Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009685.1 Corchorus capsularis cultivar CVL-1 contig09706, 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: 12978
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26


Found at i:3279 original size:48 final size:48

Alignment explanation


    Indices: 3227--3404  Score: 216
    Period size: 48  Copynumber: 3.6  Consensus size: 48

       3217 TCCCGTTATA

                                                            
       3227 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTTT
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTTT

                              *                           *  
       3275 TCCCAAAATGCCCTTCCCAGACGGAAGGCATTTGATTTTACCTGCTATT
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG-TTTT

                              *     *   * **                     
       3324 TCCCAAAACTGCCCTTCCTGGACGAAAGACGCTT-ATTTTTACTCACT-TTTT
          1 TCCCAAAA-TGCCCTTCCCGGACGGAAGGCATTTGA-TTTTA--C-CTGTTTT

                   *                      
       3375 TCCCAAAGTGCCCTTCCCGGACGGAAGGCA
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCA

       3405 CTAATTTCCA


Statistics
Matches: 110,  Mismatches: 14, Indels: 10
        0.82            0.10        0.07

Matches are distributed among these distances:
  48   43  0.39
  49   12  0.11
  50   42  0.38
  51   10  0.09
  52    1  0.01
  53    2  0.02

ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30


Consensus pattern (48 bp):   
TCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTTT

Found at i:3423 original size:50 final size:49

Alignment explanation


    Indices: 3227--3502  Score: 213
    Period size: 49  Copynumber: 5.6  Consensus size: 49

       3217 TCCCGTTATA

                                           *                 
       3227 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG-TTTT
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACCTGCTTTT

                              *            *              *  
       3275 TCCCAAAATGCCCTTCCCAGACGGAAGGCATTTGATTTTACCTGCTATT
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACCTGCTTTT

                              *     *   *  *  *           *      
       3324 TCCCAAAACTGCCCTTCCTGGACGAAAGAC-GCTTATTTTTA-CTCACTTTTT
          1 TCCCAAAA-TGCCCTTCCCGGACGGAAGGCATCTGA-TTTTACCT-GC-TTTT

                   *                         *     *  *       
       3375 TCCCAAAGTGCCCTTCCCGGACGGAAGGCA-CTAATTTCCACTTGCTTTT
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTT-TACCTGCTTTT

               *    **       *   *       *   *            *   
       3424 TCCTAAAACACCCTTCCTGGATGGAAGGCGT-TAATTTTA-CTCGCGTTT
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACCT-GCTTTT

               **           *       *      
       3472 TCTTAAAAATGCCCTTTCCGGACGAAAGGCA
          1 TC-CCAAAATGCCCTTCCCGGACGGAAGGCA

       3503 AGTTCATTTT


Statistics
Matches: 179,  Mismatches: 38, Indels: 21
        0.75            0.16        0.09

Matches are distributed among these distances:
  47    1  0.01
  48   51  0.28
  49   70  0.39
  50   46  0.26
  51   11  0.06

ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31


Consensus pattern (49 bp):   
TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACCTGCTTTT

Found at i:3495 original size:148 final size:148

Alignment explanation


    Indices: 3227--3499  Score: 322
    Period size: 148  Copynumber: 1.8  Consensus size: 148

       3217 TCCCGTTATA

                                           * *    *                 **       
       3227 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTTTTCCCAAAATGCCCTTCC
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTAATTTCACCTGTTTTTCCCAAAACACCCTTCC

                         *  *                       *                        
       3292 CAGACGGAAGGCATTTGATTTTACCTGCTATTTCCCAAAACTGCCCTTCCTGGACGAAAGACGCT
         66 CAGACGGAAGGCAGTTAATTTTACCTGCTATTTCCCAAAAATGCCCTTCCTGGACGAAAGACGCT

                              
       3357 TATTTTTACTCACTTTTT
        131 TATTTTTACTCACTTTTT

                   *                                  *          *           
       3375 TCCCAAAGTGCCCTTCCCGGACGGAAGGCA-CTAATTTCCACTTGCTTTTTCCTAAAACACCCTT
          1 TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTAATTT-CACCTG-TTTTTCCCAAAACACCCTT

              **  *                               **                         
       3439 CCTGGATGGAAGGC-GTTAATTTTA-CTCGCGT-TTTCTTAAAAATGCCCTTTCC-GGACGAAAG
         64 CCCAGACGGAAGGCAGTTAATTTTACCT-GC-TATTTCCCAAAAATGCCC-TTCCTGGACGAAAG

       3500 GCAAGTTCAT


Statistics
Matches: 104,  Mismatches: 16, Indels: 10
        0.80            0.12        0.08

Matches are distributed among these distances:
 147    7  0.07
 148   65  0.62
 149   32  0.31

ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32


Consensus pattern (148 bp):   
TCCCAAAATGCCCTTCCCGGACGGAAGGCATCTAATTTCACCTGTTTTTCCCAAAACACCCTTCC
CAGACGGAAGGCAGTTAATTTTACCTGCTATTTCCCAAAAATGCCCTTCCTGGACGAAAGACGCT
TATTTTTACTCACTTTTT
Done.