Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010798.1 Corchorus olitorius cultivar O-4 contig10830, 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: 11599
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30


Found at i:1637 original size:20 final size:20

Alignment explanation


    Indices: 1609--1669  Score: 113
    Period size: 20  Copynumber: 3.0  Consensus size: 20

       1599 TCTCTCTACC

                                
       1609 TAAGGGTTCAGACAATTTAG
          1 TAAGGGTTCAGACAATTTAG

                *               
       1629 TAAGAGTTCAGACAATTTAG
          1 TAAGGGTTCAGACAATTTAG

                                
       1649 TAAGGGTTCAGACAATTTAG
          1 TAAGGGTTCAGACAATTTAG

             
       1669 T
          1 T

       1670 TGGTTGATGG


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   39  1.00

ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31


Consensus pattern (20 bp):   
TAAGGGTTCAGACAATTTAG

Found at i:1827 original size:26 final size:26

Alignment explanation


    Indices: 1791--1842  Score: 95
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1781 CCCAATCCTC

                                      
       1791 ATTAAATGATCGAGAGGTATCAGAAT
          1 ATTAAATGATCGAGAGGTATCAGAAT

                       *              
       1817 ATTAAATGATCTAGAGGTATCAGAAT
          1 ATTAAATGATCGAGAGGTATCAGAAT

       1843 CTTCGGTAGC


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29


Consensus pattern (26 bp):   
ATTAAATGATCGAGAGGTATCAGAAT

Found at i:2496 original size:20 final size:20

Alignment explanation


    Indices: 2471--2511  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       2461 GCAATCATGA

                                
       2471 AACTGGGAAACTAGCCTTTT
          1 AACTGGGAAACTAGCCTTTT

                                
       2491 AACTGGGAAACTAGCCTTTT
          1 AACTGGGAAACTAGCCTTTT

             
       2511 A
          1 A

       2512 CTCTACCTTC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29


Consensus pattern (20 bp):   
AACTGGGAAACTAGCCTTTT

Found at i:2706 original size:31 final size:31

Alignment explanation


    Indices: 2668--2729  Score: 124
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2658 TTTCGCCTAG

                                           
       2668 TAAGTGCTTATGAAAGCCTCTTCCTTTTGGT
          1 TAAGTGCTTATGAAAGCCTCTTCCTTTTGGT

                                           
       2699 TAAGTGCTTATGAAAGCCTCTTCCTTTTGGT
          1 TAAGTGCTTATGAAAGCCTCTTCCTTTTGGT

       2730 CCGGTAATGG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42


Consensus pattern (31 bp):   
TAAGTGCTTATGAAAGCCTCTTCCTTTTGGT

Found at i:8627 original size:21 final size:21

Alignment explanation


    Indices: 8601--8642  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8591 TAAGCCGAGC

                                 
       8601 CAAAGCAAAGTACTTCAGTTT
          1 CAAAGCAAAGTACTTCAGTTT

                                 
       8622 CAAAGCAAAGTACTTCAGTTT
          1 CAAAGCAAAGTACTTCAGTTT

       8643 TAGGATTTCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29


Consensus pattern (21 bp):   
CAAAGCAAAGTACTTCAGTTT

Found at i:9538 original size:16 final size:16

Alignment explanation


    Indices: 9513--9550  Score: 67
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       9503 CTGGCTTAGT

                 *          
       9513 AGTTGTAGGGCAGGAC
          1 AGTTGCAGGGCAGGAC

                            
       9529 AGTTGCAGGGCAGGAC
          1 AGTTGCAGGGCAGGAC

                  
       9545 AGTTGC
          1 AGTTGC

       9551 CCCTAATCTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.24, C:0.16, G:0.42, T:0.18


Consensus pattern (16 bp):   
AGTTGCAGGGCAGGAC
Done.