Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021882.1 Corchorus olitorius cultivar O-4 contig21915, 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: 15682
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:5896 original size:45 final size:46

Alignment explanation


    Indices: 5819--5906  Score: 142
    Period size: 45  Copynumber: 1.9  Consensus size: 46

       5809 AGCAACTATT

                         *    *        *                  
       5819 AATATTAGCTTTTTTTTTTATGAATTATCTAGAGATGGAGTAGTAG
          1 AATATTAGCTTTTATTTTGATGAATTACCTAGAGATGGAGTAGTAG

                                                       
       5865 AATATTAGC-TTTATTTTGATGAATTACCTAGAGATGGAGTAG
          1 AATATTAGCTTTTATTTTGATGAATTACCTAGAGATGGAGTAG

       5907 CATTTAGGTA


Statistics
Matches: 39,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  45   30  0.77
  46    9  0.23

ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42


Consensus pattern (46 bp):   
AATATTAGCTTTTATTTTGATGAATTACCTAGAGATGGAGTAGTAG

Found at i:11325 original size:22 final size:21

Alignment explanation


    Indices: 11277--11325  Score: 53
    Period size: 22  Copynumber: 2.3  Consensus size: 21

      11267 TTACCCTTCT

                  *             *
      11277 TCTCTCTTCCCCCACTAACTC
          1 TCTCTCCTCCCCCACTAACTA

             *               *    
      11298 TTTCTCCTCCTCCCACTCACTA
          1 TCTCTCCTCC-CCCACTAACTA

                  
      11320 TCTCTC
          1 TCTCTC

      11326 TTCATAAATT


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  21    8  0.36
  22   14  0.64

ACGTcount: A:0.12, C:0.51, G:0.00, T:0.37


Consensus pattern (21 bp):   
TCTCTCCTCCCCCACTAACTA

Found at i:11872 original size:19 final size:19

Alignment explanation


    Indices: 11848--11888  Score: 82
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      11838 GGCAGTCGCC

                               
      11848 CTTCCAAAGTTTAAAAATA
          1 CTTCCAAAGTTTAAAAATA

                               
      11867 CTTCCAAAGTTTAAAAATA
          1 CTTCCAAAGTTTAAAAATA

               
      11886 CTT
          1 CTT

      11889 ATATATGTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34


Consensus pattern (19 bp):   
CTTCCAAAGTTTAAAAATA

Found at i:14665 original size:9 final size:9

Alignment explanation


    Indices: 14651--14676  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      14641 ATTCTAAAAT

                     
      14651 TTTCTTTTA
          1 TTTCTTTTA

                     
      14660 TTTCTTTTA
          1 TTTCTTTTA

                    
      14669 TTTCTTTT
          1 TTTCTTTT

      14677 TCCCCTTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81


Consensus pattern (9 bp):   
TTTCTTTTA

Found at i:14806 original size:18 final size:18

Alignment explanation


    Indices: 14783--14820  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      14773 CAATCGGCCC

                              
      14783 CTTTCTCTCTCTTTTTTT
          1 CTTTCTCTCTCTTTTTTT

                  *   *       
      14801 CTTTCTTTCTTTTTTTTT
          1 CTTTCTCTCTCTTTTTTT

              
      14819 CT
          1 CT

      14821 CTATTTGGCT


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

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (18 bp):   
CTTTCTCTCTCTTTTTTT
Done.