Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017209.1 Corchorus olitorius cultivar O-4 contig17242, 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: 21102
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:4239 original size:19 final size:18

Alignment explanation


    Indices: 4215--4251  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       4205 TTGAAGATTT

                               
       4215 TTTGAAGACAATTTGAAGA
          1 TTTGAAGACAA-TTGAAGA

                     *        
       4234 TTTGAAGACCATTGAAGA
          1 TTTGAAGACAATTGAAGA

       4252 ATTATTTCCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30


Consensus pattern (18 bp):   
TTTGAAGACAATTGAAGA

Found at i:13122 original size:17 final size:18

Alignment explanation


    Indices: 13089--13127  Score: 62
    Period size: 17  Copynumber: 2.2  Consensus size: 18

      13079 AAAGTTCGTG

                               
      13089 TTTGAAGACAATTTGAAGA
          1 TTTGAAGAC-ATTTGAAGA

                              
      13108 TTTGAAGAC-TTTGAAGA
          1 TTTGAAGACATTTGAAGA

               
      13125 TTT
          1 TTT

      13128 ATTTCAAGAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  17   11  0.55
  19    9  0.45

ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38


Consensus pattern (18 bp):   
TTTGAAGACATTTGAAGA

Found at i:14527 original size:15 final size:15

Alignment explanation


    Indices: 14494--14535  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      14484 TTACTTTGCT

                          * 
      14494 TTGTTTTCTAGTTTCA
          1 TTGTTTTCT-GTTTAA

                           
      14510 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
      14525 TTGCTTTCTGT
          1 TTGTTTTCTGT

      14536 CAACCTCTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:17874 original size:21 final size:21

Alignment explanation


    Indices: 17837--17878  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      17827 CCCAAGCCGC

                        *        
      17837 CCCGAGCCACATGCCCGGCCA
          1 CCCGAGCCACATACCCGGCCA

                                  
      17858 CCCGAGCCATC-TACCCGGCCA
          1 CCCGAGCCA-CATACCCGGCCA

      17879 GCCGTGCCTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21   18  0.95
  22    1  0.05

ACGTcount: A:0.19, C:0.52, G:0.21, T:0.07


Consensus pattern (21 bp):   
CCCGAGCCACATACCCGGCCA

Found at i:18112 original size:22 final size:21

Alignment explanation


    Indices: 18087--18135  Score: 62
    Period size: 22  Copynumber: 2.3  Consensus size: 21

      18077 CCACTACCAA

                 *         *      
      18087 GCCATTACCGGCCATTCACCGT
          1 GCCATCACCGGCCATGC-CCGT

                *                
      18109 GCCACCACCGGCCATGCCCGT
          1 GCCATCACCGGCCATGCCCGT

                  
      18130 GCCATC
          1 GCCATC

      18136 GCCATTCCAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  21    9  0.39
  22   14  0.61

ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16


Consensus pattern (21 bp):   
GCCATCACCGGCCATGCCCGT

Found at i:18131 original size:21 final size:22

Alignment explanation


    Indices: 18093--18133  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      18083 CCAAGCCATT

                     *            
      18093 ACCGGCCATTCACCGTGCCACC
          1 ACCGGCCATGCACCGTGCCACC

                                
      18115 ACCGGCCATGC-CCGTGCCA
          1 ACCGGCCATGCACCGTGCCA

      18134 TCGCCATTCC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    8  0.44
  22   10  0.56

ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12


Consensus pattern (22 bp):   
ACCGGCCATGCACCGTGCCACC

Found at i:19966 original size:17 final size:18

Alignment explanation


    Indices: 19933--19971  Score: 62
    Period size: 17  Copynumber: 2.2  Consensus size: 18

      19923 AAAGTTCGCG

                               
      19933 TTTGAAGACAATTTGAAGA
          1 TTTGAAGAC-ATTTGAAGA

                              
      19952 TTTGAAGAC-TTTGAAGA
          1 TTTGAAGACATTTGAAGA

               
      19969 TTT
          1 TTT

      19972 ATTTCAAGAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  17   11  0.55
  19    9  0.45

ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38


Consensus pattern (18 bp):   
TTTGAAGACATTTGAAGA
Done.