Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012439.1 Corchorus olitorius cultivar O-4 contig12472, 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: 11656
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:1996 original size:16 final size:15

Alignment explanation


    Indices: 1975--2016  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1965 TTACTCTGCT

                            
       1975 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                   *       
       1991 TTGTTTTATGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       2006 TTGCTTTCTGT
          1 TTGTTTTCTGT

       2017 CAATCTTTGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2262 original size:29 final size:29

Alignment explanation


    Indices: 2189--2260  Score: 117
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       2179 TTTGGCGCCG

                                         
       2189 TTGCCGGGGAAGGGAACTTTTTCTGGTAT
          1 TTGCCGGGGAAGGGAACTTTTTCTGGTAT

                  *                    * 
       2218 TTGCCGAGGAAGGGAACTTTTTCTGGTTT
          1 TTGCCGGGGAAGGGAACTTTTTCTGGTAT

                          
       2247 TTGCCAGGGGAAGG
          1 TTGCC-GGGGAAGG

       2261 AAAAATAGAC


Statistics
Matches: 39,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  29   32  0.82
  30    7  0.18

ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32


Consensus pattern (29 bp):   
TTGCCGGGGAAGGGAACTTTTTCTGGTAT

Found at i:2416 original size:18 final size:18

Alignment explanation


    Indices: 2393--2432  Score: 71
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2383 TGTTTTGTGT

                              
       2393 TTTGCGTCAAAAAAAAAA
          1 TTTGCGTCAAAAAAAAAA

                     *        
       2411 TTTGCGTCATAAAAAAAA
          1 TTTGCGTCAAAAAAAAAA

                
       2429 TTTG
          1 TTTG

       2433 TTTATGCGTC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30


Consensus pattern (18 bp):   
TTTGCGTCAAAAAAAAAA

Found at i:5698 original size:21 final size:21

Alignment explanation


    Indices: 5672--5719  Score: 78
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5662 GCCATTCACT

                          *      
       5672 GTGCCACCACCGGTTAAGCCC
          1 GTGCCACCACCGGTCAAGCCC

                            *    
       5693 GTGCCACCACCGGTCATGCCC
          1 GTGCCACCACCGGTCAAGCCC

                  
       5714 GTGCCA
          1 GTGCCA

       5720 TCGCCATTCC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.17, C:0.44, G:0.25, T:0.15


Consensus pattern (21 bp):   
GTGCCACCACCGGTCAAGCCC

Found at i:6096 original size:15 final size:14

Alignment explanation


    Indices: 6076--6105  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       6066 ATCTTTTTAA

                           
       6076 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       6091 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       6105 T
          1 T

       6106 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT

Found at i:6633 original size:15 final size:16

Alignment explanation


    Indices: 6615--6647  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       6605 AAAAGGGTAG

                       *    
       6615 TTAAAAAA-AATTGTT
          1 TTAAAAAAGAAGTGTT

                            
       6630 TTAAAAAAGAAGTGTT
          1 TTAAAAAAGAAGTGTT

              
       6646 TT
          1 TT

       6648 CATGCAAGAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39


Consensus pattern (16 bp):   
TTAAAAAAGAAGTGTT

Found at i:9011 original size:15 final size:15

Alignment explanation


    Indices: 8981--9022  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       8971 TTACTCTGCT

                            
       8981 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       8997 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
       9012 TTGTTTTCTGT
          1 TTGTTTTCTGT

       9023 CAATCTTTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA
Done.