Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013719.1 Corchorus olitorius cultivar O-4 contig13752, 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: 14649
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30


Found at i:2378 original size:31 final size:31

Alignment explanation


    Indices: 2343--2481  Score: 143
    Period size: 31  Copynumber: 4.5  Consensus size: 31

       2333 TGTCCGACGA

                                    *    * 
       2343 TGGCATGCCACGTGTACCAAAAAACGACATG
          1 TGGCATGCCACGTGTACCAAAAAATGACACG

                 *                 *      *
       2374 TGGCACGCCACGTGTACCAAAAAGTGACACA
          1 TGGCATGCCACGTGTACCAAAAAATGACACG

             **  *    *                   * 
       2405 TATCACGCCATGTGTACCAAAAAAGTGACATG
          1 TGGCATGCCACGTGTACCAAAAAA-TGACACG

                      *    **      *       
       2437 TGGCATGCCATGTGTTTCAAAAAGTGACACG
          1 TGGCATGCCACGTGTACCAAAAAATGACACG

                          
       2468 TGGCATGCCACGTG
          1 TGGCATGCCACGTG

       2482 CACACAAGGA


Statistics
Matches: 88,  Mismatches: 19, Indels: 2
        0.81            0.17        0.02

Matches are distributed among these distances:
  31   65  0.74
  32   23  0.26

ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19


Consensus pattern (31 bp):   
TGGCATGCCACGTGTACCAAAAAATGACACG

Found at i:2458 original size:63 final size:62

Alignment explanation


    Indices: 2349--2466  Score: 173
    Period size: 63  Copynumber: 1.9  Consensus size: 62

       2339 ACGATGGCAT

                                                                          
       2349 GCCACGTGTACCAAAAAACGACATGTGGCACGCCACGTGTACCAAAAAGTGACACATATCAC
          1 GCCACGTGTACCAAAAAACGACATGTGGCACGCCACGTGTACCAAAAAGTGACACATATCAC

                *              *           *    *    **             
       2411 GCCATGTGTACCAAAAAAGTGACATGTGGCATGCCATGTGTTTCAAAAAGTGACAC
          1 GCCACGTGTACCAAAAAA-CGACATGTGGCACGCCACGTGTACCAAAAAGTGACAC

       2467 GTGGCATGCC


Statistics
Matches: 49,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  62   17  0.35
  63   32  0.65

ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19


Consensus pattern (62 bp):   
GCCACGTGTACCAAAAAACGACATGTGGCACGCCACGTGTACCAAAAAGTGACACATATCAC

Found at i:11933 original size:16 final size:16

Alignment explanation


    Indices: 11912--11946  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      11902 TGAAATGAAT

                   *    *   
      11912 ATATAATGATAATATA
          1 ATATAATAATAAAATA

                            
      11928 ATATAATAATAAAATA
          1 ATATAATAATAAAATA

               
      11944 ATA
          1 ATA

      11947 AGGCTAATTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34


Consensus pattern (16 bp):   
ATATAATAATAAAATA

Found at i:12336 original size:16 final size:16

Alignment explanation


    Indices: 12315--12348  Score: 68
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      12305 AATTCCATTC

                            
      12315 CAAAACTCGTCAAATT
          1 CAAAACTCGTCAAATT

                            
      12331 CAAAACTCGTCAAATT
          1 CAAAACTCGTCAAATT

              
      12347 CA
          1 CA

      12349 GTTTCATGTC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24


Consensus pattern (16 bp):   
CAAAACTCGTCAAATT

Found at i:14353 original size:25 final size:25

Alignment explanation


    Indices: 14334--14404  Score: 124
    Period size: 25  Copynumber: 2.8  Consensus size: 25

      14324 TAAACGCTCA

                         * *         
      14334 TGTGCTTGCGTTTGGAAAACGAGCC
          1 TGTGCTTGCGTTTAGCAAACGAGCC

                                     
      14359 TGTGCTTGCGTTTAGCAAACGAGCC
          1 TGTGCTTGCGTTTAGCAAACGAGCC

                                 
      14384 TGTGCTTGCGTTTAGCAAACG
          1 TGTGCTTGCGTTTAGCAAACG

      14405 CATGGGCTGC


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   44  1.00

ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30


Consensus pattern (25 bp):   
TGTGCTTGCGTTTAGCAAACGAGCC
Done.