Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018506.1 Corchorus olitorius cultivar O-4 contig18539, 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: 13299
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:1577 original size:2 final size:2

Alignment explanation


    Indices: 1572--1607  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       1562 TTAAAAAAAG

                                             *        *          
       1572 AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1608 GTATGTACTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2043 original size:33 final size:33

Alignment explanation


    Indices: 1979--2044  Score: 80
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       1969 CAGGTGCAAC

                                * *  **      
       1979 AAACTATATTAATGAAACCTTTTTCCTCAAAAA
          1 AAACTATATTAATGAAACCTATATCAGCAAAAA

                                              
       2012 AAACTATATTAATGAAACCATATAT-AGCAAAAA
          1 AAACTATATTAATGAAACC-TATATCAGCAAAAA

       2045 TATACTTTCA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  33   25  0.89
  34    3  0.11

ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29


Consensus pattern (33 bp):   
AAACTATATTAATGAAACCTATATCAGCAAAAA

Found at i:2885 original size:3 final size:3

Alignment explanation


    Indices: 2877--2903  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       2867 ACAATGAAGA

                                               
       2877 ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT

       2904 GGCCATAGGA


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

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:7208 original size:14 final size:15

Alignment explanation


    Indices: 7189--7218  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       7179 AACTAGGAAA

                           
       7189 AATAAATAA-CAAGG
          1 AATAAATAAGCAAGG

                           
       7203 AATAAATAAGCAAGG
          1 AATAAATAAGCAAGG

             
       7218 A
          1 A

       7219 TTGGACTTAG


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

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

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


Consensus pattern (15 bp):   
AATAAATAAGCAAGG

Found at i:13264 original size:2 final size:2

Alignment explanation


    Indices: 13257--13299  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      13247 TCATTTCTCA

                                                                          
      13257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
      13299 A
          1 A


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.