Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005066.1 Corchorus capsularis cultivar CVL-1 contig05084, 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: 6421
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:51 original size:23 final size:24

Alignment explanation


    Indices: 13--57  Score: 65
    Period size: 23  Copynumber: 1.9  Consensus size: 24

          3 GATTAATTTG

                       *            
         13 TAAATAAAAATTAAATCTTTGAGT
          1 TAAATAAAAATGAAATCTTTGAGT

                            *     
         37 TAAA-AAAAATGAAATTTTTGA
          1 TAAATAAAAATGAAATCTTTGA

         58 CTGATTTATG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23   15  0.79
  24    4  0.21

ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36


Consensus pattern (24 bp):   
TAAATAAAAATGAAATCTTTGAGT

Found at i:2151 original size:29 final size:29

Alignment explanation


    Indices: 2100--2167  Score: 75
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       2090 GTTATGTTGA

                *                        
       2100 GGGGACAAAAAGTCCCAAAATTGAAGCTC
          1 GGGGGCAAAAAGTCCCAAAATTGAAGCTC

              *        *       *       *  
       2129 AGTGGGCAAAATGT-CCAAGATTGAAGTTC
          1 -GGGGGCAAAAAGTCCCAAAATTGAAGCTC

                      
       2158 GGGGGCAAAA
          1 GGGGGCAAAA

       2168 CATCCAAACG


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  28    9  0.28
  29   13  0.41
  30   10  0.31

ACGTcount: A:0.38, C:0.16, G:0.29, T:0.16


Consensus pattern (29 bp):   
GGGGGCAAAAAGTCCCAAAATTGAAGCTC

Found at i:2173 original size:28 final size:29

Alignment explanation


    Indices: 2114--2175  Score: 72
    Period size: 28  Copynumber: 2.2  Consensus size: 29

       2104 ACAAAAAGTC

                             *        ** 
       2114 CCAAAATTGAAGCTCAGTGGGCAAAATGT
          1 CCAAAATTGAAGCTCAGGGGGCAAAACAT

                *       *                
       2143 CCAAGATTGAAGTTC-GGGGGCAAAACAT
          1 CCAAAATTGAAGCTCAGGGGGCAAAACAT

                 
       2171 CCAAA
          1 CCAAA

       2176 CGCTACAATT


Statistics
Matches: 27,  Mismatches: 6, Indels: 1
        0.79            0.18        0.03

Matches are distributed among these distances:
  28   14  0.52
  29   13  0.48

ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18


Consensus pattern (29 bp):   
CCAAAATTGAAGCTCAGGGGGCAAAACAT

Found at i:3433 original size:4 final size:4

Alignment explanation


    Indices: 3426--3459  Score: 52
    Period size: 4  Copynumber: 8.8  Consensus size: 4

       3416 AAAAAAAAAG

                                             *         
       3426 GAAA GAAA GAAA GAAA GAAA G-AA GAAG GAAA GAA
          1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA

       3460 TGATTAAGAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   3    3  0.11
   4   24  0.89

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:5049 original size:22 final size:22

Alignment explanation


    Indices: 5021--5062  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       5011 ACCGACTGAG

                                   
       5021 ATATTATATATTTT-TTATATTT
          1 ATATTATAT-TTTTATTATATTT

                   *            
       5043 ATATTATGTTTTTATTATAT
          1 ATATTATATTTTTATTATAT

       5063 ATAATATATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    4  0.22
  22   14  0.78

ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67


Consensus pattern (22 bp):   
ATATTATATTTTTATTATATTT

Found at i:5457 original size:1 final size:1

Alignment explanation


    Indices: 5446--5476  Score: 53
    Period size: 1  Copynumber: 31.0  Consensus size: 1

       5436 TCTACTATTG

                *                          
       5446 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       5477 CTAGACGCGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03


Consensus pattern (1 bp):   
A
Done.