Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015813.1 Corchorus olitorius cultivar O-4 contig15846, 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: 2188
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:145 original size:32 final size:32

Alignment explanation


    Indices: 62--150  Score: 90
    Period size: 32  Copynumber: 2.8  Consensus size: 32

         52 TAATAGTGCA

                                         **  
         62 TATGACATCTTCAAGTGTCTATTGGAAATTTAT
          1 TATGACATCTTCAAGTGTCTATT-GAAATAAAT

            *      *    **     *             
         95 CATGACAACTTCTGGTGTCAATTG-AATAAAAT
          1 TATGACATCTTCAAGTGTCTATTGAAAT-AAAT

                                    
        127 TATGACATCTTCAAGTGTCTATTG
          1 TATGACATCTTCAAGTGTCTATTG

        151 CAAGATCATG


Statistics
Matches: 43,  Mismatches: 12, Indels: 3
        0.74            0.21        0.05

Matches are distributed among these distances:
  31    3  0.07
  32   22  0.51
  33   18  0.42

ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38


Consensus pattern (32 bp):   
TATGACATCTTCAAGTGTCTATTGAAATAAAT

Found at i:175 original size:30 final size:30

Alignment explanation


    Indices: 95--454  Score: 432
    Period size: 30  Copynumber: 11.7  Consensus size: 30

         85 GGAAATTTAT

                                      *  * *
         95 CATGACAACTTCTGGTGTCAATTGAATAAAAT
          1 CATGACAACTTCTGGTGTCAATTG--CAAGAC

            *      *    **     *         *
        127 TATGACATCTTCAAGTGTCTATTGCAAGAT
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                   *                   * *
        157 CATGACAGCTTCTGGTGTCAATTGCAACAT
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                   *                      
        187 CATGACAGCTTCTGGTGTCAATTGCAAGAC
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                         *                
        217 CATGACAACTTCTAGTGTCAATTGCAAGAC
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                                                 
        247 CATGACAACTTCTGGTGTCAATTGCAAATTGCAAGGC
          1 CATGACAACTTCTGGTGTCAATTGC-AA--G--A--C

                         *              * 
        284 CATGACAACTTCTAGTGTCAATTGCAAGGC
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                                        * 
        314 CATGACAACTTCTGGTGTCAATTGCAAGGC
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                                *       * 
        344 CATGACAACTTCTGGTGTCATTTGCAAGGC
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                                *       * 
        374 CATGACAACTTCTGGTGTCATTTGCAAGGC
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                                *       * 
        404 CATGACAACTTCTGGTGTCATTTGCAAGGC
          1 CATGACAACTTCTGGTGTCAATTGCAAGAC

                                 
        434 CATGACAACTTCTGGTGTCAA
          1 CATGACAACTTCTGGTGTCAA

        455 CGTATATTAG


Statistics
Matches: 298,  Mismatches: 23, Indels: 16
        0.88            0.07        0.05

Matches are distributed among these distances:
  30  247  0.83
  31    2  0.01
  32   19  0.06
  33    1  0.00
  34    1  0.00
  35    1  0.00
  36    2  0.01
  37   25  0.08

ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29


Consensus pattern (30 bp):   
CATGACAACTTCTGGTGTCAATTGCAAGAC

Found at i:377 original size:157 final size:157

Alignment explanation


    Indices: 128--430  Score: 462
    Period size: 157  Copynumber: 1.9  Consensus size: 157

        118 GAATAAAATT

                  *           *         *       *                     *      
        128 ATGACATCTTCAAGTGTCTATTGCAAGATCATGACAGCTTCTGGTGTCAATTGCAACATCATGAC
          1 ATGACAACTTCAAGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAACACCATGAC

             *                                                               
        193 AGCTTCTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCAATTGCAAGACCATGACAACTT
         66 AACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCAATTGCAAGACCATGACAACTT

                                       
        258 CTGGTGTCAATTGCAAATTGCAAGGCC
        131 CTGGTGTCAATTGCAAATTGCAAGGCC

                       *               *                            **       
        285 ATGACAACTTCTAGTGTCAATTGCAAGGCCATGACAACTTCTGGTGTCAATTGCAAGGCCATGAC
          1 ATGACAACTTCAAGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAACACCATGAC

                          *       *              *      *       *            
        350 AACTTCTGGTGTCATTTGCAAGGCCATGACAACTTCTGGTGTCATTTGCAAGGCCATGACAACTT
         66 AACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCAATTGCAAGACCATGACAACTT

                     *      
        415 CTGGTGTCATTTGCAA
        131 CTGGTGTCAATTGCAA

        431 GGCCATGACA


Statistics
Matches: 130,  Mismatches: 16, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
 157  130  1.00

ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29


Consensus pattern (157 bp):   
ATGACAACTTCAAGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAACACCATGAC
AACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTAGTGTCAATTGCAAGACCATGACAACTT
CTGGTGTCAATTGCAAATTGCAAGGCC

Found at i:2151 original size:2 final size:2

Alignment explanation


    Indices: 2144--2181  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       2134 TCTTTTCAAC

                                                                    
       2144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2182 CTAACAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.