Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008118.1 Corchorus capsularis cultivar CVL-1 contig08139, 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: 10613
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:996 original size:31 final size:32

Alignment explanation


    Indices: 958--1036  Score: 126
    Period size: 31  Copynumber: 2.5  Consensus size: 32

        948 TTACAAAACA

                             *              
        958 AGCAATTAAGGATATAACA-TTTTCAATTTCG
          1 AGCAATTAAGGATATAAAAGTTTTCAATTTCG

                                     *      
        989 AGCAATTAAGGATA-AAAAGTTTTCGATTTCG
          1 AGCAATTAAGGATATAAAAGTTTTCAATTTCG

                             
       1020 AGCAATTAAGGATATAA
          1 AGCAATTAAGGATATAA

       1037 TCAGTTAGGG


Statistics
Matches: 44,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  30    3  0.07
  31   39  0.89
  32    2  0.05

ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32


Consensus pattern (32 bp):   
AGCAATTAAGGATATAAAAGTTTTCAATTTCG

Found at i:1221 original size:29 final size:31

Alignment explanation


    Indices: 1155--1221  Score: 102
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       1145 TCTAACGGAC

                      *                    
       1155 TATATCCTTATTTGCTCGATTTTCGTAACGT
          1 TATATCCTTAATTGCTCGATTTTCGTAACGT

                            *              
       1186 TATATCCTTAATTGCTTG-TTTT-GTAACGT
          1 TATATCCTTAATTGCTCGATTTTCGTAACGT

                   
       1215 TATATCC
          1 TATATCC

       1222 CAAATTGCAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  29   14  0.41
  30    4  0.12
  31   16  0.47

ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49


Consensus pattern (31 bp):   
TATATCCTTAATTGCTCGATTTTCGTAACGT

Found at i:3774 original size:16 final size:16

Alignment explanation


    Indices: 3753--3858  Score: 88
    Period size: 16  Copynumber: 6.6  Consensus size: 16

       3743 GGAGAGTGTG

                             
       3753 GGTGAGTATCT-CACCA
          1 GGTGAGTAT-TACACCA

                            
       3769 GGTGAGTATTACACCA
          1 GGTGAGTATTACACCA

                      **  **
       3785 GGTGAGTATTGTACTG
          1 GGTGAGTATTACACCA

                      **  **
       3801 GGTGAGTATTGTACTG
          1 GGTGAGTATTACACCA

                      *     
       3817 GGTGAGTATTGCACCA
          1 GGTGAGTATTACACCA

                      **    
       3833 GGTGAGTATTGTACCA
          1 GGTGAGTATTACACCA

             *        
       3849 GATGAGTATT
          1 GGTGAGTATT

       3859 TGTATTGGGT


Statistics
Matches: 80,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  15    1  0.01
  16   79  0.99

ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31


Consensus pattern (16 bp):   
GGTGAGTATTACACCA

Found at i:3805 original size:32 final size:32

Alignment explanation


    Indices: 3769--3873  Score: 111
    Period size: 32  Copynumber: 3.2  Consensus size: 32

       3759 TATCTCACCA

                      **                    
       3769 GGTGAGTATTACACCAGGTGAGTATTGTACTG
          1 GGTGAGTATTGTACCAGGTGAGTATTGTACTG

                          **           *  **
       3801 GGTGAGTATTGTACTGGGTGAGTATTGCACCA
          1 GGTGAGTATTGTACCAGGTGAGTATTGTACTG

                             *            *  
       3833 GGTGAGTATTGTACCAGATGAGTATTTGTATTG
          1 GGTGAGTATTGTACCAGGTGAGTA-TTGTACTG

               *    
       3866 GGTAAGTA
          1 GGTGAGTA

       3874 GGGTAGGAAC


Statistics
Matches: 57,  Mismatches: 15, Indels: 1
        0.78            0.21        0.01

Matches are distributed among these distances:
  32   46  0.81
  33   11  0.19

ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33


Consensus pattern (32 bp):   
GGTGAGTATTGTACCAGGTGAGTATTGTACTG

Found at i:3822 original size:48 final size:49

Alignment explanation


    Indices: 3769--3873  Score: 149
    Period size: 48  Copynumber: 2.2  Consensus size: 49

       3759 TATCTCACCA

                                          ** *               
       3769 GGTGAGTATTACACCAGGTGAGTATTGTACTGGGTGAGTA-TTGTACTG
          1 GGTGAGTATTACACCAGGTGAGTATTGTACCAGATGAGTATTTGTACTG

                      *                                   *  
       3817 GGTGAGTATTGCACCAGGTGAGTATTGTACCAGATGAGTATTTGTATTG
          1 GGTGAGTATTACACCAGGTGAGTATTGTACCAGATGAGTATTTGTACTG

               *    
       3866 GGTAAGTA
          1 GGTGAGTA

       3874 GGGTAGGAAC


Statistics
Matches: 50,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  48   36  0.72
  49   14  0.28

ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33


Consensus pattern (49 bp):   
GGTGAGTATTACACCAGGTGAGTATTGTACCAGATGAGTATTTGTACTG

Found at i:7432 original size:17 final size:19

Alignment explanation


    Indices: 7410--7452  Score: 54
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       7400 TGGCCATCTC

                               
       7410 AAGAAAGAC-T-GTCCGAA
          1 AAGAAAGACTTGGTCCGAA

                   *      *    
       7427 AAGAAAGGCTTGGTTCGAA
          1 AAGAAAGACTTGGTCCGAA

                   
       7446 AAGAAAG
          1 AAGAAAG

       7453 GTACATATTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  17    8  0.36
  18    1  0.05
  19   13  0.59

ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14


Consensus pattern (19 bp):   
AAGAAAGACTTGGTCCGAA
Done.