Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001396.1 Corchorus capsularis cultivar CVL-1 contig01396, 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: 6080
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Found at i:188 original size:22 final size:20

Alignment explanation


    Indices: 123--214  Score: 58
    Period size: 22  Copynumber: 4.2  Consensus size: 20

        113 TTTTGATAAT

                                  
        123 TAAACACCCTATGAAATTTTGA
          1 TAAACA-CCTATGAAA-TTTGA

               ** *          *   
        145 TAATTATCTATGAAATAATGA
          1 TAAACACCTATGAAAT-TTGA

                                  
        166 TAAACACCATATGAAACTTTGA
          1 TAAACACC-TATGAAA-TTTGA

               *   *     *        
        188 TAACCTAACTATGGAATTTGAA
          1 TAAAC-ACCTATGAAATTTG-A

                 
        210 TAAAC
          1 TAAAC

        215 CTTCCTATCA


Statistics
Matches: 53,  Mismatches: 12, Indels: 10
        0.71            0.16        0.13

Matches are distributed among these distances:
  20    1  0.02
  21   20  0.38
  22   29  0.55
  23    3  0.06

ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32


Consensus pattern (20 bp):   
TAAACACCTATGAAATTTGA

Found at i:2724 original size:3 final size:3

Alignment explanation


    Indices: 2699--2753  Score: 78
    Period size: 3  Copynumber: 18.7  Consensus size: 3

       2689 TTTTATTCAT

                  *                                                     
       2699 TTA TTT TTA TT- TT- TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA

                          
       2743 TTA TTA TTA TT
          1 TTA TTA TTA TT

       2754 TTCGACATGA


Statistics
Matches: 48,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
   2    4  0.08
   3   41  0.85
   4    3  0.06

ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73


Consensus pattern (3 bp):   
TTA

Found at i:2921 original size:76 final size:76

Alignment explanation


    Indices: 2795--2946  Score: 295
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       2785 ATTCTACCAT

                                                                *            
       2795 GTGACACTTCTTGTGGCAACACCCTATAGTACTTTTGCCTTTTGGCATATGTTGTGGCAATATCT
          1 GTGACACTTCTTGTGGCAACACCCTATAGTACTTTTGCCTTTTGGCATATGTCGTGGCAATATCT

                       
       2860 TATGTCCATAC
         66 TATGTCCATAC

                                                                             
       2871 GTGACACTTCTTGTGGCAACACCCTATAGTACTTTTGCCTTTTGGCATATGTCGTGGCAATATCT
          1 GTGACACTTCTTGTGGCAACACCCTATAGTACTTTTGCCTTTTGGCATATGTCGTGGCAATATCT

                       
       2936 TATGTCCATAC
         66 TATGTCCATAC

       2947 CTTCAGGGGC


Statistics
Matches: 75,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  76   75  1.00

ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38


Consensus pattern (76 bp):   
GTGACACTTCTTGTGGCAACACCCTATAGTACTTTTGCCTTTTGGCATATGTCGTGGCAATATCT
TATGTCCATAC

Found at i:3012 original size:43 final size:43

Alignment explanation


    Indices: 2951--3036  Score: 172
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       2941 CCATACCTTC

                                                       
       2951 AGGGGCTGTTTGGTTCGCATAATTGGGATATACCCATGGTCGT
          1 AGGGGCTGTTTGGTTCGCATAATTGGGATATACCCATGGTCGT

                                                       
       2994 AGGGGCTGTTTGGTTCGCATAATTGGGATATACCCATGGTCGT
          1 AGGGGCTGTTTGGTTCGCATAATTGGGATATACCCATGGTCGT

       3037 GGAAATAGAC


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   43  1.00

ACGTcount: A:0.19, C:0.16, G:0.33, T:0.33


Consensus pattern (43 bp):   
AGGGGCTGTTTGGTTCGCATAATTGGGATATACCCATGGTCGT

Found at i:3968 original size:14 final size:15

Alignment explanation


    Indices: 3949--3982  Score: 61
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       3939 TGAAGATGAT

                           
       3949 AAAAAAGTGGG-GAA
          1 AAAAAAGTGGGAGAA

                           
       3963 AAAAAAGTGGGAGAA
          1 AAAAAAGTGGGAGAA

                 
       3978 AAAAA
          1 AAAAA

       3983 CGACACATGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14   11  0.58
  15    8  0.42

ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06


Consensus pattern (15 bp):   
AAAAAAGTGGGAGAA

Found at i:5848 original size:13 final size:13

Alignment explanation


    Indices: 5830--5909  Score: 61
    Period size: 13  Copynumber: 6.1  Consensus size: 13

       5820 TAGCAATACG

                         
       5830 TACCTTATGGCAA
          1 TACCTTATGGCAA

                   *  *   
       5843 TACCTTTTTGACAA
          1 TACC-TTATGGCAA

                * * *    
       5857 TACCCTCTAGCAA
          1 TACCTTATGGCAA

                  * *   *
       5870 TACCTTCTTGCAC
          1 TACCTTATGGCAA

              *   *      
       5883 TAACTTGTGGCAA
          1 TACCTTATGGCAA

                         
       5896 TACCTTATGGCAA
          1 TACCTTATGGCAA

             
       5909 T
          1 T

       5910 TACCCTGCTG


Statistics
Matches: 51,  Mismatches: 15, Indels: 2
        0.75            0.22        0.03

Matches are distributed among these distances:
  13   40  0.78
  14   11  0.22

ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34


Consensus pattern (13 bp):   
TACCTTATGGCAA
Done.