Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009770.1 Corchorus capsularis cultivar CVL-1 contig09791, 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: 27647
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:11813 original size:33 final size:33

Alignment explanation


    Indices: 11768--11832  Score: 112
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      11758 AACCTTTCCC

                               *             
      11768 ATCCTATAAATCTTACTCTGTTTCCAAAATTCT
          1 ATCCTATAAATCTTACTCTATTTCCAAAATTCT

                   *                        
      11801 ATCCTATCAATCTTACTCTATTTCCAAAATTC
          1 ATCCTATAAATCTTACTCTATTTCCAAAATTC

      11833 AAACTTGTGA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.31, C:0.26, G:0.02, T:0.42


Consensus pattern (33 bp):   
ATCCTATAAATCTTACTCTATTTCCAAAATTCT

Found at i:12303 original size:2 final size:2

Alignment explanation


    Indices: 12296--12321  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      12286 CGAAGGGCGT

                                                  
      12296 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

      12322 ACTTTTCCTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:13789 original size:9 final size:9

Alignment explanation


    Indices: 13775--13800  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      13765 AAATTTTGAA

                     
      13775 TGTTCTTGG
          1 TGTTCTTGG

                     
      13784 TGTTCTTGG
          1 TGTTCTTGG

                    
      13793 TGTTCTTG
          1 TGTTCTTG

      13801 ATGAATTCAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.00, C:0.12, G:0.31, T:0.58


Consensus pattern (9 bp):   
TGTTCTTGG

Found at i:17639 original size:52 final size:50

Alignment explanation


    Indices: 17556--17698  Score: 177
    Period size: 52  Copynumber: 2.9  Consensus size: 50

      17546 GATGTGTTGT

                                   *                *          
      17556 TGAGAGAAAGGGGATGGAT-AGAGTTCTACTCTTTGGGATAGATGGATGGA
          1 TGAGAGAAAGGGGATGGATGA-AATTCTACTCTTTGGGATGGATGGATGGA

                                                *               
      17606 TGAGAGAAAGGGGGGATGGATGAAATTCTACTCTTTAGGATGGATGGAT-GA
          1 TGAGAGAAA--GGGGATGGATGAAATTCTACTCTTTGGGATGGATGGATGGA

                                *    * *                
      17657 -GAGA-AAAGGGGATGGATGGAATTATGCTCTTTGGGATGGATG
          1 TGAGAGAAAGGGGATGGATGAAATTCTACTCTTTGGGATGGATG

      17699 AGAGAAAGGG


Statistics
Matches: 83,  Mismatches: 7, Indels: 9
        0.84            0.07        0.09

Matches are distributed among these distances:
  47   31  0.37
  49    3  0.04
  50   13  0.16
  51    2  0.02
  52   33  0.40
  53    1  0.01

ACGTcount: A:0.30, C:0.06, G:0.38, T:0.26


Consensus pattern (50 bp):   
TGAGAGAAAGGGGATGGATGAAATTCTACTCTTTGGGATGGATGGATGGA

Found at i:17687 original size:47 final size:48

Alignment explanation


    Indices: 17596--17698  Score: 154
    Period size: 47  Copynumber: 2.2  Consensus size: 48

      17586 CTTTGGGATA

                                *                *          
      17596 GATGGATGGATGAGAGAAAGGGGGGATGGATGAAATTCTACTCTTTAG
          1 GATGGATGGATGAGAGAAAGAGGGGATGGATGAAATTATACTCTTTAG

                                            *      *      * 
      17644 GATGGATGGATGAGAGAAA-AGGGGATGGATGGAATTATGCTCTTTGG
          1 GATGGATGGATGAGAGAAAGAGGGGATGGATGAAATTATACTCTTTAG

                    
      17691 GATGGATG
          1 GATGGATG

      17699 AGAGAAAGGG


Statistics
Matches: 50,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  47   31  0.62
  48   19  0.38

ACGTcount: A:0.30, C:0.05, G:0.40, T:0.25


Consensus pattern (48 bp):   
GATGGATGGATGAGAGAAAGAGGGGATGGATGAAATTATACTCTTTAG
Done.