Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007734.1 Corchorus olitorius cultivar O-4 contig07760, 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, 628

Length: 1047
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24


Found at i:198 original size:87 final size:86

Alignment explanation


    Indices: 1--331  Score: 501
    Period size: 85  Copynumber: 3.8  Consensus size: 86

                                         *       *         *                *
          1 CCCAAACACATACTATAACACAGGGG-CATCTCTATTCCAAAAGTCCCCAAACACATATATAACG
          1 CCCAAACACATACTATAACACAGGGGACACCTCTATTAC-AAAGTCCTCAAACACATATATAACA

                    *  *           
         65 CAGAGGCACCTGTATTC-AAGTC
         65 CAGAGGCATCTATA-TCAAAGTC

                                                                             
         87 CCCAAACACATACTATAACACAGGGGACGACCT-TATTACAAAGTCCTCTAAACACATATATAAC
          1 CCCAAACACATACTATAACACAGGGGAC-ACCTCTATTACAAAGTCCTC-AAACACATATATAAC

                                    
        151 ACACGAGGCATCTATATCAAAGTC
         64 ACA-GAGGCATCTATATCAAAGTC

                                                                             
        175 CCCAAACACATA-TATAACACAGGGGACACCTCTATTACAAAGTCCTCAAACACATATATAACAC
          1 CCCAAACACATACTATAACACAGGGGACACCTCTATTACAAAGTCCTCAAACACATATATAACAC

                    *            
        239 AGAGGCATTTATATCAAAGTC
         66 AGAGGCATCTATATCAAAGTC

                                      *  *                                   
        260 CCCAAACACATA-TATAACACAGGGGGCATCTCTATTACAAAGTCCTCAAACACATATATAACAC
          1 CCCAAACACATACTATAACACAGGGGACACCTCTATTACAAAGTCCTCAAACACATATATAACAC

                    
        324 AGAGGCAT
         66 AGAGGCAT

        332 TTCTCCTCAT


Statistics
Matches: 230,  Mismatches: 9, Indels: 13
        0.91            0.04        0.05

Matches are distributed among these distances:
  85   89  0.39
  86   56  0.24
  87   55  0.24
  88   30  0.13

ACGTcount: A:0.40, C:0.27, G:0.12, T:0.20


Consensus pattern (86 bp):   
CCCAAACACATACTATAACACAGGGGACACCTCTATTACAAAGTCCTCAAACACATATATAACAC
AGAGGCATCTATATCAAAGTC

Found at i:216 original size:44 final size:43

Alignment explanation


    Indices: 1--330  Score: 381
    Period size: 44  Copynumber: 7.6  Consensus size: 43

                                        *       *        
          1 CCCAAACACATACTATAACACAGGGGCATCTCTATTCCAAAAGTC
          1 CCCAAACACATA-TATAACACAGGGGCACCTCTATTAC-AAAGTC

                              *   *       *            
         46 CCCAAACACATATATAACGCAGAGGCACCTGTATT-C-AAGTC
          1 CCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTC

                                                          
         87 CCCAAACACATACTATAACACAGGGGACGACCT-TATTACAAAGTC
          1 CCCAAACACATA-TATAACACAGGGG-C-ACCTCTATTACAAAGTC

               *                    *                     
        132 CTCTAAACACATATATAACACACGAGGCA--TCTA-TATCAAAGTC
          1 C-CCAAACACATATATAACACA-GGGGCACCTCTATTA-CAAAGTC

                                                        
        175 CCCAAACACATATATAACACAGGGGACACCTCTATTACAAAGTC
          1 CCCAAACACATATATAACACAGGGG-CACCTCTATTACAAAGTC

             *                    *       *             
        219 CTCAAACACATATATAACACAGAGGCA--TTTA-TATCAAAGTC
          1 CCCAAACACATATATAACACAGGGGCACCTCTATTA-CAAAGTC

                                        *               
        260 CCCAAACACATATATAACACAGGGGGCATCTCTATTACAAAGTC
          1 CCCAAACACATATATAACACA-GGGGCACCTCTATTACAAAGTC

             *                    *    
        304 CTCAAACACATATATAACACAGAGGCA
          1 CCCAAACACATATATAACACAGGGGCA

        331 TTTCTCCTCA


Statistics
Matches: 249,  Mismatches: 18, Indels: 38
        0.82            0.06        0.12

Matches are distributed among these distances:
  40    2  0.01
  41   50  0.20
  42   40  0.16
  43   23  0.09
  44   89  0.36
  45   32  0.13
  46   13  0.05

ACGTcount: A:0.41, C:0.28, G:0.12, T:0.20


Consensus pattern (43 bp):   
CCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTC

Found at i:487 original size:2 final size:2

Alignment explanation


    Indices: 440--478  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        430 ACCAAATTCC

                                                                       
        440 TA TA T- 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 TA

        479 CACATATATG


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   35  0.97

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.