Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010784.1 Corchorus olitorius cultivar O-4 contig10816, 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: 17166
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:34 original size:12 final size:10

Alignment explanation


    Indices: 5--45  Score: 55
    Period size: 10  Copynumber: 3.9  Consensus size: 10

          1 TTTT

                      
          5 TTTTTTTTAA
          1 TTTTTTTTAA

             *         
         15 TCTTTTTTAGA
          1 TTTTTTTTA-A

                       
         26 TTTTCTTTTAA
          1 TTTT-TTTTAA

                     
         37 TTTTTTTTA
          1 TTTTTTTTA

         46 TCTTTTAATA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  10   13  0.48
  11    9  0.33
  12    5  0.19

ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76


Consensus pattern (10 bp):   
TTTTTTTTAA

Found at i:51 original size:22 final size:22

Alignment explanation


    Indices: 4--45  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

          1 TTT

                *                 
          4 TTTTTTTTTAATCTTTTTTAGA
          1 TTTTCTTTTAATCTTTTTTAGA

                        *       
         26 TTTTCTTTTAATTTTTTTTA
          1 TTTTCTTTTAATCTTTTTTA

         46 TCTTTTAATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76


Consensus pattern (22 bp):   
TTTTCTTTTAATCTTTTTTAGA

Found at i:703 original size:21 final size:21

Alignment explanation


    Indices: 671--710  Score: 55
    Period size: 20  Copynumber: 1.9  Consensus size: 21

        661 TTTTTTTTTC

                                 
        671 ATTTTATTAGTA-GTAAAATA
          1 ATTTTATTAGTAGGTAAAATA

                 *              
        691 ATTTTTTTGAGTAGGTAAAA
          1 ATTTTATT-AGTAGGTAAAA

        711 ATAAAATAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    7  0.41
  21    4  0.24
  22    6  0.35

ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45


Consensus pattern (21 bp):   
ATTTTATTAGTAGGTAAAATA

Found at i:718 original size:5 final size:5

Alignment explanation


    Indices: 708--738  Score: 62
    Period size: 5  Copynumber: 6.2  Consensus size: 5

        698 TGAGTAGGTA

                                                 
        708 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
          1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A

        739 TTTTAGAATG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   26  1.00

ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19


Consensus pattern (5 bp):   
AAAAT

Found at i:7385 original size:12 final size:12

Alignment explanation


    Indices: 7368--7395  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

       7358 CAGATCATGT

                        
       7368 ATTCCCAGATTC
          1 ATTCCCAGATTC

                        
       7380 ATTCCCAGATTC
          1 ATTCCCAGATTC

                
       7392 ATTC
          1 ATTC

       7396 TCCATTATAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.25, C:0.32, G:0.07, T:0.36


Consensus pattern (12 bp):   
ATTCCCAGATTC

Found at i:15012 original size:120 final size:119

Alignment explanation


    Indices: 14791--15023  Score: 355
    Period size: 120  Copynumber: 1.9  Consensus size: 119

      14781 ACTTTTGTAG

                      *                 *          *                         
      14791 TTTTACTCAATTAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACTATTTTTTTT
          1 TTTTACTCAACTAAAAACTCTATATTTAGTTAATTAAATATAATATCCTTATAACTATTTTTTTT

                        *                  *                      
      14856 TACTATTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAATAT
         66 TACTATTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTTAATAT

                                    *                                        
      14910 TTTTACTCAACTAAAAACTCTATTTTTTAGTTAATTAAATATAATATCCTTATAACTATTTTATT
          1 TTTTACTCAACTAAAAACTCTA-TATTTAGTTAATTAAATATAATATCCTTATAACTATTTT-TT

                                                                
      14975 TTTA-TCATTTTACTAATTTAATT-AAAAAACTT-GATATATTAGAATTTTT
         64 TTTACT-A-TTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTT

      15024 AAAATATATT


Statistics
Matches: 104,  Mismatches: 6, Indels: 7
        0.89            0.05        0.06

Matches are distributed among these distances:
 119   21  0.20
 120   53  0.51
 121   16  0.15
 122   14  0.13

ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51


Consensus pattern (119 bp):   
TTTTACTCAACTAAAAACTCTATATTTAGTTAATTAAATATAATATCCTTATAACTATTTTTTTT
TACTATTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTTAATAT
Done.