Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019877.1 Corchorus olitorius cultivar O-4 contig19910, 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: 21363
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:16053 original size:37 final size:36

Alignment explanation


    Indices: 16011--16155  Score: 139
    Period size: 37  Copynumber: 3.8  Consensus size: 36

      16001 TAAAACCTGG

                                                 
      16011 TGGGAACTTTCCCAATTTGAAAACTTTGAGAACTTGA
          1 TGGGAACTTTCCCAATTTGAAAACTTTGA-AACTTGA

                          *  * *                    
      16048 TGGGAACTTTCCCACTTAGTAAACTAAAATTGAAAC-TGA
          1 TGGGAACTTTCCCAATTTGAAAACT----TTGAAACTTGA

            * *             *             *      * 
      16087 CGAGAACTTTCCCTAAATTGAAAAACTTTAAAAACTTTA
          1 TGGGAACTTTCCC-AATTTG-AAAACTTT-GAAACTTGA

                                          
      16126 TGGGAACTTTCCCAATTTGAAAACTTTGAA
          1 TGGGAACTTTCCCAATTTGAAAACTTTGAA

      16156 GGAAATTCCT


Statistics
Matches: 85,  Mismatches: 15, Indels: 17
        0.73            0.13        0.15

Matches are distributed among these distances:
  36    2  0.02
  37   32  0.38
  38    9  0.11
  39   27  0.32
  40    6  0.07
  41    9  0.11

ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31


Consensus pattern (36 bp):   
TGGGAACTTTCCCAATTTGAAAACTTTGAAACTTGA

Found at i:18290 original size:42 final size:42

Alignment explanation


    Indices: 18223--18306  Score: 141
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      18213 CGAATCCTGT

                             *              *         
      18223 CGTGCCAAGACCGGCCATAGCCGAGCCACCTTGTGCTTCCAC
          1 CGTGCCAAGACCGGCCACAGCCGAGCCACCTTCTGCTTCCAC

                                *                     
      18265 CGTGCCAAGACCGGCCACAGTCGAGCCACCTTCTGCTTCCAC
          1 CGTGCCAAGACCGGCCACAGCCGAGCCACCTTCTGCTTCCAC

      18307 TGAGACACGA


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.19, C:0.42, G:0.23, T:0.17


Consensus pattern (42 bp):   
CGTGCCAAGACCGGCCACAGCCGAGCCACCTTCTGCTTCCAC

Found at i:18319 original size:42 final size:42

Alignment explanation


    Indices: 18228--18331  Score: 129
    Period size: 42  Copynumber: 2.5  Consensus size: 42

      18218 CCTGTCGTGC

                        *              *           * *
      18228 CAAGACCGGCCATAGCCGAGCCACCTTGTGCTTCCACCGTGC
          1 CAAGACCGGCCACAGCCGAGCCACCTTCTGCTTCCACCGAGA

                           *                     *    
      18270 CAAGACCGGCCACAGTCGAGCCACCTTCTGCTTCCACTGAGA
          1 CAAGACCGGCCACAGCCGAGCCACCTTCTGCTTCCACCGAGA

              *                  
      18312 CACGACCGGCCATCA-CCGAG
          1 CAAGACCGGCCA-CAGCCGAG

      18332 TCAGAGTCGC


Statistics
Matches: 53,  Mismatches: 8, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  42   51  0.96
  43    2  0.04

ACGTcount: A:0.22, C:0.40, G:0.23, T:0.14


Consensus pattern (42 bp):   
CAAGACCGGCCACAGCCGAGCCACCTTCTGCTTCCACCGAGA

Found at i:18386 original size:21 final size:21

Alignment explanation


    Indices: 18362--18414  Score: 61
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      18352 ACCCAACACG

                         **     *
      18362 GTGCCATCACCGGTTAAGCCT
          1 GTGCCATCACCGGCCAAGCCC

                  *         *    
      18383 GTGCCACCACCGGCCATGCCC
          1 GTGCCATCACCGGCCAAGCCC

                       
      18404 GTGCCATCACC
          1 GTGCCATCACC

      18415 ATTCCGTGCT


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17


Consensus pattern (21 bp):   
GTGCCATCACCGGCCAAGCCC

Found at i:19618 original size:18 final size:18

Alignment explanation


    Indices: 19597--19635  Score: 69
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      19587 ACTAATTACC

                            * 
      19597 CTTTGAAAATCATGAATA
          1 CTTTGAAAATCATGAACA

                              
      19615 CTTTGAAAATCATGAACA
          1 CTTTGAAAATCATGAACA

               
      19633 CTT
          1 CTT

      19636 CGAGGTTAGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33


Consensus pattern (18 bp):   
CTTTGAAAATCATGAACA
Done.