Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016107.1 Corchorus olitorius cultivar O-4 contig16140, 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: 30436
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:2894 original size:16 final size:16

Alignment explanation


    Indices: 2863--2927  Score: 58
    Period size: 17  Copynumber: 3.9  Consensus size: 16

       2853 AGTTTTGATT

                 *            
       2863 ATTAAAAAATATATATTA
          1 ATTAATAAATATATA--A

               *            
       2881 ATTCATAAATATATAA
          1 ATTAATAAATATATAA

                     *    *  
       2897 ATTAATAAAAATAAAAA
          1 ATTAATAAATAT-ATAA

                  *       
       2914 ATTAATTAATATAT
          1 ATTAATAAATATAT

       2928 TTTTTTTGGT


Statistics
Matches: 38,  Mismatches: 8, Indels: 4
        0.76            0.16        0.08

Matches are distributed among these distances:
  16   12  0.32
  17   13  0.34
  18   13  0.34

ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37


Consensus pattern (16 bp):   
ATTAATAAATATATAA

Found at i:4640 original size:12 final size:13

Alignment explanation


    Indices: 4618--4650  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

       4608 CATCTAAATA

                *        
       4618 AAAAAAAAGAAAG
          1 AAAAGAAAGAAAG

                         
       4631 -AAAGAAAGAAAG
          1 AAAAGAAAGAAAG

                    
       4643 AAAAGAAA
          1 AAAAGAAA

       4651 AGATAAGTGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  12   11  0.61
  13    7  0.39

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (13 bp):   
AAAAGAAAGAAAG

Found at i:5330 original size:161 final size:162

Alignment explanation


    Indices: 5056--5377  Score: 574
    Period size: 161  Copynumber: 2.0  Consensus size: 162

       5046 ATATCTGAAT

                                  *         *        *    *                  
       5056 CTTAAAGCAAAAACTTCATCTCTTTCTTCAACCTCAGCTCTTTTCTGGGCCTCAACTTCTTGAAT
          1 CTTAAAGCAAAAACTTCATCTCCTTCTTCAACATCAGCTCTCTTCTAGGCCTCAACTTCTTGAAT

                                     *                                       
       5121 ATGGAGCTCCTCATCCACCTTGGAATGAAGGATGACAGGGACAGAGCAACACGTACACATAACGG
         66 ATGGAGCTCCTCATCCACCTTGGAACGAAGGATGACAGGGACAGAGCAACACGTACACATAACGG

                                            
       5186 CACCATGTTTCTCATGCAGCCTTTCGAAATGG
        131 CACCATGTTTCTCATGCAGCCTTTCGAAATGG

                *                                                            
       5218 CTTACAGC-AAAACTTCATCTCCTTCTTCAACATCAGCTCTCTTCTAGGCCTCAACTTCTTGAAT
          1 CTTAAAGCAAAAACTTCATCTCCTTCTTCAACATCAGCTCTCTTCTAGGCCTCAACTTCTTGAAT

                                                                             
       5282 ATGGAGCTCCTCATCCACCTTGGAACGAAGGATGACAGGGACAGAGCAACACGTACACATAACGG
         66 ATGGAGCTCCTCATCCACCTTGGAACGAAGGATGACAGGGACAGAGCAACACGTACACATAACGG

                *                          
       5347 CACCGTGTTTCTCATGCAGCCTTTCGAAATG
        131 CACCATGTTTCTCATGCAGCCTTTCGAAATG

       5378 ACGTCTAAAA


Statistics
Matches: 153,  Mismatches: 7, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
 161  146  0.95
 162    7  0.05

ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26


Consensus pattern (162 bp):   
CTTAAAGCAAAAACTTCATCTCCTTCTTCAACATCAGCTCTCTTCTAGGCCTCAACTTCTTGAAT
ATGGAGCTCCTCATCCACCTTGGAACGAAGGATGACAGGGACAGAGCAACACGTACACATAACGG
CACCATGTTTCTCATGCAGCCTTTCGAAATGG

Found at i:6805 original size:16 final size:16

Alignment explanation


    Indices: 6784--6817  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       6774 ATATATCATT

                            
       6784 AAAAAATAAATCCTTA
          1 AAAAAATAAATCCTTA

                    *  *    
       6800 AAAAAATAGATTCTTA
          1 AAAAAATAAATCCTTA

              
       6816 AA
          1 AA

       6818 TATCCTTAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26


Consensus pattern (16 bp):   
AAAAAATAAATCCTTA

Found at i:29280 original size:15 final size:16

Alignment explanation


    Indices: 29260--29289  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      29250 TGTAAGTTAA

                            
      29260 TCAAAA-ATCAATTTT
          1 TCAAAAGATCAATTTT

                           
      29275 TCAAAAGATCAATTT
          1 TCAAAAGATCAATTT

      29290 GAATTCACAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37


Consensus pattern (16 bp):   
TCAAAAGATCAATTTT

Done.