Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024861.1 Corchorus olitorius cultivar O-4 contig24894, 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: 11631
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29


Found at i:2336 original size:13 final size:13

Alignment explanation


    Indices: 2320--2346  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       2310 TAAATCTGAC

                         
       2320 AAACATTCAAAAG
          1 AAACATTCAAAAG

                         
       2333 AAACATTCAAAAG
          1 AAACATTCAAAAG

             
       2346 A
          1 A

       2347 GATTGTCAGC


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

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15


Consensus pattern (13 bp):   
AAACATTCAAAAG

Found at i:4004 original size:2 final size:2

Alignment explanation


    Indices: 3997--4049  Score: 51
    Period size: 2  Copynumber: 28.5  Consensus size: 2

       3987 AAGCTAATTA

                                        * *           *                   
       3997 AT AT AT AT AT AT AT AT A- AC CT -T AT AT TT AT AT -T AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                  
       4036 AT AT A- AT AT AT AT A
          1 AT AT AT AT AT AT AT A

       4050 AACTTTATAT


Statistics
Matches: 43,  Mismatches: 4, Indels: 8
        0.78            0.07        0.15

Matches are distributed among these distances:
   1    4  0.09
   2   39  0.91

ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:4033 original size:11 final size:11

Alignment explanation


    Indices: 3997--4049  Score: 56
    Period size: 11  Copynumber: 4.8  Consensus size: 11

       3987 AAGCTAATTA

                       
       3997 ATATATATA-T
          1 ATATATATATT

                         
       4007 ATATATA-ACCTT
          1 ATATATATA--TT

                *      
       4019 ATATTTATATT
          1 ATATATATATT

                      *
       4030 ATATATATATA
          1 ATATATATATT

                     
       4041 ATATATATA
          1 ATATATATA

       4050 AACTTTATAT


Statistics
Matches: 36,  Mismatches: 3, Indels: 7
        0.78            0.07        0.15

Matches are distributed among these distances:
   9    1  0.03
  10    7  0.19
  11   20  0.56
  12    7  0.19
  13    1  0.03

ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49


Consensus pattern (11 bp):   
ATATATATATT

Found at i:7108 original size:2 final size:2

Alignment explanation


    Indices: 7101--7141  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       7091 TTAAGACTAG

                                                                         
       7101 TA TA TA TA TA TA 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 TA TA TA TA TA TA T

       7142 GAGGAGGGAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:7802 original size:19 final size:19

Alignment explanation


    Indices: 7774--7818  Score: 81
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       7764 CAATGGGACT

                 *             
       7774 ATCACTAATTGTGTTGTTA
          1 ATCACCAATTGTGTTGTTA

                               
       7793 ATCACCAATTGTGTTGTTA
          1 ATCACCAATTGTGTTGTTA

                   
       7812 ATCACCA
          1 ATCACCA

       7819 CAATAGTTAG


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   25  1.00

ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40


Consensus pattern (19 bp):   
ATCACCAATTGTGTTGTTA
Done.