Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016040.1 Corchorus capsularis cultivar CVL-1 contig16061, 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: 17722
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:5804 original size:21 final size:21

Alignment explanation


    Indices: 5778--5845  Score: 88
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       5768 GTTTGTTGTT

                                 
       5778 CTGTTTTTGGCAATTTTACTG
          1 CTGTTTTTGGCAATTTTACTG

                            *    
       5799 CTGTTTTTGGCAATTTCACTG
          1 CTGTTTTTGGCAATTTTACTG

                                   
       5820 -TAG-TTTTGGC-ATTTTAGCTG
          1 CT-GTTTTTGGCAATTTTA-CTG

                  
       5840 CTGTTT
          1 CTGTTT

       5846 GGAGCATAAG


Statistics
Matches: 41,  Mismatches: 2, Indels: 8
        0.80            0.04        0.16

Matches are distributed among these distances:
  19    5  0.12
  20   12  0.29
  21   24  0.59

ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51


Consensus pattern (21 bp):   
CTGTTTTTGGCAATTTTACTG

Found at i:6138 original size:2 final size:2

Alignment explanation


    Indices: 6131--6169  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       6121 CAGGAGGTAC

                                                                      
       6131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6170 ATTAACCATA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:10864 original size:21 final size:21

Alignment explanation


    Indices: 10838--10890  Score: 72
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      10828 TTTGTTGTTC

                             *  * 
      10838 TGTTTTTGGCAACTTT-GCTGT
          1 TGTTTTTGGCAA-TTTCCCTAT

                                 
      10859 TGTTTTTGGCAATTTCCCTAT
          1 TGTTTTTGGCAATTTCCCTAT

                       
      10880 TGTTTTTGGCA
          1 TGTTTTTGGCA

      10891 TTTTAGCTGC


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  20    3  0.10
  21   26  0.90

ACGTcount: A:0.11, C:0.15, G:0.21, T:0.53


Consensus pattern (21 bp):   
TGTTTTTGGCAATTTCCCTAT

Found at i:10904 original size:21 final size:20

Alignment explanation


    Indices: 10837--10905  Score: 66
    Period size: 21  Copynumber: 3.3  Consensus size: 20

      10827 GTTTGTTGTT

                                 
      10837 CTGTTTTTGGCAACTTTGCTG
          1 CTGTTTTTGGCAA-TTTGCTG

            *                *  *
      10858 TTGTTTTTGGCAATTTCCCTA
          1 CTGTTTTTGGCAATTT-GCTG

            *           *        
      10879 TTGTTTTTGGCATTTTAGCTG
          1 CTGTTTTTGGCAATTT-GCTG

                  
      10900 CTGTTT
          1 CTGTTT

      10906 GGAGCATAAA


Statistics
Matches: 39,  Mismatches: 8, Indels: 2
        0.80            0.16        0.04

Matches are distributed among these distances:
  20    3  0.08
  21   36  0.92

ACGTcount: A:0.10, C:0.16, G:0.20, T:0.54


Consensus pattern (20 bp):   
CTGTTTTTGGCAATTTGCTG

Found at i:14466 original size:2 final size:2

Alignment explanation


    Indices: 14459--14496  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      14449 AACAGGAGGA

                                                                    
      14459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      14497 TCAACCATAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
AT

Done.