Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014595.1 Corchorus capsularis cultivar CVL-1 contig14616, 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: 18939
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33


Found at i:51 original size:22 final size:22

Alignment explanation


    Indices: 18--471  Score: 256
    Period size: 22  Copynumber: 20.8  Consensus size: 22

          8 AAAATTCAGG

                *                 
         18 GAGGATATCAAAATTTCAT-GT
          1 GAGGTTATCAAAATTTCATAGT

                                    
         39 GAAGGTTATCAAAATTTCATAGTT
          1 G-AGGTTATCAAAATTTCATAG-T

            *     *           *  *
         63 TA-GTTTTCAAAATTTCACA-A
          1 GAGGTTATCAAAATTTCATAGT

                             *     
         83 GAGGGTTATCAAAATTTTATAGT
          1 GA-GGTTATCAAAATTTCATAGT

              *   *               *
        106 -ATGTAGATCAAAATTTCATAGG
          1 GAGGT-TATCAAAATTTCATAGT

               *   *            * 
        128 GAGATTAACAAAATTTCATAAT
          1 GAGGTTATCAAAATTTCATAGT

                         **      *
        150 GAGGTTATCAAAAAATCATAGG
          1 GAGGTTATCAAAATTTCATAGT

                                  
        172 GAGGTTATCAAAA-TT--T-GT
          1 GAGGTTATCAAAATTTCATAGT

                       *           
        190 -A-GTTATCAAGATTTCATAAG-
          1 GAGGTTATCAAAATTTCAT-AGT

            * *             *    *
        210 AAAGTTATCAAAATTTTATAGG
          1 GAGGTTATCAAAATTTCATAGT

                                   
        232 GAGGTTTATCAAAATTTCATAG-
          1 GAGG-TTATCAAAATTTCATAGT

                 *                 *
        254 GAAGATTTATCAAAATTTCATAGC
          1 G-AG-GTTATCAAAATTTCATAGT

                      *           
        278 GAGGTTATCACAATTTCATAGT
          1 GAGGTTATCAAAATTTCATAGT

             * *              * * 
        300 GTGATTATCAAAATTTCAGAAT
          1 GAGGTTATCAAAATTTCATAGT

             * *     * *           
        322 GTGATTACTGACAA-TTCATA-T
          1 GAGGTTA-TCAAAATTTCATAGT

                   * *   *       **
        343 GGAGGTTTTTAAATTTTCATAAC
          1 -GAGGTTATCAAAATTTCATAGT

             *         *  **      
        366 GTGGTTATCAATATACCATA-T
          1 GAGGTTATCAAAATTTCATAGT

                        *  *       
        387 GGAGGTTATCAACATCTCATAGT
          1 -GAGGTTATCAAAATTTCATAGT

              *                 * *
        410 GTTGGTTATCAAAATTTCATTGG
          1 G-AGGTTATCAAAATTTCATAGT

              *                 * 
        433 GAAGTTATCAAAATTTCATATT
          1 GAGGTTATCAAAATTTCATAGT

                              
        455 GAGGTCT-TCAAAATTTC
          1 GAGGT-TATCAAAATTTC

        472 GAGGTTAATT


Statistics
Matches: 329,  Mismatches: 76, Indels: 55
        0.72            0.17        0.12

Matches are distributed among these distances:
  16    9  0.03
  17    3  0.01
  18    1  0.00
  19    2  0.01
  20    1  0.00
  21   12  0.04
  22  235  0.71
  23   64  0.19
  24    2  0.01

ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36


Consensus pattern (22 bp):   
GAGGTTATCAAAATTTCATAGT

Found at i:1834 original size:18 final size:18

Alignment explanation


    Indices: 1813--1847  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1803 TCGATATTTA

                   *  *       
       1813 TCGATATCTCGATAAATC
          1 TCGATATATCCATAAATC

                             
       1831 TCGATATATCCATAAAT
          1 TCGATATATCCATAAAT

       1848 ATCCGTAAAT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34


Consensus pattern (18 bp):   
TCGATATATCCATAAATC

Found at i:5315 original size:14 final size:14

Alignment explanation


    Indices: 5296--5324  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       5286 TTTTATTTTT

                          
       5296 CTTCTATTAAGATA
          1 CTTCTATTAAGATA

                          
       5310 CTTCTATTAAGATA
          1 CTTCTATTAAGATA

             
       5324 C
          1 C

       5325 CAATTATAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41


Consensus pattern (14 bp):   
CTTCTATTAAGATA
Done.