Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012229.1 Corchorus capsularis cultivar CVL-1 contig12250, 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: 7581
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30


Found at i:156 original size:30 final size:30

Alignment explanation


    Indices: 107--164  Score: 91
    Period size: 30  Copynumber: 1.9  Consensus size: 30

         97 GTCTTCAAGT

                 *                        
        107 CCATAGTAAGTCCTTGGCGCATCATTCCTG
          1 CCATAATAAGTCCTTGGCGCATCATTCCTG

                                         
        137 CCATAATAAG-CCTTGGGCGCATCATTCC
          1 CCATAATAAGTCCTT-GGCGCATCATTCC

        165 CTCCCCCTTG


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  29    4  0.15
  30   22  0.85

ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28


Consensus pattern (30 bp):   
CCATAATAAGTCCTTGGCGCATCATTCCTG

Found at i:592 original size:33 final size:33

Alignment explanation


    Indices: 545--661  Score: 171
    Period size: 33  Copynumber: 3.5  Consensus size: 33

        535 CTTTTCACCT

                                 *           
        545 AAAACAGAATTATTTTCAATGTTATGATCAACC
          1 AAAACAGAATTATTTTCAATGCTATGATCAACC

                *          *                 
        578 AAAATAGAATTATTTGCAATGCTATGATCAACC
          1 AAAACAGAATTATTTTCAATGCTATGATCAACC

                            *         *      
        611 AAAACAGAATTATTTTTAATGCTATGTTCAACC
          1 AAAACAGAATTATTTTCAATGCTATGATCAACC

                    *  *      
        644 AAAACAGATTTGTTTTCA
          1 AAAACAGAATTATTTTCA

        662 TCACAATTAG


Statistics
Matches: 74,  Mismatches: 10, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   74  1.00

ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34


Consensus pattern (33 bp):   
AAAACAGAATTATTTTCAATGCTATGATCAACC

Found at i:679 original size:66 final size:66

Alignment explanation


    Indices: 545--684  Score: 156
    Period size: 66  Copynumber: 2.1  Consensus size: 66

        535 CTTTTCACCT

                                 *               *               * *    *    
        545 AAAACAGAATTATTTTCAATGTTATGATCAACCAAAATAGAATTATTTGCAATGCTATGATCAAC
          1 AAAACAGAATTATTTTCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAAC

             
        610 C
         66 C

                            *         *              *  *   *          *    *
        611 AAAACAGAATTATTTTTAATGCTATGTTCAACCAAAACAGATTTGTTTTC-ATCACAATTAGCAT
          1 AAAACAGAATTATTTTCAATGCTATGATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGCAA

              
        675 CC
         65 CC

                    
        677 AAAACAGA
          1 AAAACAGA

        685 TTTAGTACCA


Statistics
Matches: 61,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  65    2  0.03
  66   59  0.97

ACGTcount: A:0.42, C:0.16, G:0.10, T:0.31


Consensus pattern (66 bp):   
AAAACAGAATTATTTTCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAAC
C

Found at i:714 original size:33 final size:32

Alignment explanation


    Indices: 677--781  Score: 111
    Period size: 33  Copynumber: 3.2  Consensus size: 32

        667 ATTAGCATCC

                           *    *            
        677 AAAACAGATTTAGTACCATCACAAACAACACTT
          1 AAAACAGATTTAGTATCATCGCAAACAACA-TT

                  *       *    *             
        710 AAAACAAATTTAGTGTCATTGCAAACAACATTT
          1 AAAACAGATTTAGTATCATCGCAAACAACA-TT

               **  *                         
        743 AAATTAGGTTTAGTATCATCGCAAACAACATCT
          1 AAAACAGATTTAGTATCATCGCAAACAACAT-T

                  
        776 AAAACA
          1 AAAACA

        782 CTCTTTCCAA


Statistics
Matches: 57,  Mismatches: 14, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   56  0.98

ACGTcount: A:0.47, C:0.19, G:0.09, T:0.26


Consensus pattern (32 bp):   
AAAACAGATTTAGTATCATCGCAAACAACATT
Done.