Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005888.1 Corchorus olitorius cultivar O-4 contig05913, 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, 786

Length: 1310
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32


Found at i:131 original size:33 final size:32

Alignment explanation


    Indices: 59--156  Score: 99
    Period size: 33  Copynumber: 3.0  Consensus size: 32

         49 CTATGATCAA

                    *                 ** *   
         59 CCAAAACATATTTGTTTTCATCACAATTAGCAT
          1 CCAAAACAAATTTG-TTTCATCACAAACAACAT

                                             
         92 CCAAAACAAAATTTGTTTCATCACAAACAACA-
          1 CCAAAAC-AAATTTGTTTCATCACAAACAACAT

                     *       *               
        124 CCTAAAACAGATTTAGTGTCATCACAAACAACA
          1 CC-AAAACAAATTT-GTTTCATCACAAACAACA

        157 ATTAAATCAG


Statistics
Matches: 56,  Mismatches: 6, Indels: 6
        0.82            0.09        0.09

Matches are distributed among these distances:
  32    7  0.12
  33   43  0.77
  34    6  0.11

ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27


Consensus pattern (32 bp):   
CCAAAACAAATTTGTTTCATCACAAACAACAT

Found at i:172 original size:33 final size:33

Alignment explanation


    Indices: 109--198  Score: 108
    Period size: 33  Copynumber: 2.7  Consensus size: 33

         99 AAAATTTGTT

                           *                *
        109 TCATCACAAACAACACCTAAAACAGATTTAGTG
          1 TCATCACAAACAACAACTAAAACAGATTTAGTA

                            *    *   *       
        142 TCATCACAAACAACAATTAAATCAGGTTTAGTA
          1 TCATCACAAACAACAACTAAAACAGATTTAGTA

                   *  *    *        
        175 TCATCACTAATAACATCTAAAACA
          1 TCATCACAAACAACAACTAAAACA

        199 CTCTTTGCAA


Statistics
Matches: 47,  Mismatches: 10, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  33   47  1.00

ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24


Consensus pattern (33 bp):   
TCATCACAAACAACAACTAAAACAGATTTAGTA
Done.