Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015777.1 Corchorus olitorius cultivar O-4 contig15810, 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: 7482
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33


Found at i:1662 original size:52 final size:52

Alignment explanation


    Indices: 1603--1707  Score: 192
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       1593 AACAAGAATT

                                        *                       
       1603 GCAGGACAACATCGGCCCAGAACTTGTTTAACTTCGGGACAGAAGTTGTTGC
          1 GCAGGACAACATCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC

                      *                                         
       1655 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
          1 GCAGGACAACATCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC

             
       1707 G
          1 G

       1708 GAAAGAAAAA


Statistics
Matches: 51,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  52   51  1.00

ACGTcount: A:0.26, C:0.24, G:0.28, T:0.23


Consensus pattern (52 bp):   
GCAGGACAACATCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC

Found at i:1697 original size:22 final size:22

Alignment explanation


    Indices: 1661--1704  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1651 TTGCGCAGGA

                      *           
       1661 CAACTTCGGCCCAGAACTTGTT
          1 CAACTTCGGCACAGAACTTGTT

                     *      *     
       1683 CAACTTCGGGACAGAAGTTGTT
          1 CAACTTCGGCACAGAACTTGTT

       1705 GCGGAAAGAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27


Consensus pattern (22 bp):   
CAACTTCGGCACAGAACTTGTT

Found at i:3966 original size:33 final size:31

Alignment explanation


    Indices: 3860--4005  Score: 123
    Period size: 33  Copynumber: 4.5  Consensus size: 31

       3850 GAGTAATTCT

                         *         *         
       3860 AAATCTGTTTTAGATGTTGTTTGCGAT-AATAC
          1 AAATCTGTTTT-GGTGTTGTTTGTGATGAA-AC

                *  **                     *  
       3892 TAAACCTAATTTGAGTGTTGTTTGTGATGACAC
          1 -AAATCTGTTTTG-GTGTTGTTTGTGATGAAAC

                                             
       3925 TAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
          1 -AAATCTGTTTT-GGTGTTGTTTGTGATGAAAC

                             * **             
       3958 AAATTCTGTTTTGGATGCTAATTGTGATGTAAAC
          1 AAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAAC

                          
       3992 AAATCTGTTTTGGT
          1 AAATCTGTTTTGGT

       4006 TGATCATAGC


Statistics
Matches: 94,  Mismatches: 13, Indels: 13
        0.78            0.11        0.11

Matches are distributed among these distances:
  32    7  0.07
  33   78  0.83
  34    9  0.10

ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43


Consensus pattern (31 bp):   
AAATCTGTTTTGGTGTTGTTTGTGATGAAAC

Found at i:5835 original size:21 final size:21

Alignment explanation


    Indices: 5809--5921  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       5799 TGCTAGAAGT

                                 
       5809 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
       5830 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
       5851 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
       5872 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
       5893 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
       5914 TCATTGGA
          1 TCATTGGA

       5922 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   84  0.99

ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Done.