Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013798.1 Corchorus capsularis cultivar CVL-1 contig13819, 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: 10117
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:347 original size:200 final size:202

Alignment explanation


    Indices: 1--447  Score: 731
    Period size: 200  Copynumber: 2.2  Consensus size: 202

                                                       *                     
          1 ATGGAGTCCAAAATTTACACTGAACAGTGTTATTGTATAATAATCCTATAAGAAAATTTATATAA
          1 ATGGAGTCCAAAATTTACACTG-ACAGTG-TATTGTATAATAACCCTATAAGAAAATTTATATAA

                                      *                                      
         66 TACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGATTTAACTTTAAGAGTTGACATGTGTA
         64 TACACCGTCAGTGGAGTTTAGCAGACCGCACGTGCGGGATTTAACTTTAAGAGTTGACATGTGTA

                                                                     *       
        131 CCCTTAGAGAATATGTATTAATATTAAATA-T-TTAATTATGAAATAGGGTATGTGTTAACTTCT
        129 CCCTTAGAGAATATGTATTAATATTAAATATTATTAATTATGAAAT-GGGTATGTGTCAACTTCT

                      
        194 TAACCCGCTT
        193 TAACCCGCTT

                                                                             
        204 ATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAACCCTATAAGAAAATTT-TATAATA
          1 ATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAACCCTATAAGAAAATTTATATAATA

                                  *                           *              
        268 CACCGTCAGTGGAGTTTAGCAGGCCGCACGTGCGAGG-TTTAACTTTAAGGGTTGACATGTGTAC
         66 CACCGTCAGTGGAGTTTAGCAGACCGCACGTGCG-GGATTTAACTTTAAGAGTTGACATGTGTAC

                  *                                                          
        332 CCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGTATGTGTCAACTTCT
        130 CCTTAGAGAATATGTATTAATATTAAATA-TT-ATTAATTATGAAATGGGTATGTGTCAACTTCT

                 *    
        397 TAACCTGCTT
        193 TAACCCGCTT

                               *     *               
        407 ATGGAGTCCAAAATTTACATTGACATTGTATTGTATAATAA
          1 ATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAA

        448 TCCTTATTAT


Statistics
Matches: 230,  Mismatches: 9, Indels: 10
        0.92            0.04        0.04

Matches are distributed among these distances:
 200   93  0.40
 201   30  0.13
 202    7  0.03
 203   87  0.38
 204   13  0.06

ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34


Consensus pattern (202 bp):   
ATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAACCCTATAAGAAAATTTATATAATA
CACCGTCAGTGGAGTTTAGCAGACCGCACGTGCGGGATTTAACTTTAAGAGTTGACATGTGTACC
CTTAGAGAATATGTATTAATATTAAATATTATTAATTATGAAATGGGTATGTGTCAACTTCTTAA
CCCGCTT

Found at i:2833 original size:16 final size:18

Alignment explanation


    Indices: 2804--2837  Score: 54
    Period size: 16  Copynumber: 2.0  Consensus size: 18

       2794 AGTATAGTAT

                              
       2804 TATTATCTTAATTACTTA
          1 TATTATCTTAATTACTTA

                              
       2822 TATTA-CTT-ATTACTTA
          1 TATTATCTTAATTACTTA

       2838 GACTTAGTGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    8  0.50
  17    3  0.19
  18    5  0.31

ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56


Consensus pattern (18 bp):   
TATTATCTTAATTACTTA

Found at i:5989 original size:28 final size:28

Alignment explanation


    Indices: 5929--5989  Score: 70
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       5919 TTCGTGTGTT

                    *     *       *    *
       5929 AAAATTACCGTTTTGCCCCTACTAGGCT
          1 AAAATTACAGTTTTACCCCTACGAGGCC

                                        
       5957 AAAATTACAGTTTTACCCCTA-GAGGCC
          1 AAAATTACAGTTTTACCCCTACGAGGCC

                  
       5984 AGAAAT
          1 A-AAAT

       5990 GATTAAATGA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  27    5  0.18
  28   23  0.82

ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28


Consensus pattern (28 bp):   
AAAATTACAGTTTTACCCCTACGAGGCC
Done.