Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014308.1 Corchorus olitorius cultivar O-4 contig14341, 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: 11520
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:7303 original size:41 final size:41

Alignment explanation


    Indices: 7172--7318  Score: 129
    Period size: 41  Copynumber: 3.6  Consensus size: 41

       7162 TTGTGATTTC

                    **                  *        *    
       7172 ATTCAATTGGGTCCCTAATTTAG-GCTATTATTTATTCATTG
          1 ATTCAATTTTGTCCCTAATTTAGAG-TAATATTTATTAATTG

                    *  *    *  *              *       
       7213 ATTCAATTCTGCCCCTGATCTA-AGGTAATATTTGTTAATTG
          1 ATTCAATTTTGTCCCTAATTTAGA-GTAATATTTATTAATTG

                                                      
       7254 ATTCAATTTTGTCCCTAATTTAGAGTAATATTTACTT-ATTG
          1 ATTCAATTTTGTCCCTAATTTAGAGTAATATTTA-TTAATTG

             *        *    **       
       7295 AGTCAATTTTATCCCGGATTTAGA
          1 ATTCAATTTTGTCCCTAATTTAGA

       7319 ATTTTATTTT


Statistics
Matches: 85,  Mismatches: 17, Indels: 8
        0.77            0.15        0.07

Matches are distributed among these distances:
  41   81  0.95
  42    4  0.05

ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44


Consensus pattern (41 bp):   
ATTCAATTTTGTCCCTAATTTAGAGTAATATTTATTAATTG

Found at i:8263 original size:22 final size:22

Alignment explanation


    Indices: 8224--8265  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       8214 AAATGAGAGT

                         *        
       8224 TTTCAAAAATAAAGTAAAAGAC
          1 TTTCAAAAATAAAATAAAAGAC

                                 
       8246 TTTCAAAACA-AAAATAAAAG
          1 TTTCAAAA-ATAAAATAAAAG

       8266 GTTTTGACAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  22   17  0.94
  23    1  0.06

ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21


Consensus pattern (22 bp):   
TTTCAAAAATAAAATAAAAGAC

Found at i:10081 original size:18 final size:19

Alignment explanation


    Indices: 10048--10087  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 19

      10038 GAAGTTCGTG

                     *         
      10048 ATTGAAGATTTATTGAAGA
          1 ATTGAAGATCTATTGAAGA

                               
      10067 ATTGAAGA-CTATTGAAGA
          1 ATTGAAGATCTATTGAAGA

               
      10085 ATT
          1 ATT

      10088 ATCTCAAGAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18   12  0.60
  19    8  0.40

ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35


Consensus pattern (19 bp):   
ATTGAAGATCTATTGAAGA

Found at i:11082 original size:128 final size:128

Alignment explanation


    Indices: 10854--11109  Score: 494
    Period size: 128  Copynumber: 2.0  Consensus size: 128

      10844 AGGGGGTGTA

                            *                                                
      10854 GACACCCATTTTTACCTTATATCCTTCAATTTTAAGTTAATACGTTTTTAATTGCGTTTAGGGGG
          1 GACACCCATTTTTACCCTATATCCTTCAATTTTAAGTTAATACGTTTTTAATTGCGTTTAGGGGG

                                                                           
      10919 CACTTGGGTCCATTCTTAAATTTATGCTCATATGTTGATAGATTAGCTCATTACTTTTCACAT
         66 CACTTGGGTCCATTCTTAAATTTATGCTCATATGTTGATAGATTAGCTCATTACTTTTCACAT

                                                              *              
      10982 GACACCCATTTTTACCCTATATCCTTCAATTTTAAGTTAATACGTTTTTACTTGCGTTTAGGGGG
          1 GACACCCATTTTTACCCTATATCCTTCAATTTTAAGTTAATACGTTTTTAATTGCGTTTAGGGGG

                                                                           
      11047 CACTTGGGTCCATTCTTAAATTTATGCTCATATGTTGATAGATTAGCTCATTACTTTTCACAT
         66 CACTTGGGTCCATTCTTAAATTTATGCTCATATGTTGATAGATTAGCTCATTACTTTTCACAT

      11110 TACATTTCTT


Statistics
Matches: 126,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 128  126  1.00

ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43


Consensus pattern (128 bp):   
GACACCCATTTTTACCCTATATCCTTCAATTTTAAGTTAATACGTTTTTAATTGCGTTTAGGGGG
CACTTGGGTCCATTCTTAAATTTATGCTCATATGTTGATAGATTAGCTCATTACTTTTCACAT

Found at i:11208 original size:29 final size:29

Alignment explanation


    Indices: 11175--11233  Score: 118
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      11165 ATTTTACATG

                                         
      11175 GCATTTTGTTATTTAGGCACTTTTGCAAA
          1 GCATTTTGTTATTTAGGCACTTTTGCAAA

                                         
      11204 GCATTTTGTTATTTAGGCACTTTTGCAAA
          1 GCATTTTGTTATTTAGGCACTTTTGCAAA

             
      11233 G
          1 G

      11234 GGTCATTTCC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.24, C:0.14, G:0.19, T:0.44


Consensus pattern (29 bp):   
GCATTTTGTTATTTAGGCACTTTTGCAAA
Done.