Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019917.1 Corchorus olitorius cultivar O-4 contig19950, 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: 10486
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:1887 original size:15 final size:16

Alignment explanation


    Indices: 1854--1893  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       1844 TTACTTTGCT

                            
       1854 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       1870 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

                     
       1885 TTGTTTTCT
          1 TTGTTTTCT

       1894 TTCAACCTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:9137 original size:13 final size:12

Alignment explanation


    Indices: 9111--9136  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       9101 GGAACTTTTC

                        
       9111 AAGTGCAAAAAA
          1 AAGTGCAAAAAA

                        
       9123 AAGTGCAAAAAA
          1 AAGTGCAAAAAA

              
       9135 AA
          1 AA

       9137 AAGAAGGGAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (12 bp):   
AAGTGCAAAAAA

Found at i:10350 original size:145 final size:149

Alignment explanation


    Indices: 10095--10486  Score: 569
    Period size: 145  Copynumber: 2.6  Consensus size: 149

      10085 GTCTCAATTC

                                   **     *                                  
      10095 AGAATTTGCATTTGTAAGACCTCTAGGCACAATTTCAGAAACC-TCTGGGTATTAATTCTGATAA
          1 AGAATTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTTC-GGGTATTAATTCTGATAA

                 **     *    *                                               
      10159 ATCCTATGGGTACCATTCCATTTCATCAAATTTTTAATCAAAGCTGTGTTTAAATTTCAAAATCA
         65 ATCCTCCGGGTATCATTTCATTTCATCAAATTTTTAATCAAAGCTGTGTTTAAATTTCAAAATCA

                                
      10224 AAACCTTG-CTC-AAGG-TT
        130 AAACCTTGACTCAAAGGATT

               *        *                                                    
      10241 -GAGTTTGCATTGGTAAGACCTCCGGGCACCATTTCAGAAACCTTCGGGTATTAATTCTGATAAA
          1 AGAATTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTTCGGGTATTAATTCTGATAAA

                                        *                       *           *
      10305 TCCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAGTTTCAAAATCAC
         66 TCCTCCGGGTATCATTTCATTTCATCAAATTTTTAATCAAAGCTGTGTTTAAATTTCAAAATCAA

                                    
      10370 AACCTTGACTCAAAGGTCTCAATT
        131 AACCTTGACTCAAAGG-----ATT

                                                         *                   
      10394 CAGAATTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTATTAATTCTGATAA
          1 -AGAATTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTTCGGGTATTAATTCTGATAA

                                        
      10459 ATCCTCCGGGTATCATTTCATTTCATCA
         65 ATCCTCCGGGTATCATTTCATTTCATCA


Statistics
Matches: 220,  Mismatches: 15, Indels: 13
        0.89            0.06        0.05

Matches are distributed among these distances:
 145  121  0.55
 146    5  0.02
 147    4  0.02
 153    2  0.01
 155   88  0.40

ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34


Consensus pattern (149 bp):   
AGAATTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTTCGGGTATTAATTCTGATAAA
TCCTCCGGGTATCATTTCATTTCATCAAATTTTTAATCAAAGCTGTGTTTAAATTTCAAAATCAA
AACCTTGACTCAAAGGATT
Done.