Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010446.1 Corchorus olitorius cultivar O-4 contig10478, 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: 3248
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:308 original size:154 final size:152

Alignment explanation


    Indices: 1--323  Score: 504
    Period size: 154  Copynumber: 2.1  Consensus size: 152

                                    *           *         *                  
          1 AGGCCATAAACAATGGAAAGAAAAGCATCGTGGGTTGCCAAATCGAGGAAGATTCAAAACGGAAC
          1 AGGCCATAAACAATGGAAAGAAAAACATCGTGGGTTACCAAATCGAAGAAGATTCAAAACGGAAC

                                                                             
         66 TAATGGGCCCGAAAGGCCTAAAATAACAAGTGTTCCAATGAGCTAAAAACTTCACAGTGGACTAA
         66 TAATGGGCCCGAAAGGCCTAAAATAACAAGTGTTCCAATGAGCTAAAAACTTCACAGTGGACTAA

                                  
        131 TCTCACCAAAATGATTATAGTT
        131 TCTCACCAAAATGATTATAGTT

                                        *    *               *    *      **  
        153 AGGCCATAAACAATGGAAAGAAAAACATTGTGGTTTACCAAATCGAAGATGATTTAAAACGTCAC
          1 AGGCCATAAACAATGGAAAGAAAAACATCGTGGGTTACCAAATCGAAGAAGATTCAAAACGGAAC

                      *  *                                                   
        218 TAATGGGCCTTGATAGGCAC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
         66 TAATGGGCC-CGAAAGGC-CTAAAATAACAAGTGTTCC-AATGAGCTAAAAACTTCACAGTGGAC

                                 *   
        282 TAATCTCACCAAAATGATTATTGTT
        128 TAATCTCACCAAAATGATTATAGTT

                             
        307 AGGCCATAAACAATGGA
          1 AGGCCATAAACAATGGA

        324 TCAACTCTCC


Statistics
Matches: 156,  Mismatches: 12, Indels: 4
        0.91            0.07        0.02

Matches are distributed among these distances:
 152   65  0.42
 153   23  0.15
 154   68  0.44

ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22


Consensus pattern (152 bp):   
AGGCCATAAACAATGGAAAGAAAAACATCGTGGGTTACCAAATCGAAGAAGATTCAAAACGGAAC
TAATGGGCCCGAAAGGCCTAAAATAACAAGTGTTCCAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATAGTT

Found at i:1422 original size:25 final size:24

Alignment explanation


    Indices: 1385--1431  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1375 CTAGAAAATT

                                      
       1385 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       1411 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1432 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA
Done.