Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023150.1 Corchorus olitorius cultivar O-4 contig23183, 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: 15879
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:443 original size:27 final size:27

Alignment explanation


    Indices: 413--488  Score: 107
    Period size: 27  Copynumber: 2.8  Consensus size: 27

        403 TGACCGAGAC

                *     *                
        413 GCCCTTGAACGTGCAAATGACCAAAAT
          1 GCCCCTGAACATGCAAATGACCAAAAT

                   *             *     
        440 GCCCCTGGACATGCAAATGACTAAAAT
          1 GCCCCTGAACATGCAAATGACCAAAAT

            *                     
        467 ACCCCTGAACATGCAAATGACC
          1 GCCCCTGAACATGCAAATGACC

        489 CCAAAATTCC


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   42  1.00

ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17


Consensus pattern (27 bp):   
GCCCCTGAACATGCAAATGACCAAAAT

Found at i:9172 original size:19 final size:18

Alignment explanation


    Indices: 9148--9186  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       9138 AAATATCTCC

                               
       9148 AATTAGGGCTAATTGCACA
          1 AATTAGGGC-AATTGCACA

                  **          
       9167 AATTAGTTCAATTGCACA
          1 AATTAGGGCAATTGCACA

              
       9185 AA
          1 AA

       9187 AACAAGAACC


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18   11  0.61
  19    7  0.39

ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28


Consensus pattern (18 bp):   
AATTAGGGCAATTGCACA

Found at i:11950 original size:145 final size:144

Alignment explanation


    Indices: 11687--12267  Score: 828
    Period size: 145  Copynumber: 4.0  Consensus size: 144

      11677 TTATCCTTTT

                                                  *     *                    
      11687 GTATCATCTCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAAGTTTCAAAATCAAAACCTTGC
          1 GTATCATCTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATCAAAACCTTGC

                       *  *                      *    *                      
      11752 TCAAGGTCGAGGTTACATTTGTAAGACCTCCGGGCACCATTTTAGAAACCTCCGGGTATTAATTC
         66 TCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTC

                           
      11817 TGATAAATCCTCTAG
        131 TGATAAATCCTCT-G

                                          *             *                    
      11832 GTATCATCTCATTTCATCAAGTTTTTAATCGAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGC
          1 GTATCATCTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATCAAAACCTTGC

                                                                             
      11897 TCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTC
         66 TCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTC

                     *     
      11962 TGATAAATCTTCCTG
        131 TGATAAATCCT-CTG

                   *                                                         
      11977 GTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATCAAAACCTTGC
          1 GTATCATCTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATCAAAACCTTGC

                                         *       *      *      *             
      12042 TCAAGGTCGAGTTTGCATTTGTAAGACCTTCGGGCACCATTTCATAAACCTTCGGGTATTAATTC
         66 TCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTC

                         * 
      12107 TGATAAATCCTCCGG
        131 TGATAAATCCT-CTG

                                             *                          *    
      12122 GTATCATCTCATTTCATCAAGTTTTTAATCAAATTTGCGTTTAAATTTC--AAT--AAACTTTGC
          1 GTATCATCTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATCAAAACCTTGC

                                                  *           *    *    *    
      12183 TCAAGGTCTTTACTCAGAGTTTGCATTTGTAAGACCTCGGGGCACAATTTAAGAATCCTCTGGGT
         66 TCAAGG-------TC-GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGT

                       *  *     
      12248 ATTAATTCTGACAAGTCCTC
        123 ATTAATTCTGATAAATCCTC

      12268 CGGGCATTCC


Statistics
Matches: 398,  Mismatches: 29, Indels: 15
        0.90            0.07        0.03

Matches are distributed among these distances:
 141   14  0.04
 143    3  0.01
 145  318  0.80
 146    2  0.01
 148    3  0.01
 149   58  0.15

ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35


Consensus pattern (144 bp):   
GTATCATCTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATCAAAACCTTGC
TCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTC
TGATAAATCCTCTG

Found at i:15522 original size:47 final size:47

Alignment explanation


    Indices: 15469--15575  Score: 119
    Period size: 47  Copynumber: 2.3  Consensus size: 47

      15459 TATTTGCCAT

                        *               *       *            
      15469 TTAGTTTAATTATCT-GGACTTAAACCAGCCTCTT-TTCCTTTTACTAC
          1 TTAGTTTAATTACCTAGGA-TTAAACCAACCTCTTCCT-CTTTTACTAC

                                    **  *                  
      15516 TTAGTTTAATTACCTAGGATTAAATTAATCTCTTCCTCTTTTACTAC
          1 TTAGTTTAATTACCTAGGATTAAACCAACCTCTTCCTCTTTTACTAC

                         
      15563 TTAGTTGTAATTA
          1 TTAGTT-TAATTA

      15576 AACTAATCTC


Statistics
Matches: 51,  Mismatches: 6, Indels: 5
        0.82            0.10        0.08

Matches are distributed among these distances:
  47   41  0.80
  48   10  0.20

ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47


Consensus pattern (47 bp):   
TTAGTTTAATTACCTAGGATTAAACCAACCTCTTCCTCTTTTACTAC
Done.