Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015783.1 Corchorus capsularis cultivar CVL-1 contig15804, 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: 27592
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:2668 original size:27 final size:27

Alignment explanation


    Indices: 2638--2690  Score: 88
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       2628 TTGGTAAATG

                                       
       2638 GTGATGACAAATAAAAAGGAACAGAGC
          1 GTGATGACAAATAAAAAGGAACAGAGC

                     *     *          
       2665 GTGATGACATATAAATAGGAACAGAG
          1 GTGATGACAAATAAAAAGGAACAGAG

       2691 GGAGTACTAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.49, C:0.09, G:0.26, T:0.15


Consensus pattern (27 bp):   
GTGATGACAAATAAAAAGGAACAGAGC

Found at i:19928 original size:20 final size:21

Alignment explanation


    Indices: 19915--19958  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 21

      19905 TTGTAAGCTT

                                 
      19915 CCTATGATTTTTGTTAACCTC
          1 CCTATGATTTTTGTTAACCTC

                    *         *   
      19936 CCTATGAGATTTTGTTAATCTC
          1 CCTATGA-TTTTTGTTAACCTC

             
      19958 C
          1 C

      19959 TTAAATTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21    7  0.35
  22   13  0.65

ACGTcount: A:0.20, C:0.23, G:0.11, T:0.45


Consensus pattern (21 bp):   
CCTATGATTTTTGTTAACCTC

Found at i:19951 original size:22 final size:21

Alignment explanation


    Indices: 19895--19958  Score: 67
    Period size: 21  Copynumber: 3.0  Consensus size: 21

      19885 TAAACCTTTT

                             *  * 
      19895 CTATGAAATTTTG-TAAGCTTC
          1 CTATG-AATTTTGTTAACCTCC

                  *              
      19916 CTATGATTTTTGTTAACCTCC
          1 CTATGAATTTTGTTAACCTCC

                             *    
      19937 CTATGAGATTTTGTTAATCTCC
          1 CTATGA-ATTTTGTTAACCTCC

      19959 TTAAATTTTT


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  20    6  0.17
  21   17  0.47
  22   13  0.36

ACGTcount: A:0.23, C:0.19, G:0.12, T:0.45


Consensus pattern (21 bp):   
CTATGAATTTTGTTAACCTCC

Found at i:21037 original size:35 final size:35

Alignment explanation


    Indices: 20981--21047  Score: 98
    Period size: 35  Copynumber: 1.9  Consensus size: 35

      20971 TAAGCTGACT

                                    *          
      20981 AAACACCTTAAGACCCCACTAACTTCAATATCTCC
          1 AAACACCTTAAGACCCCACTAACTCCAATATCTCC

                       * *  *               
      21016 AAACACCTTAATATCCTACTAACTCCAATATC
          1 AAACACCTTAAGACCCCACTAACTCCAATATC

      21048 AAAGAGGATC


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  35   28  1.00

ACGTcount: A:0.39, C:0.34, G:0.01, T:0.25


Consensus pattern (35 bp):   
AAACACCTTAAGACCCCACTAACTCCAATATCTCC

Found at i:25415 original size:16 final size:16

Alignment explanation


    Indices: 25377--25426  Score: 57
    Period size: 17  Copynumber: 3.0  Consensus size: 16

      25367 CTATGTTTGG

                  *         
      25377 TAGGAAAGAAAGAAAA
          1 TAGGAAGGAAAGAAAA

                              
      25393 TAGGGAAGGAAATG-AAA
          1 TA-GGAAGGAAA-GAAAA

                             
      25410 TAGGAAGGAAGAGAAAA
          1 TAGGAAGGAA-AGAAAA

      25427 GAAAGTTCCA


Statistics
Matches: 29,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  16   11  0.38
  17   17  0.59
  18    1  0.03

ACGTcount: A:0.60, C:0.00, G:0.32, T:0.08


Consensus pattern (16 bp):   
TAGGAAGGAAAGAAAA
Done.