Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020118.1 Corchorus olitorius cultivar O-4 contig20151, 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: 12746
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:37 original size:22 final size:22

Alignment explanation


    Indices: 6--279  Score: 115
    Period size: 22  Copynumber: 12.7  Consensus size: 22

          1 TAAGA

                                  
          6 TGGTTATCAAAATTTCATGAGG
          1 TGGTTATCAAAATTTCATGAGG

                 *         *      
         28 TGGTTTTCAAAATTTTATGA--
          1 TGGTTATCAAAATTTCATGAGG

                              *    
         48 -GGTTATCAAAATTTCA-AATGG
          1 TGGTTATCAAAATTTCATGA-GG

            *              *       
         69 AGGTTATCAAAATTTTAT-AGGG
          1 TGGTTATCAAAATTTCATGA-GG

            *       *              
         91 AGGTTTATAAAAATTTCAT-A-G
          1 TGG-TTATCAAAATTTCATGAGG

                **    *     *      *
        112 TGAGGCATCACAATTTTATG-GTA
          1 TG-GTTATCAAAATTTCATGAG-G

               *              * * 
        135 TGGCTATCAAAATTTCATAATG
          1 TGGTTATCAAAATTTCATGAGG

              *   *   *    *      *
        157 TGATTACCAATATTTTATCG-GA
          1 TGGTTATCAAAATTTCAT-GAGG

            *            *    * * 
        179 AGGTTATCAAAATATCATAATG
          1 TGGTTATCAAAATTTCATGAGG

                *      *            
        201 TGCGCT-TC-ACATTTCATTGA-G
          1 TG-GTTATCAAAATTTCA-TGAGG

              *                   
        222 TGATTATCAAAATTTCATG-GG
          1 TGGTTATCAAAATTTCATGAGG

                *             *   
        243 TGGTCATCAAAATTTCATTAGG
          1 TGGTTATCAAAATTTCATGAGG

                   *       
        265 TGGTTATTAAAATTT
          1 TGGTTATCAAAATTT

        280 TTATGATCCG


Statistics
Matches: 180,  Mismatches: 53, Indels: 38
        0.66            0.20        0.14

Matches are distributed among these distances:
  18    1  0.01
  19   14  0.08
  20    1  0.01
  21   42  0.23
  22  104  0.58
  23   18  0.10

ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38


Consensus pattern (22 bp):   
TGGTTATCAAAATTTCATGAGG

Found at i:79 original size:41 final size:45

Alignment explanation


    Indices: 7--202  Score: 171
    Period size: 44  Copynumber: 4.5  Consensus size: 45

          1 TAAGAT

                             *     *    *                
          7 GGTTATCAAAATTTCATGA-G-GTGGTTTTCAAAATTTTAT-G-A
          1 GGTTATCAAAATTTCATAATGTGAGGTTATCAAAATTTTATGGAA

                                                        * 
         48 GGTTATCAAAATTTCA-AATG-GAGGTTATCAAAATTTTATAGGGA
          1 GGTTATCAAAATTTCATAATGTGAGGTTATCAAAATTTTAT-GGAA

                   *                    *    *            *
         92 GGTTTATAAAAATTTCAT-A-GTGAGG-CATCACAATTTTATGGTAT
          1 GG-TTATCAAAATTTCATAATGTGAGGTTATCAAAATTTTATGG-AA

              *                          *   *            
        136 GGCTATCAAAATTTCATAATGTGA--TTACCAATATTTTATCGGAA
          1 GGTTATCAAAATTTCATAATGTGAGGTTATCAAAATTTTAT-GGAA

                        *          
        180 GGTTATCAAAATATCATAATGTG
          1 GGTTATCAAAATTTCATAATGTG

        203 CGCTTCACAT


Statistics
Matches: 126,  Mismatches: 17, Indels: 21
        0.77            0.10        0.13

Matches are distributed among these distances:
  40    1  0.01
  41   34  0.27
  43   16  0.13
  44   51  0.40
  45   24  0.19

ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37


Consensus pattern (45 bp):   
GGTTATCAAAATTTCATAATGTGAGGTTATCAAAATTTTATGGAA

Found at i:406 original size:20 final size:21

Alignment explanation


    Indices: 365--409  Score: 65
    Period size: 22  Copynumber: 2.1  Consensus size: 21

        355 TATCGTCATA

                                  
        365 AAAACTTTATAGTGTAATTATC
          1 AAAACTTTATAGTG-AATTATC

                *                
        387 AAAATTTTATAGTG-ATTATC
          1 AAAACTTTATAGTGAATTATC

               
        407 AAA
          1 AAA

        410 TTTCATAAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    9  0.41
  22   13  0.59

ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40


Consensus pattern (21 bp):   
AAAACTTTATAGTGAATTATC

Found at i:10236 original size:14 final size:14

Alignment explanation


    Indices: 10217--10248  Score: 55
    Period size: 14  Copynumber: 2.3  Consensus size: 14

      10207 AGTCCTTTGT

                          
      10217 AAAGTTAGAAACAA
          1 AAAGTTAGAAACAA

                      *   
      10231 AAAGTTAGAAGCAA
          1 AAAGTTAGAAACAA

                
      10245 AAAG
          1 AAAG

      10249 ATATTTAAGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.62, C:0.06, G:0.19, T:0.12


Consensus pattern (14 bp):   
AAAGTTAGAAACAA
Done.