Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009633.1 Corchorus capsularis cultivar CVL-1 contig09654, 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: 16441
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:1926 original size:1 final size:1

Alignment explanation


    Indices: 1920--1946  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

       1910 AGTTTGCAAC

                                       
       1920 AAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA

       1947 GAAAGAAGAG


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

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:7709 original size:3 final size:3

Alignment explanation


    Indices: 7703--7747  Score: 90
    Period size: 3  Copynumber: 15.0  Consensus size: 3

       7693 TACTACTAAT

                                                                       
       7703 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

       7748 GATGTATACA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   42  1.00

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


Consensus pattern (3 bp):   
TAA

Found at i:8191 original size:6 final size:6

Alignment explanation


    Indices: 8180--8218  Score: 69
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       8170 CTTATATAAT

                               *                         
       8180 ATAAAG ATAAAG ATAAAA ATAAAG ATAAAG ATAAAG ATA
          1 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATA

       8219 TATATATGTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   31  1.00

ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18


Consensus pattern (6 bp):   
ATAAAG

Found at i:9945 original size:41 final size:41

Alignment explanation


    Indices: 9887--9968  Score: 137
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       9877 TTTTCGTATC

                                                     
       9887 GTTCAGATGGCTAAATTGAATTAGTAAGCAGAAACCAATTT
          1 GTTCAGATGGCTAAATTGAATTAGTAAGCAGAAACCAATTT

                        *               *     *      
       9928 GTTCAGATGGCTCAATTGAATTAGTAAGTAGAAAGCAATTT
          1 GTTCAGATGGCTAAATTGAATTAGTAAGCAGAAACCAATTT

       9969 CGTCCGGCTT


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  41   38  1.00

ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30


Consensus pattern (41 bp):   
GTTCAGATGGCTAAATTGAATTAGTAAGCAGAAACCAATTT

Found at i:10900 original size:2 final size:2

Alignment explanation


    Indices: 10895--10923  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      10885 TGGGAGTTAT

                                                       
      10895 TA TA 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 TA TA T

      10924 GGACCTGAGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:13558 original size:12 final size:12

Alignment explanation


    Indices: 13541--13565  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      13531 TTAAGACAGA

                        
      13541 TATGATTCAAAG
          1 TATGATTCAAAG

                        
      13553 TATGATTCAAAG
          1 TATGATTCAAAG

             
      13565 T
          1 T

      13566 GTAATTCCAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36


Consensus pattern (12 bp):   
TATGATTCAAAG
Done.