Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002019.1 Corchorus olitorius cultivar O-4 contig02019, 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: 3364
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:182 original size:31 final size:29

Alignment explanation


    Indices: 116--195  Score: 97
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        106 CTCATTTTTG

                *          *        *    
        116 AAACGTAAGGGATTAATTTGTACCGAAAA
          1 AAACATAAGGGATTATTTTGTACCAAAAA

                                 *         
        145 AAACATAAGGGATTATTTTGTCCCAAAAGCA
          1 AAACATAAGGGATTATTTTGTACCAAAA--A

                          *     
        176 AAACATAAGGGATTTTTTTG
          1 AAACATAAGGGATTATTTTG

        196 GGTATTTAGC


Statistics
Matches: 44,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  29   24  0.55
  31   20  0.45

ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29


Consensus pattern (29 bp):   
AAACATAAGGGATTATTTTGTACCAAAAA

Found at i:228 original size:6 final size:6

Alignment explanation


    Indices: 217--255  Score: 60
    Period size: 6  Copynumber: 6.2  Consensus size: 6

        207 TTTATATAAT

                                                         
        217 ATAAAG ATAAAG ATATAAAG ATAAAG ATAAAG ATAAAG A
          1 ATAAAG ATAAAG --ATAAAG ATAAAG ATAAAG ATAAAG A

        256 ATCTAATCCT


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   6   25  0.81
   8    6  0.19

ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18


Consensus pattern (6 bp):   
ATAAAG

Found at i:234 original size:14 final size:14

Alignment explanation


    Indices: 215--255  Score: 68
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        205 CCTTTATATA

                          
        215 ATATAAAGATAAAG
          1 ATATAAAGATAAAG

                          
        229 ATATAAAGATAAAG
          1 ATATAAAGATAAAG

                          
        243 --ATAAAGATAAAG
          1 ATATAAAGATAAAG

             
        255 A
          1 A

        256 ATCTAATCCT


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

Matches are distributed among these distances:
  12   12  0.46
  14   14  0.54

ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20


Consensus pattern (14 bp):   
ATATAAAGATAAAG

Found at i:2765 original size:6 final size:6

Alignment explanation


    Indices: 2756--2790  Score: 52
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       2746 TTTATATAAT

                                                    
       2756 ATAAAG ATAAAG ATATAAAG ATAAAG ATAAAG ATA
          1 ATAAAG ATAAAG --ATAAAG ATAAAG ATAAAG ATA

       2791 TATATATCTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
   6   21  0.78
   8    6  0.22

ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20


Consensus pattern (6 bp):   
ATAAAG

Found at i:2773 original size:14 final size:14

Alignment explanation


    Indices: 2754--2784  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       2744 GATTTATATA

                          
       2754 ATATAAAGATAAAG
          1 ATATAAAGATAAAG

                          
       2768 ATATAAAGATAAAG
          1 ATATAAAGATAAAG

               
       2782 ATA
          1 ATA

       2785 AAGATATATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23


Consensus pattern (14 bp):   
ATATAAAGATAAAG
Done.