Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024145.1 Corchorus olitorius cultivar O-4 contig24178, 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: 4433
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:289 original size:29 final size:29

Alignment explanation


    Indices: 254--455  Score: 271
    Period size: 29  Copynumber: 7.0  Consensus size: 29

        244 TAAAGTATGC

                        *        *     * 
        254 AAAATGACCAAACTGCCCCAGAATGTGTA
          1 AAAATGACCAAAATGCCCCAGGATGTGCA

              *      *         *       * 
        283 AAGATGACCGAAATGCCCCCGGATGTGTA
          1 AAAATGACCAAAATGCCCCAGGATGTGCA

                                    *    
        312 AAAATGACCAAAATGCCCCAGGATATGCA
          1 AAAATGACCAAAATGCCCCAGGATGTGCA

                                     *    
        341 AAAATGACCAAAATGTCCCC-GGATATGCA
          1 AAAATGACCAAAATG-CCCCAGGATGTGCA

                    *          *         
        370 AAAATGACAAAAATGCCCCCGGATGTGCA
          1 AAAATGACCAAAATGCCCCAGGATGTGCA

                               *         
        399 AAAATGACCAAAATGCCCCTGGATGTGCA
          1 AAAATGACCAAAATGCCCCAGGATGTGCA

                               *        
        428 AAAATGACCAAAATGCCCCTGGATGTGC
          1 AAAATGACCAAAATGCCCCAGGATGTGC

        456 GAATGGTTGA


Statistics
Matches: 157,  Mismatches: 14, Indels: 4
        0.90            0.08        0.02

Matches are distributed among these distances:
  28    4  0.03
  29  149  0.95
  30    4  0.03

ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCAGGATGTGCA

Found at i:2241 original size:46 final size:45

Alignment explanation


    Indices: 2148--2242  Score: 111
    Period size: 46  Copynumber: 2.1  Consensus size: 45

       2138 TTTAATCCTC

                   *         *            *    *    * *  
       2148 TTTTTTAGAAAAACAAATTTTCATTCTTCCTTTTAGTCTCTTTTT
          1 TTTTTTAAAAAAACAAACTTTCATTCTTCCCTTTAATCTCATCTT

                                                           
       2193 TTTTTTAAAGAAAACAAACTTTCATTCTCTCCCTTTAATCT-ATCTT
          1 TTTTTTAAA-AAAACAAACTTTCATTCT-TCCCTTTAATCTCATCTT

                
       2239 TTTT
          1 TTTT

       2243 ATTTCTCATG


Statistics
Matches: 42,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  45    8  0.19
  46   24  0.57
  47   10  0.24

ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53


Consensus pattern (45 bp):   
TTTTTTAAAAAAACAAACTTTCATTCTTCCCTTTAATCTCATCTT

Found at i:3024 original size:15 final size:16

Alignment explanation


    Indices: 2999--3036  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       2989 TTTAGGCTGT

                *           
       2999 ACTTCCTTCCTTCCTC
          1 ACTTTCTTCCTTCCTC

                         *  
       3015 -CTTTCTTCCTTCTTC
          1 ACTTTCTTCCTTCCTC

                   
       3030 ACTTTCT
          1 ACTTTCT

       3037 ATTTTTTCTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  15   13  0.68
  16    6  0.32

ACGTcount: A:0.05, C:0.42, G:0.00, T:0.53


Consensus pattern (16 bp):   
ACTTTCTTCCTTCCTC

Found at i:3941 original size:28 final size:27

Alignment explanation


    Indices: 3910--3989  Score: 79
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       3900 GGCATTTCGG

                  *         *           
       3910 TCATTTTCAAAATCTATGGGCATTTTAA
          1 TCATTTGCAAAATC-AGGGGCATTTTAA

                     * *              *
       3938 TCATTTGCACATTCAGGGGCATTTTAG
          1 TCATTTGCAAAATCAGGGGCATTTTAA

                     * * *           
       3965 TCATTTGCATATTGAGGGGCATTTT
          1 TCATTTGCAAAATCAGGGGCATTTT

       3990 GGCCATTTTA


Statistics
Matches: 45,  Mismatches: 7, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  27   34  0.76
  28   11  0.24

ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41


Consensus pattern (27 bp):   
TCATTTGCAAAATCAGGGGCATTTTAA

Found at i:3962 original size:27 final size:27

Alignment explanation


    Indices: 3927--3989  Score: 99
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       3917 CAAAATCTAT

                                       
       3927 GGGCATTTTAATCATTTGCACATTCAG
          1 GGGCATTTTAATCATTTGCACATTCAG

                      *         *   *  
       3954 GGGCATTTTAGTCATTTGCATATTGAG
          1 GGGCATTTTAATCATTTGCACATTCAG

                     
       3981 GGGCATTTT
          1 GGGCATTTT

       3990 GGCCATTTTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   33  1.00

ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40


Consensus pattern (27 bp):   
GGGCATTTTAATCATTTGCACATTCAG

Found at i:3996 original size:27 final size:27

Alignment explanation


    Indices: 3927--3997  Score: 88
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       3917 CAAAATCTAT

                      **               
       3927 GGGCATTTTAATCATTTGCACATTCAG
          1 GGGCATTTTAGCCATTTGCACATTCAG

                       *        *   *  
       3954 GGGCATTTTAGTCATTTGCATATTGAG
          1 GGGCATTTTAGCCATTTGCACATTCAG

                     *       
       3981 GGGCATTTTGGCCATTT
          1 GGGCATTTTAGCCATTT

       3998 TAAGTTAAGG


Statistics
Matches: 39,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   39  1.00

ACGTcount: A:0.21, C:0.15, G:0.24, T:0.39


Consensus pattern (27 bp):   
GGGCATTTTAGCCATTTGCACATTCAG
Done.