Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013892.1 Corchorus olitorius cultivar O-4 contig13925, 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: 14698
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:3106 original size:65 final size:65

Alignment explanation


    Indices: 3031--3229  Score: 398
    Period size: 65  Copynumber: 3.1  Consensus size: 65

       3021 TCTATTTCTA

                                                                             
       3031 TTTTATTTAGTACCCTTTTTAGACATTTTATCTCTTAACCACATTTTTCTACAACAATACCAAGT
          1 TTTTATTTAGTACCCTTTTTAGACATTTTATCTCTTAACCACATTTTTCTACAACAATACCAAGT

                                                                             
       3096 TTTTATTTAGTACCCTTTTTAGACATTTTATCTCTTAACCACATTTTTCTACAACAATACCAAGT
          1 TTTTATTTAGTACCCTTTTTAGACATTTTATCTCTTAACCACATTTTTCTACAACAATACCAAGT

                                                                             
       3161 TTTTATTTAGTACCCTTTTTAGACATTTTATCTCTTAACCACATTTTTCTACAACAATACCAAGT
          1 TTTTATTTAGTACCCTTTTTAGACATTTTATCTCTTAACCACATTTTTCTACAACAATACCAAGT

                
       3226 TTTT
          1 TTTT

       3230 TCAAAATTTA


Statistics
Matches: 134,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  65  134  1.00

ACGTcount: A:0.29, C:0.21, G:0.05, T:0.46


Consensus pattern (65 bp):   
TTTTATTTAGTACCCTTTTTAGACATTTTATCTCTTAACCACATTTTTCTACAACAATACCAAGT

Found at i:3706 original size:2 final size:2

Alignment explanation


    Indices: 3685--3723  Score: 51
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       3675 TGTCTTTATG

                      *     *     *                                   
       3685 AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3724 AATTAACCGA


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41


Consensus pattern (2 bp):   
AT

Found at i:6636 original size:16 final size:17

Alignment explanation


    Indices: 6604--6637  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       6594 TTTTATTTTT

                 *           
       6604 TATTTGTTGATATATAA
          1 TATTTATTGATATATAA

                             
       6621 TATTTATTGA-ATATAA
          1 TATTTATTGATATATAA

             
       6637 T
          1 T

       6638 TTATACGTAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53


Consensus pattern (17 bp):   
TATTTATTGATATATAA

Found at i:6783 original size:14 final size:13

Alignment explanation


    Indices: 6747--6785  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 13

       6737 ATTTTATATT

                        * 
       6747 TATAATTATATTTA
          1 TATAATTA-ATTAA

                         
       6761 TATAATTAATTAA
          1 TATAATTAATTAA

                        
       6774 TATAATTTAATT
          1 TATAA-TTAATT

       6786 TTTAAAATAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  13    9  0.39
  14   14  0.61

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (13 bp):   
TATAATTAATTAA

Found at i:6829 original size:12 final size:12

Alignment explanation


    Indices: 6809--6845  Score: 56
    Period size: 12  Copynumber: 3.1  Consensus size: 12

       6799 TTAAAAAATA

                        
       6809 TTAGACGGGCTT
          1 TTAGACGGGCTT

              *         
       6821 TTGGACGGGCTT
          1 TTAGACGGGCTT

               *        
       6833 TTAAACGGGCTT
          1 TTAGACGGGCTT

             
       6845 T
          1 T

       6846 GGTCTAAGTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35


Consensus pattern (12 bp):   
TTAGACGGGCTT

Found at i:12598 original size:51 final size:51

Alignment explanation


    Indices: 12520--12625  Score: 194
    Period size: 51  Copynumber: 2.1  Consensus size: 51

      12510 GGTGAAAGGA

                                                               
      12520 AAGGAGCGGGTTCCTAGGCAGAATTTTAGTCGAAAGGATGATCATGTGGAG
          1 AAGGAGCGGGTTCCTAGGCAGAATTTTAGTCGAAAGGATGATCATGTGGAG

                           *      *                            
      12571 AAGGAGCGGGTTCCTCGGCAGATTTTTAGTCGAAAGGATGATCATGTGGAG
          1 AAGGAGCGGGTTCCTAGGCAGAATTTTAGTCGAAAGGATGATCATGTGGAG

                
      12622 AAGG
          1 AAGG

      12626 TTTCGGGATC


Statistics
Matches: 53,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  51   53  1.00

ACGTcount: A:0.28, C:0.12, G:0.36, T:0.24


Consensus pattern (51 bp):   
AAGGAGCGGGTTCCTAGGCAGAATTTTAGTCGAAAGGATGATCATGTGGAG
Done.