Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018872.1 Corchorus olitorius cultivar O-4 contig18905, 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: 32202
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:3149 original size:13 final size:13

Alignment explanation


    Indices: 3131--3163  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       3121 AAAATTAAGA

                   *     
       3131 AAAGATTTACAAG
          1 AAAGATTCACAAG

                         
       3144 AAAGATTCACAAG
          1 AAAGATTCACAAG

                   
       3157 AAAGATT
          1 AAAGATT

       3164 GAAAAACTAG


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

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.55, C:0.09, G:0.15, T:0.21


Consensus pattern (13 bp):   
AAAGATTCACAAG

Found at i:7983 original size:29 final size:30

Alignment explanation


    Indices: 7934--8020  Score: 90
    Period size: 29  Copynumber: 3.0  Consensus size: 30

       7924 AACGATGAGC

                           *            ** 
       7934 GTCTTGGACCA-TGGTAAATGAACGAC-TTT
          1 GTCTTGGA-CATTGGCAAATGAACGACGAAT

                            *             
       7963 GTCTTGGACATTGGCACATGAACGACGAAT
          1 GTCTTGGACATTGGCAAATGAACGACGAAT

               *         *               
       7993 GTCCTGGACATTGCCAAATGAAC-ACGAA
          1 GTCTTGGACATTGGCAAATGAACGACGAA

       8021 CGCCCTGGAC


Statistics
Matches: 49,  Mismatches: 7, Indels: 4
        0.82            0.12        0.07

Matches are distributed among these distances:
  28    2  0.04
  29   26  0.53
  30   21  0.43

ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24


Consensus pattern (30 bp):   
GTCTTGGACATTGGCAAATGAACGACGAAT

Found at i:8029 original size:29 final size:30

Alignment explanation


    Indices: 7967--8033  Score: 91
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       7957 GACTTTGTCT

                     *  *            * *  
       7967 TGGACATTGGCACATGAACGACGAATGTCC
          1 TGGACATTGCCAAATGAACGACGAACGCCC

                                          
       7997 TGGACATTGCCAAATGAAC-ACGAACGCCC
          1 TGGACATTGCCAAATGAACGACGAACGCCC

                    
       8026 TGGACATT
          1 TGGACATT

       8034 ACCATTGGAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 1
        0.87            0.11        0.03

Matches are distributed among these distances:
  29   16  0.48
  30   17  0.52

ACGTcount: A:0.31, C:0.25, G:0.24, T:0.19


Consensus pattern (30 bp):   
TGGACATTGCCAAATGAACGACGAACGCCC

Found at i:13429 original size:25 final size:24

Alignment explanation


    Indices: 13379--13429  Score: 57
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      13369 ATGATTTAGG

                      *  *      **  
      13379 GGTTACTAACTCCCTTTTTTTTGA
          1 GGTTACTAACACCATTTTTTCAGA

                                     
      13403 GGTTACTAACACTCATTTTTTCAGA
          1 GGTTACTAACAC-CATTTTTTCAGA

              
      13428 GG
          1 GG

      13430 GACAATACTT


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  24   11  0.50
  25   11  0.50

ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43


Consensus pattern (24 bp):   
GGTTACTAACACCATTTTTTCAGA

Found at i:29157 original size:205 final size:205

Alignment explanation


    Indices: 28805--29216  Score: 752
    Period size: 205  Copynumber: 2.0  Consensus size: 205

      28795 TGATGGAACT

                                                             *               
      28805 AAACATCCAACACTTTACCAGCAGACCAAATGCCTAATGACTTTTTAGTGACATTAATTACAAGC
          1 AAACATCCAACACTTTACCAGCAGACCAAATGCCTAATGACTTTTTAGTAACATTAATTACAAGC

                                                                       *  *  
      28870 AAGATAAATTTTGGCTATCTTAAACCATCTCAAACTCAAAATGCAAATGGGGCAAGGATTCTTTC
         66 AAGATAAATTTTGGCTATCTTAAACCATCTCAAACTCAAAATGCAAATGGGGCAAGGATCCTCTC

                                             *                               
      28935 CGCTAGTGGAGAGGTCTACTGATTTTCCAAAGCCAGTTTAATGGCTTTAAGTGAAACTGGACATT
        131 CGCTAGTGGAGAGGTCTACTGATTTTCCAAAGCAAGTTTAATGGCTTTAAGTGAAACTGGACATT

                      
      29000 TGGAGAGAGA
        196 TGGAGAGAGA

                                 *  *                                     *  
      29010 AAACATCCAACACTTTACCAGTAGGCCAAATGCCTAATGACTTTTTAGTAACATTAATTACATGC
          1 AAACATCCAACACTTTACCAGCAGACCAAATGCCTAATGACTTTTTAGTAACATTAATTACAAGC

                          *                                                  
      29075 AAGATAAATTTTGGTTATCTTAAACCATCTCAAACTCAAAATGCAAATGGGGCAAGGATCCTCTC
         66 AAGATAAATTTTGGCTATCTTAAACCATCTCAAACTCAAAATGCAAATGGGGCAAGGATCCTCTC

                                                                             
      29140 CGCTAGTGGAGAGGTCTACTGATTTTCCAAAGCAAGTTTAATGGCTTTAAGTGAAACTGGACATT
        131 CGCTAGTGGAGAGGTCTACTGATTTTCCAAAGCAAGTTTAATGGCTTTAAGTGAAACTGGACATT

                      
      29205 TGGAGAGAGA
        196 TGGAGAGAGA

              
      29215 AA
          1 AA

      29217 TTGAAATAAC


Statistics
Matches: 199,  Mismatches: 8, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 205  199  1.00

ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28


Consensus pattern (205 bp):   
AAACATCCAACACTTTACCAGCAGACCAAATGCCTAATGACTTTTTAGTAACATTAATTACAAGC
AAGATAAATTTTGGCTATCTTAAACCATCTCAAACTCAAAATGCAAATGGGGCAAGGATCCTCTC
CGCTAGTGGAGAGGTCTACTGATTTTCCAAAGCAAGTTTAATGGCTTTAAGTGAAACTGGACATT
TGGAGAGAGA
Done.