Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001051.1 Corchorus capsularis cultivar CVL-1 contig01051, 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: 1770
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31


Found at i:136 original size:75 final size:75

Alignment explanation


    Indices: 13--167  Score: 274
    Period size: 75  Copynumber: 2.1  Consensus size: 75

          3 CGGTAAGTCG

                                              *                              
         13 CGATCAAGTCGCGCCCCACCGCCGGCTCGTCGCTTGCGACCCAGGGTCGGTCGCGACCTAAACCT
          1 CGATCAAGTCGCGCCCCACCGCCGGCTCGTCGCTCGCGACCCAGGGTCGGTCGCGACCTAAACCT

                      
         78 CGGTGGGTCC
         66 CGGTGGGTCC

                       *                              *                      
         88 CGATCAAGTCGTGCCCCACCGCCGGCTCGTCGCTCGCGACCCGGGGTCGGTCGCGACCTAAACCT
          1 CGATCAAGTCGCGCCCCACCGCCGGCTCGTCGCTCGCGACCCAGGGTCGGTCGCGACCTAAACCT

                     *
        153 CGGTGGGTCG
         66 CGGTGGGTCC

                 
        163 CGATC
          1 CGATC

        168 CAGCCGCGAC


Statistics
Matches: 76,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  75   76  1.00

ACGTcount: A:0.13, C:0.39, G:0.32, T:0.16


Consensus pattern (75 bp):   
CGATCAAGTCGCGCCCCACCGCCGGCTCGTCGCTCGCGACCCAGGGTCGGTCGCGACCTAAACCT
CGGTGGGTCC

Found at i:266 original size:11 final size:13

Alignment explanation


    Indices: 237--290  Score: 60
    Period size: 11  Copynumber: 4.3  Consensus size: 13

        227 GACGGCCTTT

                      *  
        237 TTTAATT-TTTTA
          1 TTTAATTATTATA

                         
        249 TTTAATTATTA-A
          1 TTTAATTATTATA

                          
        261 -TTAATTATTATTA
          1 TTTAATTATTA-TA

                        *
        274 TTTAATTATTATT
          1 TTTAATTATTATA

                
        287 TTTA
          1 TTTA

        291 GATAATTGTT


Statistics
Matches: 36,  Mismatches: 2, Indels: 7
        0.80            0.04        0.16

Matches are distributed among these distances:
  11   10  0.28
  12    8  0.22
  13    8  0.22
  14   10  0.28

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (13 bp):   
TTTAATTATTATA

Found at i:272 original size:14 final size:14

Alignment explanation


    Indices: 253--286  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

        243 TTTTTATTTA

                          
        253 ATTATTAATTAATT
          1 ATTATTAATTAATT

                   *      
        267 ATTATTATTTAATT
          1 ATTATTAATTAATT

                  
        281 ATTATT
          1 ATTATT

        287 TTTAGATAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (14 bp):   
ATTATTAATTAATT

Found at i:276 original size:25 final size:23

Alignment explanation


    Indices: 238--284  Score: 76
    Period size: 25  Copynumber: 2.0  Consensus size: 23

        228 ACGGCCTTTT

                                   
        238 TTAATTTTTTATTTAATTATTAA
          1 TTAATTTTTTATTTAATTATTAA

                                    
        261 TTAATTATTATTATTTAATTATTA
          1 TTAATT-TT-TTATTTAATTATTA

        285 TTTTTAGATA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  23    6  0.27
  24    2  0.09
  25   14  0.64

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (23 bp):   
TTAATTTTTTATTTAATTATTAA

Found at i:1165 original size:33 final size:33

Alignment explanation


    Indices: 1128--1212  Score: 107
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       1118 AGCACTAGTG

                    *              *         
       1128 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                     **    *     *           
       1161 ACCGGCCACATGACTCGGAGATGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                          *    
       1194 ACCGGCCACGCGACATGGA
          1 ACCGGCCACGCGACTTGGA

       1213 CATGTTCGGC


Statistics
Matches: 42,  Mismatches: 10, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  33   42  1.00

ACGTcount: A:0.25, C:0.36, G:0.29, T:0.09


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

Found at i:1223 original size:33 final size:32

Alignment explanation


    Indices: 1128--1224  Score: 104
    Period size: 33  Copynumber: 2.9  Consensus size: 32

       1118 AGCACTAGTG

                    *            *           
       1128 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
          1 ACCGGCCACGCGAC-TGGAGATGTCCGGCCAAC

                     **            *         
       1161 ACCGGCCACATGACTCGGAGATGCCCGGCCAAC
          1 ACCGGCCACGCGACT-GGAGATGTCCGGCCAAC

                               *    *      
       1194 ACCGGCCACGCGACATGGACATGTTCGGCCA
          1 ACCGGCCACGCGAC-TGGAGATGTCCGGCCA

       1225 CAACCGACCA


Statistics
Matches: 52,  Mismatches: 10, Indels: 4
        0.79            0.15        0.06

Matches are distributed among these distances:
  32    1  0.02
  33   50  0.96
  34    1  0.02

ACGTcount: A:0.24, C:0.36, G:0.29, T:0.11


Consensus pattern (32 bp):   
ACCGGCCACGCGACTGGAGATGTCCGGCCAAC
Done.