Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014467.1 Corchorus capsularis cultivar CVL-1 contig14488, 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: 15300
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:3512 original size:2 final size:2

Alignment explanation


    Indices: 3505--3532  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       3495 CATTTCTTTT

                                                     
       3505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3533 CTTACTATTT


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):   
TA

Found at i:4947 original size:129 final size:121

Alignment explanation


    Indices: 4731--5083  Score: 454
    Period size: 114  Copynumber: 2.9  Consensus size: 121

       4721 TGCAAGAGAA

                                                                             
       4731 TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTGTCACCTCCTGCAAT
          1 TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTGTCACCTCCTGCAAT

                                                                            
       4796 AGAATGCCTGCTAATGCTTCCTGTTGACTTTTGTTCAACATCTTCACTACCTTCTTCAAATGAG
         66 AGAATGCCTGCTAATGCTTCCTG-TGACTTTTGTTCAACATCTTCAC-A------TCAAATGAG

                                                              *              
       4860 TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTATCACCTCCTGCAAT
          1 TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTGTCACCTCCTGCAAT

                         *                                           
       4925 AGAATGCCTGCTACTGCTTCCTGGTGACTTTTGTT---CA-----ACATCAAATGAG
         66 AGAATGCCTGCTAATGCTTCCT-GTGACTTTTGTTCAACATCTTCACATCAAATGAG

                                       *     *  **          *    *   *       
       4974 TGTCCTACGCCAGGGCTGTGTCCTGGGGTAG-TTGGTTGGAAATCTTCTTTGTTACCACCTGCAA
          1 TGTCCTACGCCAGGGCTGTGTCCTGGGCT-GCTAGGGCGGAAATCTTCCTTGTCACCTCCTGCAA

                       *                                  
       5038 TAGAATGCCTGTTAATGCTTCCTAGTGACTTTTGTTCAACATCTTC
         65 TAGAATGCCTGCTAATGCTTCCT-GTGACTTTTGTTCAACATCTTC

       5084 GTCATGATCT


Statistics
Matches: 201,  Mismatches: 13, Indels: 27
        0.83            0.05        0.11

Matches are distributed among these distances:
 114   96  0.48
 115    1  0.00
 117    2  0.01
 120    1  0.00
 121    2  0.01
 126    2  0.01
 129   96  0.48
 130    1  0.00

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


Consensus pattern (121 bp):   
TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTGTCACCTCCTGCAAT
AGAATGCCTGCTAATGCTTCCTGTGACTTTTGTTCAACATCTTCACATCAAATGAG

Found at i:5166 original size:243 final size:242

Alignment explanation


    Indices: 4731--5172  Score: 529
    Period size: 243  Copynumber: 1.8  Consensus size: 242

       4721 TGCAAGAGAA

                                                                    *        
       4731 TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTGTCACCTCCTGCAAT
          1 TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTGTCACCACCTGCAAT

                                                                   *    *  * 
       4796 AGAATGCCTGCTAATGCTTCCTGTTGACTTTTGTTCAACATCTTCACTACCTTCTTCAAATGAGT
         66 AGAATGCCTGCTAATGCTTCCTGTTGACTTTTGTTCAACATCTTCACTACCTTCTGCAAAAGAAT

                   *     *   ***                 *     *           *       * 
       4861 GTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTATCACCTCCTGCAATA
        131 GTCCTACACCAGGACTGACCCCTGGGCTGCTAGGGCGAAAATCATCCTTATCA-CACCTGCAACA

                                                            
       4926 GAATGCCTGCTACTGCTTCCTGGTGACTTTTGTTCAACATCAAATGAG
        195 GAATGCCTGCTACTGCTTCCTGGTGACTTTTGTTCAACATCAAATGAG

                                       *     *  **          *    *           
       4974 TGTCCTACGCCAGGGCTGTGTCCTGGGGTAG-TTGGTTGGAAATCTTCTTTGTTACCACCTGCAA
          1 TGTCCTACGCCAGGGCTGTGTCCTGGGCT-GCTAGGGCGGAAATCTTCCTTGTCACCACCTGCAA

                       *                                    *     *      *   
       5038 TAGAATGCCTGTTAATGCTTCCTAG-TGACTTTTGTTCAACATCTTCGTCATGATCTTCTGGAAA
         65 TAGAATGCCTGCTAATGCTTCCT-GTTGACTTTTGTTCAACATCTTC-AC-T-ACCTTCTGCAAA

                 *                                                   *       
       5102 AGAATTTCCTACACCAGGACTGACCCCT-GG-TG-TAGTTGGTCGAAAATCATCCTTGT-A-ACC
        126 AGAATGTCCTACACCAGGACTGACCCCTGGGCTGCTAG--GG-CGAAAATCATCCTTATCACACC

                       
       5162 TGCAACAGAAT
        188 TGCAACAGAAT

       5173 CATCAAAATC


Statistics
Matches: 166,  Mismatches: 25, Indels: 16
        0.80            0.12        0.08

Matches are distributed among these distances:
 243  113  0.68
 244    5  0.03
 245    6  0.04
 246   42  0.25

ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32


Consensus pattern (242 bp):   
TGTCCTACGCCAGGGCTGTGTCCTGGGCTGCTAGGGCGGAAATCTTCCTTGTCACCACCTGCAAT
AGAATGCCTGCTAATGCTTCCTGTTGACTTTTGTTCAACATCTTCACTACCTTCTGCAAAAGAAT
GTCCTACACCAGGACTGACCCCTGGGCTGCTAGGGCGAAAATCATCCTTATCACACCTGCAACAG
AATGCCTGCTACTGCTTCCTGGTGACTTTTGTTCAACATCAAATGAG

Found at i:10985 original size:38 final size:38

Alignment explanation


    Indices: 10934--11012  Score: 158
    Period size: 38  Copynumber: 2.1  Consensus size: 38

      10924 ATTAGATGAA

                                                  
      10934 AAGTGGACAGATAATATGGGACGGAGGGAGTATAAAAC
          1 AAGTGGACAGATAATATGGGACGGAGGGAGTATAAAAC

                                                  
      10972 AAGTGGACAGATAATATGGGACGGAGGGAGTATAAAAC
          1 AAGTGGACAGATAATATGGGACGGAGGGAGTATAAAAC

               
      11010 AAG
          1 AAG

      11013 AAGAATATCC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   41  1.00

ACGTcount: A:0.43, C:0.08, G:0.34, T:0.15


Consensus pattern (38 bp):   
AAGTGGACAGATAATATGGGACGGAGGGAGTATAAAAC
Done.