Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014464.1 Corchorus capsularis cultivar CVL-1 contig14485, 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: 10562
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36


Found at i:1850 original size:20 final size:20

Alignment explanation


    Indices: 1834--1874  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1824 AAATCAAAGT

                             *  
       1834 AAAACCAAGATAATCAATCC
          1 AAAACCAAGATAATCAAACC

                       *  *     
       1854 AAAACCAAGATTATAAAACC
          1 AAAACCAAGATAATCAAACC

             
       1874 A
          1 A

       1875 GATCAGTCAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.59, C:0.22, G:0.05, T:0.15


Consensus pattern (20 bp):   
AAAACCAAGATAATCAAACC

Found at i:4189 original size:20 final size:19

Alignment explanation


    Indices: 4155--4192  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       4145 GATTACTAAA

                      *        
       4155 AAAACAATTAGAGGTTATC
          1 AAAACAATTAAAGGTTATC

                               
       4174 AAAACAATTATAAGGTTAT
          1 AAAACAATTA-AAGGTTAT

       4193 TAATAAATTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29


Consensus pattern (19 bp):   
AAAACAATTAAAGGTTATC

Found at i:7855 original size:4 final size:4

Alignment explanation


    Indices: 7846--7907  Score: 79
    Period size: 4  Copynumber: 15.5  Consensus size: 4

       7836 CTTACTAAGT

                                       *                   *    *      
       7846 TATA TATA TATA TATA TATA TACA TATA TATA TATA TACA TACA TATA
          1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA

            *    *           
       7894 CATA CATA TATA TA
          1 TATA TATA TATA TA

       7908 AGGTTAAAAA


Statistics
Matches: 52,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   4   52  1.00

ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42


Consensus pattern (4 bp):   
TATA

Found at i:7857 original size:6 final size:6

Alignment explanation


    Indices: 7846--7907  Score: 79
    Period size: 6  Copynumber: 10.3  Consensus size: 6

       7836 CTTACTAAGT

                                     *                  *    *     
       7846 TATATA TATATA TATATA TATACA TATATA TATATA TACATA CATATA
          1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA

            *   *           
       7894 CATACA TATATA TA
          1 TATATA TATATA TA

       7908 AGGTTAAAAA


Statistics
Matches: 48,  Mismatches: 8, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   6   48  1.00

ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42


Consensus pattern (6 bp):   
TATATA

Found at i:7861 original size:10 final size:10

Alignment explanation


    Indices: 7849--7907  Score: 82
    Period size: 10  Copynumber: 5.9  Consensus size: 10

       7839 ACTAAGTTAT

                     *
       7849 ATATATATAT
          1 ATATATATAC

                      
       7859 ATATATATAC
          1 ATATATATAC

                     *
       7869 ATATATATAT
          1 ATATATATAC

                 *    
       7879 ATATACATAC
          1 ATATATATAC

                 *    
       7889 ATATACATAC
          1 ATATATATAC

                     
       7899 ATATATATA
          1 ATATATATA

       7908 AGGTTAAAAA


Statistics
Matches: 44,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   44  1.00

ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41


Consensus pattern (10 bp):   
ATATATATAC
Done.