Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020141.1 Corchorus olitorius cultivar O-4 contig20174, 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: 11485
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33


Found at i:768 original size:26 final size:26

Alignment explanation


    Indices: 710--771  Score: 70
    Period size: 26  Copynumber: 2.4  Consensus size: 26

        700 ACACGGGCCA

                *            *        
        710 GTGCAGCCCAGCGTGCTGGGCTAGGC
          1 GTGCGGCCCAGCGTGCTAGGCTAGGC

            ***                   *   
        736 ACACGGCCCAGCGTGCTAGGCTTGGC
          1 GTGCGGCCCAGCGTGCTAGGCTAGGC

                      
        762 GTGCGGCCCA
          1 GTGCGGCCCA

        772 ATCCGTATGG


Statistics
Matches: 27,  Mismatches: 9, Indels: 0
        0.75            0.25        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.13, C:0.34, G:0.39, T:0.15


Consensus pattern (26 bp):   
GTGCGGCCCAGCGTGCTAGGCTAGGC

Found at i:1252 original size:29 final size:29

Alignment explanation


    Indices: 1219--1280  Score: 124
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       1209 TGAAGGAGGT

                                         
       1219 AAAGTATTGGAATTATACAAGAGCAATAG
          1 AAAGTATTGGAATTATACAAGAGCAATAG

                                         
       1248 AAAGTATTGGAATTATACAAGAGCAATAG
          1 AAAGTATTGGAATTATACAAGAGCAATAG

                
       1277 AAAG
          1 AAAG

       1281 ACTACTCTAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23


Consensus pattern (29 bp):   
AAAGTATTGGAATTATACAAGAGCAATAG

Found at i:2104 original size:13 final size:13

Alignment explanation


    Indices: 2086--2115  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       2076 GCTTTTACTC

                         
       2086 TGATTTATGACTT
          1 TGATTTATGACTT

                      *  
       2099 TGATTTATGATTT
          1 TGATTTATGACTT

                
       2112 TGAT
          1 TGAT

       2116 ATTAACGGTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57


Consensus pattern (13 bp):   
TGATTTATGACTT

Found at i:7071 original size:29 final size:29

Alignment explanation


    Indices: 7039--7100  Score: 124
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       7029 TGAAGCAGAT

                                         
       7039 AAAGTATTGGAATTATACAAGAGCAATAG
          1 AAAGTATTGGAATTATACAAGAGCAATAG

                                         
       7068 AAAGTATTGGAATTATACAAGAGCAATAG
          1 AAAGTATTGGAATTATACAAGAGCAATAG

                
       7097 AAAG
          1 AAAG

       7101 ACTACTCTAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23


Consensus pattern (29 bp):   
AAAGTATTGGAATTATACAAGAGCAATAG

Found at i:7924 original size:13 final size:13

Alignment explanation


    Indices: 7906--7935  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       7896 GCTTTTACTC

                         
       7906 TGATTTATGACTT
          1 TGATTTATGACTT

                      *  
       7919 TGATTTATGATTT
          1 TGATTTATGACTT

                
       7932 TGAT
          1 TGAT

       7936 ATTAACGATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57


Consensus pattern (13 bp):   
TGATTTATGACTT

Found at i:11391 original size:17 final size:16

Alignment explanation


    Indices: 11351--11401  Score: 66
    Period size: 17  Copynumber: 3.1  Consensus size: 16

      11341 CATGTAATCT

                    *       
      11351 TTGATCACCGGTGATC
          1 TTGATCACTGGTGATC

                             
      11367 TTGCATCACTGGTGATC
          1 TTG-ATCACTGGTGATC

                      *      
      11384 TTAGATCACTAGTGATC
          1 TT-GATCACTGGTGATC

             
      11401 T
          1 T

      11402 GGGGGTGATC


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   27  0.87
  18    1  0.03

ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35


Consensus pattern (16 bp):   
TTGATCACTGGTGATC
Done.