Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010484.1 Corchorus capsularis cultivar CVL-1 contig10505, 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: 9125
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:581 original size:19 final size:19

Alignment explanation


    Indices: 554--591  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        544 TTCCAAGATA

                               
        554 AAAAAAGAAAAAATCAATC
          1 AAAAAAGAAAAAATCAATC

                *         *    
        573 AAAACAGAAAAAATGAATC
          1 AAAAAAGAAAAAATCAATC

        592 TTTCAAAATT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.71, C:0.11, G:0.08, T:0.11


Consensus pattern (19 bp):   
AAAAAAGAAAAAATCAATC

Found at i:726 original size:52 final size:52

Alignment explanation


    Indices: 665--807  Score: 268
    Period size: 52  Copynumber: 2.8  Consensus size: 52

        655 AAAAATTTTT

                                                                
        665 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
          1 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC

                                                                
        717 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
          1 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC

                             *         *           
        769 CATCAAGTTTTCAAAGTGTTCAATTTAAGTCTTTTCAAA
          1 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAA

        808 ACATTCAAAT


Statistics
Matches: 89,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  52   89  1.00

ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39


Consensus pattern (52 bp):   
CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC

Found at i:1517 original size:42 final size:42

Alignment explanation


    Indices: 1458--1543  Score: 136
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1448 AAGGGTCAAG

                                 *       * *       *  
       1458 TGGCCGGTTGTGGCCGGATGGTCCGTGCGTTGGCCCGTGTGA
          1 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATAGCCCGTGCGA

                                                      
       1500 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATAGCCCGTGCGA
          1 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATAGCCCGTGCGA

              
       1542 TG
          1 TG

       1544 TCCCATGCAT


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.07, C:0.26, G:0.44, T:0.23


Consensus pattern (42 bp):   
TGGCCGGTTGTGGCCGGATGGCCCGTGCGATAGCCCGTGCGA

Found at i:1521 original size:18 final size:18

Alignment explanation


    Indices: 1458--1522  Score: 51
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       1448 AAGGGTCAAG

                              
       1458 TGGCCGGTTGTGGCCGGA
          1 TGGCCGGTTGTGGCCGGA

                            *        
       1476 TGGTCCGTGCGTTG-GCCCGTGTGA
          1 TGG-CC--G-GTTGTGGCC--G-GA

                              
       1500 TGGCCGGTTGTGGCCGGA
          1 TGGCCGGTTGTGGCCGGA

                 
       1518 TGGCC
          1 TGGCC

       1523 CGTGCGATAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 16
        0.67            0.04        0.29

Matches are distributed among these distances:
  18   10  0.27
  19    3  0.08
  20    4  0.11
  21    8  0.22
  22    4  0.11
  23    3  0.08
  24    5  0.14

ACGTcount: A:0.05, C:0.25, G:0.46, T:0.25


Consensus pattern (18 bp):   
TGGCCGGTTGTGGCCGGA
Done.