Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013552.1 Corchorus capsularis cultivar CVL-1 contig13573, 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: 31531
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:12411 original size:52 final size:52

Alignment explanation


    Indices: 12329--12433  Score: 201
    Period size: 52  Copynumber: 2.0  Consensus size: 52

      12319 TGGACCCATA

                                     *                          
      12329 CTTCCTTGCCAACCCTAAGAAAGACTAACCTACCACCACCAATGCCCCTAGC
          1 CTTCCTTGCCAACCCTAAGAAAGACCAACCTACCACCACCAATGCCCCTAGC

                                                                
      12381 CTTCCTTGCCAACCCTAAGAAAGACCAACCTACCACCACCAATGCCCCTAGC
          1 CTTCCTTGCCAACCCTAAGAAAGACCAACCTACCACCACCAATGCCCCTAGC

             
      12433 C
          1 C

      12434 AGTGGCGTAG


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  52   52  1.00

ACGTcount: A:0.30, C:0.44, G:0.10, T:0.16


Consensus pattern (52 bp):   
CTTCCTTGCCAACCCTAAGAAAGACCAACCTACCACCACCAATGCCCCTAGC

Found at i:12671 original size:47 final size:49

Alignment explanation


    Indices: 12605--12699  Score: 158
    Period size: 48  Copynumber: 2.0  Consensus size: 49

      12595 TTGACCCCAT

                                                             
      12605 AAAATATTGGCTATTTTCACATATT-TGATATTTAAACTATATTTATAA
          1 AAAATATTGGCTATTTTCACATATTCTGATATTTAAACTATATTTATAA

                                  *    *                    
      12653 AAAAT-TTGGCTATTTTCACATTTTCTTATATTTAAACTATATTTATA
          1 AAAATATTGGCTATTTTCACATATTCTGATATTTAAACTATATTTATA

      12700 TCTTATCCTC


Statistics
Matches: 44,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  47   18  0.41
  48   26  0.59

ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48


Consensus pattern (49 bp):   
AAAATATTGGCTATTTTCACATATTCTGATATTTAAACTATATTTATAA

Found at i:19854 original size:144 final size:143

Alignment explanation


    Indices: 19601--19913  Score: 409
    Period size: 144  Copynumber: 2.2  Consensus size: 143

      19591 ATGAAAGAGA

                             *                                           *   
      19601 AAGATGACTAAGAGAAGCCAGGTTCCCTATCAAACTTGAAACTTCACCTACCAACTTGTTATAGC
          1 AAGATG-CTAAGAGAAGTCAGGTTCCCTATCAAACTTGAAACTTCACCTACCAACTTGTTAGAGC

                  *                                                          
      19666 CAAGGTTAAGAAACCGAAGAGAATTGAGGCCGAACAACTCGTCAGGTATTGAAGAGTTGAAAGAG
         65 CAAGGTCAAGAAACCGAAGAGAATTGAGGCCGAACAACTCGTCAGGTATTGAAGAGTTGAAAGAG

                        *  
      19731 TT-GAATGAAAGGTC
        130 TTAGAA-GAAAGATC

                                *            *        *       *              
      19745 AAGATGCGTAAGAGAAGTCATGTTCCCTAT-AGCACTTGAAATTTCACCTTCCAACTTGTTAGAG
          1 AAGATGC-TAAGAGAAGTCAGGTTCCCTATCA-AACTTGAAACTTCACCTACCAACTTGTTAGAG

                           *    *  *     ***                                 
      19809 CCAAGGTCAAGAAACTGAAGGGAGTTGAGTTTGAA-AAGC-CAGTCAGGTATTGAAGAGTTGAAA
         64 CCAAGGTCAAGAAACCGAAGAGAATTGAGGCCGAACAA-CTC-GTCAGGTATTGAAGAGTTGAAA

                             
      19872 GAGTTAGAAGAAAGATC
        127 GAGTTAGAAGAAAGATC

                                     
      19889 AAGATGCCTAAGAGAAGTCAGGTTC
          1 AAGATG-CTAAGAGAAGTCAGGTTC

      19914 GCAAGGCCAT


Statistics
Matches: 148,  Mismatches: 15, Indels: 12
        0.85            0.09        0.07

Matches are distributed among these distances:
 143    5  0.03
 144  139  0.94
 145    4  0.03

ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23


Consensus pattern (143 bp):   
AAGATGCTAAGAGAAGTCAGGTTCCCTATCAAACTTGAAACTTCACCTACCAACTTGTTAGAGCC
AAGGTCAAGAAACCGAAGAGAATTGAGGCCGAACAACTCGTCAGGTATTGAAGAGTTGAAAGAGT
TAGAAGAAAGATC

Found at i:26908 original size:21 final size:20

Alignment explanation


    Indices: 26869--26910  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 20

      26859 TCCTTTGCTT

                          *     
      26869 ATTGACTTCAATGCTCTTCA
          1 ATTGACTTCAATGCACTTCA

                          *      
      26889 ATTGATCTTCAATGGACTTCA
          1 ATTGA-CTTCAATGCACTTCA

             
      26910 A
          1 A

      26911 ACCTTCAAGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20    5  0.26
  21   14  0.74

ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38


Consensus pattern (20 bp):   
ATTGACTTCAATGCACTTCA

Found at i:30900 original size:18 final size:19

Alignment explanation


    Indices: 30877--30920  Score: 65
    Period size: 18  Copynumber: 2.4  Consensus size: 19

      30867 CTAGCTAGTA

                                
      30877 ATTAATACT-TAATTAA-TT
          1 ATTAATACTATAA-TAATTT

                               
      30895 ATTAATACTATAATAATTT
          1 ATTAATACTATAATAATTT

                   
      30914 ATTAATA
          1 ATTAATA

      30921 TTCCATCGTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   12  0.50
  19   12  0.50

ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48


Consensus pattern (19 bp):   
ATTAATACTATAATAATTT
Done.