Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001646.1 Corchorus capsularis cultivar CVL-1 contig01646, 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: 4055
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:113 original size:25 final size:26

Alignment explanation


    Indices: 76--127  Score: 61
    Period size: 25  Copynumber: 2.0  Consensus size: 26

         66 CAACACATGG

                    *                 
         76 TATGGGAATGTAT-CATTACCATCTA
          1 TATGGGAAGGTATACATTACCATCTA

                  *            *       
        101 TATGGGTAGGTATGACATTCCCATCTA
          1 TATGGGAAGGTAT-ACATTACCATCTA

        128 GTGGCGGATC


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  25   11  0.50
  27   11  0.50

ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Consensus pattern (26 bp):   
TATGGGAAGGTATACATTACCATCTA

Found at i:796 original size:30 final size:29

Alignment explanation


    Indices: 740--801  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 29

        730 ATAAACTTCT

                                          
        740 AAAGACACATTTTCTTTGAATTCAAAAAAA
          1 AAAGACACATTTTCTTTGAA-TCAAAAAAA

                                           
        770 AAAGACACATTTTCTTTGGTAA-CAAAAAAA
          1 AAAGACACATTTTCTTT-G-AATCAAAAAAA

              
        800 AA
          1 AA

        802 TTCAAAAGAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  30   27  0.90
  31    1  0.03
  32    2  0.07

ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27


Consensus pattern (29 bp):   
AAAGACACATTTTCTTTGAATCAAAAAAA

Found at i:1735 original size:28 final size:28

Alignment explanation


    Indices: 1694--1750  Score: 105
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1684 TAATCCGGAT

                     *                  
       1694 TCGACATGTGTCGCGCACCTGATTATGG
          1 TCGACATGTATCGCGCACCTGATTATGG

                                        
       1722 TCGACATGTATCGCGCACCTGATTATGG
          1 TCGACATGTATCGCGCACCTGATTATGG

             
       1750 T
          1 T

       1751 AGGTGAGTCT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30


Consensus pattern (28 bp):   
TCGACATGTATCGCGCACCTGATTATGG

Found at i:2253 original size:56 final size:56

Alignment explanation


    Indices: 2191--2352  Score: 234
    Period size: 59  Copynumber: 2.8  Consensus size: 56

       2181 TGCAAGTATA

                               *       *                            
       2191 ACTAAACTCACCTATATATAAGAATTAGATTAGTGTGTGTTTGGTATCGAGTGATT
          1 ACTAAACTCACCTATATATTAGAATTAAATTAGTGTGTGTTTGGTATCGAGTGATT

                                        *                     *        
       2247 ACTAAACTCACCTACAATATATTAGAATCAAATTAGTGTGTGTTTGGTATTGAGTGATT
          1 ACTAAACTCACCT---ATATATTAGAATTAAATTAGTGTGTGTTTGGTATCGAGTGATT

                        *                   *         *    
       2306 ACTAAACTCACCAATATATTAGAATTAAATTATTGTGTGTTTAGTAT
          1 ACTAAACTCACCTATATATTAGAATTAAATTAGTGTGTGTTTGGTAT

       2353 GAAGAGAATA


Statistics
Matches: 95,  Mismatches: 8, Indels: 6
        0.87            0.07        0.06

Matches are distributed among these distances:
  56   44  0.46
  59   51  0.54

ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38


Consensus pattern (56 bp):   
ACTAAACTCACCTATATATTAGAATTAAATTAGTGTGTGTTTGGTATCGAGTGATT

Done.