Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015698.1 Corchorus olitorius cultivar O-4 contig15731, 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: 9436
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Found at i:990 original size:15 final size:15

Alignment explanation


    Indices: 970--1004  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        960 AAATTGAGGC

                   *       
        970 TAATTAAGTTGGATT
          1 TAATTAAATTGGATT

                        *  
        985 TAATTAAATTGGTTT
          1 TAATTAAATTGGATT

                 
       1000 TAATT
          1 TAATT

       1005 TTTGGGCTAG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51


Consensus pattern (15 bp):   
TAATTAAATTGGATT

Found at i:2065 original size:18 final size:18

Alignment explanation


    Indices: 2044--2084  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       2034 GTAATAGTAG

                     *        
       2044 GCTCAGGAGTAGCAGCCA
          1 GCTCAGGAGCAGCAGCCA

                   *         *
       2062 GCTCAGGGGCAGCAGCCG
          1 GCTCAGGAGCAGCAGCCA

                 
       2080 GCTCA
          1 GCTCA

       2085 AGATAACATC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.22, C:0.32, G:0.37, T:0.10


Consensus pattern (18 bp):   
GCTCAGGAGCAGCAGCCA

Found at i:4200 original size:17 final size:17

Alignment explanation


    Indices: 4178--4213  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       4168 TGATTTGTAA

                             
       4178 AGTTTGTTACACCAGAT
          1 AGTTTGTTACACCAGAT

                     *  *    
       4195 AGTTTGTTATACTAGAT
          1 AGTTTGTTACACCAGAT

              
       4212 AG
          1 AG

       4214 CTCTTTGTAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39


Consensus pattern (17 bp):   
AGTTTGTTACACCAGAT

Found at i:6846 original size:18 final size:18

Alignment explanation


    Indices: 6778--6846  Score: 57
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       6768 TACAAAATAT

                *    *        
       6778 TGTTACACTGCCGCAGGA
          1 TGTTCCACTACCGCAGGA

                       *    * 
       6796 TGTTCCACTACTGCAGAA
          1 TGTTCCACTACCGCAGGA

                *  * **       
       6814 TGTTGCATTGTCGCAGGA
          1 TGTTCCACTACCGCAGGA

                  *        
       6832 TGTTCCGCTACCGCA
          1 TGTTCCACTACCGCA

       6847 AGAACCTTTG


Statistics
Matches: 36,  Mismatches: 15, Indels: 0
        0.71            0.29        0.00

Matches are distributed among these distances:
  18   36  1.00

ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28


Consensus pattern (18 bp):   
TGTTCCACTACCGCAGGA

Found at i:8641 original size:17 final size:17

Alignment explanation


    Indices: 8619--8653  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       8609 GATTTGTAAT

                             
       8619 GTTTGTTACACCAGATA
          1 GTTTGTTACACCAGATA

                    *  *     
       8636 GTTTGTTATACTAGATA
          1 GTTTGTTACACCAGATA

             
       8653 G
          1 G

       8654 CTCTTTGTAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40


Consensus pattern (17 bp):   
GTTTGTTACACCAGATA
Done.