Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013456.1 Corchorus capsularis cultivar CVL-1 contig13477, 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: 4518
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:41 original size:27 final size:27

Alignment explanation


    Indices: 1--80  Score: 97
    Period size: 28  Copynumber: 2.9  Consensus size: 27

                           *           
          1 AAAAATGACCAAAATGCCCCTGGGTGC
          1 AAAAATGACCAAAATACCCCTGGGTGC

             *     *        *            
         28 ATAAATGNCCAAAAATNCCCCTTGGGTGC
          1 AAAAATGACC-AAAATACCCC-TGGGTGC

                               *    
         57 AAAAATGACCAAAATACCCTTGGG
          1 AAAAATGACCAAAATACCCCTGGG

         81 CGACCCTATT


Statistics
Matches: 44,  Mismatches: 7, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  27   12  0.27
  28   17  0.39
  29   15  0.34

ACGTcount: A:0.38, C:0.24, G:0.19, T:0.17


Consensus pattern (27 bp):   
AAAAATGACCAAAATACCCCTGGGTGC

Found at i:62 original size:29 final size:28

Alignment explanation


    Indices: 1--70  Score: 97
    Period size: 29  Copynumber: 2.5  Consensus size: 28

                                        
          1 AAAAATGACC-AAAATGCCCCTGGGTGC
          1 AAAAATGACCAAAAATGCCCCTGGGTGC

             *     *        *            
         28 ATAAATGNCCAAAAATNCCCCTTGGGTGC
          1 AAAAATGACCAAAAATGCCCC-TGGGTGC

                          
         57 AAAAATGACCAAAA
          1 AAAAATGACCAAAA

         71 TACCCTTGGG


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
  27    8  0.22
  28    9  0.25
  29   19  0.53

ACGTcount: A:0.41, C:0.23, G:0.17, T:0.16


Consensus pattern (28 bp):   
AAAAATGACCAAAAATGCCCCTGGGTGC

Found at i:70 original size:28 final size:27

Alignment explanation


    Indices: 1--80  Score: 99
    Period size: 27  Copynumber: 2.9  Consensus size: 27

                                        
          1 AAAAATGACCAAAATGCCCC-TGGGTGC
          1 AAAAATGACCAAAAT-CCCCTTGGGTGC

             *     *                     
         28 ATAAATGNCCAAAAATNCCCCTTGGGTGC
          1 AAAAATGACC-AAAAT-CCCCTTGGGTGC

                           *        
         57 AAAAATGACCAAAATACCCTTGGG
          1 AAAAATGACCAAAATCCCCTTGGG

         81 CGACCCTATT


Statistics
Matches: 45,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  27   16  0.36
  28   14  0.31
  29   15  0.33

ACGTcount: A:0.38, C:0.24, G:0.19, T:0.17


Consensus pattern (27 bp):   
AAAAATGACCAAAATCCCCTTGGGTGC

Found at i:1130 original size:27 final size:27

Alignment explanation


    Indices: 1100--1183  Score: 73
    Period size: 27  Copynumber: 3.1  Consensus size: 27

       1090 CTTCCACCTG

                                       
       1100 AGTCGCCCTTTTCGGGTTTTCAACTCA
          1 AGTCGCCCTTTTCGGGTTTTCAACTCA

                 *         **  *       **
       1127 AGTCCCCCCTTTTC-CATCCTTC-ACTTG
          1 AGT-CGCCCTTTTCGGGT-TTTCAACTCA

              *                        
       1154 AGCCGCCCTTTTCGGGTTTTCAACTCA
          1 AGTCGCCCTTTTCGGGTTTTCAACTCA

               
       1181 AGT
          1 AGT

       1184 GATCCCAATG


Statistics
Matches: 39,  Mismatches: 14, Indels: 8
        0.64            0.23        0.13

Matches are distributed among these distances:
  26   12  0.31
  27   15  0.38
  28   12  0.31

ACGTcount: A:0.14, C:0.35, G:0.15, T:0.36


Consensus pattern (27 bp):   
AGTCGCCCTTTTCGGGTTTTCAACTCA
Done.