Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000642.1 Corchorus capsularis cultivar CVL-1 contig00642, 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, 798

Length: 1330
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28


Found at i:53 original size:32 final size:31

Alignment explanation


    Indices: 12--177  Score: 127
    Period size: 33  Copynumber: 5.1  Consensus size: 31

          2 AAAATAGCCG

                              *    * *      
         12 AGCCGCCCCATCGAGGCGACCTGTCGTGGCGA
          1 AGCCGCCCCAT-GAGGCGGCCTGCCATGGCGA

                       *              *    * 
         44 AGCCGCCCCACCG-GGACGGCCTGCCCTGGCTA
          1 AGCCGCCCCA-TGAGG-CGGCCTGCCATGGCGA

                         *         **     *  
         76 AGCCGCCCCAGTGGGGCGGCCTTTTCATGGGGA
          1 AGCCGCCCCA-TGAGGCGGCC-TGCCATGGCGA

                         *                *  
        109 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
          1 AGCCGCCCCA-TGAGGCGGCCTG-CCATGGCGA

                                *    *      
        142 AGCCGCCCCATGAGGGCGGCTTGCCGTGGCGA
          1 AGCCGCCCCATGA-GGCGGCCTGCCATGGCGA

                
        174 AGCC
          1 AGCC

        178 TCCCAAGTGG


Statistics
Matches: 109,  Mismatches: 19, Indels: 12
        0.78            0.14        0.09

Matches are distributed among these distances:
  31    2  0.02
  32   53  0.49
  33   54  0.50

ACGTcount: A:0.13, C:0.37, G:0.37, T:0.13


Consensus pattern (31 bp):   
AGCCGCCCCATGAGGCGGCCTGCCATGGCGA

Found at i:153 original size:16 final size:16

Alignment explanation


    Indices: 101--153  Score: 54
    Period size: 16  Copynumber: 3.2  Consensus size: 16

         91 GCGGCCTTTT

                            
        101 CATGGGGAAGCCGCCC
          1 CATGGGGAAGCCGCCC

                    **        
        117 CAGTGGGGCGGCCTG-CC
          1 CA-TGGGGAAGCC-GCCC

                 *          
        134 CATGGTGAAGCCGCCC
          1 CATGGGGAAGCCGCCC

                
        150 CATG
          1 CATG

        154 AGGGCGGCTT


Statistics
Matches: 29,  Mismatches: 5, Indels: 6
        0.73            0.12        0.15

Matches are distributed among these distances:
  15    1  0.03
  16   15  0.52
  17   12  0.41
  18    1  0.03

ACGTcount: A:0.15, C:0.36, G:0.38, T:0.11


Consensus pattern (16 bp):   
CATGGGGAAGCCGCCC

Found at i:176 original size:65 final size:64

Alignment explanation


    Indices: 12--193  Score: 199
    Period size: 65  Copynumber: 2.8  Consensus size: 64

          2 AAAATAGCCG

                               * *                     **   *                
         12 AGCCGCCCCATCGA-GGCGACCTGTCGTGGCGAAGCCGCCCCACCGGGACGGCCTGCCCTGGCTA
          1 AGCCGCCCCAT-GAGGGCGGCTTGTCGTGGCGAAGCCGCCCCAGTGGGGCGGCCTGCCCTGGCTA

                                    *  *   *                                 
         76 AGCCGCCCCAGTG-GGGCGGCCTTTTCATGGGGAAGCCGCCCCAGTGGGGCGGCCTGCCCATGG-
          1 AGCCGCCCCA-TGAGGGCGG-CTTGTCGTGGCGAAGCCGCCCCAGTGGGGCGGCCTGCCC-TGGC

               
        139 TGA
         63 T-A

                                   *            *   *           
        142 AGCCGCCCCATGAGGGCGGCTTGCCGTGGCGAAGCCTCCCAAGTGGGGCGGC
          1 AGCCGCCCCATGAGGGCGGCTTGTCGTGGCGAAGCCGCCCCAGTGGGGCGGC

        194 TTCACCACGG


Statistics
Matches: 98,  Mismatches: 14, Indels: 11
        0.80            0.11        0.09

Matches are distributed among these distances:
  64   15  0.15
  65   63  0.64
  66   20  0.20

ACGTcount: A:0.13, C:0.37, G:0.37, T:0.13


Consensus pattern (64 bp):   
AGCCGCCCCATGAGGGCGGCTTGTCGTGGCGAAGCCGCCCCAGTGGGGCGGCCTGCCCTGGCTA

Found at i:191 original size:32 final size:32

Alignment explanation


    Indices: 38--195  Score: 156
    Period size: 33  Copynumber: 4.9  Consensus size: 32

         28 CGACCTGTCG

                            **   *    *    *
         38 TGGCGAAGCCGCCCCACCGGGACGGCCTGCCC
          1 TGGCGAAGCCGCCCCAGTGGGGCGGCTTGCCA

                *                        **  
         70 TGGCTAAGCCGCCCCAGTGGGGCGGCCTTTTCA
          1 TGGCGAAGCCGCCCCAGTGGGGCGG-CTTGCCA

               *                      *      
        103 TGGGGAAGCCGCCCCAGTGGGGCGGCCTGCCCA
          1 TGGCGAAGCCGCCCCAGTGGGGCGGCTTG-CCA

               *                            *
        136 TGGTGAAGCCGCCCCA-TGAGGGCGGCTTGCCG
          1 TGGCGAAGCCGCCCCAGTG-GGGCGGCTTGCCA

                      *   *             
        168 TGGCGAAGCCTCCCAAGTGGGGCGGCTT
          1 TGGCGAAGCCGCCCCAGTGGGGCGGCTT

        196 CACCACGGTA


Statistics
Matches: 103,  Mismatches: 19, Indels: 8
        0.79            0.15        0.06

Matches are distributed among these distances:
  32   49  0.48
  33   54  0.52

ACGTcount: A:0.13, C:0.35, G:0.38, T:0.14


Consensus pattern (32 bp):   
TGGCGAAGCCGCCCCAGTGGGGCGGCTTGCCA

Found at i:681 original size:22 final size:23

Alignment explanation


    Indices: 642--684  Score: 79
    Period size: 22  Copynumber: 1.9  Consensus size: 23

        632 AATCCTAATC

                                   
        642 CTGTTAGGAATAGTAAAACCTTT
          1 CTGTTAGGAATAGTAAAACCTTT

                                 
        665 CTGTTAGGAA-AGTAAAACCT
          1 CTGTTAGGAATAGTAAAACCT

        685 ACTCCTTCTA


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

Matches are distributed among these distances:
  22   10  0.50
  23   10  0.50

ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30


Consensus pattern (23 bp):   
CTGTTAGGAATAGTAAAACCTTT
Done.