Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015198.1 Corchorus capsularis cultivar CVL-1 contig15219, 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: 9010
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:1794 original size:6 final size:6

Alignment explanation


    Indices: 1783--1809  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       1773 AAAGCAAAGC

                                           
       1783 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

       1810 GCAAATTAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:2766 original size:10 final size:10

Alignment explanation


    Indices: 2751--2775  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       2741 GAGGACTCTA

                      
       2751 GAATTTTCTG
          1 GAATTTTCTG

                      
       2761 GAATTTTCTG
          1 GAATTTTCTG

                 
       2771 GAATT
          1 GAATT

       2776 GAGCAGGGAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48


Consensus pattern (10 bp):   
GAATTTTCTG

Found at i:3371 original size:20 final size:22

Alignment explanation


    Indices: 3347--3396  Score: 59
    Period size: 20  Copynumber: 2.4  Consensus size: 22

       3337 CAAAATAGGG

                                  
       3347 TAAAAACACATAAAAATAGC-A
          1 TAAAAACACATAAAAATAGCTA

                 ** *             
       3368 -AAAAGTATATAAAAATAGCTA
          1 TAAAAACACATAAAAATAGCTA

                    
       3389 TAAAAACA
          1 TAAAAACA

       3397 TGCATAATTT


Statistics
Matches: 22,  Mismatches: 5, Indels: 3
        0.73            0.17        0.10

Matches are distributed among these distances:
  20   16  0.73
  21    1  0.05
  22    5  0.23

ACGTcount: A:0.66, C:0.10, G:0.06, T:0.18


Consensus pattern (22 bp):   
TAAAAACACATAAAAATAGCTA

Found at i:8107 original size:107 final size:107

Alignment explanation


    Indices: 7921--8165  Score: 370
    Period size: 107  Copynumber: 2.3  Consensus size: 107

       7911 CATTTCATTT

                                                                       *     
       7921 CTAATTTCACTAAGTTTAG-TCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAA
          1 CTAATTTCACTAAGTTTAGCT-CCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAA

                                *                      
       7985 TAAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAGAA
         65 TAAATAATTTATTGTTATAGAGTTTTAGAAATAAAATACAGAA

                                  *                                      **  
       8028 CTAATTTCACTAAGTTTAGCTCGAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATGAT
          1 CTAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT

            *                                    * *  
       8093 TAATAATTTATTGTTATAGAGTTTTAGAAATAAAATATATAA
         66 AAATAATTTATTGTTATAGAGTTTTAGAAATAAAATACAGAA

                *        *                   
       8135 CT-AGTTCACTAAATTTAGC-CCAAATTAAAAT
          1 CTAATTTCACTAAGTTTAGCTCCAAATTAAAAT

       8166 AAAATTAAAA


Statistics
Matches: 126,  Mismatches: 11, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
 105   11  0.09
 106   15  0.12
 107   99  0.79
 108    1  0.01

ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41


Consensus pattern (107 bp):   
CTAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
AAATAATTTATTGTTATAGAGTTTTAGAAATAAAATACAGAA

Found at i:8202 original size:107 final size:102

Alignment explanation


    Indices: 7921--8202  Score: 246
    Period size: 107  Copynumber: 2.6  Consensus size: 102

       7911 CATTTCATTT

                *        *                      * *                          
       7921 CTAATTTCACTAAGTTTAG-TCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAA
          1 CTAAGTTCACTAAATTTAGCT-CCAAATTAAAATTTAAATTTTATTTTAAGGGT-AA----AAAA

             *                  *                      
       7985 TAAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAGAA
         60 TTAATAATTTATTGTTATAGAGTTTTAGAAATAAAATACAGAA

                *        *        *            * *                        *  
       8028 CTAATTTCACTAAGTTTAGCTCGAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATGAT
          1 CTAAGTTCACTAAATTTAGCTCCAAATTAAAATTTAAATTTTATTTTAAGGGTAAA----A-AAT

                                                 * *  
       8093 TAATAATTTATTGTTATAGAGTTTTAGAAATAAAATATATAA
         61 TAATAATTTATTGTTATAGAGTTTTAGAAATAAAATACAGAA

                                                                     *       
       8135 CT-AGTTCACTAAATTTAGC-CCAAATTAAAATAAAATTAAAATTTTATTTTAAAGGTTAGAAAA
          1 CTAAGTTCACTAAATTTAGCTCCAAATTAAAAT----TT-AAATTTTATTTT-AAGGGTA-AAAA

                 
       8198 ATTAA
         59 ATTAA

       8203 GATTTGTAAA


Statistics
Matches: 149,  Mismatches: 13, Indels: 26
        0.79            0.07        0.14

Matches are distributed among these distances:
 102    1  0.01
 105   11  0.07
 106   18  0.12
 107   97  0.65
 108    2  0.01
 109    2  0.01
 110   10  0.07
 111    6  0.04
 112    2  0.01

ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41


Consensus pattern (102 bp):   
CTAAGTTCACTAAATTTAGCTCCAAATTAAAATTTAAATTTTATTTTAAGGGTAAAAAATTAATA
ATTTATTGTTATAGAGTTTTAGAAATAAAATACAGAA
Done.