Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018330.1 Corchorus olitorius cultivar O-4 contig18363, 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: 16704
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:773 original size:13 final size:13

Alignment explanation


    Indices: 755--779  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        745 CAGTAAACCT

                         
        755 TAAATAAAGACAC
          1 TAAATAAAGACAC

                        
        768 TAAATAAAGACA
          1 TAAATAAAGACA

        780 TATTTTTTTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16


Consensus pattern (13 bp):   
TAAATAAAGACAC

Found at i:1999 original size:16 final size:16

Alignment explanation


    Indices: 1978--2016  Score: 60
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1968 GACAGTTTTC

                         *  
       1978 TCGGGTCATTCGGGTT
          1 TCGGGTCATTCGGATT

                            
       1994 TCGGGTCATTCGGATT
          1 TCGGGTCATTCGGATT

            *      
       2010 CCGGGTC
          1 TCGGGTC

       2017 TCGGGTTGGG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.08, C:0.23, G:0.36, T:0.33


Consensus pattern (16 bp):   
TCGGGTCATTCGGATT

Found at i:2889 original size:16 final size:16

Alignment explanation


    Indices: 2868--2939  Score: 67
    Period size: 16  Copynumber: 4.5  Consensus size: 16

       2858 TTCTCGGGTT

                            
       2868 ATTCGGGTTTCGGATC
          1 ATTCGGGTTTCGGATC

             *       *       
       2884 ACTCGGGTTAC-GAGTC
          1 ATTCGGGTTTCGGA-TC

                         *  
       2900 ATTCGGGTTTCGGGTC
          1 ATTCGGGTTTCGGATC

                 *        *  
       2916 A-TCTAGGTTTCGGGTC
          1 ATTC-GGGTTTCGGATC

                    
       2932 ATTCGGGT
          1 ATTCGGGT

       2940 CTCAGGTAGG


Statistics
Matches: 45,  Mismatches: 7, Indels: 8
        0.75            0.12        0.13

Matches are distributed among these distances:
  15    4  0.09
  16   38  0.84
  17    3  0.07

ACGTcount: A:0.12, C:0.19, G:0.33, T:0.35


Consensus pattern (16 bp):   
ATTCGGGTTTCGGATC

Found at i:2909 original size:32 final size:32

Alignment explanation


    Indices: 2868--2939  Score: 92
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       2858 TTCTCGGGTT

                                 *           
       2868 ATTCGGGTTTCGGATCA-CTCGGGTTACGAGTC
          1 ATTCGGGTTTCGGATCATCT-AGGTTACGAGTC

                         *           *  *   
       2900 ATTCGGGTTTCGGGTCATCTAGGTTTCGGGTC
          1 ATTCGGGTTTCGGATCATCTAGGTTACGAGTC

                    
       2932 ATTCGGGT
          1 ATTCGGGT

       2940 CTCAGGTAGG


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  32   33  0.94
  33    2  0.06

ACGTcount: A:0.12, C:0.19, G:0.33, T:0.35


Consensus pattern (32 bp):   
ATTCGGGTTTCGGATCATCTAGGTTACGAGTC

Found at i:3052 original size:2 final size:2

Alignment explanation


    Indices: 3040--3083  Score: 65
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       3030 AATAGTAAGG

                  *                                                       
       3040 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T- TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                 
       3080 TA TA
          1 TA TA

       3084 GGTAAGATAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   36  0.95

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:9985 original size:4 final size:4

Alignment explanation


    Indices: 9976--10000  Score: 50
    Period size: 4  Copynumber: 6.2  Consensus size: 4

       9966 TTTACATGTT

                                           
       9976 TATG TATG TATG TATG TATG TATG T
          1 TATG TATG TATG TATG TATG TATG T

      10001 TCATGCATGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   21  1.00

ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52


Consensus pattern (4 bp):   
TATG

Done.