Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014839.1 Corchorus olitorius cultivar O-4 contig14872, 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: 18466
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:1879 original size:58 final size:57

Alignment explanation


    Indices: 1771--1884  Score: 138
    Period size: 58  Copynumber: 2.0  Consensus size: 57

       1761 ATTAATCAAA

                                    *              ***   *           
       1771 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGATGTTTTCGGACCAAGACT
          1 TATCAAGTGACATGTTCTTTATTAAATGCATAAAAAAGACACTTTAGGACCAAGACT

                *            *            *                     *    
       1828 TATCGAGTGACATGTTTTTTTATTAAATGCCTAAAAAAGACACTTTAGGACCGAGAC
          1 TATCAAGTGACATG-TTCTTTATTAAATGCATAAAAAAGACACTTTAGGACCAAGAC

       1885 ATGATGCTAT


Statistics
Matches: 47,  Mismatches: 9, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  57   13  0.28
  58   34  0.72

ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Consensus pattern (57 bp):   
TATCAAGTGACATGTTCTTTATTAAATGCATAAAAAAGACACTTTAGGACCAAGACT

Found at i:4818 original size:25 final size:24

Alignment explanation


    Indices: 4768--4819  Score: 68
    Period size: 25  Copynumber: 2.1  Consensus size: 24

       4758 CCTTGAATTT

                          *      *  
       4768 TTTAATGCTTAATTCTTAAATTTA
          1 TTTAATGCTTAATTATTAAATCTA

                              *      
       4792 TTTAATGTCTTAATTATTCAATCTA
          1 TTTAATG-CTTAATTATTAAATCTA

               
       4817 TTT
          1 TTT

       4820 TACAATTCAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  24    7  0.29
  25   17  0.71

ACGTcount: A:0.31, C:0.10, G:0.04, T:0.56


Consensus pattern (24 bp):   
TTTAATGCTTAATTATTAAATCTA

Found at i:5752 original size:25 final size:24

Alignment explanation


    Indices: 5718--5764  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       5708 ACGTTTGCAC

                                     
       5718 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
       5743 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

       5765 TGTAAGTATT


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

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:5775 original size:17 final size:17

Alignment explanation


    Indices: 5750--5814  Score: 58
    Period size: 17  Copynumber: 3.5  Consensus size: 17

       5740 AAAAAATACC

                *            
       5750 TAAGAATTTAATTAATG
          1 TAAGTATTTAATTAATG

                                 
       5767 TAAGTATTTCAATTATTATCG
          1 TAAGTATTT-AATTA--AT-G

              **              
       5788 TATTTCATTTAATTAATG
          1 TAAGT-ATTTAATTAATG

                     
       5806 TAAGTATTT
          1 TAAGTATTT

       5815 TAGTTATTAT


Statistics
Matches: 38,  Mismatches: 5, Indels: 10
        0.72            0.09        0.19

Matches are distributed among these distances:
  17   12  0.32
  18    9  0.24
  19    2  0.05
  20    2  0.05
  21    9  0.24
  22    4  0.11

ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49


Consensus pattern (17 bp):   
TAAGTATTTAATTAATG

Found at i:5816 original size:18 final size:18

Alignment explanation


    Indices: 5756--5816  Score: 52
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       5746 TACCTAAGAA

                              
       5756 TTTAATTAATGTAAGTAT
          1 TTTAATTAATGTAAGTAT

              *             **    
       5774 TTCAATTATTATCGTATTTCA-
          1 TTTAATTA--AT-GTAAGT-AT

                              
       5795 TTTAATTAATGTAAGTAT
          1 TTTAATTAATGTAAGTAT

                
       5813 TTTA
          1 TTTA

       5817 GTTATTATAT


Statistics
Matches: 32,  Mismatches: 6, Indels: 10
        0.67            0.12        0.21

Matches are distributed among these distances:
  17    1  0.03
  18   15  0.47
  19    2  0.06
  20    2  0.06
  21   11  0.34
  22    1  0.03

ACGTcount: A:0.34, C:0.05, G:0.08, T:0.52


Consensus pattern (18 bp):   
TTTAATTAATGTAAGTAT

Found at i:6070 original size:6 final size:6

Alignment explanation


    Indices: 6052--6147  Score: 138
    Period size: 6  Copynumber: 15.8  Consensus size: 6

       6042 ATTTAGACTT

                                    *                           *   
       6052 ATATAG TATATAG ATATAG ATGTAG ATATAG ATATAG ATATAG ATGTAG
          1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG

                                           * *               *    
       6101 ATATAG ATATAG ATATAG ATATAG ATACAT ATATAG ATATAG TTATA
          1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA

       6148 TGATGCATCT


Statistics
Matches: 80,  Mismatches: 9, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
   6   74  0.93
   7    6  0.08

ACGTcount: A:0.47, C:0.01, G:0.17, T:0.35


Consensus pattern (6 bp):   
ATATAG

Done.