Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010321.1 Corchorus olitorius cultivar O-4 contig10353, 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: 3629
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28


Found at i:1826 original size:38 final size:38

Alignment explanation


    Indices: 1775--2179  Score: 506
    Period size: 38  Copynumber: 10.6  Consensus size: 38

       1765 AACTCAAAGA

                      *    *                      
       1775 AGTTATCAAAGTTGAGTGGAAACAGGTCATCTTTCAGC
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                   *  *                       * **
       1813 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTTAAA
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

               *        *                 *      *
       1851 AGTAATCAAAATCGACTGGAAACAGGTCATTTTTCAGA
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                 *      *                         
       1889 AGTTACCAAAATCGACTGGAAACAGGTCATCTTTCAGC
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                   *                              
       1927 AGTTATCGAAATTGACTGGAAACAGGTCATCTTTCAGC
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                   *  *                           
       1965 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                        *                        *
       2003 AGTTATCAAAATCGACTGGAAACAGGTCATCTTTCAGA
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                        *                *       *
       2041 AGTTATCAAAATCGACTGGAAACAGGTCACCTTTCAGT
          1 AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                   *  *           *    *          *
       2079 AGTTATCGAAGTTGACTGGAAATAGGTTA-CTTTTCAGA
          1 AGTTATCAAAATTGACTGGAAACAGGTCATC-TTTCAGC

                 *     *      **                   
       2117 AGTTTGTCAAAGTTGACTCAAAACAGGTCATCTTTCAGC
          1 AG-TTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

                             *      
       2156 AGTTATCAAAATTGACTAGAAACA
          1 AGTTATCAAAATTGACTGGAAACA

       2180 AGTCCTTTTC


Statistics
Matches: 321,  Mismatches: 43, Indels: 6
        0.87            0.12        0.02

Matches are distributed among these distances:
  37    1  0.00
  38  290  0.90
  39   29  0.09
  40    1  0.00

ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28


Consensus pattern (38 bp):   
AGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGC

Found at i:3134 original size:12 final size:11

Alignment explanation


    Indices: 3089--3135  Score: 58
    Period size: 12  Copynumber: 4.0  Consensus size: 11

       3079 AAAGGGTGTT

                       
       3089 AAAAAAAAAGG
          1 AAAAAAAAAGG

                      * 
       3100 AAAAGAAAAAAG
          1 AAAA-AAAAAGG

                        
       3112 AAAGAAAAAAGG
          1 AAA-AAAAAAGG

                        
       3124 AAAAAGAAAAGG
          1 AAAAA-AAAAGG

       3136 GGTGCACGTG


Statistics
Matches: 31,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  11    6  0.19
  12   24  0.77
  13    1  0.03

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (11 bp):   
AAAAAAAAAGG

Found at i:3191 original size:16 final size:16

Alignment explanation


    Indices: 3172--3208  Score: 56
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       3162 AAAGAAAAAG

                *           
       3172 AAAAGGAAGAAAGGAA
          1 AAAAAGAAGAAAGGAA

                         *  
       3188 AAAAAGAAGAAAGTAA
          1 AAAAAGAAGAAAGGAA

                 
       3204 AAAAA
          1 AAAAA

       3209 AAAAAAAAGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03


Consensus pattern (16 bp):   
AAAAAGAAGAAAGGAA

Found at i:3221 original size:16 final size:16

Alignment explanation


    Indices: 3162--3221  Score: 57
    Period size: 17  Copynumber: 3.5  Consensus size: 16

       3152 CCCCAAAATT

                               
       3162 AAAGAAAAAGAAAAGGAAG
          1 AAAGAAAAA-AAAA--AAG

                *       *   
       3181 AAAGGAAAAAAAGAAG
          1 AAAGAAAAAAAAAAAG

                            *
       3197 AAAGTAAAAAAAAAAAA
          1 AAAG-AAAAAAAAAAAG

                    
       3214 AAAGAAAA
          1 AAAGAAAA

       3222 GGGGTGGGAC


Statistics
Matches: 35,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  16   11  0.31
  17   13  0.37
  18    3  0.09
  19    8  0.23

ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02


Consensus pattern (16 bp):   
AAAGAAAAAAAAAAAG
Done.