Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021990.1 Corchorus olitorius cultivar O-4 contig22023, 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: 10754
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30


Found at i:469 original size:21 final size:21

Alignment explanation


    Indices: 445--536  Score: 150
    Period size: 21  Copynumber: 4.4  Consensus size: 21

        435 CTTAGGCAAT

                         *       
        445 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                        *        
        466 TCCAATGAGCTTCGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
        487 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        508 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        529 TCCAATGA
          1 TCCAATGA

        537 TATCCTAGCA


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   64  0.96

ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:2214 original size:15 final size:16

Alignment explanation


    Indices: 2196--2228  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2186 GAAAGAAAGT

                            
       2196 AATTAAAC-AGAAAAC
          1 AATTAAACTAGAAAAC

                 *          
       2211 AATTATACTAGAAAAC
          1 AATTAAACTAGAAAAC

              
       2227 AA
          1 AA

       2229 AGCAAAGTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    7  0.44
  16    9  0.56

ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18


Consensus pattern (16 bp):   
AATTAAACTAGAAAAC

Found at i:7191 original size:21 final size:22

Alignment explanation


    Indices: 7167--7209  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       7157 TTTGCCTCAT

                                  
       7167 GCATTCATTCAT-CATGCCATG
          1 GCATTCATTCATGCATGCCATG

                  *         *     
       7188 GCATTCGTTCATGCATTCCATG
          1 GCATTCATTCATGCATGCCATG

       7210 AAGCTTTAGC


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

Matches are distributed among these distances:
  21   11  0.58
  22    8  0.42

ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35


Consensus pattern (22 bp):   
GCATTCATTCATGCATGCCATG

Found at i:9423 original size:76 final size:76

Alignment explanation


    Indices: 9272--9415  Score: 168
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       9262 ACAAGGACCC

                                                               *  * *      * 
       9272 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGGGGACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT

                       
       9337 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            *      
       9348 CGACTCCAGCTGGGTGCCCACATGGATTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCA

                  
       9410 GATGGG
         63 GATGGG

       9416 TTGTGTCATA


Statistics
Matches: 57,  Mismatches: 8, Indels: 6
        0.80            0.11        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   47  0.82
  77    6  0.11

ACGTcount: A:0.17, C:0.30, G:0.31, T:0.23


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
GGGCAGTGTCA
Done.