Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006955.1 Corchorus capsularis cultivar CVL-1 contig06976, 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: 17881
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:4696 original size:33 final size:33

Alignment explanation


    Indices: 4658--4764  Score: 126
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       4648 GGCGCGAGTG

                    *            *           
       4658 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC

                     *     *               * 
       4691 ACCGGCCACACGACTCGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC

                          *    *   *         
       4724 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
          1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC

                     
       4756 AACCGGCCA
          1 -ACCGGCCA

       4765 TCACCTGGCG


Statistics
Matches: 62,  Mismatches: 11, Indels: 2
        0.83            0.15        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   61  0.98

ACGTcount: A:0.23, C:0.40, G:0.28, T:0.08


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC

Found at i:4763 original size:10 final size:11

Alignment explanation


    Indices: 4748--4797  Score: 52
    Period size: 10  Copynumber: 4.6  Consensus size: 11

       4738 ATGGACATGT

                       
       4748 CCGGCCA-CAA
          1 CCGGCCACCAA

                   *   
       4758 CCGGCCATC-A
          1 CCGGCCACCAA

                         
       4768 CCTGGCGCACCAA
          1 CC-GGC-CACCAA

                       
       4781 CCGGCCA-CAA
          1 CCGGCCACCAA

                   
       4791 CCGGCCA
          1 CCGGCCA

       4798 TCGATTGGGC


Statistics
Matches: 35,  Mismatches: 1, Indels: 8
        0.80            0.02        0.18

Matches are distributed among these distances:
  10   20  0.57
  11    6  0.17
  12    6  0.17
  13    3  0.09

ACGTcount: A:0.24, C:0.50, G:0.22, T:0.04


Consensus pattern (11 bp):   
CCGGCCACCAA

Found at i:7855 original size:23 final size:23

Alignment explanation


    Indices: 7829--7872  Score: 79
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       7819 TAGTCTTATC

                                   
       7829 AGGAAATTAACATTGAGGCCATA
          1 AGGAAATTAACATTGAGGCCATA

                 *               
       7852 AGGAATTTAACATTGAGGCCA
          1 AGGAAATTAACATTGAGGCCA

       7873 AAAGACATTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23


Consensus pattern (23 bp):   
AGGAAATTAACATTGAGGCCATA

Found at i:7882 original size:23 final size:23

Alignment explanation


    Indices: 7835--7882  Score: 71
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       7825 TATCAGGAAA

                              *    
       7835 TTAACATTGAGGCCATAAGGAAT
          1 TTAACATTGAGGCCATAAAGAAT

                                    
       7858 TTAACATTGAGGCCA-AAAGACAT
          1 TTAACATTGAGGCCATAAAGA-AT

              
       7881 TT
          1 TT

       7883 GACCTATGAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22    4  0.17
  23   19  0.83

ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27


Consensus pattern (23 bp):   
TTAACATTGAGGCCATAAAGAAT

Found at i:11256 original size:21 final size:21

Alignment explanation


    Indices: 11230--11270  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11220 TCTGTCAAAT

                                 
      11230 TTGACAGCAAATTTACCTCCC
          1 TTGACAGCAAATTTACCTCCC

                          *     
      11251 TTGACAGCAAATTTTCCTCC
          1 TTGACAGCAAATTTACCTCC

      11271 TTATTGCTCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32


Consensus pattern (21 bp):   
TTGACAGCAAATTTACCTCCC

Found at i:14030 original size:84 final size:87

Alignment explanation


    Indices: 13865--14030  Score: 239
    Period size: 88  Copynumber: 1.9  Consensus size: 87

      13855 GCACATTTAT

                                             *  **                           
      13865 TAAAGACCCCAATCAACTTTTGATGAGAATCAATATTGCTACTCTATTTTGGTATTTTCTTTTAC
          1 TAAAGACCCCAATCAACTTTTGATGAGAATCAAGATAACTACTCTATTTT-GTATTTTCTTTTAC

                                   
      13930 GTGTTTAAGAGTTGTAACAGGTC
         65 GTGTTTAAGAGTTGTAACAGGTC

                                       *   *                    *          * 
      13953 TAAAGACCCCAATCAACTTTTGATGAGGATCGAGATAACTA-TCT-TTTT-TCTTTTCTTTTATG
          1 TAAAGACCCCAATCAACTTTTGATGAGAATCAAGATAACTACTCTATTTTGTATTTTCTTTTACG

                            
      14015 TGTTTAAGAGTTGTAA
         66 TGTTTAAGAGTTGTAA

      14031 TAGCCTTTTT


Statistics
Matches: 71,  Mismatches: 7, Indels: 4
        0.87            0.09        0.05

Matches are distributed among these distances:
  84   28  0.39
  86    4  0.06
  87    3  0.04
  88   36  0.51

ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41


Consensus pattern (87 bp):   
TAAAGACCCCAATCAACTTTTGATGAGAATCAAGATAACTACTCTATTTTGTATTTTCTTTTACG
TGTTTAAGAGTTGTAACAGGTC
Done.