Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019527.1 Corchorus olitorius cultivar O-4 contig19560, 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: 33032
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:2311 original size:20 final size:20

Alignment explanation


    Indices: 2288--2336  Score: 98
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       2278 ATCACATGCC

                                
       2288 AAGATCACCACAAGTGATCA
          1 AAGATCACCACAAGTGATCA

                                
       2308 AAGATCACCACAAGTGATCA
          1 AAGATCACCACAAGTGATCA

                     
       2328 AAGATCACC
          1 AAGATCACC

       2337 CCCAACCAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   29  1.00

ACGTcount: A:0.45, C:0.27, G:0.14, T:0.14


Consensus pattern (20 bp):   
AAGATCACCACAAGTGATCA

Found at i:3526 original size:3 final size:3

Alignment explanation


    Indices: 3518--3542  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       3508 GAAATGGATT

                                             
       3518 TGA TGA TGA TGA TGA TGA TGA TGA T
          1 TGA TGA TGA TGA TGA TGA TGA TGA T

       3543 TATTTTTGTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36


Consensus pattern (3 bp):   
TGA

Found at i:7233 original size:20 final size:21

Alignment explanation


    Indices: 7208--7247  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7198 TAACACTTGA

                                 
       7208 TTATAC-ATAGATTTTGTTAC
          1 TTATACTATAGATTTTGTTAC

                       *        
       7228 TTATACTATAGCTTTTGTTA
          1 TTATACTATAGATTTTGTTA

       7248 AAATGTCATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    6  0.33
  21   12  0.67

ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53


Consensus pattern (21 bp):   
TTATACTATAGATTTTGTTAC

Found at i:17200 original size:9 final size:9

Alignment explanation


    Indices: 17183--17231  Score: 80
    Period size: 9  Copynumber: 5.4  Consensus size: 9

      17173 TTTTTCAACA

                     
      17183 AGTTATACT
          1 AGTTATACT

                *    
      17192 AGTTGTACT
          1 AGTTATACT

                     
      17201 AGTTATACT
          1 AGTTATACT

                   * 
      17210 AGTTATATT
          1 AGTTATACT

                     
      17219 AGTTATACT
          1 AGTTATACT

                
      17228 AGTT
          1 AGTT

      17232 GCATAAAGTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   9   36  1.00

ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47


Consensus pattern (9 bp):   
AGTTATACT

Found at i:31185 original size:21 final size:20

Alignment explanation


    Indices: 31155--31214  Score: 66
    Period size: 21  Copynumber: 2.9  Consensus size: 20

      31145 AACAACTTCA

                 *            * *
      31155 TCCGCAACCATCTCCACCTCT
          1 TCCGCCACCAT-TCCACCACC

                                 
      31176 TCCGCCACCAGTTCCACCACC
          1 TCCGCCACCA-TTCCACCACC

                              
      31197 TCCGCCACACATTCCACC
          1 TCCGCCAC-CATTCCACC

      31215 GTTTCTACAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  21   31  0.91
  22    3  0.09

ACGTcount: A:0.20, C:0.55, G:0.07, T:0.18


Consensus pattern (20 bp):   
TCCGCCACCATTCCACCACC

Found at i:32964 original size:24 final size:24

Alignment explanation


    Indices: 32934--32981  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      32924 AATGAGATGG

                        *           
      32934 TGAATGAAACCATTACAAAGACGA
          1 TGAATGAAACCACTACAAAGACGA

                                    
      32958 TGAATGAAACCACTACAAAGACGA
          1 TGAATGAAACCACTACAAAGACGA

      32982 GGGAGATGAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.50, C:0.19, G:0.17, T:0.15


Consensus pattern (24 bp):   
TGAATGAAACCACTACAAAGACGA
Done.