Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013064.1 Corchorus olitorius cultivar O-4 contig13097, 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: 19453
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:2927 original size:38 final size:38

Alignment explanation


    Indices: 2811--3337  Score: 245
    Period size: 39  Copynumber: 13.9  Consensus size: 38

       2801 TTTATCTAAC

                                              *  * 
       2811 TAAACCTGCTTAGGTCTCTGTTTAGAAGTTTC--AT-CG
          1 TAAACCTGCTTAGGTCTCTGTTTAG-AGTTTCGTTTAAG

                   *     *    *     * *     *      
       2847 --AACCTACTTAGATCTCCGTTTACAATTTCCATTTAAG
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTT-CGTTTAAG

                                *                 
       2884 TAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTTTAAG
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTTTAAG

            *     **  *  *      *      *    *    * 
       2922 AAAACCCACTCAGCTCTCTGCTTAGAATTTTCATTTATG
          1 TAAACCTGCTTAGGTCTCTGTTTAG-AGTTTCGTTTAAG

                     *       *    *            * *   
       2961 -AAGACCTGTTTAGGATTTCTGCTTAGAGCTTT-GATCAAG
          1 TAA-ACCTGCTTAGG-TCTCTGTTTAGAG-TTTCGTTTAAG

                 *        * *             * *      
       3000 TAAACTTGCTTAGGCCCCTGTTTAGAGTTGCCATTTAAG
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTT-TCGTTTAAG

                 *           *        *    *      
       3039 TAAACATGCTTAGGTCTATGTTTAGAATTTCATTTAAG
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTTTAAG

            *     *         * ***     * *      * *
       3077 AAAACCCGCTTAGGTCCCCACTTAGAATCTCGTTTGAT
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTTTAAG

               *  * *                              
       3115 TAAGCCCGTTTAGGTCTCTGTTTAGAGTTTCCGTTTAAG
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTT-CGTTTAAG

                        *      *     * *    *      
       3154 TAAACCTGCTTAAGTCTCTATTTATAATTTTCATTTAAG
          1 TAAACCTGCTTAGGTCTCTGTTTA-GAGTTTCGTTTAAG

             *      *  *        *                 
       3193 TGAACCTGTTTTGGTCTCTGATTAGAGTTTCGTTT-AG
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTTTAAG

                 *   *  *    **    *   *      *       
       3230 -AAACTTGTGTTTGAGTGACTGTCTAGTGTTTCATTTTGAA-
          1 TAAACCTG-CTTAG-GTCTCTGTTTAGAGTTTC-GTTT-AAG

            *       *                  *          
       3270 AAAACCTGTTTAGGTCTCTGTTTAGAGCTTCG--T-A-
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTTTAAG

                             *                
       3304 TAAACCTGCTTAGGTCTTTGTTTAGAGTTTCGTT
          1 TAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTT

       3338 CAGAAAATTT


Statistics
Matches: 357,  Mismatches: 111, Indels: 46
        0.69            0.22        0.09

Matches are distributed among these distances:
  33    4  0.01
  34   49  0.14
  36    7  0.02
  37    9  0.03
  38  114  0.32
  39  145  0.41
  40   22  0.06
  41    7  0.02

ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40


Consensus pattern (38 bp):   
TAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTTTAAG

Found at i:3309 original size:34 final size:34

Alignment explanation


    Indices: 3271--3336  Score: 105
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       3261 CATTTTGAAA

                   *                          
       3271 AAACCTGTTTAGGTCTCTGTTTAGAGCTTCGTAT
          1 AAACCTGCTTAGGTCTCTGTTTAGAGCTTCGTAT

                            *         *     
       3305 AAACCTGCTTAGGTCTTTGTTTAGAGTTTCGT
          1 AAACCTGCTTAGGTCTCTGTTTAGAGCTTCGT

       3337 TCAGAAAATT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   29  1.00

ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42


Consensus pattern (34 bp):   
AAACCTGCTTAGGTCTCTGTTTAGAGCTTCGTAT

Found at i:16959 original size:2 final size:2

Alignment explanation


    Indices: 16952--16980  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      16942 ATGCAATCAA

                                                       
      16952 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A

      16981 TATATATATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:17472 original size:26 final size:27

Alignment explanation


    Indices: 17443--17514  Score: 101
    Period size: 27  Copynumber: 2.7  Consensus size: 27

      17433 AGTGAACTTG

                   *                   
      17443 AAATGACCAAAATGCCCCTA-ATGCAC
          1 AAATGACTAAAATGCCCCTAGATGCAC

                                    ** 
      17469 AAATGACTAAAATGCCCCTAGATGTGC
          1 AAATGACTAAAATGCCCCTAGATGCAC

                  *            
      17496 AAATGAGTAAAATGCCCCT
          1 AAATGACTAAAATGCCCCT

      17515 GGACGACCCT


Statistics
Matches: 41,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  26   19  0.46
  27   22  0.54

ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19


Consensus pattern (27 bp):   
AAATGACTAAAATGCCCCTAGATGCAC

Done.