Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020951.1 Corchorus olitorius cultivar O-4 contig20984, 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: 25670
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30


Found at i:1238 original size:2 final size:2

Alignment explanation


    Indices: 1231--1265  Score: 61
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1221 ATATAAACCC

                                                               
       1231 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

       1266 TATTTGAAAC


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   30  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:5829 original size:20 final size:22

Alignment explanation


    Indices: 5806--5846  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5796 TCGAGCTCGG

                                  
       5806 CTCGAA-TTTTC-CGAGTCGAA
          1 CTCGAATTTTTCTCGAGTCGAA

                                 
       5826 CTCGAATTTTTCTCGAGTCGA
          1 CTCGAATTTTTCTCGAGTCGA

       5847 GCCCGAGTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    6  0.32
  21    5  0.26
  22    8  0.42

ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34


Consensus pattern (22 bp):   
CTCGAATTTTTCTCGAGTCGAA

Found at i:9251 original size:5 final size:5

Alignment explanation


    Indices: 9241--9269  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       9231 AATTTACAAG

                                              
       9241 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
          1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA

       9270 CAACAACTAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79


Consensus pattern (5 bp):   
TTTAT

Found at i:16949 original size:24 final size:24

Alignment explanation


    Indices: 16917--16963  Score: 94
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      16907 ACCTTTCTGC

                                    
      16917 AACACAGAATATTAGTGCGACCAT
          1 AACACAGAATATTAGTGCGACCAT

                                   
      16941 AACACAGAATATTAGTGCGACCA
          1 AACACAGAATATTAGTGCGACCA

      16964 GATAGATAGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19


Consensus pattern (24 bp):   
AACACAGAATATTAGTGCGACCAT

Found at i:17023 original size:66 final size:66

Alignment explanation


    Indices: 16941--17064  Score: 248
    Period size: 66  Copynumber: 1.9  Consensus size: 66

      16931 GTGCGACCAT

                                                                             
      16941 AACACAGAATATTAGTGCGACCAGATAGATAGAAGAAACCAATGGGAATAAAATGAACCTTTCTG
          1 AACACAGAATATTAGTGCGACCAGATAGATAGAAGAAACCAATGGGAATAAAATGAACCTTTCTG

             
      17006 C
         66 C

                                                                      
      17007 AACACAGAATATTAGTGCGACCAGATAGATAGAAGAAACCAATGGGAATAAAATGAAC
          1 AACACAGAATATTAGTGCGACCAGATAGATAGAAGAAACCAATGGGAATAAAATGAAC

      17065 AGAGCAGACA


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  66   58  1.00

ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18


Consensus pattern (66 bp):   
AACACAGAATATTAGTGCGACCAGATAGATAGAAGAAACCAATGGGAATAAAATGAACCTTTCTG
C

Found at i:23000 original size:30 final size:30

Alignment explanation


    Indices: 22964--23025  Score: 124
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      22954 CAAAGCTCTG

                                          
      22964 AATACCATTTGGGAAAACTAAACAAAAAAA
          1 AATACCATTTGGGAAAACTAAACAAAAAAA

                                          
      22994 AATACCATTTGGGAAAACTAAACAAAAAAA
          1 AATACCATTTGGGAAAACTAAACAAAAAAA

              
      23024 AA
          1 AA

      23026 ACAGATTCAC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   32  1.00

ACGTcount: A:0.61, C:0.13, G:0.10, T:0.16


Consensus pattern (30 bp):   
AATACCATTTGGGAAAACTAAACAAAAAAA

Found at i:24043 original size:30 final size:29

Alignment explanation


    Indices: 23983--24042  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      23973 GAAAGCTCTG

                                         
      23983 AATACCATTTGGGAAAACTAAACAAAAAA
          1 AATACCATTTGGGAAAACTAAACAAAAAA

                                         
      24012 AATACCATTTGGGAAAACTAAACAAAAAA
          1 AATACCATTTGGGAAAACTAAACAAAAAA

              
      24041 AA
          1 AA

      24043 AACATATTCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.60, C:0.13, G:0.10, T:0.17


Consensus pattern (29 bp):   
AATACCATTTGGGAAAACTAAACAAAAAA
Done.