Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012324.1 Corchorus olitorius cultivar O-4 contig12357, 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: 15107
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:3776 original size:19 final size:19

Alignment explanation


    Indices: 3752--3789  Score: 60
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       3742 ACACATTAAA

                                
       3752 GCAAAATGTA-ATATATTTT
          1 GCAAAATGTATA-ATATTTT

                               
       3771 GCAAAATGTATAATATTTT
          1 GCAAAATGTATAATATTTT

       3790 CTTTCCCACA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  19   17  0.94
  20    1  0.06

ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42


Consensus pattern (19 bp):   
GCAAAATGTATAATATTTT

Found at i:5428 original size:139 final size:132

Alignment explanation


    Indices: 5185--5456  Score: 368
    Period size: 139  Copynumber: 2.0  Consensus size: 132

       5175 CTGAATTGCA

                                              *                          *   
       5185 TACTTTTCTTTAGAGTATTCATCAGATACATCTTTACTCCTGCAAAGTACTTACCTTGCTTTTCA
          1 TACTTTTCTTTAGAGTATTCATCAGATACATCTTAACTCCTGCAAAGTACTTACCTTGCTTCTCA

                                                                          *  
       5250 AGAAATATATTCGATTTATGTTAAAGCATTCCGAGAGTAAAATCCTAAATGCATCAATGTAGGAA
         66 AGAAATATATTCGATTTATGTTAAAGCATTCCGAGAGTAAAATCCTAAATGCATCAATGTAGAAA

              
       5315 TG
        131 TG

                                    *                                 *      
       5317 TACTTTTCTTTAGAGTATTCATCATATACAAT-TTAAACTCCTGCAATTTAAAAGTATTTTA-CT
          1 TACTTTTCTTTAGAGTATTCATCAGATAC-ATCTT-AACTCCTGC------AAAGTA-CTTACCT

                                 *                 *               *         
       5380 TGCTTCTCAAGAAATATATTCTATTTATGTTAAAGCATTTCGAGAGTAAAATCCTGAATGCATCA
         57 TGCTTCTCAAGAAATATATTCGATTTATGTTAAAGCATTCCGAGAGTAAAATCCTAAATGCATCA

            *          
       5445 GTGTAGAAATG
        122 ATGTAGAAATG

             
       5456 T
          1 T

       5457 CCACATTACT


Statistics
Matches: 122,  Mismatches: 9, Indels: 11
        0.86            0.06        0.08

Matches are distributed among these distances:
 132   30  0.25
 133   10  0.08
 139   79  0.65
 140    3  0.02

ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38


Consensus pattern (132 bp):   
TACTTTTCTTTAGAGTATTCATCAGATACATCTTAACTCCTGCAAAGTACTTACCTTGCTTCTCA
AGAAATATATTCGATTTATGTTAAAGCATTCCGAGAGTAAAATCCTAAATGCATCAATGTAGAAA
TG

Found at i:14645 original size:17 final size:19

Alignment explanation


    Indices: 14599--14645  Score: 55
    Period size: 17  Copynumber: 2.6  Consensus size: 19

      14589 AGTATAATAA

                               
      14599 TTTT-TTAATTAATATTCT
          1 TTTTATTAATTAATATTCT

                 * *           
      14617 TTTTAGTCATTAA-ATT-T
          1 TTTTATTAATTAATATTCT

                        
      14634 TTTTATTAATTA
          1 TTTTATTAATTA

      14646 TAAAAAGATA


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  17   11  0.46
  18    7  0.29
  19    6  0.25

ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64


Consensus pattern (19 bp):   
TTTTATTAATTAATATTCT

Found at i:15096 original size:117 final size:116

Alignment explanation


    Indices: 14847--15107  Score: 395
    Period size: 117  Copynumber: 2.2  Consensus size: 116

      14837 TGGAAGAACA

                                                          *      *           
      14847 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTCATTTTCCATTTCAAACCACT
          1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTCAATTTCCACTTCAAACCACT

                                                         *  *  
      14912 CTACCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCGAAGGC
         66 CTACCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAACGC

                                                                             
      14963 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCTCAAGTCC-TCAAATTTCCACTTCAAACC
          1 TCCACCACAACCATGAATATTGTTTTGAGGAA-TT-TCAAGTCCTTC-AATTTCCACTTCAAACC

                  *                                     *           
      15027 AACTCTTCC-ATAAAAATAGTAT-AATTACTCCTTAATTCTTAGGT-TCCAAACGC
         63 -ACTCTACCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCT-CAAACGC

                                        
      15080 TCCACCACAACCATGAATATTGTTTTGA
          1 TCCACCACAACCATGAATATTGTTTTGA


Statistics
Matches: 134,  Mismatches: 6, Indels: 9
        0.90            0.04        0.06

Matches are distributed among these distances:
 116   33  0.25
 117   58  0.43
 118   36  0.27
 119    7  0.05

ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33


Consensus pattern (116 bp):   
TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTCAATTTCCACTTCAAACCACT
CTACCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAACGC
Done.