Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013124.1 Corchorus olitorius cultivar O-4 contig13157, 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: 3834
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37


Found at i:156 original size:58 final size:58

Alignment explanation


    Indices: 53--167  Score: 153
    Period size: 58  Copynumber: 2.0  Consensus size: 58

         43 ATAGCATCAT

                      *                                               
         53 GCCTCGGTCCTAAAACATCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA
          1 GCCTCGGTCCGAAAACATCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA

                *           *                         *           *    
        111 GCCTTGGTCCGAAAACGTCTTTTTTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
          1 GCCTCGGTCCGAAAACATC-TTTTTTA-GACATCTAATAAAAAAACATGTCACTCGATA

        168 TTTGATTAAT


Statistics
Matches: 50,  Mismatches: 5, Indels: 4
        0.85            0.08        0.07

Matches are distributed among these distances:
  58   34  0.68
  59   15  0.30
  60    1  0.02

ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32


Consensus pattern (58 bp):   
GCCTCGGTCCGAAAACATCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA

Found at i:2777 original size:124 final size:125

Alignment explanation


    Indices: 2627--2878  Score: 382
    Period size: 124  Copynumber: 2.0  Consensus size: 125

       2617 CATTGTTTAA

                   *                                            *    ***     
       2627 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTATTAT-TTTTA-TA
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATCACCTACTA

                                                                         
       2690 ATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
         66 ATTTTTACCATTTTACTATTTT-ATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT

                                            * *                              
       2751 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCACCTACT
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATAT-CACCTAC-

             *                         *                                  
       2816 TTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAATAT
         64 TAATTTTTACCATTTTACTATTTTATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT

             
       2878 A
          1 A

       2879 TTTCTTAAAT


Statistics
Matches: 115,  Mismatches: 9, Indels: 5
        0.89            0.07        0.04

Matches are distributed among these distances:
 124   52  0.45
 126    2  0.02
 127   38  0.33
 128   23  0.20

ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49


Consensus pattern (125 bp):   
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATCACCTACTA
ATTTTTACCATTTTACTATTTTATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT

Found at i:2900 original size:14 final size:13

Alignment explanation


    Indices: 2864--2902  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

       2854 TATATATTAG

                         
       2864 AATTTTTTAAATA
          1 AATTTTTTAAATA

            *    *        
       2877 TATTTCTTAAATGA
          1 AATTTTTTAAAT-A

                        
       2891 AATTTTTTAAAT
          1 AATTTTTTAAAT

       2903 TTTACAATTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54


Consensus pattern (13 bp):   
AATTTTTTAAATA
Done.