Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015248.1 Corchorus capsularis cultivar CVL-1 contig15269, 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: 5047
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37


Found at i:1244 original size:15 final size:15

Alignment explanation


    Indices: 1220--1253  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1210 ATGGCATAGG

                      *    
       1220 AGAAAAGAATCAAAT
          1 AGAAAAGAATAAAAT

                 *         
       1235 AGAAAGGAATAAAAT
          1 AGAAAAGAATAAAAT

                
       1250 AGAA
          1 AGAA

       1254 TCAGGGGATG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.68, C:0.03, G:0.18, T:0.12


Consensus pattern (15 bp):   
AGAAAAGAATAAAAT

Found at i:2939 original size:2 final size:2

Alignment explanation


    Indices: 2932--2958  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       2922 AGCATCTGCC

                                                    
       2932 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2959 ATGCGTTTCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3159 original size:2 final size:2

Alignment explanation


    Indices: 3152--3176  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3142 ATTAAGTCTC

                                                 
       3152 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       3177 TTTTGTGTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4036 original size:46 final size:45

Alignment explanation


    Indices: 3958--4049  Score: 139
    Period size: 46  Copynumber: 2.0  Consensus size: 45

       3948 AAACTAGATT

                *                      *                  
       3958 GACCTATTATGGGTAAAACTCTCCCAATAATTATCTGTATATTATC
          1 GACCCATTATGGGTAAAACTCTCCCAACAATTATCTGTATA-TATC

                                    **                   
       4004 GACCCATTATGGGTAAAACTCTCCTGACAATTATCTGTATATATC
          1 GACCCATTATGGGTAAAACTCTCCCAACAATTATCTGTATATATC

             
       4049 G
          1 G

       4050 CTTTCAAAGA


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  45    5  0.12
  46   37  0.88

ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35


Consensus pattern (45 bp):   
GACCCATTATGGGTAAAACTCTCCCAACAATTATCTGTATATATC

Found at i:4926 original size:20 final size:20

Alignment explanation


    Indices: 4901--4944  Score: 70
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       4891 TCAACAATAC

                       **       
       4901 CCATTTCCTAATTCCTAAAG
          1 CCATTTCCTAAACCCTAAAG

                                
       4921 CCATTTCCTAAACCCTAAAG
          1 CCATTTCCTAAACCCTAAAG

                
       4941 CCAT
          1 CCAT

       4945 GACCTATAAC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.32, C:0.34, G:0.05, T:0.30


Consensus pattern (20 bp):   
CCATTTCCTAAACCCTAAAG
Done.