Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011308.1 Corchorus capsularis cultivar CVL-1 contig11329, 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: 8131
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:77 original size:2 final size:2

Alignment explanation


    Indices: 70--108  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

         60 CGAGACGTGT

                                                                      
         70 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        109 CTTAATACAG


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


Consensus pattern (2 bp):   
TA

Found at i:649 original size:22 final size:23

Alignment explanation


    Indices: 600--653  Score: 65
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        590 TTTATTTTAA

                                 **
        600 AAAAAAAACATTAAATAGTAGTG
          1 AAAAAAAACATTAAATAGTAGCC

            *               *      
        623 TAAAAAAACATTAAATTGT-GCC
          1 AAAAAAAACATTAAATAGTAGCC

                     
        645 AAAAAAAAC
          1 AAAAAAAAC

        654 TTTATTTAAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  22    9  0.35
  23   17  0.65

ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20


Consensus pattern (23 bp):   
AAAAAAAACATTAAATAGTAGCC

Found at i:919 original size:16 final size:16

Alignment explanation


    Indices: 898--932  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        888 AGTATGGAAA

                            
        898 AGACAAGAGAATAGAG
          1 AGACAAGAGAATAGAG

                  *      *  
        914 AGACAATAGAATATAG
          1 AGACAAGAGAATAGAG

               
        930 AGA
          1 AGA

        933 AGAAGAAAAT


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

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.57, C:0.06, G:0.26, T:0.11


Consensus pattern (16 bp):   
AGACAAGAGAATAGAG

Found at i:1165 original size:11 final size:11

Alignment explanation


    Indices: 1151--1184  Score: 68
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       1141 ATTCATAACA

                       
       1151 AATTTATAATT
          1 AATTTATAATT

                       
       1162 AATTTATAATT
          1 AATTTATAATT

                       
       1173 AATTTATAATT
          1 AATTTATAATT

             
       1184 A
          1 A

       1185 TTTGATTAAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:1853 original size:11 final size:11

Alignment explanation


    Indices: 1810--1847  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       1800 TTTCTATATA

                *      
       1810 AAATAAATTAT
          1 AAATTAATTAT

                        
       1821 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       1832 AAATTAATTAT
          1 AAATTAATTAT

                 
       1843 AAATT
          1 AAATT

       1848 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:8079 original size:32 final size:32

Alignment explanation


    Indices: 8043--8107  Score: 121
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       8033 ATCTGACATG

                                  *         
       8043 CCCTGTTGATGAAGCAATTTGCGGCATCTTCT
          1 CCCTGTTGATGAAGCAATTTGCAGCATCTTCT

                                            
       8075 CCCTGTTGATGAAGCAATTTGCAGCATCTTCT
          1 CCCTGTTGATGAAGCAATTTGCAGCATCTTCT

             
       8107 C
          1 C

       8108 ATGTCTTTTT


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34


Consensus pattern (32 bp):   
CCCTGTTGATGAAGCAATTTGCAGCATCTTCT
Done.