Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011590.1 Corchorus capsularis cultivar CVL-1 contig11611, 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: 12431
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:116 original size:66 final size:66

Alignment explanation


    Indices: 1--141  Score: 167
    Period size: 66  Copynumber: 2.1  Consensus size: 66

                                       *               *       *       *     
          1 TGCCGTCCTAGGAGGATGGCACACCATTGTTGATGCTGTCATAGGAGGACGGCACACCATGGTTG
          1 TGCCGTCCTAGGAGGATGGCACACCATGGTTGATGCTGTCATACGAGGACGACACACCACGGTTG

             
         66 A
         66 A

                *              *            *        * * *                   
         67 TGCCATCCTAGGAGGATGGTACACCATGGTTGGTGCCT-TCCTTCTAGGACGACACACCACGGTT
          1 TGCCGTCCTAGGAGGATGGCACACCATGGTTGATG-CTGTCATACGAGGACGACACACCACGGTT

             *
        131 GG
         65 GA

                     
        133 TGCCGTCCT
          1 TGCCGTCCT

        142 CCGAGGACGG


Statistics
Matches: 62,  Mismatches: 12, Indels: 2
        0.82            0.16        0.03

Matches are distributed among these distances:
  66   60  0.97
  67    2  0.03

ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24


Consensus pattern (66 bp):   
TGCCGTCCTAGGAGGATGGCACACCATGGTTGATGCTGTCATACGAGGACGACACACCACGGTTG
A

Found at i:124 original size:33 final size:33

Alignment explanation


    Indices: 1--154  Score: 128
    Period size: 33  Copynumber: 4.7  Consensus size: 33

                *     *     *          *    *
          1 TGCCGTCCTAGGAGGATGGCACACCATTGTTGA
          1 TGCCATCCTACGAGGACGGCACACCATGGTTGG

               **  *  *                     *
         34 TGCTGTCATAGGAGGACGGCACACCATGGTTGA
          1 TGCCATCCTACGAGGACGGCACACCATGGTTGG

                      *     *  *             
         67 TGCCATCCTAGGAGGATGGTACACCATGGTTGG
          1 TGCCATCCTACGAGGACGGCACACCATGGTTGG

                *    * *      *       *      
        100 TGCCTTCCTTCTAGGACGACACACCACGGTTGG
          1 TGCCATCCTACGAGGACGGCACACCATGGTTGG

                *    *            
        133 TGCCGTCCTCCGAGGACGGCAC
          1 TGCCATCCTACGAGGACGGCAC

        155 CGCGCCTAGA


Statistics
Matches: 99,  Mismatches: 22, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  33   99  1.00

ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22


Consensus pattern (33 bp):   
TGCCATCCTACGAGGACGGCACACCATGGTTGG

Found at i:9368 original size:19 final size:21

Alignment explanation


    Indices: 9341--9382  Score: 61
    Period size: 19  Copynumber: 2.1  Consensus size: 21

       9331 CATTAAACCA

                *                
       9341 TTGATCCGGAT-GG-TTTTGT
          1 TTGAACCGGATGGGTTTTTGT

                                 
       9360 TTGAACCGGATGGGTTTTTGT
          1 TTGAACCGGATGGGTTTTTGT

              
       9381 TT
          1 TT

       9383 AAATAATTTA


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

Matches are distributed among these distances:
  19   10  0.50
  20    2  0.10
  21    8  0.40

ACGTcount: A:0.12, C:0.10, G:0.31, T:0.48


Consensus pattern (21 bp):   
TTGAACCGGATGGGTTTTTGT

Found at i:10037 original size:25 final size:27

Alignment explanation


    Indices: 9977--10037  Score: 94
    Period size: 25  Copynumber: 2.4  Consensus size: 27

       9967 TAGAAGCATG

                                       
       9977 ATTAAATAA--AATATATATAAATACT
          1 ATTAAATAATTAATATATATAAATACT

                                       
      10002 ATTAAATAATTAATATA-A-AAATACT
          1 ATTAAATAATTAATATATATAAATACT

                       
      10027 ATTAAATAATT
          1 ATTAAATAATT

      10038 TTTCGAAGTA


Statistics
Matches: 34,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  25   27  0.79
  26    1  0.03
  27    6  0.18

ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38


Consensus pattern (27 bp):   
ATTAAATAATTAATATATATAAATACT
Done.