Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022009.1 Corchorus olitorius cultivar O-4 contig22042, 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: 19315
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34


Found at i:2905 original size:20 final size:20

Alignment explanation


    Indices: 2877--2914  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2867 GGTTGGTGGT

                *     *         
       2877 TATCTTGGGATATTACCGGG
          1 TATCCTGGGAGATTACCGGG

                              
       2897 TATCCTGGGAGATTACCG
          1 TATCCTGGGAGATTACCG

       2915 TCGGATGGCC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32


Consensus pattern (20 bp):   
TATCCTGGGAGATTACCGGG

Found at i:3193 original size:28 final size:27

Alignment explanation


    Indices: 3125--3201  Score: 118
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       3115 TTTAAGGTCA

                          *            
       3125 TTCAGGGGCATTTTAGTCATTTGCACG
          1 TTCAGGGGCATTTTGGTCATTTGCACG

             *                       * 
       3152 TCCAGGGGCATTTTGGTCATTTGCATG
          1 TTCAGGGGCATTTTGGTCATTTGCACG

                                   
       3179 TTCATGGGGCATTTTGGTCATTT
          1 TTCA-GGGGCATTTTGGTCATTT

       3202 TAGGTTCACT


Statistics
Matches: 45,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  27   27  0.60
  28   18  0.40

ACGTcount: A:0.16, C:0.17, G:0.27, T:0.40


Consensus pattern (27 bp):   
TTCAGGGGCATTTTGGTCATTTGCACG

Found at i:8030 original size:21 final size:21

Alignment explanation


    Indices: 7975--8030  Score: 76
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       7965 TAATGTGGAT

                         *       
       7975 TGTTTGTGGATTTATCTTGAA
          1 TGTTTGTGGATTTTTCTTGAA

               *           *     
       7996 TGTCTGTGGATTTTTTTTGAA
          1 TGTTTGTGGATTTTTCTTGAA

                     *    
       8017 TGTTTGTGGGTTTT
          1 TGTTTGTGGATTTT

       8031 GTATGTTGAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.12, C:0.04, G:0.27, T:0.57


Consensus pattern (21 bp):   
TGTTTGTGGATTTTTCTTGAA

Found at i:8201 original size:16 final size:16

Alignment explanation


    Indices: 8181--8217  Score: 56
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       8171 GTTTTGATGG

                     *      
       8181 CTTATGATTGTGAGAT
          1 CTTATGATTCTGAGAT

            *               
       8197 GTTATGATTCTGAGAT
          1 CTTATGATTCTGAGAT

                 
       8213 CTTAT
          1 CTTAT

       8218 CTTTCACTAG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46


Consensus pattern (16 bp):   
CTTATGATTCTGAGAT

Found at i:13825 original size:234 final size:233

Alignment explanation


    Indices: 13409--13872  Score: 851
    Period size: 234  Copynumber: 2.0  Consensus size: 233

      13399 TTGTTATATA

                                                                             
      13409 ATCTTACTATCTTACTACTATTTAAAATCACGAACTCAACAATCCTAATTGGGAAATTTCATAAA
          1 ATCTTACTATCTTACTACTATTTAAAATCACGAACTCAACAATCCTAATTGGGAAATTTCATAAA

                                          *                        *         
      13474 TACCCTTATTATTGTAGTATAATATTTTTTTTAATCAGTATTCTTTTTGGTCATTGAACTTTTTT
         66 TACCCTTATTATTGTAGTATAATATTTTTTCTAATCAGTATTCTTTTTGGTCATTAAACTTTTTT

                        *                                                    
      13539 ATTAATTATGCAGAGATATTGCAAATCTGCTATAATTATAATTAATAATTTATTTCTCATTGATA
        131 ATTAATTATGCAAAGATATTGCAAATCTGCTATAATTATAATTAATAATTTATTTCTCATTGATA

                                                  
      13604 TTGTTATTTATATAATTTATATTT-TTAATTTAATCTT
        196 TTGTTATTTATATAATTTATATTTATTAATTTAATCTT

                                                                             
      13641 ATCTTATCTTATCTTACTACTATTTAAAATCACGAACTCAACAATCCTAATTGGGAAATTTCATA
          1 ATCTTA-C-TATCTTACTACTATTTAAAATCACGAACTCAACAATCCTAATTGGGAAATTTCATA

                                                                             
      13706 AATACCCTTATTATTGTAGTATAATA-TTTTTCTAATCAGTATTCTTTTTGGTCATTAAACTTTT
         64 AATACCCTTATTATTGTAGTATAATATTTTTTCTAATCAGTATTCTTTTTGGTCATTAAACTTTT

                                    *                                        
      13770 TTGATTAATTATGCAAAGATATTGTAAATCTGCTATAATTATAATTAATAATTTATTTCTCATTG
        129 TT-ATTAATTATGCAAAGATATTGCAAATCTGCTATAATTATAATTAATAATTTATTTCTCATTG

                                                  
      13835 ATATTGTTATTTATATAATTTATATTTATTAATTTAAT
        193 ATATTGTTATTTATATAATTTATATTTATTAATTTAAT

      13873 TTACTCAATA


Statistics
Matches: 224,  Mismatches: 4, Indels: 5
        0.96            0.02        0.02

Matches are distributed among these distances:
 232    6  0.03
 233   39  0.17
 234  169  0.75
 235   10  0.04

ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48


Consensus pattern (233 bp):   
ATCTTACTATCTTACTACTATTTAAAATCACGAACTCAACAATCCTAATTGGGAAATTTCATAAA
TACCCTTATTATTGTAGTATAATATTTTTTCTAATCAGTATTCTTTTTGGTCATTAAACTTTTTT
ATTAATTATGCAAAGATATTGCAAATCTGCTATAATTATAATTAATAATTTATTTCTCATTGATA
TTGTTATTTATATAATTTATATTTATTAATTTAATCTT
Done.