Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011517.1 Corchorus capsularis cultivar CVL-1 contig11538, 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: 3381
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38


Found at i:1081 original size:10 final size:10

Alignment explanation


    Indices: 1066--1091  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       1056 AGTTGCTGCC

                      
       1066 AAATTCCAGA
          1 AAATTCCAGA

                      
       1076 AAATTCCAGA
          1 AAATTCCAGA

                  
       1086 AAATTC
          1 AAATTC

       1092 TAGAGTCCTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23


Consensus pattern (10 bp):   
AAATTCCAGA

Found at i:2054 original size:6 final size:6

Alignment explanation


    Indices: 2043--2069  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       2033 TTAATTCTAC

                                           
       2043 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       2070 GCTTTGCTTT


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

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:3058 original size:22 final size:22

Alignment explanation


    Indices: 3018--3110  Score: 70
    Period size: 22  Copynumber: 4.2  Consensus size: 22

       3008 CTGATTATTC

                                   
       3018 TTTACT-TTGTACTGATTACTAT
          1 TTTACTCTTGTA-TGATTACTAT

                                    
       3040 TTTACTCTTGT-TGATTTACCT-T
          1 TTTACTCTTGTATGA-TTA-CTAT

            *        *             
       3062 CTTACT-TTTTACTGATTACTAT
          1 TTTACTCTTGTA-TGATTACTAT

                          *     *  
       3084 TTTACTCTT-TACTAATTACCAT
          1 TTTACTCTTGTA-TGATTACTAT

                 
       3106 TTTAC
          1 TTTAC

       3111 CCTTTCAGAT


Statistics
Matches: 59,  Mismatches: 5, Indels: 14
        0.76            0.06        0.18

Matches are distributed among these distances:
  21    8  0.14
  22   40  0.68
  23   11  0.19

ACGTcount: A:0.22, C:0.18, G:0.05, T:0.55


Consensus pattern (22 bp):   
TTTACTCTTGTATGATTACTAT

Found at i:3115 original size:22 final size:22

Alignment explanation


    Indices: 3069--3115  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3059 CTTCTTACTT

                  *     *       * 
       3069 TTTACTGATTACTATTTTACTC
          1 TTTACTAATTACCATTTTACCC

                                  
       3091 TTTACTAATTACCATTTTACCC
          1 TTTACTAATTACCATTTTACCC

               
       3113 TTT
          1 TTT

       3116 CAGATACCTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.23, C:0.21, G:0.02, T:0.53


Consensus pattern (22 bp):   
TTTACTAATTACCATTTTACCC
Done.