Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013904.1 Corchorus olitorius cultivar O-4 contig13937, 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: 52314
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:8930 original size:27 final size:27

Alignment explanation


    Indices: 8900--8965  Score: 105
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       8890 AGTGTATTTG

                *                 *    
       8900 AAATTACCAAAATGCCCATGGATGTGC
          1 AAATGACCAAAATGCCCATGGACGTGC

                             *         
       8927 AAATGACCAAAATGCCCCTGGACGTGC
          1 AAATGACCAAAATGCCCATGGACGTGC

                        
       8954 AAATGACCAAAA
          1 AAATGACCAAAA

       8966 GAAGTAAGTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   36  1.00

ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCATGGACGTGC

Found at i:11561 original size:76 final size:76

Alignment explanation


    Indices: 11429--11580  Score: 177
    Period size: 76  Copynumber: 2.0  Consensus size: 76

      11419 TGACGAGCTA

                      *                                                      
      11429 TGACACAGCCTACCTGGGTGATCAGGCACAACACATGGGTCCTCAGACAAACCATGTGGGCACCC
          1 TGACACAGCCCACCTGGGTGATCAGGCACAACACATGGGTCCTCAGACAAACCATGTGGGCACCC

                        
      11494 -AGGTAGAGTCG
         66 AAGG-AGAGTCG

                  *             *                     **     *              *
      11505 TGACACTGCCCACCTGGGTGCTCAAGG-A-AATCACATGGGTGTTCAAGGCAAA-CATGTGGGCG
          1 TGACACAGCCCACCTGGGTGATC-AGGCACAA-CACATGGGTCCTC-AGACAAACCATGTGGGCA

                          
      11567 CCCAAGGAGAGTCG
         63 CCCAAGGAGAGTCG

      11581 GGGACAGCCC


Statistics
Matches: 65,  Mismatches: 7, Indels: 8
        0.81            0.09        0.10

Matches are distributed among these distances:
  75    2  0.03
  76   51  0.78
  77   12  0.18

ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16


Consensus pattern (76 bp):   
TGACACAGCCCACCTGGGTGATCAGGCACAACACATGGGTCCTCAGACAAACCATGTGGGCACCC
AAGGAGAGTCG

Found at i:30802 original size:13 final size:13

Alignment explanation


    Indices: 30784--30809  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      30774 AAGGTAACAA

                         
      30784 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
      30797 CAAAAATCATCAC
          1 CAAAAATCATCAC

      30810 TCATGCCAAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATCATCAC

Found at i:35842 original size:21 final size:22

Alignment explanation


    Indices: 35805--35848  Score: 65
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      35795 ATTAGAAATT

                                   
      35805 GCTACCCCTAGAAAAAATTGTTG
          1 GCTACCCCTAGAAAAAATT-TTG

                                  
      35828 GCTACCCC-A-AAAAAATTTTG
          1 GCTACCCCTAGAAAAAATTTTG

             
      35848 G
          1 G

      35849 TTAAGAAAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  20    4  0.19
  21    8  0.38
  22    1  0.05
  23    8  0.38

ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25


Consensus pattern (22 bp):   
GCTACCCCTAGAAAAAATTTTG

Found at i:36331 original size:22 final size:22

Alignment explanation


    Indices: 36283--36331  Score: 55
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      36273 TTGCCCTTCT

                                 *
      36283 TCTCT-CTCCCCCCACTAACTC
          1 TCTCTCCTCCCCCCACTAACTA

             *        *      *    
      36304 TTTCTCCTCCTCCCACTCACTA
          1 TCTCTCCTCCCCCCACTAACTA

                  
      36326 TCTCTC
          1 TCTCTC

      36332 TTCATCAATT


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  21    4  0.18
  22   18  0.82

ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35


Consensus pattern (22 bp):   
TCTCTCCTCCCCCCACTAACTA

Found at i:37089 original size:1 final size:1

Alignment explanation


    Indices: 37083--37114  Score: 55
    Period size: 1  Copynumber: 32.0  Consensus size: 1

      37073 TCCCTCATAT

                                   *        
      37083 AAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      37115 CCACTGCCCC


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:46374 original size:3 final size:3

Alignment explanation


    Indices: 46366--46416  Score: 102
    Period size: 3  Copynumber: 17.0  Consensus size: 3

      46356 CGACTCTCCA

                                                                           
      46366 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

               
      46414 ATT
          1 ATT

      46417 TATATATATA


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   48  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Done.