Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015768.1 Corchorus capsularis cultivar CVL-1 contig15789, 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: 14972
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:834 original size:21 final size:22

Alignment explanation


    Indices: 789--837  Score: 59
    Period size: 21  Copynumber: 2.3  Consensus size: 22

        779 TAAAATGGGT

                                 *
        789 AATCA-AGAGTTTTCAAGATTT
          1 AATCAGAGAGTTTTCAAGATTA

                                   
        810 AATCAGAG-GTTTTCAA-ATTCA
          1 AATCAGAGAGTTTTCAAGATT-A

                   
        831 AATCAGA
          1 AATCAGA

        838 TTTAGTGAGA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  20    3  0.12
  21   20  0.80
  22    2  0.08

ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33


Consensus pattern (22 bp):   
AATCAGAGAGTTTTCAAGATTA

Found at i:2828 original size:29 final size:28

Alignment explanation


    Indices: 2783--2838  Score: 76
    Period size: 29  Copynumber: 2.0  Consensus size: 28

       2773 ATGTGGCATG

                        *               
       2783 AAACATTATAGATTGGGAATTAAGTTTA
          1 AAACATTATAGAATGGGAATTAAGTTTA

                    *             *     
       2811 AAACTATTGTAGAATGGGAATTCAGTTT
          1 AAAC-ATTATAGAATGGGAATTAAGTTT

       2839 TCAAGGTATT


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

Matches are distributed among these distances:
  28    4  0.17
  29   20  0.83

ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36


Consensus pattern (28 bp):   
AAACATTATAGAATGGGAATTAAGTTTA

Found at i:3850 original size:19 final size:19

Alignment explanation


    Indices: 3810--3847  Score: 60
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       3800 GATTTATCCT

                               
       3810 ATCTATCTGTTGAATTTGA
          1 ATCTATCTGTTGAATTTGA

                        *      
       3829 ATCT-TCTGTTGGATTTGA
          1 ATCTATCTGTTGAATTTGA

             
       3847 A
          1 A

       3848 ATCCTATTTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47


Consensus pattern (19 bp):   
ATCTATCTGTTGAATTTGA

Found at i:8112 original size:47 final size:47

Alignment explanation


    Indices: 8057--8167  Score: 213
    Period size: 47  Copynumber: 2.4  Consensus size: 47

       8047 AGAAGATCTG

                                                           
       8057 AGGAAAAGAAAGAGAGAGCGGGAGGAGAGTGGGAAGAAGAAAAACCC
          1 AGGAAAAGAAAGAGAGAGCGGGAGGAGAGTGGGAAGAAGAAAAACCC

                                                           
       8104 AGGAAAAGAAAGAGAGAGCGGGAGGAGAGTGGGAAGAAGAAAAACCC
          1 AGGAAAAGAAAGAGAGAGCGGGAGGAGAGTGGGAAGAAGAAAAACCC

                       *     
       8151 AGGAAAAGAAAAAGAGA
          1 AGGAAAAGAAAGAGAGA

       8168 CTCGTTAGAG


Statistics
Matches: 63,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  47   63  1.00

ACGTcount: A:0.52, C:0.07, G:0.39, T:0.02


Consensus pattern (47 bp):   
AGGAAAAGAAAGAGAGAGCGGGAGGAGAGTGGGAAGAAGAAAAACCC

Found at i:14089 original size:56 final size:56

Alignment explanation


    Indices: 14020--14148  Score: 258
    Period size: 56  Copynumber: 2.3  Consensus size: 56

      14010 TAAATGACTC

                                                                    
      14020 AATTACCCTGAATTAAGCCATTTTATTTCCCCTAATCTCTGCTTCTTACTAAACTT
          1 AATTACCCTGAATTAAGCCATTTTATTTCCCCTAATCTCTGCTTCTTACTAAACTT

                                                                    
      14076 AATTACCCTGAATTAAGCCATTTTATTTCCCCTAATCTCTGCTTCTTACTAAACTT
          1 AATTACCCTGAATTAAGCCATTTTATTTCCCCTAATCTCTGCTTCTTACTAAACTT

                             
      14132 AATTACCCTGAATTAAG
          1 AATTACCCTGAATTAAG

      14149 TCGATCAATG


Statistics
Matches: 73,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  56   73  1.00

ACGTcount: A:0.29, C:0.26, G:0.06, T:0.40


Consensus pattern (56 bp):   
AATTACCCTGAATTAAGCCATTTTATTTCCCCTAATCTCTGCTTCTTACTAAACTT

Found at i:14171 original size:35 final size:35

Alignment explanation


    Indices: 14128--14346  Score: 186
    Period size: 35  Copynumber: 6.3  Consensus size: 35

      14118 TTCTTACTAA

                                  *   *        
      14128 ACTTAATTACCCTGAATTAAGTCGATCAATGACTT
          1 ACTTAATTACCCTGAATTAAGTTGATTAATGACTT

               *                        *     *
      14163 ACTCAATTACCCTGAATTAAGTTGATTACTGACTC
          1 ACTTAATTACCCTGAATTAAGTTGATTAATGACTT

                                         * *    
      14198 ACTTAATTACCCTGAATTAAGTTGATTACTTAAC-T
          1 ACTTAATTACCCTGAATTAAGTTGATTA-ATGACTT

                                        *  *   
      14233 ACTTAATTACCCTGAATTAA---G-TTACTGCCTT
          1 ACTTAATTACCCTGAATTAAGTTGATTAATGACTT

                             *        *            
      14264 ACTTAACTT-CCCTGAACTAAGTT-ACTAACTGACTTTT
          1 ACTTAA-TTACCCTGAATTAAGTTGATTAA-TGAC--TT

                                 *       *      
      14301 A-TTAATTACCCTGAATTAAGCT-ACTTACTGACTT
          1 ACTTAATTACCCTGAATTAAGTTGA-TTAATGACTT

             *          
      14335 AATTAAGTTACC
          1 ACTTAA-TTACC

      14347 TATTACTTAC


Statistics
Matches: 150,  Mismatches: 20, Indels: 27
        0.76            0.10        0.14

Matches are distributed among these distances:
  30    2  0.01
  31   20  0.13
  32    3  0.02
  34    5  0.03
  35   86  0.57
  36   29  0.19
  37    5  0.03

ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37


Consensus pattern (35 bp):   
ACTTAATTACCCTGAATTAAGTTGATTAATGACTT

Done.