Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018779.1 Corchorus olitorius cultivar O-4 contig18812, 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: 8663
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:691 original size:15 final size:15

Alignment explanation


    Indices: 671--708  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        661 ACAAAGATTG

                           
        671 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                           
        686 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                    
        701 ACTAGAAA
          1 AC-AGAAA

        709 ACAAAGCAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.77
  16    5  0.23

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


Consensus pattern (15 bp):   
ACAGAAAGCAATTAA

Found at i:3989 original size:21 final size:21

Alignment explanation


    Indices: 3963--4006  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3953 GGAATGGCGA

                         *       
       3963 TGGCACGGGCATAGCCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                      *          
       3984 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATAACCGGTGG

              
       4005 TG
          1 TG

       4007 TGGCACTCGG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18


Consensus pattern (21 bp):   
TGGCACGGGCATAACCGGTGG

Found at i:7322 original size:31 final size:28

Alignment explanation


    Indices: 7251--7322  Score: 72
    Period size: 29  Copynumber: 2.4  Consensus size: 28

       7241 AATGACGCAA

                                         
       7251 AAAACTCTTTTTTTTTTCGACGCAAAAAC
          1 AAAAC-CTTTTTTTTTTCGACGCAAAAAC

                 **                *        
       7280 AAACAGATTTTTTTTTTCTTGACTCAAAACAC
          1 AAA-ACCTTTTTTTTTTC--GACGCAAAA-AC

                       
       7312 AAAACCTTTTT
          1 AAAACCTTTTT

       7323 AAAAAAAAAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 6
        0.76            0.11        0.13

Matches are distributed among these distances:
  29   14  0.41
  30    1  0.03
  31   14  0.41
  32    5  0.15

ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40


Consensus pattern (28 bp):   
AAAACCTTTTTTTTTTCGACGCAAAAAC

Found at i:7345 original size:19 final size:18

Alignment explanation


    Indices: 7323--7364  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       7313 AAACCTTTTT

                               
       7323 AAAAAAAAAAAACGCAACA
          1 AAAAAAAAAAAACGCAA-A

                 **           
       7342 AAAAATTAAAAACGCAAA
          1 AAAAAAAAAAAACGCAAA

                 
       7360 AAAAA
          1 AAAAA

       7365 TCAAAATTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18    6  0.29
  19   15  0.71

ACGTcount: A:0.79, C:0.12, G:0.05, T:0.05


Consensus pattern (18 bp):   
AAAAAAAAAAAACGCAAA

Found at i:7365 original size:18 final size:19

Alignment explanation


    Indices: 7330--7370  Score: 66
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       7320 TTTAAAAAAA

                              *
       7330 AAAAACGCAACAAAAAATT
          1 AAAAACGCAACAAAAAATC

                               
       7349 AAAAACGCAA-AAAAAATC
          1 AAAAACGCAACAAAAAATC

                
       7367 AAAA
          1 AAAA

       7371 TTTTTTTTAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  18   11  0.52
  19   10  0.48

ACGTcount: A:0.73, C:0.15, G:0.05, T:0.07


Consensus pattern (19 bp):   
AAAAACGCAACAAAAAATC
Done.