Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022272.1 Corchorus olitorius cultivar O-4 contig22305, 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: 11171
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:4498 original size:26 final size:28

Alignment explanation


    Indices: 4460--4514  Score: 69
    Period size: 26  Copynumber: 2.0  Consensus size: 28

       4450 GTCACACTCT

                         *              
       4460 TAGATGGGAGATGGA-AA-TCTTCCTTC
          1 TAGATGGGAGATGAATAATTCTTCCTTC

                   **                   
       4486 TAGATGGTTGATGAATAATTCTTCCTTC
          1 TAGATGGGAGATGAATAATTCTTCCTTC

             
       4514 T
          1 T

       4515 TCCTATCACA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  26   12  0.50
  27    2  0.08
  28   10  0.42

ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38


Consensus pattern (28 bp):   
TAGATGGGAGATGAATAATTCTTCCTTC

Found at i:6335 original size:18 final size:17

Alignment explanation


    Indices: 6312--6349  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       6302 CCCAAATTAC

                              
       6312 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
       6330 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
       6347 TTA
          1 TTA

       6350 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:6347 original size:8 final size:9

Alignment explanation


    Indices: 6316--6349  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       6306 AATTACTTAT

                     
       6316 GGAAATTAG
          1 GGAAATTAG

                    *
       6325 GGAAATTAT
          1 GGAAATTAG

                     
       6334 GGAAATTA-
          1 GGAAATTAG

                    
       6342 GGAAATTA
          1 GGAAATTA

       6350 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:7706 original size:49 final size:47

Alignment explanation


    Indices: 7628--7768  Score: 153
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       7618 GAAGCAATCC

                                     *                       
       7628 TTTACTTTTTAC-TGCACTTTTTCTTAATTTTTACTACAAAATTGAACT
          1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                                               * *        *  
       7676 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGATAAAATTGATCT
          1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                *                  *                      
       7725 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       7769 TTGGCACGCT


Statistics
Matches: 80,  Mismatches: 8, Indels: 11
        0.81            0.08        0.11

Matches are distributed among these distances:
  47   16  0.20
  48   24  0.30
  49   39  0.49
  50    1  0.01

ACGTcount: A:0.28, C:0.13, G:0.06, T:0.53


Consensus pattern (47 bp):   
TTTATTTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:8633 original size:15 final size:15

Alignment explanation


    Indices: 8592--8641  Score: 73
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       8582 TGCTAGGGTG

                    *      
       8592 AATGGTGCAAACAAC
          1 AATGGTGCGAACAAC

                           
       8607 AATGGTGCGAACAAC
          1 AATGGTGCGAACAAC

                   *      *
       8622 AATGGTGTGAACAAT
          1 AATGGTGCGAACAAC

                 
       8637 AATGG
          1 AATGG

       8642 AAACGATGCA


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   32  1.00

ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18


Consensus pattern (15 bp):   
AATGGTGCGAACAAC
Done.