Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020773.1 Corchorus olitorius cultivar O-4 contig20806, 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: 44275
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:7686 original size:25 final size:25

Alignment explanation


    Indices: 7639--7687  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       7629 TCTATGCCCC

                 *            *      
       7639 AAAATGCAAGAGTAGTAAGTAGAGG
          1 AAAATCCAAGAGTAGTAACTAGAGG

                                     
       7664 AAAATCCAAGAAGTAGT-ACTAGAG
          1 AAAATCCAAG-AGTAGTAACTAGAG

       7688 TTTAGGTTTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25   15  0.71
  26    6  0.29

ACGTcount: A:0.49, C:0.08, G:0.27, T:0.16


Consensus pattern (25 bp):   
AAAATCCAAGAGTAGTAACTAGAGG

Found at i:26886 original size:13 final size:15

Alignment explanation


    Indices: 26864--26900  Score: 60
    Period size: 14  Copynumber: 2.6  Consensus size: 15

      26854 GGCTCTTAAT

                           
      26864 TTTTTCTTTC-TTTC
          1 TTTTTCTTTCATTTC

                           
      26878 TTTTT-TTTCATTTC
          1 TTTTTCTTTCATTTC

                     
      26892 TTTTTCTTT
          1 TTTTTCTTT

      26901 TGTTTGGTGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  13    4  0.19
  14   14  0.67
  15    3  0.14

ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81


Consensus pattern (15 bp):   
TTTTTCTTTCATTTC

Found at i:37815 original size:68 final size:68

Alignment explanation


    Indices: 37706--37840  Score: 243
    Period size: 68  Copynumber: 2.0  Consensus size: 68

      37696 CATAGGAAGG

                                                                             
      37706 CTATTGTATAAAAGGCCATGGTTTATTAATCCTAAAGCATGGAAAAGGTATCAAAACAGTCCGAG
          1 CTATTGTATAAAAGGCCATGGTTTATTAATCCTAAAGCATGGAAAAGGTATCAAAACAGTCCGAG

               
      37771 AAC
         66 AAC

                           *           *   *                                 
      37774 CTATTGTATAAAAGGGCATGGTTTATTGATCTTAAAGCATGGAAAAGGTATCAAAACAGTCCGAG
          1 CTATTGTATAAAAGGCCATGGTTTATTAATCCTAAAGCATGGAAAAGGTATCAAAACAGTCCGAG

              
      37839 AA
         66 AA

      37841 TCACCATCTA


Statistics
Matches: 64,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  68   64  1.00

ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26


Consensus pattern (68 bp):   
CTATTGTATAAAAGGCCATGGTTTATTAATCCTAAAGCATGGAAAAGGTATCAAAACAGTCCGAG
AAC

Found at i:38424 original size:21 final size:22

Alignment explanation


    Indices: 38393--38440  Score: 64
    Period size: 21  Copynumber: 2.2  Consensus size: 22

      38383 ACCCAGATCC

                                   
      38393 CAAACAGTAAAA-CTAAATCCAA
          1 CAAACAGTAAAATC-AAATCCAA

            *                     
      38415 TAAACA-TAAAATCAAATCCAA
          1 CAAACAGTAAAATCAAATCCAA

                 
      38436 CAAAC
          1 CAAAC

      38441 CAAAAAAGCA


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  21   17  0.74
  22    6  0.26

ACGTcount: A:0.60, C:0.23, G:0.02, T:0.15


Consensus pattern (22 bp):   
CAAACAGTAAAATCAAATCCAA

Found at i:42127 original size:63 final size:63

Alignment explanation


    Indices: 41987--42181  Score: 255
    Period size: 66  Copynumber: 3.0  Consensus size: 63

      41977 CCCACTAAAA

                 *   *                                  *                  * 
      41987 AGCCTCCCTTGGCTTGGCTTTTCAATCCAACGTTTGATGGCCGCTGCTCCTCGATGACCACATCG
          1 AGCCTGCCTCGGCTTGGCTTTTCAATCCAACGTTTGAT-G--GCAGCTCCTCGATGACCACATTG

             
      42052 T
         63 T

                                                             *             
      42053 AGCCTGCCTCGGCTTGGCTTTTCAATCCAACGTTTGATGGCAGCTCCTCCATGACCACATTGT
          1 AGCCTGCCTCGGCTTGGCTTTTCAATCCAACGTTTGATGGCAGCTCCTCGATGACCACATTGT

                            *            *   *  *                            
      42116 AGCCTGCCTCGGCTTGTCTTCTGATCAATTCAAGGTCTGATGGCAGCTCCTCGATGACCACATTG
          1 AGCCTGCCTCGGCTTGGCTT-T--TCAATCCAACGTTTGATGGCAGCTCCTCGATGACCACATTG

             
      42181 T
         63 T

      42182 CGAAATTCTG


Statistics
Matches: 116,  Mismatches: 10, Indels: 6
        0.88            0.08        0.05

Matches are distributed among these distances:
  63   40  0.34
  64    1  0.01
  65    1  0.01
  66   74  0.64

ACGTcount: A:0.17, C:0.31, G:0.22, T:0.30


Consensus pattern (63 bp):   
AGCCTGCCTCGGCTTGGCTTTTCAATCCAACGTTTGATGGCAGCTCCTCGATGACCACATTGT

Found at i:42718 original size:42 final size:42

Alignment explanation


    Indices: 42659--42782  Score: 187
    Period size: 42  Copynumber: 3.0  Consensus size: 42

      42649 ACCACATTGT

                                       *              
      42659 AGCCTGCCTCGGCTTGGCTTTTCAATGTAATGTTTGATGGGA
          1 AGCCTGCCTCGGCTTGGCTTTTCAATGCAATGTTTGATGGGA

                               *                       
      42701 AGCCTGCCTCGGCTTGGCTCTTCAATGCAACT-TTTGATGGGA
          1 AGCCTGCCTCGGCTTGGCTTTTCAATGCAA-TGTTTGATGGGA

                          *      *        *         
      42743 AGCCTGCCTCGGCTAGGCTTTCCAATGCAACGTTTGATGG
          1 AGCCTGCCTCGGCTTGGCTTTTCAATGCAATGTTTGATGG

      42783 CAGCTCCTCG


Statistics
Matches: 74,  Mismatches: 6, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  42   73  0.99
  43    1  0.01

ACGTcount: A:0.17, C:0.24, G:0.27, T:0.31


Consensus pattern (42 bp):   
AGCCTGCCTCGGCTTGGCTTTTCAATGCAATGTTTGATGGGA
Done.