Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009529.1 Corchorus capsularis cultivar CVL-1 contig09550, 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: 19215
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:2822 original size:3 final size:3

Alignment explanation


    Indices: 2816--2856  Score: 64
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       2806 ATCTTCTTGA

                                  *   *                           
       2816 ACC ACC ACC ACC ACC ACT ACT ACC ACC ACC ACC ACC ACC AC
          1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC

       2857 TACCTCCAGG


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.34, C:0.61, G:0.00, T:0.05


Consensus pattern (3 bp):   
ACC

Found at i:6214 original size:22 final size:22

Alignment explanation


    Indices: 6186--6231  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       6176 AGAAAAAATA

                                  
       6186 AAGGAAAGTTTGTATACATTAG
          1 AAGGAAAGTTTGTATACATTAG

                                  
       6208 AAGGAAAGTTTGTATACATTAG
          1 AAGGAAAGTTTGTATACATTAG

              
       6230 AA
          1 AA

       6232 ACCATAACAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30


Consensus pattern (22 bp):   
AAGGAAAGTTTGTATACATTAG

Found at i:7951 original size:12 final size:12

Alignment explanation


    Indices: 7934--7981  Score: 51
    Period size: 12  Copynumber: 4.0  Consensus size: 12

       7924 TGGGTCATTG

                        
       7934 CCAGAAGCAGAA
          1 CCAGAAGCAGAA

                      * 
       7946 CCAGAAGCAGCA
          1 CCAGAAGCAGAA

            *   *    *  
       7958 GCAGGAGCATAA
          1 CCAGAAGCAGAA

                   *    
       7970 CCAGAAGAAGAA
          1 CCAGAAGCAGAA

       7982 GCATTGTTCA


Statistics
Matches: 27,  Mismatches: 9, Indels: 0
        0.75            0.25        0.00

Matches are distributed among these distances:
  12   27  1.00

ACGTcount: A:0.48, C:0.23, G:0.27, T:0.02


Consensus pattern (12 bp):   
CCAGAAGCAGAA

Found at i:7984 original size:24 final size:24

Alignment explanation


    Indices: 7939--7984  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       7929 CATTGCCAGA

                          *  *      
       7939 AGCAGAACCAGAAGCAGCAGCAGG
          1 AGCAGAACCAGAAGAAGAAGCAGG

                *                 
       7963 AGCATAACCAGAAGAAGAAGCA
          1 AGCAGAACCAGAAGAAGAAGCA

       7985 TTGTTCATTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.48, C:0.22, G:0.28, T:0.02


Consensus pattern (24 bp):   
AGCAGAACCAGAAGAAGAAGCAGG

Found at i:10532 original size:12 final size:13

Alignment explanation


    Indices: 10511--10539  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

      10501 TTTTGCTCCC

                         
      10511 CTTTTATCTTTAT
          1 CTTTTATCTTTAT

                         
      10524 CTTTT-TCTTTAT
          1 CTTTTATCTTTAT

                
      10536 CTTT
          1 CTTT

      10540 ATTTTTGTCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.69
  13    5  0.31

ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72


Consensus pattern (13 bp):   
CTTTTATCTTTAT

Found at i:13718 original size:2 final size:2

Alignment explanation


    Indices: 13711--13738  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      13701 TTTTATAATA

                                                     
      13711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13739 TATCCTGATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.