Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017615.1 Corchorus olitorius cultivar O-4 contig17648, 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: 30115
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31


Found at i:931 original size:2 final size:2

Alignment explanation


    Indices: 924--967  Score: 65
    Period size: 2  Copynumber: 23.0  Consensus size: 2

        914 CTCGATACAA

                                                       *                  
        924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT A- AT AT -T AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 
        964 AT AT
          1 AT AT

        968 TTAATTAAAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   36  0.95

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:972 original size:14 final size:15

Alignment explanation


    Indices: 926--972  Score: 60
    Period size: 16  Copynumber: 3.1  Consensus size: 15

        916 CGATACAAAT

                           
        926 ATATATATATATATA
          1 ATATATATATATATA

                        *   
        941 TATATATATATACATA
          1 -ATATATATATATATA

                        *  
        957 ATAT-TATATATTTA
          1 ATATATATATATATA

              
        971 AT
          1 AT

        973 TAAAAAAATT


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  14   10  0.36
  15    4  0.14
  16   14  0.50

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (15 bp):   
ATATATATATATATA

Found at i:13325 original size:1 final size:1

Alignment explanation


    Indices: 13319--13346  Score: 56
    Period size: 1  Copynumber: 28.0  Consensus size: 1

      13309 AGCAATCAGG

                                        
      13319 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA

      13347 CGCCTGGGGT


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

Matches are distributed among these distances:
   1   27  1.00

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


Consensus pattern (1 bp):   
A

Found at i:21144 original size:19 final size:18

Alignment explanation


    Indices: 21120--21155  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      21110 TGAATACTTA

                               
      21120 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      21139 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      21156 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:28262 original size:18 final size:18

Alignment explanation


    Indices: 28239--28303  Score: 85
    Period size: 18  Copynumber: 3.6  Consensus size: 18

      28229 CAAAATATTT

                              
      28239 TTCCACTGCCGCAGGATG
          1 TTCCACTGCCGCAGGATG

                   * *    *   
      28257 TTCCACTACTGCAGAATG
          1 TTCCACTGCCGCAGGATG

                 *            
      28275 TTCCATTGCCGCAGGATG
          1 TTCCACTGCCGCAGGATG

                *      
      28293 TTCCGCTGCCG
          1 TTCCACTGCCG

      28304 TAAGAACCTT


Statistics
Matches: 38,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  18   38  1.00

ACGTcount: A:0.17, C:0.32, G:0.25, T:0.26


Consensus pattern (18 bp):   
TTCCACTGCCGCAGGATG
Done.