Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012932.1 Corchorus olitorius cultivar O-4 contig12965, 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: 20399
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:4454 original size:41 final size:41

Alignment explanation


    Indices: 4351--4681  Score: 359
    Period size: 41  Copynumber: 7.9  Consensus size: 41

       4341 CCATAAGGAG

                   *                                   
       4351 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTG-TAAT
          1 AAATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGAT-AT

                                          *            
       4393 AGAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATAT
          1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT

                   *                                  
       4436 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
          1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT

                *                         *            
       4477 AGAGTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATAT
          1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT

             *     *                                  
       4520 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
          1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT

                 *      *                 *      *     
       4561 AAAGGCGCCCCTATG-T-TATATGTGTTTGGGGACTTGGATAT
          1 AAA--TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT

             **    *                                   
       4602 ATGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGA-AT
          1 AAATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTT-GATAT

                                          *       
       4644 AGAATTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
          1 A-AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTT

       4682 TTGGTTATTG


Statistics
Matches: 244,  Mismatches: 28, Indels: 33
        0.80            0.09        0.11

Matches are distributed among these distances:
  39    7  0.03
  40    3  0.01
  41  110  0.45
  42   10  0.04
  43   55  0.23
  44   59  0.24

ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42


Consensus pattern (41 bp):   
AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT

Found at i:4505 original size:84 final size:85

Alignment explanation


    Indices: 4351--4681  Score: 535
    Period size: 84  Copynumber: 3.9  Consensus size: 85

       4341 CCATAAGGAG

                                                          *                  
       4351 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT

                                
       4416 GTGTTTGGGGACTTTGATAT
         66 GTGTTTGGGGACTTTGATAT

                                                                             
       4436 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGTTGCCCCTGTGTTATATAT
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT

                                
       4500 GTGTTTGGGGACTTTGATAT
         66 GTGTTTGGGGACTTTGATAT

             *                                         *  **      *          
       4520 AGATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAAAGGCGCCCCTATG-T-TATAT
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT

                          *     
       4582 GTGTTTGGGGACTTGGATAT
         66 GTGTTTGGGGACTTTGATAT

             **                                   *      *                   
       4602 ATGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAATTGCCCCTGTGTTATATAT
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT

                           
       4667 GTGTTTGGGGACTTT
         66 GTGTTTGGGGACTTT

       4682 TTGGTTATTG


Statistics
Matches: 227,  Mismatches: 16, Indels: 6
        0.91            0.06        0.02

Matches are distributed among these distances:
  82   55  0.24
  83   18  0.08
  84  102  0.45
  85   52  0.23

ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42


Consensus pattern (85 bp):   
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
GTGTTTGGGGACTTTGATAT

Found at i:5459 original size:27 final size:27

Alignment explanation


    Indices: 5416--5487  Score: 74
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       5406 AAGTGGACTT

                       **             *
       5416 AAAATGACCAACGTGCCCCTGAATATG
          1 AAAATGACCAAAATGCCCCTGAATATA

            *                   * * *  
       5443 CAAATGACCAAAATG-CCCTTAGTGTA
          1 AAAATGACCAAAATGCCCCTGAATATA

                               
       5469 AAAATGACCAAAATGCCCC
          1 AAAATGACCAAAATGCCCC

       5488 CCCTAGGTGA


Statistics
Matches: 36,  Mismatches: 8, Indels: 2
        0.78            0.17        0.04

Matches are distributed among these distances:
  26   21  0.58
  27   15  0.42

ACGTcount: A:0.40, C:0.26, G:0.15, T:0.18


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGAATATA

Found at i:20290 original size:21 final size:24

Alignment explanation


    Indices: 20265--20315  Score: 63
    Period size: 23  Copynumber: 2.2  Consensus size: 24

      20255 TATCTTAGAT

                                    
      20265 ATAAT-ATATATTATT-A-AATAA
          1 ATAATAATATATTATTAATAATAA

                          *          
      20286 ATAATTAATATATTTTTAATAATAA
          1 ATAA-TAATATATTATTAATAATAA

                 
      20311 ATAAT
          1 ATAAT

      20316 GAGTTCAAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  21    4  0.16
  22    1  0.04
  23    9  0.36
  24    2  0.08
  25    9  0.36

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (24 bp):   
ATAATAATATATTATTAATAATAA
Done.