCCTCATCTTCATCCTCA

                 *     *       
      12301 TCCTCCTCTTCCT-CTCCA
          1 TCCTCATCTTCATCCT-CA

              *     *  *  *   
      12319 TCATCATCATCGTCGTCA
          1 TCCTCATCTTCATCCTCA

              *           *   
      12337 TCTTCATCTTCATCGTCA
          1 TCCTCATCTTCATCCTCA

              
      12355 TC
          1 TC

      12357 GTCTCCAGTG


Statistics
Matches: 55,  Mismatches: 12, Indels: 8
        0.73            0.16        0.11

Matches are distributed among these distances:
  15   12  0.22
  16    1  0.02
  17    2  0.04
  18   39  0.71
  19    1  0.02

ACGTcount: A:0.12, C:0.42, G:0.03, T:0.43


Consensus pattern (18 bp):   
TCCTCATCTTCATCCTCA

Found at i:12433 original size:21 final size:18

Alignment explanation


    Indices: 12407--12456  Score: 64
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      12397 TCAGGATCTC

                                 
      12407 CTTCATCTTCACCAGATGCAT
          1 CTTCATCTTCACC-G-T-CAT

                   *          
      12428 CTTCATCCTCACCGTCAT
          1 CTTCATCTTCACCGTCAT

                       
      12446 CTTCATCTTCA
          1 CTTCATCTTCA

      12457 TCTTGATCAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  18   13  0.48
  19    1  0.04
  20    1  0.04
  21   12  0.44

ACGTcount: A:0.20, C:0.38, G:0.06, T:0.36


Consensus pattern (18 bp):   
CTTCATCTTCACCGTCAT
Done.