Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017452.1 Corchorus olitorius cultivar O-4 contig17485, 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: 4249
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:1375 original size:15 final size:15

Alignment explanation


    Indices: 1349--1386  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       1339 TTTGCTTTGT

                            
       1349 TTTCTAGTTTAATTGC
          1 TTTCT-GTTTAATTGC

                           
       1365 TTTCTGTTTAATTGC
          1 TTTCTGTTTAATTGC

                   
       1380 TTTCTGT
          1 TTTCTGT

       1387 CAACCTCTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.77
  16    5  0.23

ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61


Consensus pattern (15 bp):   
TTTCTGTTTAATTGC

Found at i:1617 original size:28 final size:29

Alignment explanation


    Indices: 1559--1618  Score: 111
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       1549 TTTGGCGCCG

                                         
       1559 TTGCCGGGGAAAGGAACTTTTTCTGGTTT
          1 TTGCCGGGGAAAGGAACTTTTTCTGGTTT

                       *                 
       1588 TTGCCGGGGAAGGGAACTTTTTCTGGTTT
          1 TTGCCGGGGAAAGGAACTTTTTCTGGTTT

              
       1617 TT
          1 TT

       1619 TGACAGGGGA


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.15, C:0.13, G:0.32, T:0.40


Consensus pattern (29 bp):   
TTGCCGGGGAAAGGAACTTTTTCTGGTTT

Found at i:1631 original size:31 final size:29

Alignment explanation


    Indices: 1559--1631  Score: 101
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       1549 TTTGGCGCCG

                *      *                 
       1559 TTGCCGGGGAAAGGAACTTTTTCTGGTTT
          1 TTGCAGGGGAAGGGAACTTTTTCTGGTTT

                *                         
       1588 TTGCCGGGGAAGGGAACTTTTTCTGGTTTT
          1 TTGCAGGGGAAGGGAACTTTTTCTGG-TTT

                          
       1618 TTGACAGGGGAAGG
          1 TTG-CAGGGGAAGG

       1632 AAAATAGACT


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  29   25  0.62
  30    6  0.15
  31    9  0.22

ACGTcount: A:0.18, C:0.12, G:0.36, T:0.34


Consensus pattern (29 bp):   
TTGCAGGGGAAGGGAACTTTTTCTGGTTT

Found at i:1721 original size:29 final size:29

Alignment explanation


    Indices: 1676--1733  Score: 107
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       1666 TTTCTCTTTG

                                         
       1676 TTTCTGCGTTTTCTCTAAAAAAAAAAAAT
          1 TTTCTGCGTTTTCTCTAAAAAAAAAAAAT

                        *                
       1705 TTTCTGCGTTTTTTCTAAAAAAAAAAAAT
          1 TTTCTGCGTTTTCTCTAAAAAAAAAAAAT

       1734 AAAATTATTT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40


Consensus pattern (29 bp):   
TTTCTGCGTTTTCTCTAAAAAAAAAAAAT

Found at i:1870 original size:21 final size:22

Alignment explanation


    Indices: 1835--1878  Score: 63
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1825 GTTTCAGTTT

                                  
       1835 TGCGTCGAAAAAAAAAAATTTC
          1 TGCGTCGAAAAAAAAAAATTTC

                    *        *    
       1857 TGCGTC-ATAAAAAAAATTTTC
          1 TGCGTCGAAAAAAAAAAATTTC

             
       1878 T
          1 T

       1879 TGTTCCGGCG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21   14  0.70
  22    6  0.30

ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30


Consensus pattern (22 bp):   
TGCGTCGAAAAAAAAAAATTTC
Done.