Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002035.1 Corchorus olitorius cultivar O-4 contig02035, 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: 1693
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36


Found at i:538 original size:48 final size:48

Alignment explanation


    Indices: 483--608  Score: 252
    Period size: 48  Copynumber: 2.6  Consensus size: 48

        473 AACTCTTGTT

                                                            
        483 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
          1 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG

                                                            
        531 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
          1 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG

                                          
        579 TGATCAACCCTATCTTTTACTTTTCATCAC
          1 TGATCAACCCTATCTTTTACTTTTCATCAC

        609 TTGTCATTTA


Statistics
Matches: 78,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   78  1.00

ACGTcount: A:0.21, C:0.26, G:0.07, T:0.45


Consensus pattern (48 bp):   
TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG

Found at i:569 original size:21 final size:21

Alignment explanation


    Indices: 497--640  Score: 78
    Period size: 22  Copynumber: 6.3  Consensus size: 21

        487 CAACCCTATC

                                 
        497 TTTTACTTTTCATCACCCTTG
          1 TTTTACTTTTCATCACCCTTG

                        * *           *
        518 TTTTTACAAGTTGTGATCAACCCTATC
          1 -TTTTAC---TTTTCATC-ACCCT-TG

                                 
        545 TTTTACTTTTCATCACCCTTG
          1 TTTTACTTTTCATCACCCTTG

                        * *           *
        566 TTTTTACAAGTTGTGATCAACCCTATC
          1 -TTTTAC---TTTTCATC-ACCCT-TG

                                 
        593 TTTTACTTTTCATCA--CTTG
          1 TTTTACTTTTCATCACCCTTG

                                   
        612 TCATTTACTTTTCATCA-CCTTG
          1 T--TTTACTTTTCATCACCCTTG

                   
        634 TTGTTAC
          1 TT-TTAC

        641 AAGGTGTAAT


Statistics
Matches: 95,  Mismatches: 12, Indels: 31
        0.69            0.09        0.22

Matches are distributed among these distances:
  19    2  0.02
  20    3  0.03
  21   19  0.20
  22   23  0.24
  23   12  0.13
  25   12  0.13
  26   22  0.23
  27    2  0.02

ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49


Consensus pattern (21 bp):   
TTTTACTTTTCATCACCCTTG

Found at i:1627 original size:52 final size:54

Alignment explanation


    Indices: 1537--1643  Score: 182
    Period size: 52  Copynumber: 2.0  Consensus size: 54

       1527 CTAATCTAAT

                                                                   
       1537 TTATTAAATTACTCCTATATATACAGTTAGATTACCTGTTATA-TTTTTTTCTAC
          1 TTATTAAATTACTCC-ATATATACAGTTAGATTACCTGTTATATTTTTTTTCTAC

                                   *                              
       1591 TTATTAAATTACTCC-TATATACGGTTAGATTACCTGTTATATTTTTTTTCTAC
          1 TTATTAAATTACTCCATATATACAGTTAGATTACCTGTTATATTTTTTTTCTAC

       1644 AAATTAGATT


Statistics
Matches: 51,  Mismatches: 1, Indels: 3
        0.93            0.02        0.05

Matches are distributed among these distances:
  52   25  0.49
  53   11  0.22
  54   15  0.29

ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50


Consensus pattern (54 bp):   
TTATTAAATTACTCCATATATACAGTTAGATTACCTGTTATATTTTTTTTCTAC

Done.