Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024349.1 Corchorus olitorius cultivar O-4 contig24382, 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: 8634
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:2531 original size:17 final size:18

Alignment explanation


    Indices: 2491--2568  Score: 77
    Period size: 19  Copynumber: 4.2  Consensus size: 18

       2481 TGGGTATGAA

                     *  *       
       2491 TTTTGGTATGAACTGTGCTT
          1 TTTTGGTATCAATTGTG--T

                      *       
       2511 TTTTGGTATCTATTGT-T
          1 TTTTGGTATCAATTGTGT

                   * *        
       2528 TTTTGGTGTGAATTGTGT
          1 TTTTGGTATCAATTGTGT

                               
       2546 TTCTTGGTATCAATTGTGT
          1 TT-TTGGTATCAATTGTGT

                
       2565 TTTT
          1 TTTT

       2569 TTCGGGTACC


Statistics
Matches: 48,  Mismatches: 8, Indels: 6
        0.77            0.13        0.10

Matches are distributed among these distances:
  17   14  0.29
  18    5  0.10
  19   16  0.33
  20   13  0.27

ACGTcount: A:0.13, C:0.06, G:0.23, T:0.58


Consensus pattern (18 bp):   
TTTTGGTATCAATTGTGT

Found at i:2555 original size:36 final size:38

Alignment explanation


    Indices: 2491--2568  Score: 106
    Period size: 37  Copynumber: 2.1  Consensus size: 38

       2481 TGGGTATGAA

                                 *        *       
       2491 TTTTGGTATGAACTGTGCTTTTTTGGTATCTATTGT-T
          1 TTTTGGTATGAACTGTGCTTTCTTGGTATCAATTGTGT

                   *    *                         
       2528 TTTTGGTGTGAATTGTG-TTTCTTGGTATCAATTGTGT
          1 TTTTGGTATGAACTGTGCTTTCTTGGTATCAATTGTGT

                
       2565 TTTT
          1 TTTT

       2569 TTCGGGTACC


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  36   16  0.44
  37   20  0.56

ACGTcount: A:0.13, C:0.06, G:0.23, T:0.58


Consensus pattern (38 bp):   
TTTTGGTATGAACTGTGCTTTCTTGGTATCAATTGTGT

Found at i:6989 original size:11 final size:10

Alignment explanation


    Indices: 6958--7005  Score: 55
    Period size: 11  Copynumber: 4.8  Consensus size: 10

       6948 GAAGTTCGTG

                       
       6958 ATTGAAGATTA
          1 ATTGAAGA-TA

                      
       6969 ATTGAAGATA
          1 ATTGAAGATA

                       
       6979 ATTTGAAGAT-
          1 A-TTGAAGATA

                     *
       6989 A-TGAAGATC
          1 ATTGAAGATA

                    
       6998 ATTGAAGA
          1 ATTGAAGA

       7006 AATATTTCAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 7
        0.83            0.00        0.17

Matches are distributed among these distances:
   8    7  0.21
   9    1  0.03
  10   10  0.29
  11   16  0.47

ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31


Consensus pattern (10 bp):   
ATTGAAGATA
Done.