Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010866.1 Corchorus capsularis cultivar CVL-1 contig10887, 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: 27446
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:9513 original size:30 final size:29

Alignment explanation


    Indices: 9471--9529  Score: 91
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       9461 TCATTCAAAG

                                         
       9471 CCAAAATAACATATTATTATACATTAATA
          1 CCAAAATAACATATTATTATACATTAATA

                            *      *      
       9500 CCAAAATTAACATATTTTTATACTTTAATA
          1 CCAAAA-TAACATATTATTATACATTAATA

       9530 ATGTGGGATA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  29    6  0.22
  30   21  0.78

ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39


Consensus pattern (29 bp):   
CCAAAATAACATATTATTATACATTAATA

Found at i:20105 original size:39 final size:40

Alignment explanation


    Indices: 20052--20155  Score: 120
    Period size: 45  Copynumber: 2.5  Consensus size: 40

      20042 ATTTGGGACA

                    *               *               
      20052 AAAAGGATATTGAAGTACCTC-AGTACGCAAGCATTGAGC
          1 AAAAGGATGTTGAAGTACCTCGAGGACGCAAGCATTGAGC

                 *                                       
      20091 AAAAGAATGTTGAAGTACCTAATTCTGAGGACGCAAGCATTGAGC
          1 AAAAGGATGTTGAAGTACC----TC-GAGGACGCAAGCATTGAGC

                           *    
      20136 AAAAGGATGTTGAAGCACCT
          1 AAAAGGATGTTGAAGTACCT

      20156 GATGCTCAGT


Statistics
Matches: 54,  Mismatches: 5, Indels: 10
        0.78            0.07        0.14

Matches are distributed among these distances:
  39   17  0.31
  41    1  0.02
  43    2  0.04
  45   34  0.63

ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21


Consensus pattern (40 bp):   
AAAAGGATGTTGAAGTACCTCGAGGACGCAAGCATTGAGC

Found at i:20140 original size:45 final size:45

Alignment explanation


    Indices: 20070--20175  Score: 149
    Period size: 45  Copynumber: 2.4  Consensus size: 45

      20060 ATTGAAGTAC

                 *                              *       *
      20070 CTCAGTACGCAAGCATTGAGCAAAAGAATGTTGAAGTACCTAATT
          1 CTCAGGACGCAAGCATTGAGCAAAAGAATGTTGAAGCACCTAATG

              *                       *              *   
      20115 CTGAGGACGCAAGCATTGAGCAAAAGGATGTTGAAGCACCTGATG
          1 CTCAGGACGCAAGCATTGAGCAAAAGAATGTTGAAGCACCTAATG

                 *          
      20160 CTCAGTACGCAAGCAT
          1 CTCAGGACGCAAGCAT

      20176 CATCGAGCAA


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

Matches are distributed among these distances:
  45   53  1.00

ACGTcount: A:0.35, C:0.20, G:0.25, T:0.21


Consensus pattern (45 bp):   
CTCAGGACGCAAGCATTGAGCAAAAGAATGTTGAAGCACCTAATG

Found at i:22051 original size:32 final size:33

Alignment explanation


    Indices: 21992--22057  Score: 116
    Period size: 32  Copynumber: 2.0  Consensus size: 33

      21982 ATGTTTCTTG

                                             
      21992 GATTTCCTCCAAAACACAGAGTGTCCTTAATTT
          1 GATTTCCTCCAAAACACAGAGTGTCCTTAATTT

                          *                  
      22025 GATTTCCTCCAAAATAC-GAGTGTCCTTAATTT
          1 GATTTCCTCCAAAACACAGAGTGTCCTTAATTT

             
      22057 G
          1 G

      22058 CAAAGATGGA


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  32   16  0.50
  33   16  0.50

ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35


Consensus pattern (33 bp):   
GATTTCCTCCAAAACACAGAGTGTCCTTAATTT

Found at i:24284 original size:42 final size:42

Alignment explanation


    Indices: 24223--24306  Score: 143
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      24213 GAGTTACCAG

                                              *       
      24223 ATTTTCAAGTTTTTTCCGTTTAGCATCAGAAGCCTCCTCCAT
          1 ATTTTCAAGTTTTTTCCGTTTAGCATCAGAAGCCGCCTCCAT

                                                       
      24265 ATTTTC-AGTTTTTTGCCGTTTAGCATCAGAAGCCGCCTCCAT
          1 ATTTTCAAGTTTTTT-CCGTTTAGCATCAGAAGCCGCCTCCAT

      24307 CACAAATCAC


Statistics
Matches: 40,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  41    8  0.20
  42   32  0.80

ACGTcount: A:0.20, C:0.26, G:0.14, T:0.39


Consensus pattern (42 bp):   
ATTTTCAAGTTTTTTCCGTTTAGCATCAGAAGCCGCCTCCAT
Done.