Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024914.1 Corchorus olitorius cultivar O-4 contig24947, 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: 17106
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:3941 original size:18 final size:17

Alignment explanation


    Indices: 3918--3955  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       3908 CCCAAATTAC

                              
       3918 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
       3936 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
       3953 TTA
          1 TTA

       3956 AATGAATTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    8  0.40
  18   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32


Consensus pattern (17 bp):   
TTATGGAAATTAGGAAA

Found at i:3953 original size:8 final size:9

Alignment explanation


    Indices: 3922--3955  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       3912 AATTACTTAT

                     
       3922 GGAAATTAG
          1 GGAAATTAG

                    *
       3931 GGAAATTAT
          1 GGAAATTAG

                     
       3940 GGAAATTA-
          1 GGAAATTAG

                    
       3948 GGAAATTA
          1 GGAAATTA

       3956 AATGAATTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8    8  0.33
   9   16  0.67

ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26


Consensus pattern (9 bp):   
GGAAATTAG

Found at i:5308 original size:49 final size:47

Alignment explanation


    Indices: 5233--5373  Score: 171
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       5223 AAAGCAATCA

                                                             
       5233 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                                               *          *  
       5281 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                *                  *                      
       5330 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       5374 TTGGCACGTT


Statistics
Matches: 83,  Mismatches: 5, Indels: 11
        0.84            0.05        0.11

Matches are distributed among these distances:
  47   17  0.20
  48   24  0.29
  49   41  0.49
  50    1  0.01

ACGTcount: A:0.28, C:0.15, G:0.06, T:0.52


Consensus pattern (47 bp):   
TTTATTTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:6387 original size:18 final size:15

Alignment explanation


    Indices: 6342--6393  Score: 77
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       6332 TGCTAGGGTG

                   *       
       6342 AATGGTGTAAACAAC
          1 AATGGTGCAAACAAC

                           
       6357 AATGGTGCAAACAAC
          1 AATGGTGCAAACAAC

                    *  *   
       6372 AATGGTGCGAATAAC
          1 AATGGTGCAAACAAC

                   
       6387 AATGGTG
          1 AATGGTG

       6394 TGAACAATAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  15   34  1.00

ACGTcount: A:0.42, C:0.13, G:0.25, T:0.19


Consensus pattern (15 bp):   
AATGGTGCAAACAAC
Done.