Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015606.1 Corchorus capsularis cultivar CVL-1 contig15627, 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: 7544
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37


Found at i:3012 original size:2 final size:2

Alignment explanation


    Indices: 3005--3034  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       2995 ACACCTAATT

                                                 *      
       3005 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3035 CGGTATTACA


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

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:5950 original size:14 final size:15

Alignment explanation


    Indices: 5925--5953  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       5915 AACAACTAAG

                           
       5925 AAAGCAAACAGATTA
          1 AAAGCAAACAGATTA

                           
       5940 AAAGC-AACAGATTA
          1 AAAGCAAACAGATTA

       5954 TAGAAAAAAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14


Consensus pattern (15 bp):   
AAAGCAAACAGATTA

Found at i:6806 original size:3 final size:3

Alignment explanation


    Indices: 6798--6848  Score: 102
    Period size: 3  Copynumber: 17.0  Consensus size: 3

       6788 ACTATTCCAA

                                                                           
       6798 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

               
       6846 TAT
          1 TAT

       6849 CATCATCATC


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   48  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:6853 original size:3 final size:3

Alignment explanation


    Indices: 6847--6887  Score: 82
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       6837 TATTATTATT

                                                                  
       6847 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT

       6888 TATTATTATA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATC

Found at i:7151 original size:15 final size:15

Alignment explanation


    Indices: 7133--7175  Score: 54
    Period size: 14  Copynumber: 2.9  Consensus size: 15

       7123 AAATCAAATT

                           
       7133 ATATAAAATATATAA
          1 ATATAAAATATATAA

                      *    
       7148 ATAT-AAATAAATAA
          1 ATATAAAATATATAA

                           
       7162 A-ATAAAATTATATA
          1 ATATAAAA-TATATA

       7176 TATTTATATA


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  13    2  0.08
  14   13  0.54
  15    9  0.38

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (15 bp):   
ATATAAAATATATAA

Found at i:7177 original size:33 final size:31

Alignment explanation


    Indices: 7140--7214  Score: 78
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       7130 ATTATATAAA

                                            *
       7140 ATATATAAATATAAATAAATAAAATAAAATTAT
          1 ATATATAAATATAAAT-AA-AAAATAAAATTAC

                  **      *        *       
       7173 ATATATTTATATAACTAAAAAATTAAATTAC
          1 ATATATAAATATAAATAAAAAATAAAATTAC

               *       
       7204 ATAAATAAATA
          1 ATATATAAATA

       7215 CTAGGGTTTC


Statistics
Matches: 34,  Mismatches: 8, Indels: 2
        0.77            0.18        0.05

Matches are distributed among these distances:
  31   19  0.56
  32    2  0.06
  33   13  0.38

ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35


Consensus pattern (31 bp):   
ATATATAAATATAAATAAAAAATAAAATTAC
Done.