Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018304.1 Corchorus olitorius cultivar O-4 contig18337, 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: 7120
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32


Found at i:53 original size:17 final size:17

Alignment explanation


    Indices: 27--60  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

         17 AATTATTATA

                             
         27 TTGTTCATGAACAATTT
          1 TTGTTCATGAACAATTT

                 *           
         44 TTGTTTATGAACAATTT
          1 TTGTTCATGAACAATTT

         61 CAATTTTTGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50


Consensus pattern (17 bp):   
TTGTTCATGAACAATTT

Found at i:3758 original size:124 final size:125

Alignment explanation


    Indices: 3537--3800  Score: 390
    Period size: 124  Copynumber: 2.1  Consensus size: 125

       3527 TTCTCCTATG

                             *        **                         *           
       3537 AAACGCCGCTATTCCCATCAAGAAATGGTGTTTTTATCAATTGCACCAAATCTTTATTCGTTGGA
          1 AAACGCCGCTATTCCCAACAAGAAATAATGTTTTTAT--ATTGCACCAAATCTCTATTCGTTGGA

                                                                          
       3602 TAAGATTATATATAGCGGCGTTTACTTGAGAAACGCCACTATTTAGCGGCGTCTTTTGTGAA
         64 TAAGATTATATATAGCGGCGTTTACTTGAGAAACGCCACTATTTAGCGGCGTCTTTTGTGAA

                                                          *            *     
       3664 AAACGCCGCTATTCCCAACAAGAAATAATGTTTTTAGT-TT-CACCGAAT-TGCTATTCTTTGGA
          1 AAACGCCGCTATTCCCAACAAGAAATAATGTTTTTA-TATTGCACCAAATCT-CTATTCGTTGGA

                                       *                                 *
       3726 TAAGATTATATATAGCGGCGTTTACTTTAGAAACGCCACTATTTAGCGGCGTCTTTTGTGAG
         64 TAAGATTATATATAGCGGCGTTTACTTGAGAAACGCCACTATTTAGCGGCGTCTTTTGTGAA

                  *      
       3788 AAACGCTGCTATT
          1 AAACGCCGCTATT

       3801 GTATTTAGAA


Statistics
Matches: 126,  Mismatches: 9, Indels: 7
        0.89            0.06        0.05

Matches are distributed among these distances:
 123    1  0.01
 124   89  0.71
 125    2  0.02
 127   33  0.26
 128    1  0.01

ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Consensus pattern (125 bp):   
AAACGCCGCTATTCCCAACAAGAAATAATGTTTTTATATTGCACCAAATCTCTATTCGTTGGATA
AGATTATATATAGCGGCGTTTACTTGAGAAACGCCACTATTTAGCGGCGTCTTTTGTGAA

Found at i:5501 original size:16 final size:16

Alignment explanation


    Indices: 5480--5511  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       5470 GGAATAGGCA

                            
       5480 ATCAATAAAAGCAATG
          1 ATCAATAAAAGCAATG

                  *         
       5496 ATCAATCAAAGCAATG
          1 ATCAATAAAAGCAATG

       5512 CAAGAAAAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19


Consensus pattern (16 bp):   
ATCAATAAAAGCAATG

Found at i:6329 original size:20 final size:20

Alignment explanation


    Indices: 6273--6331  Score: 68
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       6263 TCTTGATATA

                                *
       6273 TTCTTTCAATGCTTTTGGTTT
          1 TTCTTTCAATGC-TTTGGTTC

                                  
       6294 TTCTTGTACAA-G-TTTGGTTC
          1 TTCTT-T-CAATGCTTTGGTTC

                              
       6314 TTCTTTCAATGCTTTGGT
          1 TTCTTTCAATGCTTTGGT

       6332 AGAGTAGGGA


Statistics
Matches: 33,  Mismatches: 1, Indels: 9
        0.77            0.02        0.21

Matches are distributed among these distances:
  18    3  0.09
  19    2  0.06
  20   18  0.55
  21    5  0.15
  22    2  0.06
  23    3  0.09

ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56


Consensus pattern (20 bp):   
TTCTTTCAATGCTTTGGTTC
Done.