Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013665.1 Corchorus olitorius cultivar O-4 contig13698, 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: 16113
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35


Found at i:874 original size:27 final size:27

Alignment explanation


    Indices: 836--887  Score: 95
    Period size: 27  Copynumber: 1.9  Consensus size: 27

        826 AGTACTGTAG

                                       
        836 AAATTGAATTTTTCTAAATAAAATAAA
          1 AAATTGAATTTTTCTAAATAAAATAAA

                   *                 
        863 AAATTGATTTTTTCTAAATAAAATA
          1 AAATTGAATTTTTCTAAATAAAATA

        888 TTTTGATAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40


Consensus pattern (27 bp):   
AAATTGAATTTTTCTAAATAAAATAAA

Found at i:7378 original size:21 final size:21

Alignment explanation


    Indices: 7340--7379  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       7330 GTTTGTAATA

                        *        
       7340 ATTTGATGAGTTGGCTTTCTT
          1 ATTTGATGAGTTCGCTTTCTT

                         *     
       7361 ATTTGATGAGTTCTCTTTC
          1 ATTTGATGAGTTCGCTTTC

       7380 GCTCACATAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53


Consensus pattern (21 bp):   
ATTTGATGAGTTCGCTTTCTT

Found at i:7459 original size:140 final size:140

Alignment explanation


    Indices: 7207--7475  Score: 520
    Period size: 140  Copynumber: 1.9  Consensus size: 140

       7197 TGAGATTCAG

                                            *                                
       7207 GAGTTGGCTTTCTTATTTGATGAGTTCTCTTTTGCTCACATAAATAGGGAGGCCAATGTTTTGGC
          1 GAGTTGGCTTTCTTATTTGATGAGTTCTCTTTCGCTCACATAAATAGGGAGGCCAATGTTTTGGC

                                                                             
       7272 ACATAAGTTAACTGGTTTACTAGTTGATCATGTGTGGTGCGGGTCTTTACCACCCGACGTTTGTA
         66 ACATAAGTTAACTGGTTTACTAGTTGATCATGTGTGGTGCGGGTCTTTACCACCCGACGTTTGTA

                      
       7337 ATAATTTGAT
        131 ATAATTTGAT

                                                                             
       7347 GAGTTGGCTTTCTTATTTGATGAGTTCTCTTTCGCTCACATAAATAGGGAGGCCAATGTTTTGGC
          1 GAGTTGGCTTTCTTATTTGATGAGTTCTCTTTCGCTCACATAAATAGGGAGGCCAATGTTTTGGC

                                                                      *     
       7412 ACATAAGTTAACTGGTTTACTAGTTGATCATGTGTGGTGCGGGTCTTTACCACCCGACTTTTGT
         66 ACATAAGTTAACTGGTTTACTAGTTGATCATGTGTGGTGCGGGTCTTTACCACCCGACGTTTGT

       7476 CTCAGTAATG


Statistics
Matches: 127,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 140  127  1.00

ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38


Consensus pattern (140 bp):   
GAGTTGGCTTTCTTATTTGATGAGTTCTCTTTCGCTCACATAAATAGGGAGGCCAATGTTTTGGC
ACATAAGTTAACTGGTTTACTAGTTGATCATGTGTGGTGCGGGTCTTTACCACCCGACGTTTGTA
ATAATTTGAT

Found at i:15881 original size:14 final size:13

Alignment explanation


    Indices: 15838--15884  Score: 51
    Period size: 13  Copynumber: 3.5  Consensus size: 13

      15828 TTTCCTTTAG

                          
      15838 TTTTGTTTTTAT-T
          1 TTTTGTTTTT-TGT

               *  *      
      15851 TTTCGTATTTTGT
          1 TTTTGTTTTTTGT

                          
      15864 TTTTGTTTTTGTGT
          1 TTTTGTTTTT-TGT

                   
      15878 TTTTGTT
          1 TTTTGTT

      15885 AATTTTGCAG


Statistics
Matches: 28,  Mismatches: 4, Indels: 3
        0.80            0.11        0.09

Matches are distributed among these distances:
  12    1  0.04
  13   17  0.61
  14   10  0.36

ACGTcount: A:0.04, C:0.02, G:0.15, T:0.79


Consensus pattern (13 bp):   
TTTTGTTTTTTGT

Found at i:15884 original size:6 final size:6

Alignment explanation


    Indices: 15838--15880  Score: 50
    Period size: 6  Copynumber: 6.7  Consensus size: 6

      15828 TTTCCTTTAG

                       *                                     
      15838 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTTGT GTTTT
          1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT -TTTT

      15881 TGTTAATTTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
   6   21  0.66
   7    7  0.22
   8    4  0.12

ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79


Consensus pattern (6 bp):   
TTTTGT
Done.