Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013481.1 Corchorus olitorius cultivar O-4 contig13514, 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: 4190
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:267 original size:33 final size:33

Alignment explanation


    Indices: 230--356  Score: 114
    Period size: 33  Copynumber: 3.8  Consensus size: 33

        220 ATTAGCATCC

                           *                  
        230 AAAACAGAATTT-GTTTCATCACAAACAATACCT
          1 AAAACAG-ATTTAGTGTCATCACAAACAATACCT

                                *   *        
        263 AAAACAGATTTAGTGTCATCGCAAGCAATA-CT
          1 AAAACAGATTTAGTGTCATCACAAACAATACCT

                **  *      *       *     * *  
        295 CAAATTAGGTTTAGTATCATCACTAACAACATCT
          1 -AAAACAGATTTAGTGTCATCACAAACAATACCT

                       *       *        
        329 AAAACAGATTTCGTGTCATTACAAACAA
          1 AAAACAGATTTAGTGTCATCACAAACAA

        357 CACTCAAATT


Statistics
Matches: 73,  Mismatches: 18, Indels: 6
        0.75            0.19        0.06

Matches are distributed among these distances:
  32    6  0.08
  33   65  0.89
  34    2  0.03

ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28


Consensus pattern (33 bp):   
AAAACAGATTTAGTGTCATCACAAACAATACCT

Found at i:323 original size:66 final size:66

Alignment explanation


    Indices: 245--371  Score: 182
    Period size: 66  Copynumber: 1.9  Consensus size: 66

        235 AGAATTTGTT

                         *                        *   *   *                  
        245 TCATCACAAACAATACCTAAAACAGATTTAGTGTCATCGCAAGCAATACTCAAATTAGGTTTAGT
          1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAGT

             
        310 A
         66 A

                   *       *             *       *                       
        311 TCATCACTAACAACATCTAAAACAGATTTCGTGTCATTACAAACAACACTCAAATTAGGTT
          1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTT

        372 CAGAATTACT


Statistics
Matches: 53,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  66   53  1.00

ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28


Consensus pattern (66 bp):   
TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAGT
A

Found at i:2550 original size:22 final size:22

Alignment explanation


    Indices: 2522--2564  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2512 TTTTCCGCAA

                      *     *     
       2522 CAAGTCCTGGGCAGGAGTTGTC
          1 CAAGTCCTGGACAGGACTTGTC

                                 
       2544 CAAGTCCTGGACAGGACTTGT
          1 CAAGTCCTGGACAGGACTTGT

       2565 TCTGAATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23


Consensus pattern (22 bp):   
CAAGTCCTGGACAGGACTTGTC

Found at i:2618 original size:21 final size:21

Alignment explanation


    Indices: 2594--2635  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2584 TTCAACAGAC

                  *              
       2594 CAAGTCTTGGGCAGGAGTTGT
          1 CAAGTCCTGGGCAGGAGTTGT

                         *       
       2615 CAAGTCCTGGGCATGAGTTGT
          1 CAAGTCCTGGGCAGGAGTTGT

       2636 TCTGATTTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.19, C:0.17, G:0.36, T:0.29


Consensus pattern (21 bp):   
CAAGTCCTGGGCAGGAGTTGT

Found at i:2640 original size:71 final size:71

Alignment explanation


    Indices: 2522--2706  Score: 298
    Period size: 71  Copynumber: 2.6  Consensus size: 71

       2512 TTTTCCGCAA

                                            *                           *    
       2522 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTTTTTC
          1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTC

                   
       2587 AACAGAC
         65 AACAGAC

                  *                           *  *         *                 
       2594 CAAGTCTTGGGCAGGAGTTGTCAAGTCCTGGGCATGAGTTGTTCTGATTTTTCTTCCGTCTTTCA
          1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA

                  
       2659 ACAGAC
         66 ACAGAC

              *                                       
       2665 CAGGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
          1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT

       2707 CCTGCTTTTA


Statistics
Matches: 103,  Mismatches: 10, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  71   83  0.81
  72   20  0.19

ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31


Consensus pattern (71 bp):   
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
ACAGAC

Found at i:2694 original size:21 final size:21

Alignment explanation


    Indices: 2668--2707  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2658 AACAGACCAG

                         *       
       2668 GTCCTGGGCAGGAGTTGTCAA
          1 GTCCTGGGCAGGACTTGTCAA

                               
       2689 GTCCTGGGCAGGACTTGTC
          1 GTCCTGGGCAGGACTTGTC

       2708 CTGCTTTTAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25


Consensus pattern (21 bp):   
GTCCTGGGCAGGACTTGTCAA
Done.