Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009756.1 Corchorus olitorius cultivar O-4 contig09788, 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: 3016
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Found at i:728 original size:61 final size:63

Alignment explanation


    Indices: 645--778  Score: 161
    Period size: 61  Copynumber: 2.2  Consensus size: 63

        635 AAAAGGTTGT

                                                                 *      * * 
        645 TTTAGAGGC--AGATAAATCATTTGCCTTTGTATCCAA-AGTTATTTGCCTCTGATTCTTGATA
          1 TTTAGAGGCAAAGATAAATCATTTGCCTTTGTATCCAATA-TTATTTGCCTCTAATTCTTAACA

                                              **           *        *      
        706 TTTAGAGGCAAAGAT-AAT-ATTTGCCTTTGTATGTAATATTATTTGTCTCTAATTTTTAACA
          1 TTTAGAGGCAAAGATAAATCATTTGCCTTTGTATCCAATATTATTTGCCTCTAATTCTTAACA

                        
        767 TTTAGAGGCAAA
          1 TTTAGAGGCAAA

        779 AAAGTATATG


Statistics
Matches: 63,  Mismatches: 7, Indels: 6
        0.83            0.09        0.08

Matches are distributed among these distances:
  61   55  0.87
  62    4  0.06
  63    4  0.06

ACGTcount: A:0.30, C:0.13, G:0.16, T:0.42


Consensus pattern (63 bp):   
TTTAGAGGCAAAGATAAATCATTTGCCTTTGTATCCAATATTATTTGCCTCTAATTCTTAACA

Found at i:2983 original size:20 final size:20

Alignment explanation


    Indices: 2954--3003  Score: 66
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       2944 GTTCTAAAAC

                           *     
       2954 TTTTACTTTTATTTCTTTTAT
          1 TTTTACTTTTATTT-ATTTAT

                                
       2975 TTTTA-TTTTATTTATTTAT
          1 TTTTACTTTTATTTATTTAT

                *     
       2994 TTTTCCTTTT
          1 TTTTACTTTT

       3004 TCTTTTTCCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  19    9  0.35
  20   12  0.46
  21    5  0.19

ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78


Consensus pattern (20 bp):   
TTTTACTTTTATTTATTTAT

Found at i:2988 original size:15 final size:15

Alignment explanation


    Indices: 2953--2991  Score: 53
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       2943 TGTTCTAAAA

                  *        
       2953 CTTTTACTTTTATTT
          1 CTTTTATTTTTATTT

                           
       2968 CTTTTATTTTTATTT
          1 CTTTTATTTTTATTT

                      
       2983 -TATTTATTT
          1 CT-TTTATTT

       2992 ATTTTTCCTT


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

Matches are distributed among these distances:
  14    1  0.05
  15   21  0.95

ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77


Consensus pattern (15 bp):   
CTTTTATTTTTATTT
Done.