Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009352.1 Corchorus capsularis cultivar CVL-1 contig09373, 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: 24329
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:344 original size:28 final size:28

Alignment explanation


    Indices: 285--344  Score: 81
    Period size: 28  Copynumber: 2.2  Consensus size: 28

        275 ATTCTTACAT

                                       *
        285 ATATATATATATATTCTTATTTACATAT
          1 ATATATATATATATTCTTATTTACATAA

                                         
        313 ATATATATATAT-TCTCTTATTTA-ATAA
          1 ATATATATATATAT-TCTTATTTACATAA

                  
        340 A-ATAT
          1 ATATAT

        345 TTTACATATT


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  26    4  0.13
  27    5  0.17
  28   21  0.70

ACGTcount: A:0.42, C:0.07, G:0.00, T:0.52


Consensus pattern (28 bp):   
ATATATATATATATTCTTATTTACATAA

Found at i:4152 original size:12 final size:12

Alignment explanation


    Indices: 4135--4160  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       4125 CGAACCTTGT

                        
       4135 CTGTCTTAAAAG
          1 CTGTCTTAAAAG

                        
       4147 CTGTCTTAAAAG
          1 CTGTCTTAAAAG

              
       4159 CT
          1 CT

       4161 ACAAATAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35


Consensus pattern (12 bp):   
CTGTCTTAAAAG

Found at i:6704 original size:12 final size:12

Alignment explanation


    Indices: 6687--6720  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       6677 TCTCCTTCAG

                      * 
       6687 CATCATCATCGT
          1 CATCATCATCCT

                        
       6699 CATCATCATCCT
          1 CATCATCATCCT

                *     
       6711 CATCTTCATC
          1 CATCATCATC

       6721 TTCGACATCA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.24, C:0.38, G:0.03, T:0.35


Consensus pattern (12 bp):   
CATCATCATCCT

Found at i:6729 original size:27 final size:27

Alignment explanation


    Indices: 6689--6745  Score: 71
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       6679 TCCTTCAGCA

                     *                  
       6689 TCATCATCGTCATCA-TCATCCTCATCT
          1 TCATCATCGACATCACT-ATCCTCATCT

                 *              *      
       6716 TCATCTTCGACATCACTATCTTCATCT
          1 TCATCATCGACATCACTATCCTCATCT

               
       6743 TCA
          1 TCA

       6746 ATTTCCTCAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  27   25  0.96
  28    1  0.04

ACGTcount: A:0.23, C:0.35, G:0.04, T:0.39


Consensus pattern (27 bp):   
TCATCATCGACATCACTATCCTCATCT

Found at i:17853 original size:15 final size:15

Alignment explanation


    Indices: 17829--17876  Score: 51
    Period size: 15  Copynumber: 3.1  Consensus size: 15

      17819 TTAGTAAATG

                           
      17829 TACTTATTTTTCATA
          1 TACTTATTTTTCATA

                 *     *  * 
      17844 TACTTTTTTTTTAGGA
          1 TACTTATTTTTCA-TA

                 *         
      17860 TACTTGTTTTTCATA
          1 TACTTATTTTTCATA

              
      17875 TA
          1 TA

      17877 TAAATATTTT


Statistics
Matches: 26,  Mismatches: 6, Indels: 2
        0.76            0.18        0.06

Matches are distributed among these distances:
  15   14  0.54
  16   12  0.46

ACGTcount: A:0.23, C:0.10, G:0.06, T:0.60


Consensus pattern (15 bp):   
TACTTATTTTTCATA
Done.