Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023793.1 Corchorus olitorius cultivar O-4 contig23826, 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: 20105
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:5227 original size:2 final size:2

Alignment explanation


    Indices: 5220--5255  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       5210 TGGAAGCGAA

                                                **               
       5220 AG AG AG AG AG AG AG AG AG AG AG AG CC AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       5256 CCCCATCTCT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.47, C:0.06, G:0.47, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:7409 original size:16 final size:16

Alignment explanation


    Indices: 7369--7402  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       7359 TTGGCCTTAA

                *           
       7369 GTCACTCGGGTTTTGG
          1 GTCATTCGGGTTTTGG

                            
       7385 GTCATTCGGGTTTTGG
          1 GTCATTCGGGTTTTGG

              
       7401 GT
          1 GT

       7403 TTTTCGGCTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.06, C:0.15, G:0.38, T:0.41


Consensus pattern (16 bp):   
GTCATTCGGGTTTTGG

Found at i:7916 original size:27 final size:27

Alignment explanation


    Indices: 7874--7930  Score: 96
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       7864 ATTTTTTTAG

                       *           *   
       7874 TTGTTTAAGTCGGTTAGAAAGAATATA
          1 TTGTTTAAGTCAGTTAGAAAGAAGATA

                                       
       7901 TTGTTTAAGTCAGTTAGAAAGAAGATA
          1 TTGTTTAAGTCAGTTAGAAAGAAGATA

               
       7928 TTG
          1 TTG

       7931 CATTGGCCGT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37


Consensus pattern (27 bp):   
TTGTTTAAGTCAGTTAGAAAGAAGATA

Found at i:8089 original size:42 final size:43

Alignment explanation


    Indices: 8038--8131  Score: 120
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       8028 AGTGCATTAC

                                   **                 *
       8038 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAA

                                *                        
       8079 CTAATATTCTACTCCTCCATTTCTAAATAATTCATCAAAATAAAA
          1 CTAATATTCTA--CCTCCATCTCTAAATAATTCATCAAAATAAAA

                    
       8124 CTAATATT
          1 CTAATATT

       8132 AATTGTTGCT


Statistics
Matches: 45,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    6  0.13
  45   35  0.78

ACGTcount: A:0.40, C:0.21, G:0.03, T:0.35


Consensus pattern (43 bp):   
CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAA

Found at i:9334 original size:19 final size:19

Alignment explanation


    Indices: 9303--9354  Score: 79
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       9293 AAACTAAAAC

                                
       9303 CCAGCTGCC-ACCATGAACA
          1 CCAGC-GCCGACCATGAACA

                               
       9322 CCAGCGCCGACCATGAACA
          1 CCAGCGCCGACCATGAACA

               *          
       9341 CCACCGCCGACCAT
          1 CCAGCGCCGACCAT

       9355 CGTCTACAGC


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  18    3  0.10
  19   28  0.90

ACGTcount: A:0.29, C:0.46, G:0.17, T:0.08


Consensus pattern (19 bp):   
CCAGCGCCGACCATGAACA

Found at i:11181 original size:22 final size:24

Alignment explanation


    Indices: 11141--11186  Score: 69
    Period size: 22  Copynumber: 2.0  Consensus size: 24

      11131 CACTTTGCTC

                                    
      11141 CTTGTCCATGAATGGAACTTGAAG
          1 CTTGTCCATGAATGGAACTTGAAG

                      *             
      11165 CTTG-CCATGGAT-GAACTTGAAG
          1 CTTGTCCATGAATGGAACTTGAAG

      11187 AACTAGATTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   10  0.48
  23    7  0.33
  24    4  0.19

ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28


Consensus pattern (24 bp):   
CTTGTCCATGAATGGAACTTGAAG

Found at i:18009 original size:72 final size:72

Alignment explanation


    Indices: 17928--18061  Score: 214
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      17918 ATTGCTCCTT

                                  *    *               *           *         
      17928 GGGCTACTTGATTGCATCACACGAACAGGAAGAGAGCAAAAAAGGTAGGCTTCACTCTTGGGATC
          1 GGGCTACTTGATTGCATCACACAAACAAGAAGAGAGCAAAAAACGTAGGCTTCACACTTGGGATC

                   
      17993 ACTTTTA
         66 ACTTTTA

                                                 *    *                   
      18000 GGGCTACTTGATTGCATCACACAAACAAGAAGAGAGCGAAAATCGTAGGCTTCACACTTGGG
          1 GGGCTACTTGATTGCATCACACAAACAAGAAGAGAGCAAAAAACGTAGGCTTCACACTTGGG

      18062 TTTCTCCCAA


Statistics
Matches: 56,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  72   56  1.00

ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22


Consensus pattern (72 bp):   
GGGCTACTTGATTGCATCACACAAACAAGAAGAGAGCAAAAAACGTAGGCTTCACACTTGGGATC
ACTTTTA
Done.