Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021433.1 Corchorus olitorius cultivar O-4 contig21466, 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: 8825
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:1638 original size:16 final size:15

Alignment explanation


    Indices: 1617--1659  Score: 68
    Period size: 16  Copynumber: 2.7  Consensus size: 15

       1607 TTATTTTGCT

                            
       1617 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                            
       1633 TTGTTTTTCTGTTTAA
          1 TTG-TTTTCTGTTTAA

                       
       1649 TTGTTTTCTGT
          1 TTGTTTTCTGT

       1660 CAACCTCTGT


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

Matches are distributed among these distances:
  15    8  0.31
  16   12  0.46
  17    6  0.23

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2104 original size:31 final size:28

Alignment explanation


    Indices: 2066--2122  Score: 78
    Period size: 31  Copynumber: 1.9  Consensus size: 28

       2056 GTCGTTTTGA

                        *                  
       2066 AAAAAAAAAATTGTTTTGTGTTTTTGCGTCG
          1 AAAAAAAAAA-TCTTTT-TG-TTTTGCGTCG

                                      
       2097 AAAAAAAAAATCTTTTTGTTTTGCGT
          1 AAAAAAAAAATCTTTTTGTTTTGCGT

       2123 TTTTAATTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  28    8  0.32
  29    2  0.08
  30    5  0.20
  31   10  0.40

ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42


Consensus pattern (28 bp):   
AAAAAAAAAATCTTTTTGTTTTGCGTCG

Found at i:4761 original size:21 final size:21

Alignment explanation


    Indices: 4714--4753  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4704 TTACCATGCA

                                 
       4714 ACCACCGGTCATGCCCGTGCC
          1 ACCACCGGTCATGCCCGTGCC

                                
       4735 ACCACCGG-CTATGCCCGTG
          1 ACCACCGGTC-ATGCCCGTG

       4754 TCATCACCAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.15, C:0.45, G:0.25, T:0.15


Consensus pattern (21 bp):   
ACCACCGGTCATGCCCGTGCC

Found at i:5137 original size:15 final size:14

Alignment explanation


    Indices: 5117--5146  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       5107 ATCTCTTTAA

                           
       5117 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       5132 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       5146 T
          1 T

       5147 GCTTTAATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT

Found at i:8013 original size:16 final size:15

Alignment explanation


    Indices: 7992--8034  Score: 59
    Period size: 16  Copynumber: 2.7  Consensus size: 15

       7982 TTACTCTGCT

                            
       7992 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                            
       8008 TTGTTTTTCTGTTTAA
          1 TTG-TTTTCTGTTTAA

              *        
       8024 TTATTTTCTGT
          1 TTGTTTTCTGT

       8035 CAACCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  15    8  0.32
  16   11  0.44
  17    6  0.24

ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:8032 original size:15 final size:16

Alignment explanation


    Indices: 7995--8034  Score: 55
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       7985 CTCTGCTTTG

                            *
       7995 TTTTCTAGTTTAATTGT
          1 TTTTCT-GTTTAATTGA

                            
       8012 TTTTCTGTTTAATT-A
          1 TTTTCTGTTTAATTGA

                    
       8027 TTTTCTGT
          1 TTTTCTGT

       8035 CAACCTCTGT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15    8  0.36
  16    8  0.36
  17    6  0.27

ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68


Consensus pattern (16 bp):   
TTTTCTGTTTAATTGA
Done.