Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006725.1 Corchorus olitorius cultivar O-4 contig06750, 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, 673

Length: 1123
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38


Found at i:78 original size:18 final size:16

Alignment explanation


    Indices: 42--72  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

         32 TGATGATATT

                            
         42 GTTTTTATAATTGTTG
          1 GTTTTTATAATTGTTG

                  *        
         58 GTTTTTCTAATTGTT
          1 GTTTTTATAATTGTT

         73 TTGGTTATGA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.16, C:0.03, G:0.16, T:0.65


Consensus pattern (16 bp):   
GTTTTTATAATTGTTG

Found at i:876 original size:22 final size:22

Alignment explanation


    Indices: 846--1054  Score: 121
    Period size: 22  Copynumber: 9.5  Consensus size: 22

        836 TCCAACGTAG

                               *   
        846 AAATATTGATAATCACACTGTGA
          1 AAAT-TTGATAATCACACTATGA

                       * *  *     
        869 AAATTTGATAACCTCATTATG-
          1 AAATTTGATAATCACACTATGA

                  *                  
        890 AAATCTGGATAA-C-CAGCTTATGA
          1 AAAT-TTGATAATCACA-C-TATGA

                       *           
        913 AAATTTGATAACCACAC-AGTGA
          1 AAATTTGATAATCACACTA-TGA

              *             *     
        935 AATTTTGATAATCACATTATGA
          1 AAATTTGATAATCACACTATGA

              *                 *   
        957 AATTTTGATAACGTCA-A-TGTG-
          1 AAATTTGATAA--TCACACTATGA

                          * *    * 
        978 AAATTGTGATAATCTCCCTATTA
          1 AAATT-TGATAATCACACTATGA

              *           *       
       1001 AATTTTGATAATCAAACTAT-A
          1 AAATTTGATAATCACACTATGA

                   *   *           
       1022 AAA-TTGGTAACCACACTATGAA
          1 AAATTTGATAATCACACTATG-A

                       
       1044 AAATTTGATAA
          1 AAATTTGATAA

       1055 CCTCCTCATA


Statistics
Matches: 144,  Mismatches: 25, Indels: 34
        0.71            0.12        0.17

Matches are distributed among these distances:
  20   17  0.12
  21   13  0.09
  22   87  0.60
  23   22  0.15
  24    5  0.03

ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33


Consensus pattern (22 bp):   
AAATTTGATAATCACACTATGA

Found at i:979 original size:44 final size:44

Alignment explanation


    Indices: 845--1101  Score: 156
    Period size: 44  Copynumber: 5.9  Consensus size: 44

        835 CTCCAACGTA

                 *              *                   * * 
        845 GAAATATTGATAATCACACTGTGAAAATTTGATAACCTCATTAT
          1 GAAATTTTGATAATCACACTATGAAAATTTGATAACCTCAATGT

                 * *                               *       
        889 GAAATCTGGATAA-C-CAGCTTATGAAAATTTGATAACCACACA-GT
          1 GAAATTTTGATAATCACA-C-TATGAAAATTTGATAACCTCA-ATGT

                              *       *         *       
        933 GAAATTTTGATAATCACATTATGAAATTTTGATAACGTCAATGT
          1 GAAATTTTGATAATCACACTATGAAAATTTGATAACCTCAATGT

                  *        * *    *   *                 * 
        977 GAAATTGTGATAATCTCCCTATTAAATTTTGATAA--TCAAACTAT
          1 GAAATTTTGATAATCACACTATGAAAATTTGATAACCTC-AA-TGT

                 *   *   *                           *  * 
       1021 -AAA-ATTGGTAACCACACTATGAAAAATTTGATAACCTC-CTCAT
          1 GAAATTTTGATAATCACACTATG-AAAATTTGATAACCTCAAT-GT

            *             *    *                    
       1064 AAAATTTTG-TAATTACACCATG-AAATTTCGATAACCTC
          1 GAAATTTTGATAATCACACTATGAAAATTT-GATAACCTC

       1102 TATATGAGAA


Statistics
Matches: 167,  Mismatches: 31, Indels: 31
        0.73            0.14        0.14

Matches are distributed among these distances:
  42   22  0.13
  43   30  0.18
  44  107  0.64
  45    6  0.04
  46    2  0.01

ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33


Consensus pattern (44 bp):   
GAAATTTTGATAATCACACTATGAAAATTTGATAACCTCAATGT

Found at i:980 original size:66 final size:64

Alignment explanation


    Indices: 845--968  Score: 149
    Period size: 66  Copynumber: 1.9  Consensus size: 64

        835 CTCCAACGTA

                         *     *                 *                        *  
        845 GAAATATTGATAATCACACTGTGAAAATTTGATAACCTCATTATGAAATCTGGATAACCAGCTTA
          1 GAAAT-TTGATAACCACACAGTGAAAATTTGATAACCACATTATGAAATCTGGATAACCA-CATA

             
        910 T
         64 T

                                      *        *             * *      
        911 GAAAATTTGATAACCACACAGTGAAATTTTGATAATCACATTATGAAATTTTGATAAC
          1 G-AAATTTGATAACCACACAGTGAAAATTTGATAACCACATTATGAAATCTGGATAAC

        969 GTCAATGTGA


Statistics
Matches: 50,  Mismatches: 7, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  66   46  0.92
  67    4  0.08

ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32


Consensus pattern (64 bp):   
GAAATTTGATAACCACACAGTGAAAATTTGATAACCACATTATGAAATCTGGATAACCACATAT
Done.