Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012680.1 Corchorus olitorius cultivar O-4 contig12713, 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: 4496
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30


Found at i:2221 original size:66 final size:65

Alignment explanation


    Indices: 2112--2304  Score: 298
    Period size: 66  Copynumber: 2.9  Consensus size: 65

       2102 CAGATTTGTT

                                     *             *                   *     
       2112 TCATCAC-AATCAACACCTAAAACAAATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAG
          1 TCATCACTAA-CAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG

              
       2176 TA
         64 TA

                                                                             
       2178 TCATCACTAACAACATCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
          1 TCATCACTAACAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT

             
       2243 A
         65 A

                                         *       *                       
       2244 TCATCACTAACAACACTCAAAACAGATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
          1 TCATCACTAACAACACT-AAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT

       2305 CAGAATTACT


Statistics
Matches: 119,  Mismatches: 6, Indels: 4
        0.92            0.05        0.03

Matches are distributed among these distances:
  65    2  0.02
  66  115  0.97
  67    2  0.02

ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27


Consensus pattern (65 bp):   
TCATCACTAACAACACTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGTA

Found at i:2293 original size:33 final size:33

Alignment explanation


    Indices: 2097--2297  Score: 210
    Period size: 33  Copynumber: 6.1  Consensus size: 33

       2087 GATATCATCC

                           *         *       
       2097 CAAAACAGATTT-GTTTCATCACAATCAACAC-
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                    *                         
       2128 CTAAAACAAATTTAGTGTCATCACAAACAACACT
          1 C-AAAACAGATTTAGTGTCATCACAAACAACACT

                **  *      *       *         
       2162 CAAATTAGTTTTAGTATCATCACTAACAACA-T
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                                  *           
       2194 CTAAAACAGATTTAGTGTCATCGCAAACAACACT
          1 C-AAAACAGATTTAGTGTCATCACAAACAACACT

                **  *      *       *         
       2228 CAAATTAGGTTTAGTATCATCACTAACAACACT
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                        *       **           
       2261 CAAAACAGATTTCGTGTCATTGCAAACAACACT
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                
       2294 CAAA
          1 CAAA

       2298 TTAGGTTCAG


Statistics
Matches: 136,  Mismatches: 29, Indels: 8
        0.79            0.17        0.05

Matches are distributed among these distances:
  31    1  0.01
  32   12  0.09
  33  120  0.88
  34    3  0.02

ACGTcount: A:0.42, C:0.23, G:0.08, T:0.26


Consensus pattern (33 bp):   
CAAAACAGATTTAGTGTCATCACAAACAACACT
Done.