Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016003.1 Corchorus olitorius cultivar O-4 contig16036, 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: 20124
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:2845 original size:26 final size:26

Alignment explanation


    Indices: 2816--2874  Score: 73
    Period size: 27  Copynumber: 2.2  Consensus size: 26

       2806 AGTGAAATGT

                 *             *      
       2816 ACCAATTGAACAACCCCCAGTAGCTA
          1 ACCAAATGAACAACCCCCAATAGCTA

                     *     *           
       2842 ACCAAAATGGACAACTCCCAATAGCTA
          1 ACC-AAATGAACAACCCCCAATAGCTA

                  
       2869 ACCAAA
          1 ACCAAA

       2875 ATGCAACTAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  26    6  0.21
  27   22  0.79

ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14


Consensus pattern (26 bp):   
ACCAAATGAACAACCCCCAATAGCTA

Found at i:2856 original size:27 final size:27

Alignment explanation


    Indices: 2825--2877  Score: 88
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       2815 TACCAATTGA

                      *                
       2825 ACAACCCCCAGTAGCTAACCAAAATGG
          1 ACAACCCCCAATAGCTAACCAAAATGG

                 *                    
       2852 ACAACTCCCAATAGCTAACCAAAATG
          1 ACAACCCCCAATAGCTAACCAAAATG

       2878 CAACTAATGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.43, C:0.32, G:0.11, T:0.13


Consensus pattern (27 bp):   
ACAACCCCCAATAGCTAACCAAAATGG

Found at i:5656 original size:106 final size:107

Alignment explanation


    Indices: 5464--5659  Score: 304
    Period size: 106  Copynumber: 1.8  Consensus size: 107

       5454 CATCAGCAAT

                                                                             
       5464 TTTCTTTTATTTTGTGACGATCAATAATTTTTGGTGGCGCTATTGTGTAATATTCCATGACGAAA
          1 TTTCTTTTATTTTGTGACGATCAAT-ATTTTTGGTGGCGCTATTGTGTAATATTCCATGACGAAA

                                                       
       5529 TCTACGTCACCAATTAGTGTGACGTTCTCATTTTCCGTCACGA
         65 TCTACGTCACCAATTAGTGTGACGTTCTCATTTTCCGTCACGA

                             *             **     *         *    *           
       5572 TTTCTTTTATTTTGTGATGATCAAT-TTTTTTTTGGCGTTATTGTGTAGTATTTCATGACGAAAT
          1 TTTCTTTTATTTTGTGACGATCAATATTTTTGGTGGCGCTATTGTGTAATATTCCATGACGAAAT

                      *    *        
       5636 CTACGTCACCTATTATTGTGACGT
         66 CTACGTCACCAATTAGTGTGACGT

       5660 CGTTGTGGTT


Statistics
Matches: 80,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
 106   56  0.70
 108   24  0.30

ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45


Consensus pattern (107 bp):   
TTTCTTTTATTTTGTGACGATCAATATTTTTGGTGGCGCTATTGTGTAATATTCCATGACGAAAT
CTACGTCACCAATTAGTGTGACGTTCTCATTTTCCGTCACGA

Found at i:10694 original size:6 final size:6

Alignment explanation


    Indices: 10678--10711  Score: 50
    Period size: 6  Copynumber: 5.3  Consensus size: 6

      10668 CCCTCCACGA

                                                   
      10678 TTTTTG CTTTTTG TTTTCTG TTTTTG TTTTTG TT
          1 TTTTTG -TTTTTG TTTT-TG TTTTTG TTTTTG TT

      10712 AGCTAGGTTC


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
   6   14  0.54
   7   12  0.46

ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79


Consensus pattern (6 bp):   
TTTTTG

Found at i:10701 original size:13 final size:12

Alignment explanation


    Indices: 10678--10711  Score: 50
    Period size: 13  Copynumber: 2.7  Consensus size: 12

      10668 CCCTCCACGA

                         
      10678 TTTTTGCTTTTTG
          1 TTTTTG-TTTTTG

                         
      10691 TTTTCTGTTTTTG
          1 TTTT-TGTTTTTG

                    
      10704 TTTTTGTT
          1 TTTTTGTT

      10712 AGCTAGGTTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  12    4  0.20
  13   14  0.70
  14    2  0.10

ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79


Consensus pattern (12 bp):   
TTTTTGTTTTTG

Found at i:12734 original size:24 final size:24

Alignment explanation


    Indices: 12702--12757  Score: 67
    Period size: 24  Copynumber: 2.3  Consensus size: 24

      12692 TGTGAAAAGA

                *           *  *    
      12702 AAAACAATAAAATAAATAAGCAAG
          1 AAAATAATAAAATAAAGAAACAAG

                         *          
      12726 AAAATAATAAAATTAAGAAACAAG
          1 AAAATAATAAAATAAAGAAACAAG

                    
      12750 ATAAATAA
          1 A-AAATAA

      12758 ATACTCCAAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  24   21  0.78
  25    6  0.22

ACGTcount: A:0.71, C:0.05, G:0.07, T:0.16


Consensus pattern (24 bp):   
AAAATAATAAAATAAAGAAACAAG

Found at i:18958 original size:12 final size:12

Alignment explanation


    Indices: 18941--18965  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      18931 CATAATTCTG

                        
      18941 AGACACATGTCA
          1 AGACACATGTCA

                        
      18953 AGACACATGTCA
          1 AGACACATGTCA

             
      18965 A
          1 A

      18966 AAAGGTTTAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16


Consensus pattern (12 bp):   
AGACACATGTCA
Done.