Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011927.1 Corchorus capsularis cultivar CVL-1 contig11948, 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: 13404
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29


Found at i:306 original size:12 final size:12

Alignment explanation


    Indices: 289--313  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        279 ACTACAATGT

                        
        289 AACTATATGCAA
          1 AACTATATGCAA

                        
        301 AACTATATGCAA
          1 AACTATATGCAA

             
        313 A
          1 A

        314 CAGAAAAGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24


Consensus pattern (12 bp):   
AACTATATGCAA

Found at i:2616 original size:18 final size:18

Alignment explanation


    Indices: 2587--2633  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       2577 CAAAAACTGA

                               
       2587 TAAAAAGTAAATAAAAATC
          1 TAAAAAG-AAATAAAAATC

                       *     *
       2606 TAAAAAGAAATCAAAATT
          1 TAAAAAGAAATAAAAATC

             *        
       2624 TGAAAAGAAA
          1 TAAAAAGAAA

       2634 AGAAAAGAAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  18   18  0.72
  19    7  0.28

ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19


Consensus pattern (18 bp):   
TAAAAAGAAATAAAAATC

Found at i:10419 original size:48 final size:49

Alignment explanation


    Indices: 10289--10475  Score: 209
    Period size: 48  Copynumber: 3.9  Consensus size: 49

      10279 CAATTTTCAG

                     *            **   *     *        *      
      10289 TTTTTACCTGCTTTTTCCCAAAGTGCCATTCCCGGACGGAAGTCACTAA
          1 TTTTTACCTACTTTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTAA

                   * *                           *          **
      10338 TTTTTACTTGC-TTTTCCCTAAAACGCCCTTCCCAGATGGAAGGCACTTG
          1 TTTTTACCTACTTTTTCCC-AAAACGCCCTTCCCAGACGGAAGGCACTAA

                          *        *                         
      10387 TTTTT-CCTACTTTGTCCCAAAATGCCCTTCCCAGACGGAAGGCACTAA
          1 TTTTTACCTACTTTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTAA

                              *              *        
      10435 TTTTTACCTA-TTTTTCCTAAAACGCCCTTCCCGGACGGAAG
          1 TTTTTACCTACTTTTTCCCAAAACGCCCTTCCCAGACGGAAG

      10476 ACACCATTCT


Statistics
Matches: 115,  Mismatches: 20, Indels: 7
        0.81            0.14        0.05

Matches are distributed among these distances:
  48   68  0.59
  49   47  0.41

ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33


Consensus pattern (49 bp):   
TTTTTACCTACTTTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTAA

Found at i:10507 original size:97 final size:96

Alignment explanation


    Indices: 10299--10512  Score: 229
    Period size: 97  Copynumber: 2.2  Consensus size: 96

      10289 TTTTTACCTG

                              *     *        *             *  *              
      10299 CTTT-TTCCCAAAGTGCCATTCCCGGACGGAAGTCACTAATTTTTACTTGCTTTTCCCTAAAACG
          1 CTTTGTTCCCAAA-TGCCCTTCCCAGACGGAAGGCACTAATTTTTACCTGATTTTCCCTAAAACG

                       *     *     **  *     
      10363 CCCTTCCCAGATGGAAGGCACTTGTTTTTCCTA
         65 CCCTTCCCAGACGGAAGACAC-TCATTCTCCTA

                                                                   *         
      10396 CTTTG-TCCCAAAATGCCCTTCCCAGACGGAAGGCACTAATTTTTACCT-ATTTTTCCTAAAACG
          1 CTTTGTTCCC-AAATGCCCTTCCCAGACGGAAGGCACTAATTTTTACCTGATTTTCCCTAAAACG

                    *                    *  
      10459 CCCTTCCCGGACGGAAGACAC-CATTCTCTTA
         65 CCCTTCCCAGACGGAAGACACTCATTCTCCTA

                                   
      10490 CTTGTTGTTCCCGAAATGCCCTT
          1 C-T-TTGTTCCC-AAATGCCCTT

      10513 TTGGACAAAG


Statistics
Matches: 98,  Mismatches: 14, Indels: 10
        0.80            0.11        0.08

Matches are distributed among these distances:
  94    7  0.07
  95    1  0.01
  96   34  0.35
  97   53  0.54
  98    3  0.03

ACGTcount: A:0.22, C:0.30, G:0.15, T:0.32


Consensus pattern (96 bp):   
CTTTGTTCCCAAATGCCCTTCCCAGACGGAAGGCACTAATTTTTACCTGATTTTCCCTAAAACGC
CCTTCCCAGACGGAAGACACTCATTCTCCTA
Done.