Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014273.1 Corchorus capsularis cultivar CVL-1 contig14294, 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: 16287
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:210 original size:31 final size:31

Alignment explanation


    Indices: 164--300  Score: 168
    Period size: 31  Copynumber: 4.4  Consensus size: 31

        154 GTGTCCGACG

                      *                  **
        164 TGGCATGCCATGTGTACCAAAAAGTGACATG
          1 TGGCATGCCACGTGTACCAAAAAGTGACACA

                 *          *              
        195 TGGCACGCCACGTGTATCAAAAAGTGACACA
          1 TGGCATGCCACGTGTACCAAAAAGTGACACA

             **  *       *                  
        226 TATCACGCCACGTTTACCCAAAAA-TGACACA
          1 TGGCATGCCACGTGTA-CCAAAAAGTGACACA

                               *           
        257 TGGCATGCCACGTGTACCAGAAAGTGACACA
          1 TGGCATGCCACGTGTACCAAAAAGTGACACA

                         
        288 TGGCATGCCACGT
          1 TGGCATGCCACGT

        301 ACACAAAAAG


Statistics
Matches: 90,  Mismatches: 14, Indels: 4
        0.83            0.13        0.04

Matches are distributed among these distances:
  30    6  0.07
  31   78  0.87
  32    6  0.07

ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19


Consensus pattern (31 bp):   
TGGCATGCCACGTGTACCAAAAAGTGACACA

Found at i:4623 original size:35 final size:35

Alignment explanation


    Indices: 4582--4834  Score: 265
    Period size: 35  Copynumber: 7.1  Consensus size: 35

       4572 TAAGTCATTT

                                     **  *   * 
       4582 ATTTACTTAATTACACCGAATTAAGCCAACTACTG
          1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG

                            *   *      *       
       4617 ATTTACTTAATTACACTGAAATAAGTTGATTACCG
          1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG

                                   *          *
       4652 ATTTACTTAATTACACCGAATTAGGTTAATTACCA
          1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG

                      *                *     **
       4687 ATTTACTTAAGTACACCGAATTAAGTTGATTACTA
          1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG

                            *        * *            
       4722 ATTTACTTAATTTAATTACC-AATTTACTTAATTACACCG
          1 ATTTACTTAA-TT-A-CACCGAATTAAGTTAATT--ACCG

                                       *      *
       4761 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
          1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG

             *                         *      *
       4796 AATTACTTAATTACACCGAATTAAGTTGATTACCA
          1 ATTTACTTAATTACACCGAATTAAGTTAATTACCG

                
       4831 ATTT
          1 ATTT

       4835 GCTTTTTCCT


Statistics
Matches: 182,  Mismatches: 30, Indels: 12
        0.81            0.13        0.05

Matches are distributed among these distances:
  35  139  0.76
  36    4  0.02
  37   22  0.12
  38    5  0.03
  39   12  0.07

ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38


Consensus pattern (35 bp):   
ATTTACTTAATTACACCGAATTAAGTTAATTACCG

Found at i:4739 original size:21 final size:21

Alignment explanation


    Indices: 4715--4754  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4705 AATTAAGTTG

                 *               
       4715 ATTACTAATTTACTTAATTTA
          1 ATTACCAATTTACTTAATTTA

                               
       4736 ATTACCAATTTACTTAATT
          1 ATTACCAATTTACTTAATT

       4755 ACACCGATTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50


Consensus pattern (21 bp):   
ATTACCAATTTACTTAATTTA

Found at i:8311 original size:28 final size:28

Alignment explanation


    Indices: 8271--8325  Score: 101
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       8261 GAATTGGATG

                                        
       8271 AAAATGCTAATTTGAAAACTAGACCCAT
          1 AAAATGCTAATTTGAAAACTAGACCCAT

                              *        
       8299 AAAATGCTAATTTGAAAATTAGACCCA
          1 AAAATGCTAATTTGAAAACTAGACCCA

       8326 CTACAAGAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   26  1.00

ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25


Consensus pattern (28 bp):   
AAAATGCTAATTTGAAAACTAGACCCAT

Found at i:16244 original size:17 final size:17

Alignment explanation


    Indices: 16222--16254  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      16212 TATTGGGTTG

                             
      16222 GCAAATTGTGAAATATT
          1 GCAAATTGTGAAATATT

                            
      16239 GCAAATTGTGAAATAT
          1 GCAAATTGTGAAATAT

      16255 ATATATATAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33


Consensus pattern (17 bp):   
GCAAATTGTGAAATATT

Found at i:16258 original size:2 final size:2

Alignment explanation


    Indices: 16251--16287  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      16241 AAATTGTGAA

                                                                   
      16251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.