Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001164.1 Corchorus capsularis cultivar CVL-1 contig01164, 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: 7529
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:93 original size:12 final size:12

Alignment explanation


    Indices: 76--104  Score: 51
    Period size: 11  Copynumber: 2.5  Consensus size: 12

         66 GTCGGTTTTT

                        
         76 GGTTTTTTAGTC
          1 GGTTTTTTAGTC

                        
         88 GG-TTTTTAGTC
          1 GGTTTTTTAGTC

                  
         99 GGTTTT
          1 GGTTTT

        105 AATTTTGAGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  11   11  0.69
  12    5  0.31

ACGTcount: A:0.07, C:0.07, G:0.28, T:0.59


Consensus pattern (12 bp):   
GGTTTTTTAGTC

Found at i:105 original size:10 final size:11

Alignment explanation


    Indices: 79--104  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

         69 GGTTTTTGGT

                       
         79 TTTTTAGTCGG
          1 TTTTTAGTCGG

                       
         90 TTTTTAGTCGG
          1 TTTTTAGTCGG

                
        101 TTTT
          1 TTTT

        105 AATTTTGAGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62


Consensus pattern (11 bp):   
TTTTTAGTCGG

Found at i:1025 original size:16 final size:17

Alignment explanation


    Indices: 995--1036  Score: 50
    Period size: 16  Copynumber: 2.5  Consensus size: 17

        985 AGAAGATTTT

                           *  
        995 TTTTTTTAATCATTTCAG
          1 TTTTTTTAA-CATTTAAG

                            *
       1013 TTTTTTTAA-ATTTAAT
          1 TTTTTTTAACATTTAAG

                    
       1029 TTTTTTTA
          1 TTTTTTTA

       1037 GTTATATTTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  16   13  0.59
  18    9  0.41

ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69


Consensus pattern (17 bp):   
TTTTTTTAACATTTAAG

Found at i:3227 original size:2 final size:2

Alignment explanation


    Indices: 3222--3250  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       3212 ACGCACACAC

                                                        
       3222 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3251 TCCATAAATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Done.