Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000273.1 Corchorus capsularis cultivar CVL-1 contig00273, 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: 12936
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:1725 original size:11 final size:11

Alignment explanation


    Indices: 1709--1739  Score: 62
    Period size: 11  Copynumber: 2.8  Consensus size: 11

       1699 CAACGCAACA

                       
       1709 AAAACAAAACG
          1 AAAACAAAACG

                       
       1720 AAAACAAAACG
          1 AAAACAAAACG

                     
       1731 AAAACAAAA
          1 AAAACAAAA

       1740 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.16, G:0.06, T:0.00


Consensus pattern (11 bp):   
AAAACAAAACG

Found at i:1755 original size:6 final size:6

Alignment explanation


    Indices: 1709--1758  Score: 50
    Period size: 6  Copynumber: 8.2  Consensus size: 6

       1699 CAACGCAACA

                                              *                       
       1709 AAAAC- AAAACG AAAAC- AAAACG AAAACAA AAAACAG AAAAACG AAAACG
          1 AAAACG AAAACG AAAACG AAAACG AAAAC-G AAAAC-G -AAAACG AAAACG

             
       1758 A
          1 A

       1759 TGCCAAACGG


Statistics
Matches: 39,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
   5   10  0.26
   6   17  0.44
   7    7  0.18
   8    5  0.13

ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00


Consensus pattern (6 bp):   
AAAACG

Found at i:6161 original size:78 final size:78

Alignment explanation


    Indices: 6079--6247  Score: 252
    Period size: 78  Copynumber: 2.2  Consensus size: 78

       6069 TTGTTTAGGT

                                                  *                  *       
       6079 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATA-TTTATAAC
          1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATA-ACCTTATAAC

                           
       6142 TATTATATTTTACCA
         64 TATTATATTTTACCA

                                                           *  *              
       6157 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTATTAACCTTATAACTA
          1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA

                      ** 
       6222 TTATATTTTAATA
         66 TTATATTTTACCA

                         
       6235 TTTTACTATTTTA
          1 TTTTACTATTTTA

       6248 ATTAAAAAAC


Statistics
Matches: 83,  Mismatches: 6, Indels: 4
        0.89            0.06        0.04

Matches are distributed among these distances:
  77    1  0.01
  78   80  0.96
  79    2  0.02

ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51


Consensus pattern (78 bp):   
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA
TTATATTTTACCA

Found at i:9029 original size:29 final size:29

Alignment explanation


    Indices: 8994--9050  Score: 78
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       8984 CTAAAATGGT

                            *            
       8994 TCCAAAAATAAAATTTTGAGGATAAAACG
          1 TCCAAAAATAAAATTTAGAGGATAAAACG

                   *    *     *         
       9023 TCCAAAATTAAAGTTTAGGGGATAAAAC
          1 TCCAAAAATAAAATTTAGAGGATAAAAC

       9051 AATAAAATCG


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.49, C:0.11, G:0.16, T:0.25


Consensus pattern (29 bp):   
TCCAAAAATAAAATTTAGAGGATAAAACG

Found at i:12918 original size:2 final size:2

Alignment explanation


    Indices: 12911--12936  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      12901 TGCTTTGATC

                                                  
      12911 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


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):   
AT

Done.