Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014561.1 Corchorus olitorius cultivar O-4 contig14594, 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: 17984
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28


Found at i:3565 original size:22 final size:21

Alignment explanation


    Indices: 3516--3573  Score: 75
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       3506 TTGTAATCTC

                           *     
       3516 TGATTATTGAT-TAATAAAAG
          1 TGATTATTGATATAAAAAAAG

                                  
       3536 TGATTATTTGATATAAAAAAAG
          1 TGATTA-TTGATATAAAAAAAG

                             
       3558 -GATATATTGATATAAA
          1 TGAT-TATTGATATAAA

       3574 CAGTTAGGAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 5
        0.85            0.03        0.12

Matches are distributed among these distances:
  20    6  0.18
  21   18  0.53
  22   10  0.29

ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38


Consensus pattern (21 bp):   
TGATTATTGATATAAAAAAAG

Found at i:7164 original size:45 final size:45

Alignment explanation


    Indices: 7100--7365  Score: 261
    Period size: 45  Copynumber: 5.9  Consensus size: 45

       7090 TGCTACAGGG

                                                         
       7100 AGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGAGCAGA
          1 AGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGAGCAGA

                 *                                       
       7145 AGGAGGAGCATTGATCGGCCTCGGAGGATCGCTAGGA-G-G-AGA
          1 AGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGAGCAGA

                   *        **    *              *            
       7187 AGGAGAAACATTGATCAACCT-TGATGGATCGCTAGTCAGGAGCTGGAGA
          1 AGGAGAAGCATTGATCGGCCTCGGA-GGATCGCTAG-GAGGAGC---AGA

                       *    **     *    *           **   
       7236 AGGAGAAGCATCGATCAACCTCGTAGGACCGCTAGGAGGAAAAGA
          1 AGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGAGCAGA

                       *                      **    **   
       7281 AGGAGAAGCATCGATCGGCCTCGGAGGATCGCTACTAGGAAAAGA
          1 AGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGAGCAGA

                   *  **                      *     
       7326 AGGAGAAACAACGATCGGCCTCGGAGGATCGCTATGAGGA
          1 AGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGA

       7366 CTGAGGAGGA


Statistics
Matches: 187,  Mismatches: 25, Indels: 18
        0.81            0.11        0.08

Matches are distributed among these distances:
  41    2  0.01
  42   30  0.16
  43    2  0.01
  44    2  0.01
  45  115  0.61
  48    4  0.02
  49   31  0.17
  50    1  0.01

ACGTcount: A:0.32, C:0.18, G:0.35, T:0.14


Consensus pattern (45 bp):   
AGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGAGCAGA

Found at i:7376 original size:136 final size:136

Alignment explanation


    Indices: 7098--7376  Score: 332
    Period size: 136  Copynumber: 2.1  Consensus size: 136

       7088 CTTGCTACAG

                         *    **          *           **        *     *      
       7098 GGAGGAGAAGCATTGATCGGCCTCGGAGGATCGCTAGGAGGAGCAGAAGGAGGAGCATTGATCGG
          1 GGAGGAGAAGCATCGATCAACCTCGGAGGACCGCTAGGAGGAAAAGAAGGAGAAGCATCGATCGG

                               **             **         *                   
       7163 CCTCGGAGGATCGCTAGGAGGAGAAGGAGAAACATTGATCAACCTTGATGGATCGCTAGTCAGGA
         66 CCTCGGAGGATCGCTAGGAAAAGAAGGAGAAACAACGATCAACCTGGATGGATCGCTAGTCAGGA

                  
       7228 GCTGGA
        131 GCTGGA

             *                       *                                       
       7234 GAAGGAGAAGCATCGATCAACCTCGTAGGACCGCTAGGAGGAAAAGAAGGAGAAGCATCGATCGG
          1 GGAGGAGAAGCATCGATCAACCTCGGAGGACCGCTAGGAGGAAAAGAAGGAGAAGCATCGATCGG

                                                       **                   *
       7299 CCTCGGAGGATCGCTACTAGGAAAAGAAGGAGAAACAACGATCGGCCTCGGA-GGATCGCTA-TG
         66 CCTCGGAGGATCG---CTAGGAAAAGAAGGAGAAACAACGATCAACCT-GGATGGATCGCTAGTC

                      
       7362 AGGA-CT-GA
        127 AGGAGCTGGA

                   
       7370 GGAGGAG
          1 GGAGGAG

       7377 GATTGGTTGT


Statistics
Matches: 120,  Mismatches: 19, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
 136   76  0.63
 137    2  0.02
 138    5  0.04
 139   35  0.29
 140    2  0.02

ACGTcount: A:0.32, C:0.18, G:0.37, T:0.14


Consensus pattern (136 bp):   
GGAGGAGAAGCATCGATCAACCTCGGAGGACCGCTAGGAGGAAAAGAAGGAGAAGCATCGATCGG
CCTCGGAGGATCGCTAGGAAAAGAAGGAGAAACAACGATCAACCTGGATGGATCGCTAGTCAGGA
GCTGGA

Found at i:8169 original size:32 final size:31

Alignment explanation


    Indices: 8133--8200  Score: 82
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       8123 AAATGTTAGT

                  *       *  *              
       8133 CCTAAATTTTAGGCTAATTGCTCAAATAAGGG
          1 CCTAAAGTTT-GGCAAAATGCTCAAATAAGGG

                 *     *                   
       8165 CCTAACGTTTGTCAAAATGCTCAAATAAGGG
          1 CCTAAAGTTTGGCAAAATGCTCAAATAAGGG

                 
       8196 CCTAA
          1 CCTAA

       8201 TCTTTCCATT


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  31   23  0.74
  32    8  0.26

ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28


Consensus pattern (31 bp):   
CCTAAAGTTTGGCAAAATGCTCAAATAAGGG
Done.