Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000416.1 Corchorus olitorius cultivar O-4 contig00416, 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, 697

Length: 1162
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28


Found at i:447 original size:21 final size:21

Alignment explanation


    Indices: 421--464  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        411 ATGTAAATGC

                      **         
        421 AAATGTGAGATTAATATGCAA
          1 AAATGTGAGACAAATATGCAA

                    *            
        442 AAATGTGATACAAATATGCAA
          1 AAATGTGAGACAAATATGCAA

              
        463 AA
          1 AA

        465 GAACCTAACA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25


Consensus pattern (21 bp):   
AAATGTGAGACAAATATGCAA

Found at i:607 original size:27 final size:26

Alignment explanation


    Indices: 577--666  Score: 81
    Period size: 27  Copynumber: 3.3  Consensus size: 26

        567 GACCACACTG

                                      
        577 CCCCCTGAAGTACAAATGACTAAAAT
          1 CCCCCTGAAGTACAAATGACTAAAAT

                     **   *       *     
        603 ACCCCCTAGGTGTAAAAATGACCAAAAT
          1 -CCCCCT-GAAGTACAAATGACTAAAAT

            *         * *              
        631 GCCCCTGAACATGCAAATGACTAAAAT
          1 CCCCCTGAA-GTACAAATGACTAAAAT

            *        
        658 GCCCCTGAA
          1 CCCCCTGAA

        667 TGACCTTAAA


Statistics
Matches: 50,  Mismatches: 11, Indels: 4
        0.77            0.17        0.06

Matches are distributed among these distances:
  26    1  0.02
  27   33  0.66
  28   16  0.32

ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18


Consensus pattern (26 bp):   
CCCCCTGAAGTACAAATGACTAAAAT

Found at i:1017 original size:35 final size:35

Alignment explanation


    Indices: 899--1162  Score: 247
    Period size: 35  Copynumber: 7.6  Consensus size: 35

        889 CAAGTTCATA

                                         *  *   
        899 TTGAAGATGCTACACCGAGTCATCAT-A-ATCTA-T
          1 TTGAAGATGCTACACCGAGTCATC-TGAGTTCAACT

                         *        *           *   
        932 TTGAAGATTTGCTGCACCGAGCCCA-CTGAG-TCCA-T
          1 TTGAAGA--TGCTACACCGAG-TCATCTGAGTTCAACT

                    *           *       *    ** 
        967 TATGAAGAAGCTACACCGAGACATCTGAATTCATTT
          1 T-TGAAGATGCTACACCGAGTCATCTGAGTTCAACT

                 *                  *       *  
       1003 TTGAATATGCTACACCGAGTCATCCGAGTTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT

                                                
       1038 TTGAAGATGCTACACCGAGTCATCTG-GATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAG-TTCAACT

             **                                
       1073 TCAAAGATGCTACACCGAGTCATCTGAGTTCAA-T
          1 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT

                        *    *                 *
       1107 TTAGAAGATGCTGCACCAAGTCATCTGAGTTCAACC
          1 TT-GAAGATGCTACACCGAGTCATCTGAGTTCAACT

                                
       1143 TTGAAGATGCTACACCGAGT
          1 TTGAAGATGCTACACCGAGT


Statistics
Matches: 191,  Mismatches: 27, Indels: 24
        0.79            0.11        0.10

Matches are distributed among these distances:
  33    9  0.05
  34   18  0.09
  35  151  0.79
  36   13  0.07

ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT

Found at i:1129 original size:105 final size:105

Alignment explanation


    Indices: 971--1162  Score: 285
    Period size: 105  Copynumber: 1.8  Consensus size: 105

        961 GTCCATTATG

                                         *   *   *          *               *
        971 AAGAAGCTACACCGAGACATCTGAATTCATTTTTGAATATGCTACACCGAGTCATCCGAGTTCAT
          1 AAGAAGCTACACCGAGACATCTGAATTCAATTTAGAAGATGCTACACCAAGTCATCCGAGTTCAA

             *                                      
       1036 CTTTGAAGATGCTACACCGAGTCATCTGGATTCAACTTCA
         66 CCTTGAAGATGCTACACCGAGTCATCTGGATTCAACTTCA

                *           *       *                  *            *        
       1076 AAGATGCTACACCGAGTCATCTGAGTTCAATTTAGAAGATGCTGCACCAAGTCATCTGAGTTCAA
          1 AAGAAGCTACACCGAGACATCTGAATTCAATTTAGAAGATGCTACACCAAGTCATCCGAGTTCAA

                                  
       1141 CCTTGAAGATGCTACACCGAGT
         66 CCTTGAAGATGCTACACCGAGT


Statistics
Matches: 76,  Mismatches: 11, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
 105   76  1.00

ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27


Consensus pattern (105 bp):   
AAGAAGCTACACCGAGACATCTGAATTCAATTTAGAAGATGCTACACCAAGTCATCCGAGTTCAA
CCTTGAAGATGCTACACCGAGTCATCTGGATTCAACTTCA
Done.