Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018189.1 Corchorus olitorius cultivar O-4 contig18222, 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: 20865
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:109 original size:9 final size:9

Alignment explanation


    Indices: 97--140  Score: 52
    Period size: 9  Copynumber: 4.8  Consensus size: 9

         87 AAATATTGTA

                   * 
         97 ATTATTACC
          1 ATTATTATC

                    *
        106 ATTATTATT
          1 ATTATTATC

                    *
        115 ATTATTATA
          1 ATTATTATC

                      
        124 ATATATTATC
          1 AT-TATTATC

                   
        134 ATTATTA
          1 ATTATTA

        141 GTTAGATTGA


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
   9   22  0.73
  10    8  0.27

ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55


Consensus pattern (9 bp):   
ATTATTATC

Found at i:3560 original size:11 final size:11

Alignment explanation


    Indices: 3544--3568  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       3534 ATTTCACAAT

                       
       3544 CAAGCTATAAC
          1 CAAGCTATAAC

                       
       3555 CAAGCTATAAC
          1 CAAGCTATAAC

               
       3566 CAA
          1 CAA

       3569 TCCTGAGTGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16


Consensus pattern (11 bp):   
CAAGCTATAAC

Found at i:5472 original size:2 final size:2

Alignment explanation


    Indices: 5465--5494  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       5455 TGGCTTCATC

                                                        
       5465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5495 GTTGTTTACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7769 original size:3 final size:3

Alignment explanation


    Indices: 7761--7797  Score: 67
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       7751 AATATTAATA

                                                              
       7761 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

       7798 CATTACTATA


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2    2  0.06
   3   31  0.94

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TAT

Found at i:11383 original size:21 final size:19

Alignment explanation


    Indices: 11346--11384  Score: 51
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      11336 AACAGGACGT

                               
      11346 TCATCATTAACAAAGAAAA
          1 TCATCATTAACAAAGAAAA

                 *              
      11365 TCATCTTTACACATAAGAAA
          1 TCATCATTA-ACA-AAGAAA

      11385 GAGGGAAAGG


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

Matches are distributed among these distances:
  19    8  0.47
  20    3  0.18
  21    6  0.35

ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26


Consensus pattern (19 bp):   
TCATCATTAACAAAGAAAA
Done.