Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017210.1 Corchorus olitorius cultivar O-4 contig17243, 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: 4751
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:1906 original size:15 final size:15

Alignment explanation


    Indices: 1876--1917  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1866 TTACTCTGCT

                            
       1876 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       1892 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       1907 TTGCTTTCTGT
          1 TTGTTTTCTGT

       1918 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2394 original size:30 final size:29

Alignment explanation


    Indices: 2355--2425  Score: 83
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       2345 TGCGTTTTTT

                                           
       2355 GAAAAAAAAAA-CGGTTTTGTGTTTTGCATC
          1 GAAAAAAAAAATCGG-TTTGT-TTTTGCATC

                          *            *  
       2385 -AAGAAAAAAAATCTGTTTGTTTTTGCGTC
          1 GAA-AAAAAAAATCGGTTTGTTTTTGCATC

                        
       2414 GAAAAAAAAAAT
          1 GAAAAAAAAAAT

       2426 GAGTTTTTTT


Statistics
Matches: 36,  Mismatches: 2, Indels: 7
        0.80            0.04        0.16

Matches are distributed among these distances:
  29   19  0.53
  30   15  0.42
  31    2  0.06

ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31


Consensus pattern (29 bp):   
GAAAAAAAAAATCGGTTTGTTTTTGCATC

Found at i:2431 original size:29 final size:28

Alignment explanation


    Indices: 2355--2440  Score: 79
    Period size: 29  Copynumber: 3.0  Consensus size: 28

       2345 TGCGTTTTTT

                       *               *  
       2355 GAAAAAAAAAACGGTTTTGTGTTTTGCATC
          1 GAAAAAAAAAATGG-TTTGT-TTTTGCGTC

                          *               
       2385 -AAGAAAAAAAATCTGTTTGTTTTTGCGTC
          1 GAA-AAAAAAAAT-GGTTTGTTTTTGCGTC

                                         
       2414 GAAAAAAAAAATGAG-TT-TTTTTGCGTC
          1 GAAAAAAAAAATG-GTTTGTTTTTGCGTC

       2441 ATATATAAAA


Statistics
Matches: 48,  Mismatches: 4, Indels: 11
        0.76            0.06        0.17

Matches are distributed among these distances:
  27   10  0.21
  28    2  0.04
  29   20  0.42
  30   15  0.31
  31    1  0.02

ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35


Consensus pattern (28 bp):   
GAAAAAAAAAATGGTTTGTTTTTGCGTC
Done.