Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023157.1 Corchorus olitorius cultivar O-4 contig23190, 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: 4723
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28


Found at i:3155 original size:91 final size:89

Alignment explanation


    Indices: 2986--3296  Score: 288
    Period size: 91  Copynumber: 3.4  Consensus size: 89

       2976 ACGGTTCAAC

                       *                *       *                   *  *     
       2986 GCAATATTTCTCCAAAGATTGGAGTTCGATGAGCTCGGTGCAGCATGTTTTC-GATTAGGTC-GA
          1 GCAATATTTCTTC-AAGATTGGA-TTCGGTGAGCTCAGTGCAGCATGTTTTCAGA-CAGTTCAG-

                               *      *  
       3049 GGTGATTCGGTGAATCAACCTGGTACAGT
         62 GGTGATTCGGTGAATCAA-ATGGTACGGT

                      *                                 *           *        
       3078 GCAATATTTCGTCAAGATTGGAATTCGGTGAGCTCAGTGCAGCAGGTTTTCAGACAATTCAGGGT
          1 GCAATATTTCTTCAAGATTGG-ATTCGGTGAGCTCAGTGCAGCATGTTTTCAGACAGTTCAGGGT

                           * *   *   
       3143 GATTCGGTGAATCAAGTTG-ATGGT
         65 GATTCGGTGAATCAAATGGTACGGT

               *                         **              *      *      *   * 
       3167 GCATTACTTT-TTCAAGATTGGATTCGGTTTGCTCAGTGCAGCATATTTTCATACAGTTAAGGAT
          1 GCAATA-TTTCTTCAAGATTGGATTCGGTGAGCTCAGTGCAGCATGTTTTCAGACAGTTCAGGGT

                           *   * *    
       3231 GATTCGGTGAATCAGGATGATGCGGT
         65 GATTCGGTGAATCA-AATGGTACGGT

               *                     *        *     
       3257 GCATTATTTCTTCAAGATTGGATTCAGTGAGCTCGGTGCA
          1 GCAATATTTCTTCAAGATTGGATTCGGTGAGCTCAGTGCA

       3297 ACACATTTTC


Statistics
Matches: 180,  Mismatches: 32, Indels: 16
        0.79            0.14        0.07

Matches are distributed among these distances:
  88   49  0.27
  89   22  0.12
  90   40  0.22
  91   54  0.30
  92   15  0.08

ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32


Consensus pattern (89 bp):   
GCAATATTTCTTCAAGATTGGATTCGGTGAGCTCAGTGCAGCATGTTTTCAGACAGTTCAGGGTG
ATTCGGTGAATCAAATGGTACGGT

Found at i:3216 original size:88 final size:89

Alignment explanation


    Indices: 3051--3307  Score: 284
    Period size: 88  Copynumber: 2.9  Consensus size: 89

       3041 TAGGTCGAGG

                            **  *   *     *      *                           
       3051 TGATTCGGTGAATCAACCTGGTACAGTGCAATATTTCGTCAAGATTGGAATTCGGTGAGCTCAGT
          1 TGATTCGGTGAATCAAGATGAT-CGGTGCATTATTTCTTCAAGATTGG-ATTCGGTGAGCTCAGT

                   *             *   *
       3116 GCAGCAGGTTTTCAGACAATTCAGGG
         64 GCAGCAGATTTTCAGACAATTAAGGA

                             *                                     **        
       3142 TGATTCGGTGAATCAAGTTGAT-GGTGCATTACTTT-TTCAAGATTGGATTCGGTTTGCTCAGTG
          1 TGATTCGGTGAATCAAGATGATCGGTGCATTA-TTTCTTCAAGATTGGATTCGGTGAGCTCAGTG

                 *       *   *       
       3205 CAGCATATTTTCATACAGTTAAGGA
         65 CAGCAGATTTTCAGACAATTAAGGA

                           *                                    *        *   
       3230 TGATTCGGTGAATCAGGATGATGCGGTGCATTATTTCTTCAAGATTGGATTCAGTGAGCTCGGTG
          1 TGATTCGGTGAATCAAGATGAT-CGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCAGTG

              *  *       
       3295 CAACACATTTTCA
         65 CAGCAGATTTTCA

       3308 AACAGTGCCA


Statistics
Matches: 140,  Mismatches: 22, Indels: 9
        0.82            0.13        0.05

Matches are distributed among these distances:
  88   54  0.39
  89   20  0.14
  90   47  0.34
  91   19  0.14

ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33


Consensus pattern (89 bp):   
TGATTCGGTGAATCAAGATGATCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCAGTGC
AGCAGATTTTCAGACAATTAAGGA

Found at i:3324 original size:90 final size:88

Alignment explanation


    Indices: 3089--3335  Score: 239
    Period size: 90  Copynumber: 2.8  Consensus size: 88

       3079 CAATATTTCG

                           *              *  **      *    *      *           
       3089 TCAAGATTGGAATTCGGTGAGCTCAGTGCAGCAGGTTTTCAGACAATTC-AGGGTGATTCGGTGA
          1 TCAAGATTGG-ATTCAGTGAGCTCAGTGCAACACATTTTCAAAC-AGTCAAGGATGATTCGGTGA

                * *                  
       3153 ATCAAGTTGATGGTGCATTACTTTT
         64 ATCAGGATGATGGTGCATTACTTTT

                          *  **          *  *       *     *                  
       3178 TCAAGATTGGATTCGGTTTGCTCAGTGCAGCATATTTTCATACAGTTAAGGATGATTCGGTGAAT
          1 TCAAGATTGGATTCAGTGAGCTCAGTGCAACACATTTTCAAACAGTCAAGGATGATTCGGTGAAT

                                      
       3243 CAGGATGATGCGGTGCATTA-TTTCT
         66 CAGGATGAT--GGTGCATTACTTT-T

                                   *                        *  **            
       3268 TCAAGATTGGATTCAGTGAGCTCGGTGCAACACATTTTCAAACAGTGCCA-TTTGATTCGGTGAA
          1 TCAAGATTGGATTCAGTGAGCTCAGTGCAACACATTTTCAAACAGT-CAAGGATGATTCGGTGAA

                
       3332 TCAG
         65 TCAG

       3336 CTAATTAGGT


Statistics
Matches: 132,  Mismatches: 21, Indels: 9
        0.81            0.13        0.06

Matches are distributed among these distances:
  87    2  0.02
  88   51  0.39
  89   13  0.10
  90   65  0.49
  91    1  0.01

ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33


Consensus pattern (88 bp):   
TCAAGATTGGATTCAGTGAGCTCAGTGCAACACATTTTCAAACAGTCAAGGATGATTCGGTGAAT
CAGGATGATGGTGCATTACTTTT

Found at i:3783 original size:15 final size:16

Alignment explanation


    Indices: 3752--3782  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       3742 ATGTTTTCAT

                            
       3752 GAATACAAAAAAAAAA
          1 GAATACAAAAAAAAAA

                           
       3768 GAATACAAAAAAAAA
          1 GAATACAAAAAAAAA

       3783 GTACTTTGGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06


Consensus pattern (16 bp):   
GAATACAAAAAAAAAA
Done.