Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021913.1 Corchorus olitorius cultivar O-4 contig21946, 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: 23309
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:2178 original size:24 final size:24

Alignment explanation


    Indices: 2161--2344  Score: 190
    Period size: 24  Copynumber: 7.7  Consensus size: 24

       2151 GGTCTTTTCT

                               *   *
       2161 CACGACCACCATGTGGTCGCATCT
          1 CACGACCACCATGTGGTCGAATCC

                     *      *       
       2185 CACGACCACTATGTGGCCGAATCC
          1 CACGACCACCATGTGGTCGAATCC

                                    
       2209 CACGACCACCATGTGGTCGAATCC
          1 CACGACCACCATGTGGTCGAATCC

                           **      *
       2233 CACGACCACCATGTGACCGAATCT
          1 CACGACCACCATGTGGTCGAATCC

                     *      *      *
       2257 CACGACCACTATGTGGCCGAATCT
          1 CACGACCACCATGTGGTCGAATCC

                *    *      *      *
       2281 CACGCCCACTATGTGGCCGAATCT
          1 CACGACCACCATGTGGTCGAATCC

               *      *             *
       2305 CATGGA-CACTATGTGGTCGAATCT
          1 CA-CGACCACCATGTGGTCGAATCC

                     *      
       2329 CACGACCACTATGTGG
          1 CACGACCACCATGTGG

       2345 CCGTGTGATT


Statistics
Matches: 142,  Mismatches: 16, Indels: 4
        0.88            0.10        0.02

Matches are distributed among these distances:
  23    2  0.01
  24  139  0.98
  25    1  0.01

ACGTcount: A:0.24, C:0.34, G:0.21, T:0.20


Consensus pattern (24 bp):   
CACGACCACCATGTGGTCGAATCC

Found at i:2237 original size:48 final size:48

Alignment explanation


    Indices: 2158--2347  Score: 274
    Period size: 48  Copynumber: 4.0  Consensus size: 48

       2148 ATTGGTCTTT

                                  *                         
       2158 TCTCACGACCACCATGTGGTCGCATCTCACGACCACTATGTGGCCGAA
          1 TCTCACGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCGAA

              *                       *         *     *     
       2206 TCCCACGACCACCATGTGGTCGAATCCCACGACCACCATGTGACCGAA
          1 TCTCACGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCGAA

                        *      *           *                
       2254 TCTCACGACCACTATGTGGCCGAATCTCACGCCCACTATGTGGCCGAA
          1 TCTCACGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCGAA

                  *      *                                 
       2302 TCTCATGGA-CACTATGTGGTCGAATCTCACGACCACTATGTGGCCG
          1 TCTCA-CGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCG

       2348 TGTGATTTTC


Statistics
Matches: 126,  Mismatches: 15, Indels: 2
        0.88            0.10        0.01

Matches are distributed among these distances:
  48  124  0.98
  49    2  0.02

ACGTcount: A:0.24, C:0.35, G:0.21, T:0.21


Consensus pattern (48 bp):   
TCTCACGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCGAA

Found at i:2267 original size:72 final size:72

Alignment explanation


    Indices: 2161--2347  Score: 268
    Period size: 72  Copynumber: 2.6  Consensus size: 72

       2151 GGTCTTTTCT

                               *                                            *
       2161 CACGACCACCATGTGGTCGCATCTCACGACCACTATGTGGCCGAATCCCACGACCACCATGTGGT
          1 CACGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCGAATCCCACGACCACCATGTGGC

                   
       2226 CGAATCC
         66 CGAATCC

                           **                              *    *    *       
       2233 CACGACCACCATGTGACCGAATCTCACGACCACTATGTGGCCGAATCTCACGCCCACTATGTGGC
          1 CACGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCGAATCCCACGACCACCATGTGGC

                  *
       2298 CGAATCT
         66 CGAATCC

               *      *                                 
       2305 CATGGA-CACTATGTGGTCGAATCTCACGACCACTATGTGGCCG
          1 CA-CGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCG

       2348 TGTGATTTTC


Statistics
Matches: 102,  Mismatches: 12, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  72  100  0.98
  73    2  0.02

ACGTcount: A:0.24, C:0.35, G:0.21, T:0.20


Consensus pattern (72 bp):   
CACGACCACCATGTGGTCGAATCTCACGACCACTATGTGGCCGAATCCCACGACCACCATGTGGC
CGAATCC
Done.