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  • #1

    H3N2, 1976

    I just noticed this one, I hadn't examined H3N2 before.

    -:not available or alignment-gaps
    .:match
    o:difference

    A/Hong Kong/1/68(H3N2) PB1
    A/Memphis/104/1976(H3N2) PB1

    Code:
    ------------------------------.............................
......o..o........o...........-...o.....o..o...........o....
.......o....................................................
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.o.....o............o.............o........o................
.o.....oo.............o.....................................
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.o...........o.....o..o..o.....o........o........o..o.......
.......o...........o..o...........o.....o.....o..o..........
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.o.....o...........o..............o.........................
.o..............oo....o.....o.....oo.o...........o..oo......
.......o.................o.....o.....oo.o..o.....o........o.
....o.....o..o..o.................o.....o..o.....o.....o....
....o..o........o..o........o.....o........o.....o.....o..o.
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.o..o...........o.....o..............oo....o.....o.....o....
...o...o..............o.....o..oo....o..o..o..o..o..........
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.o................-.......----------------------------------
--

    A/Kiev/59/1979(H1N1),PB1
    A/Memphis/104/1976(H3N2),PB1
    Code:
    ------------------------------.............................
.o....o..o..o.....o...........-...o.....o..o...........o....
.......o....................................................
..........o........o..o..........................o..o.......
.o..................o.............o........o................
.o.....oo.......o.....o........o............................
.o...o.......o..............o........o.....o.o......o.......
.o...........o.....oo.o..o.....o........o........o..o.......
.......o..o........o..o...........o.....o.....o..o..........
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.o.....o...........o..............o.........................
.o.....o........oo....o.....o.....oo.o...........o..oo......
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..................-.......----------------------------------
--

    A/Memphis/104/1976(H3N2) , PB1
    A/chicken/Dubai/338/2001(H9N2) , PB1

    Code:
    -----------------------------------------------------------
-------------.................-.............................
............................................................
....o.......................................................
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.....o......................................................
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.......o...............o.............................o.o....
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....o..o..........................o..o...........o........o.
....o..o.....o..oo.o..o..o..............o........o..o......o
.......o........o..............o..o....................o..o.
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....o...........o.....o..............o..o..............o....
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....o..o.................o........o..o..o..o.....o.....o....
.......o.....o........o.....o..o.....o..o...............o...
.......o.............................o..o.....o........o..o.
....o..o........o..o..o........o.--.o.......................
............o.....o........o..o..o........o..-------o......-
-------..............o..o....-----.......--o........o.......
.......o........o.....o..oo...................oo.o..........
.......oo.o...................o.............................
.o................-.......----------------------------------
--
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT
    Tags: None
  • #2
    Re: H3N2, 1976

    Did you pull this because of the H9N2 reference? This is the A/Victoria H3N2 strain you looked at?

    Comment

    • #3
      Re: H3N2, 1976

      no, just working on my programs and updating my databases.
      Most evident recombination in my PB1-database (all serotypes)

      I found some laboratory work on recombination in 1976
      (=swineflu-year) and even laws about it from that year,
      so is it maybe a descendant or relative from a laboratory strain ?
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment

      • #4
        Re: H3N2, 1976

        here is it again, but even clearer now and with the referrences.
        Looks as if A/Memphis/104/1976 was created in the laboratory
        by recombination of A/Memphis/103/1976 with another unpublished strain,
        which was frozen and somehow reintroduced into Dubai in 2000.

        edit: well, more likely IMO that they submitted the Dubai and the Memphis
        sequences together last year and somehow mixed it up.


        Influenza A virus (A/Memphis/103/1976(H3N2)) polymerase PB1 (PB1) and - Nucleotide - NCBI
        http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=CY006889

        Record suppressed: Influenza A virus (A/Memphis/104/1976(H3N2)) segment 2, complete seque - Nucleotide - NCBI
        http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=CY012198

        Influenza A virus (A/quail/Dubai/301/2000(H9N2)) segment 2 polymerase - Nucleotide - NCBI
        http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EF063531


        Code:
        >A/Memphis/103/1976(H3N2) segment 2
------------CAAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGCCATAAGCACCACATTCCCTTATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATATTCAGAAAAAGGGAAGTGGACAACAAACACAGAGACTGGGGCGCCCCAACTTAACCCAATTGATGGACCACTACCTGAGGATAATGAGCCAAGCGGATATGCACAAACAGACTGTGTCCTGGAAGCAATGGCTTTCCTTGAAGAATCCCACCCAGGGATTTTTGAAAACTCGTGCCTTGAAACGATGGAAGTCGTTCAACAAACAAGGGTGGACAAACTGACCCAAGGTCGTCAGACCTATGACTGGACATTAAACAGAAATCAACCGGCCGCAACTGCATTAGCCAACACTATAGAAGTCTTCAGATCGAATGGTCTAACAGCTAATGAGTCGGGAAGGCTAATAGATTTCCTCAAGGATGTGATGGAATCAATGGATAAAGAGGAAATGGAGATAACAACACACTTCCAAAGAAAAAGAAGAGTAAGAGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGAAAGAAGAAGCAGAGAGTGAACAAGAGAAGCTATCTAATAAGAGCATTAACATTGAACACAATGACCAAAGATGCAGAAAGAGGTAAATTAAAGAGAAGAGCTATTGCAACACCCGGGATGCAAATCAGAGGGTTCGTGTACTTTGTTGAAACTCTAGCTAGGAGCATTTGTGAGAAGCTTGAACAGTCTGGACTTCCAGTTGGAGGTAATGAAAAGAAGGCCAAACTGGCAAATGTTGTGAGAAAGATGATGACTAATTCACAAGACACAGAGCTTTCTTTCACAATTACTGGAGACAATACTAAGTGGAATGAAAATCAAAATCCTCGAATGTTCCTGGCGATGATTACATATATCACAAAAAATCAACCTGAATGGTTCAGAAACATTCTGAGCATCGCACCCATAATGTTCTCAAACAAAATGGCGAGACTAGGGAAAGGATACATGTTCGAAAGTAAGAGAATGAAGCTCCGAACACAAATACCAGCAGAAATGCTAGCAAGCATTGACCTAAAGTATTTCAATGAATCAACAAGAAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGTACAGCGTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACGGTTTTAGGAGTCTCAATCCTGAATCTTGGGCAAAAGAAATACACCAAAACAACATACTGGTGGGATGGACTCCAATCTTCTGATGATTTTGCTCTCATAGTGAATGCACCAAATCATGAGGGGATACAAGCAGGAGTGGATAGATTCTACAGAACCTGCAAGTTAGTCGGAATCAATATGAGCAAGAAGAAGTCCTATATAAATAGAACAGGAACATTTGAATTCACAAGCTTTTTTTACCGCTATGGATTTGTAGCCAATTTTAGTATGGAGCTGCCCAGTTTTGGGGTGTCTGGAATTAATGAGTCAGCTGATATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTAGGACCAGCAACAGCCCAGATGGCTCTTCAACTGTTCATCAAAGACTACAGATATACATATCGGTGCCACAGAGGAGACACACAAATTCAGACGAGGAGATCATTCGAGCTAAAGAAGCTGTGGGAGCAAACCCGCTCAAAGGCAGGACTATTGGTTTCAGATGGAGGGCCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTGAAGTGGGAGCTAATGGATGAGGACTATCAGGGAAGACTTTGTAATCCTCTGAATCCATTTGTCAGCCATAAGGAGATTGAATCTGTAAACAATGCTGTGATAATGCCAGCTCATGGTCCAGCCAAGAGCATGGAATATGACGCTGTTGCAACTACACACTCCTGGATTCCCAAGAGGAACCGCTCTATTCTCAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTATCAGAAATGCTGCAACCTGTTCGAGAAATTTTTTCCCAGTAGTTCATACAGGAGACCGGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGACGAATTAAGAAAGAAGAGTTCTCCGAGATCATGAAGATCTGTTTCACCATTGAAGAGCTCAGACGGCAAAAATAATGAATTTAGCTTGTCCTTCATGA------------------
>A/Memphis/104/1976(H3N2) segment 2
------------CAAACCATTTGAATGGATGTCAATCCGACTTTACTCTTTTTGAAAGTGCCAGCGCAAAATGCTATAAGTACTACATTCCCTTACACTGGAGATCCCCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATACTCAGAAAAGGGAAAGTGGACAACAAACACAGAGACTGGAGCACCCCAACTCAACCCGATTGATGGACCATTACCTGAGGATAACGAGCCAAGCGGATATGCACAAACAGATTGTGTGTTGGAAGCAATGGCCTTCCTTGAAGAATCCCACCCAGGGATCTTTGAAAACTCATGTATTGAAACGATGGAAGTTGTTCAGCAAACAAGAGTGGATAAACTGACCCAAGGTCGCCAGACCTATGACTGGACTTTGAATAGAAACCAACCGGCTGCAACTGCTTTGGCCAACACTATAGAGGTCTTCAGATCTAACGGTCTAACAGCCAATGAATCGGGGAGACTAATAGATTTCCTCAAGGATGTGATGGAGTCAATGGATAAAGAAGAAATGGAAATAACAACACATTTCCAGAGAAAGAGAAGAGTAAGGGACAACATGACCAAAAAAATGGTCACACAAAGAACAATAGGGAAGAAGAAGCAGAGGCTGAATAAGAGGAGCTACTTGATAAGAGCATTGACCCTGAACACAATGACAAAAGATGCAGAAAGAGGCAAATTGAAGAGGCGGGCAATTGCTACACCCGGAATGCAGATCAGGGGATTTGTGTACTTTGTTGAAACGCTAGCGAGAAGCATCTGTGAAAAGCTTGAGCAATCTGGACTCCCGGTTGGAGGGAATGAGAAGAAGGCTAAACTAGCAAACGTCGTGAGAAAGATGATGACTAATTCTCAAGATACAGAGCTTTCCTTTACAATTACTGGAGACAACACCAAATGGAATGAGAATCAGAATCCTCGAATGTTTATGGCAATGATAACATACATCACAAGAAACCAACCTGAATGGTTTAGAAATGTCTTGAGTATTGCCCCTATCATGTTCTCAAACAAGATGGCGAGATTAGGAAAAGGATACATGTTCGAAAGTAAGAGAATGAAGCTCCGAACACAAATACCAGCAGAAATGCTAGCAAGCATTGACCTAAAGTATTTCAATGAATCAACAAGAAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGTACAGCGTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACGGTTTTAGGAGTCTCAATCCTGAATCTTGGGCAAAAGAAATACACCAAAACAACATACTGGTGGGATGGACTCCAATCTTCTGATGATTTTGCTCTCATAGTGAATGCACCAAATCATGAGGGGATACAAGCAGGAGTGGATAGATTCTACAGAACCTGCAAGTTAGTCGGAATCAATATGAGCAAGAAGAAGTCCTATATAAATAGAACAGGAACATTTGAATTCACAAGCTTTTTTTATCGCTATGGATTTGTAGCCAATTTTAGTATGGAGCTGCCCAGTTTTGGGGTGTCTGGAATTAATGAGTCAGCTGATATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTAGGACCAGCAACAGCCCAGATGGCTCTTCAACTGTTCATCAAAGACTACAGATATACATATCGGTGCCACAGAGGAGACACACAAATTCAGACGAGGAGATCATTCGAGCTAAAGAAGCTGTGGGAGCAAACCCGCTCAAAGGCAGGACTATTGGTTTCAGATGGAGGGCCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTGAAGTGGGAGCTAATGGATGAGGACTATCAGGGAAGACTTTGTAATCCTCTGAATCCATTTGTCAGCCATAAGGAGATTGAATCTGTAAACAATGCTGTGATAATGCCAGCTCATGGTCCAGCCAAGAGCATGGAATATGACGCTGTTGCAACTACACACTCCTGGATTCCCAAGAGGAACCGCTCTATTCTCAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTATCAGAAATGCTGCAACCTGTTCGAGAAATTTTTTCCCAGTAGTTCATACAGGAGACCGGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGACGAATTAAGAAAGAAGAGTTCTCCGAGATCATGAAGATCTGTTTCACCATTGAAGAGCTCAGACGGCAAAAATAATGAATTTAGCTTGTCCTTCATGA------------------
>A/quail/Dubai/301/2000(H9N2) segment 2
AGCGAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACTTTACTCTTTTTGAAAGTGCCAGCGCAAAATGCTATAAGTACTACATTCCCTTACACTGGAGATCCCCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATACTCAGAAAAGGGAAAGTGGACAACAAACACAGAGACTGGAGCACCCCAACTCAACCCGATTGATGGACCATTACCTGAGGATAACGAGCCAAGCGGATATGCACAAACAGATTGTGTGTTGGAAGCAATGGCCTTCCTTGAAGAATCCCACCCAGGGATCTTTGAAAACTCATGTATTGAAACGATGGAAGTTGTTCAGCAAACAAGAGTGGATAAACTGACCCAAGGTCGCCAGACCTATGACTGGACTTTGAATAGAAACCAACCGGCTGCAACTGCTTTGGCCAACACTATAGAGGTCTTCAGATCTAACGGTCTAACAGCCAATGAATCGGGGAGACTAATAGATTTCCTCAAGGATGTGATGGAGTCAATGGATAAAGAAGAAATGGAAATAACAACACATTTCCAGAGAAAGAGAAGAGTAAGGGACAACATGACCAAAAAAATGGTCACACAAAGAACAATAGGGAAGAAGAAGCAGAGGCTGAATAAGAGGAGCTACTTGATAAGAGCATTGACCCTGAACACAATGACAAAAGATGCAGAAAGAGGCAAATTGAAGAGGCGGGCAATTGCTACACCCGGAATGCAGATCAGGGGATTTGTGTACTTTGTTGAAACGCTAGCGAGAAGCATCTGTGAAAAGCTTGAGCAATCTGGACTCCCGGTTGGAGGGAATGAGAAGAAGGCTAAACTAGCAAACGTCGTGAGAAAGATGATGACTAATTCTCAAGATACAGAGCTTTCCTTTACAATTACTGGAGACAACACCAAATGGAATGAGAATCAGAATCCTCGAATGTTTATGGCAATGATAACATACATCACAAGAAACCAACCTGAATGGTTTAGAAATGTCTTGAGTATTGCCCCTATCATGTTCTCAAACAAGATGGCGAGATTAGGAAAAGGATACATGTTCGAGAGTAAGAGTATGAAACTGCGGACACAAATACCAGCAGAAATGCTTGCAAACATTGACTTGAAATACTTCAATGAATCAACGAGAAAGAAAATAGAGAAAATAAGACCTCTCCTAATAGATGGCACAGCATCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTGAGCACCGTTTTAGGAGTCTCAATTCTGAACCTTGGGCAAAAGAGATACACCAAAACCACGTACTGGTGGGATGGACTCCAATCCTCTGATGATTTCGCCCTCATAGTGAATGCACCAAATCATGAAGGAATACAAGCAGGGGTGGATAGGTTCTATAGGACCTGTAAACTGGTTGGGATCAATATGAGCAAAAAGAAGTCTTACATAAATCGAACAGGGACATTTGAGTTCACAAGCTTTTTCTACCGCTATGGATTTGTAGCCAACTTCAGTATGGAGCTGCCCAGTTTTGGAGTGTCTGGGATTAACGAATCGGCTGATATGAGCATTGGAGTCACAGTGATAAAAAACAATATGATAAACAATGATCTTGGACCAGCAACAGCTCAGATGGCTCTTCAGCTATTCATCAAGGACTATAGGTACACATACCGATGCCACCGGGGTGACACCCAAATTCAAACGAGGAGATCATTCGAGCTAAAGAAGCTGTGGGAGCAGACCCGTTCGAAGGCAGGACTGTTGGTTTCAGATGGGGGACCAAACCTGTACAATATCCGGAATCTCCACATCCCAGAGGTCTGCTTGAAGTGGGAACTAATGGACGAAGATTACCAGGGCAGACTGTGTAATCCTCTTAATCCGTTTGTCAGTCATAAAGAAATTGAGTCCGTAAACAATGCTGTGGTAATGCCAGCCCATGGTCCAGCCAAGAGCATGGAATATGATGCCGTTGCCACTACACATTCATGGATCCCTAAGAGGAATCGTTCCATTCTCAATACTAGCCAAAGGGGAATTCTTGAGGATGAACAGGTGTACCAGAAGTGCTGCAATCTATTTGAGAAATTCTTCCCCAGTAGTTCATACAGGAGGCCAGTTGGAATTTCCAGCATGGTAGAGGCCATGGTGTCGAGGGCCCGAATTGACGCACGAATTGACTTCGAGTCTGGAAGGATTAAGAAAGAAGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAAAAATAGTGAATTTAGCTTGTCCTTCATGAAAAAATGCCTTGTTTCTA
        -:not both available
        .:match
        o:difference



        Code:
        >A/Memphis/103/1976(H3N2) segment 2
>A/Memphis/104/1976(H3N2) segment 2
------------...................................o..o........o
..............o.....o..o...........o...........o............
..................................................o........o
..o..........................o..o........o.....o............
o.............o..........................o.....oo...........
..o..........................o...........o..oo..............
..o.....o........o.....o.................o.................o
..o..o.....o........o........o..o..............o...........o
..o...........o.....o.....o..o.............................o
..............o........o...........o.....o.....o...........o
..............o..........................o..............oo..
..o.....o.....oo.o...........o..oo.............o............
.....o.....o.....oo.o..o.....o........o.....o.....o..o..o...
..............o.....o..o.....o.....o........o..o........o..o
........o.....o........o.....o.....o..o.....................
..o.....o...........o..o.................o..o..o........o...
..o..............oo....o.....o.....o.......o...o............
..o.....oo.oo....o..o..o..o..o..............o.........o....o
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.........................................-------------------
-
>A/Memphis/103/1976(H3N2) segment 2
>A/quail/Dubai/301/2000(H9N2) segment 2
------------...................................o..o........o
..............o.....o..o...........o...........o............
..................................................o........o
..o..........................o..o........o.....o............
o.............o..........................o.....oo...........
..o..........................o...........o..oo..............
..o.....o........o.....o.................o.................o
..o..o.....o........o........o..o..............o...........o
..o...........o.....o.....o..o.............................o
..............o........o...........o.....o.....o...........o
..............o..........................o..............oo..
..o.....o.....oo.o...........o..oo.............o............
.....o.....o.....oo.o..o.....o........o.....o.....o..o..o...
..............o.....o..o.....o.....o........o..o........o..o
........o.....o........o.....o.....o..o.....................
..o.....o...........o..o.................o..o..o........o...
..o..............oo....o.....o.....o.......o...o............
..o.....oo.oo....o..o..o..o..o..............o.........o....o
.................o........o.....o..o..o.....................
..o....o.......o.o..o..o..............o...........o.........
..o.....o...........o.....o.................................
........o..o..o.................o.....o.............o.......
.....o..o.......................o...........o..o............
..............o..o...........o........o.....o..o.....o..oo.o
..o..o..............o........o..o......o.......o........o...
...........o.......................o..o.....................
..o........o.....o..o..o....................o...........o...
..o..............o..o..............o..............o..o......
..o.....o..o..o.....o..o......o.o..o.....o........o.........
.............................o.....o..o...........o.........
.....o..o......o.o.................o........o..o............
.....o........o..o..o..o.....o.....o...........o.....o......
..o.....o..o.....o..o...............o..........o............
.................o..o.....o........o..o.....o..o........o..o
..o........o..o..............................o....o.....o...
.....o..o..o........o..o....................o..o............
........o..............o........o.....o..oo.................
...o.o.................oo.o...................o.............
.................o.......................-------------------
-
>A/Memphis/104/1976(H3N2) segment 2
>A/quail/Dubai/301/2000(H9N2) segment 2
------------................................................
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.................o........o.....o..o..o.....................
..o....o.......o.o..o..o..............o...........o.........
..o.....o...........o.....o.................................
........o..o..o.................o.....o.............o.......
.....o..o.......................o...........o..o............
..............o..o...........o........o.....o..o.....o..oo.o
..o..o..............o........o..o......o.......o........o...
...........o..o....................o..o.....................
..o........o.....o..o..o....................o...........o...
..o..............o..o..............o..............o..o......
..o.....o..o..o.....o..o......o.o..o.....o........o.........
.............................o.....o..o...........o.........
.....o..o......o.o.................o........o..o............
.....o........o..o..o..o.....o.....o...........o.....o......
..o.....o..o.....o..o...............o..........o............
.................o..o.....o........o..o.....o..o........o..o
..o........o..o..............................o....o.....o...
.....o..o..o........o..o....................o..o............
........o..............o........o.....o..oo.................
...o.o.................oo.o...................o.............
.................o.......................-------------------
-
        Last edited by gsgs; March 28, 2007, 01:58 AM.
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment

        • #5
          Re: H3N2, 1976

          sequences retracted now.

          " The sample provider was unable to confirm the source of this sample.
          The sequences associated with this virus are therefore suppressed in
          GenBank now."
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment

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