Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021551.1 Corchorus olitorius cultivar O-4 contig21584, 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: 2370
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35


Found at i:1114 original size:50 final size:50

Alignment explanation


    Indices: 1040--1708  Score: 1091
    Period size: 50  Copynumber: 13.5  Consensus size: 50

       1030 CCGAATGCTT

                                                             *
       1040 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                                                              
       1090 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                                                              
       1140 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

             *                                                
       1190 ATGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                                  *                        *  
       1240 AGGCTTTTCCACAAGCCAAACTTGTTT-C---C-AGTCAATTATCAATAC
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

             *                  *                             
       1285 AAGCTTTTCCACAAGCCAAATTCGTTTCCATACGAGTCAATTATCAACAC
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                     *              *                          
       1335 AGGCTTTTCTACAAGCC-AACTTCATTTCCATACGAGTCAATTATCAACAC
          1 AGGCTTTTCCACAAGCCAAAC-TCGTTTCCATACGAGTCAATTATCAACAC

                                                               
       1385 AGG-TTATTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC
          1 AGGCTT-TTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                                                              
       1435 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                                           *               *  
       1485 AGGCTTTTCCACAAGCCAAACTCGTTTCCATTCGAGTCAATTATCAATAC
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                     *                                     ***
       1535 AGGCTTTTCAACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAATGT
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

             *             *     *                           *
       1585 AAGCTTTTCCACAAGTCAAACCCGTTTCCATACGAGTCAATTATCAACAT
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                                              *              *
       1635 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAATTATCAACAT
          1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

                                    
       1685 AGGCTTTTCCACAAGCCAAACTCG
          1 AGGCTTTTCCACAAGCCAAACTCG

       1709 AGGATCTCTT


Statistics
Matches: 579,  Mismatches: 31, Indels: 18
        0.92            0.05        0.03

Matches are distributed among these distances:
  45   39  0.07
  46    2  0.00
  49    6  0.01
  50  527  0.91
  51    5  0.01

ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28


Consensus pattern (50 bp):   
AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAC

Found at i:2042 original size:27 final size:26

Alignment explanation


    Indices: 2005--2056  Score: 95
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       1995 TCATCTTTTT

                                       
       2005 TACATTCAGGGGCATTTTGGTCATTTG
          1 TACATTCAGGGGCATTTT-GTCATTTG

                                     
       2032 TACATTCAGGGGCATTTTGTCATTT
          1 TACATTCAGGGGCATTTTGTCATTT

       2057 TAAGTTCACT


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

Matches are distributed among these distances:
  26    7  0.28
  27   18  0.72

ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42


Consensus pattern (26 bp):   
TACATTCAGGGGCATTTTGTCATTTG
Done.