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Seq 206 Supplemental page

    1.     
    2.  
    3. Table S1: Sequence Composition

       Running the EMBOSS Compseq program

     

    #
    # Output from 'compseq'
    #
    # The Expected frequencies are calculated on the (false) assumption that every
    # word has equal frequency.
    #
    
    Word size	2
    Total count	399999
    
    #
    # Word	Obs Count	Obs Frequency	Exp Frequency	Obs/Exp Frequency
    #
    AA	32253		0.0806327	0.0625000	1.2901232
    AC	22240		0.0556001	0.0625000	0.8896022
    AG	25321		0.0633027	0.0625000	1.0128425
    AT	26591		0.0664777	0.0625000	1.0636427
    CA	27387		0.0684677	0.0625000	1.0954827
    CC	24315		0.0607877	0.0625000	0.9726024
    CG	17353		0.0433826	0.0625000	0.6941217
    CT	25041		0.0626027	0.0625000	1.0016425
    GA	25637		0.0640927	0.0625000	1.0254826
    GC	21932		0.0548301	0.0625000	0.8772822
    GG	23410		0.0585251	0.0625000	0.9364023
    GT	20733		0.0518326	0.0625000	0.8293221
    TA	21125		0.0528126	0.0625000	0.8450021
    TC	25605		0.0640127	0.0625000	1.0242026
    TG	25629		0.0640727	0.0625000	1.0251626
    TT	31553		0.0788827	0.0625000	1.2621232
    
    Other	3874		0.0096850	0.0000000	10000000000.0000000
    

      

     

    Table S2: Location of Undefined Sequences

    Length Position Segment
    Length
    Length Position

    Segment
    Length

    Length Position Segment
    Length
    100 4589  4588 100 109009  43126 100 244916  25967
    100 11963  7274 100 114786  5677 100 246605  1589
    100 28019  15956 100 129409  14523 100 248594  1889
    100 30979  2860 100 130472  963 100 281110  32416
    35 31903  824 100 132207  1635 100 295700  14490
    100 33807  1869 100 134690  2383 100 301207  5407
    100 47007  13100 100 145489  10699 100 335790

     34483

    100 47695  588 100 151264  5675 100 336771  881
    100 57524  9729 100 153427  2063 100 339971  3100
    100 58067  443 100 168304  14777 100 341119  1048
    100 59292  1125 100 171779  3375 100 342434  1215
    100 63960  4568 100 176152  4273 100 372483  29949
    100 65783  1723 100 218849  42597 100 379037  6454

    Position is the position of the first N in the sequence.  Segment is the length of the region, not including Ns, between the first N and the last N of the previous run.  

      

     Table S3: CpG analysis

    Running the EMBOSS cpgplot program

     

    CPGPLOT islands of unusual CG composition
    seq206 from 1 to 400000
    
         Observed/Expected ratio > 0.60
         Percent C + Percent G > 50.00
         Length > 200
    
     Length 298 (6657..6954)
    
     Length 887 (8774..9660)
    
     Length 284 (10838..11121)
    
     Length 214 (13617..13830)
    
     Length 317 (14964..15280)
    
     Length 1258 (15323..16580)
    
     Length 979 (16658..17636)
    
     Length 353 (17655..18007)
    
     Length 1043 (18018..19060)
    
     Length 2425 (19064..21488)
    
     Length 4419 (21492..25910)
    
     Length 1309 (25997..27305)
    
     Length 270 (27330..27599)
    
     Length 1259 (28210..29468)
    
     Length 399 (29652..30050)
    
     Length 402 (31258..31659)
    
     Length 237 (36118..36354)
    
     Length 357 (41647..42003)
    
     Length 417 (43176..43592)
    
     Length 278 (45034..45311)
    
     Length 404 (46233..46636)
    
     Length 234 (48124..48357)
    
     Length 377 (51788..52164)
    
     Length 436 (52167..52602)
    
     Length 420 (57006..57425)
    
     Length 365 (58281..58645)
    
     Length 295 (59408..59702)
    
     Length 557 (61049..61605)
    
     Length 302 (66137..66438)
    
     Length 338 (66584..66921)
    
     Length 494 (67274..67767)
    
     Length 729 (68201..68929)
    
     Length 229 (68937..69165)
    
     Length 2788 (69224..72011)
    
     Length 503 (72013..72515)
    
     Length 488 (72536..73023)
    
     Length 499 (73124..73622)
    
     Length 462 (73637..74098)
    
     Length 952 (74223..75174)
    
     Length 812 (75245..76056)
    
     Length 291 (81289..81579)
    
     Length 479 (82013..82491)
    
     Length 1511 (85216..86726)
    
     Length 454 (86914..87367)
    
     Length 598 (87402..87999)
    
     Length 381 (88923..89303)
    
     Length 713 (90548..91260)
    
     Length 367 (92180..92546)
    
     Length 493 (92646..93138)
    
     Length 350 (93151..93500)
    
     Length 214 (93518..93731)
    
     Length 755 (93736..94490)
    
     Length 812 (94761..95572)
    
     Length 628 (96179..96806)
    
     Length 542 (96882..97423)
    
     Length 1583 (97442..99024)
    
     Length 907 (100913..101819)
    
     Length 545 (102511..103055)
    
     Length 972 (103160..104131)
    
     Length 291 (104176..104466)
    
     Length 584 (107978..108561)
    
     Length 728 (113452..114179)
    
     Length 368 (120064..120431)
    
     Length 365 (120671..121035)
    
     Length 333 (121622..121954)
    
     Length 496 (125781..126276)
    
     Length 325 (126837..127161)
    
     Length 216 (127431..127646)
    
     Length 204 (128075..128278)
    
     Length 580 (132507..133086)
    
     Length 307 (136656..136962)
    
     Length 584 (141041..141624)
    
     Length 405 (142636..143040)
    
     Length 219 (143721..143939)
    
     Length 280 (144572..144851)
    
     Length 281 (147019..147299)
    
     Length 516 (149239..149754)
    
     Length 205 (153591..153795)
    
     Length 442 (156718..157159)
    
     Length 310 (160573..160882)
    
     Length 328 (161458..161785)
    
     Length 594 (161794..162387)
    
     Length 429 (162498..162926)
    
     Length 526 (162946..163471)
    
     Length 616 (163644..164259)
    
     Length 717 (164342..165058)
    
     Length 284 (166124..166407)
    
     Length 518 (166816..167333)
    
     Length 416 (170397..170812)
    
     Length 255 (172236..172490)
    
     Length 203 (172683..172885)
    
     Length 418 (175106..175523)
    
     Length 412 (178637..179048)
    
     Length 296 (179102..179397)
    
     Length 234 (185642..185875)
    
     Length 342 (186271..186612)
    
     Length 404 (186940..187343)
    
     Length 200 (191710..191909)
    
     Length 465 (192527..192991)
    
     Length 526 (193371..193896)
    
     Length 391 (194980..195370)
    
     Length 335 (196170..196504)
    
     Length 427 (201134..201560)
    
     Length 283 (202856..203138)
    
     Length 202 (203250..203451)
    
     Length 258 (207101..207358)
    
     Length 201 (208015..208215)
    
     Length 409 (208862..209270)
    
     Length 202 (209810..210011)
    
     Length 378 (210180..210557)
    
     Length 494 (214335..214828)
    
     Length 235 (216602..216836)
    
     Length 399 (217453..217851)
    
     Length 551 (219685..220235)
    
     Length 211 (226016..226226)
    
     Length 570 (227813..228382)
    
     Length 274 (228945..229218)
    
     Length 364 (229324..229687)
    
     Length 371 (235962..236332)
    
     Length 438 (237298..237735)
    
     Length 319 (237929..238247)
    
     Length 221 (240272..240492)
    
     Length 327 (240647..240973)
    
     Length 269 (246080..246348)
    
     Length 573 (249150..249722)
    
     Length 415 (249944..250358)
    
     Length 290 (256058..256347)
    
     Length 411 (257617..258027)
    
     Length 453 (259763..260215)
    
     Length 335 (260394..260728)
    
     Length 248 (260972..261219)
    
     Length 604 (261586..262189)
    
     Length 584 (262202..262785)
    
     Length 473 (263006..263478)
    
     Length 399 (263480..263878)
    
     Length 464 (264491..264954)
    
     Length 632 (265035..265666)
    
     Length 262 (266356..266617)
    
     Length 446 (266649..267094)
    
     Length 258 (267178..267435)
    
     Length 778 (267466..268243)
    
     Length 400 (268295..268694)
    
     Length 357 (270451..270807)
    
     Length 801 (272294..273094)
    
     Length 230 (278573..278802)
    
     Length 317 (279704..280020)
    
     Length 246 (280612..280857)
    
     Length 288 (281563..281850)
    
     Length 334 (283375..283708)
    
     Length 1050 (283914..284963)
    
     Length 1095 (289308..290402)
    
     Length 904 (292282..293185)
    
     Length 279 (294967..295245)
    
     Length 327 (297227..297553)
    
     Length 225 (301521..301745)
    
     Length 607 (301898..302504)
    
     Length 200 (309009..309208)
    
     Length 852 (310153..311004)
    
     Length 277 (312826..313102)
    
     Length 301 (315239..315539)
    
     Length 205 (319023..319227)
    
     Length 472 (322127..322598)
    
     Length 421 (323223..323643)
    
     Length 276 (325004..325279)
    
     Length 439 (328408..328846)
    
     Length 324 (329471..329794)
    
     Length 289 (337370..337658)
    
     Length 567 (337739..338305)
    
     Length 320 (348683..349002)
    
     Length 1323 (349035..350357)
    
     Length 898 (350429..351326)
    
     Length 727 (351414..352140)
    
     Length 347 (352153..352499)
    
     Length 475 (352567..353041)
    
     Length 750 (353103..353852)
    
     Length 235 (356464..356698)
    
     Length 368 (359382..359749)
    
     Length 228 (361509..361736)
    
     Length 1147 (361795..362941)
    
     Length 614 (363584..364197)
    
     Length 345 (369359..369703)
    
     Length 909 (369721..370629)
    
     Length 1770 (370707..372476)
    
     Length 342 (372574..372915)
    
     Length 2134 (372993..375126)
    
     Length 1673 (375147..376819)
    
     Length 911 (376919..377829)
    
     Length 1184 (377840..379023)
    
     Length 314 (379127..379440)
    
     Length 376 (379538..379913)
    
     Length 537 (379918..380454)
    
     Length 2015 (380457..382471)
    
     Length 989 (382689..383677)
    
     Length 542 (383684..384225)
    
     Length 203 (384305..384507)
    
     Length 1725 (384601..386325)
    
     Length 345 (386383..386727)
    
     Length 1023 (386745..387767)
    
     Length 328 (387845..388172)
    
     Length 270 (388536..388805)
    
     Length 312 (390787..391098)
    
     Length 208 (394357..394564)
    
     Length 240 (399705..399944)
    
    

     

     

    Table S4. Retroelement and Transposon Analysis

      Using the Repeatmasker Sever:

     

    ==================================================
    file name: RM2sequpload_1289767527  
    sequences:             1
    total length:     400000 bp  (396165 bp excl N/X-runs)
    GC level:         46.91 %
    bases masked:     318062 bp ( 79.52 %)
    ==================================================
                   number of      length   percentage
                   elements*    occupied  of sequence
    --------------------------------------------------
    Retroelements          103       292016 bp   73.00 %
       SINEs:                0            0 bp    0.00 %
       Penelope              0            0 bp    0.00 %
       LINEs:                1           63 bp    0.02 %
        CRE/SLACS            0            0 bp    0.00 %
         L2/CR1/Rex          0            0 bp    0.00 %
         R1/LOA/Jockey       0            0 bp    0.00 %
         R2/R4/NeSL          0            0 bp    0.00 %
         RTE/Bov-B           0            0 bp    0.00 %
         L1/CIN4             1           63 bp    0.02 %
       LTR elements:       102       291953 bp   72.99 %
         BEL/Pao             0            0 bp    0.00 %
         Ty1/Copia          64       147160 bp   36.79 %
         Gypsy/DIRS1        36       144484 bp   36.12 %
           Retroviral        0            0 bp    0.00 %
    
    DNA transposons         31        25162 bp    6.29 %
       hobo-Activator        3         1439 bp    0.36 %
       Tc1-IS630-Pogo        0            0 bp    0.00 %
       En-Spm                7        15445 bp    3.86 %
       MuDR-IS905            3          461 bp    0.12 %
       PiggyBac              0            0 bp    0.00 %
       Tourist/Harbinger     3          598 bp    0.15 %
       Other (Mirage,        0            0 bp    0.00 %
        P-element, Transib)
    
    Rolling-circles          0            0 bp    0.00 %
    
    Unclassified:            0            0 bp    0.00 %
    
    Total interspersed repeats:      317178 bp   79.29 %
    
    
    Small RNA:               0            0 bp    0.00 %
    
    Satellites:              0            0 bp    0.00 %
    Simple repeats:          4          229 bp    0.06 %
    Low complexity:         11          655 bp    0.16 %
    ==================================================
    
    * most repeats fragmented by insertions or deletions
      have been counted as one element
                                                          
    
    The query species was assumed to be zea           
    RepeatMasker version open-3.2.9 , default mode
                                       
    run with blastp version 3.0SE-AB [2009-10-30] [linux26-x64-I32LPF64 2009-10-30T17:06:09]
    RepBase Update 20090604, RM database version 20090604
    

     

     

     Table S5: FGENESH gene prediction

       Program: FGENESH

       Input: repeat masked sequence

     

     FGENESH 2.6 Prediction of potential genes in Monocot genomic DNA
     Time    :   Sun Nov 14 16:22:43 2010
     Seq name: seq206 
     Length of sequence: 400000 
     Number of predicted genes 10: in +chain 5, in -chain 5.
     Number of predicted exons 41: in +chain 22, in -chain 19.
     Positions of predicted genes and exons: Variant   1 from   1, Score:275.991821 
       G Str   Feature   Start        End    Score           ORF           Len
    
       1 -      PolA     49258                0.44
       1 -    1 CDSl     49302 -     49609    4.18     49302 -     49607    306
       1 -    2 CDSi     49658 -     49749    5.95     49659 -     49748     90
       1 -    3 CDSf     50239 -     50387    4.28     50241 -     50387    147
       1 -      TSS      51162               -5.08
    
       2 +      TSS      51433               -5.28
       2 +    1 CDSf     51764 -     51931   -2.55     51764 -     51931    168
       2 +    2 CDSi     52229 -     52599   -0.98     52229 -     52597    369
       2 +    3 CDSi     52795 -     52945   14.69     52796 -     52945    150
       2 +    4 CDSi     53136 -     53198    9.59     53136 -     53198     63
       2 +    5 CDSi     53963 -     54153   14.02     53963 -     54151    189
       2 +    6 CDSi     54335 -     54500   -5.63     54336 -     54500    165
       2 +    7 CDSi     55090 -     55251   15.52     55090 -     55251    162
       2 +    8 CDSi     55956 -     56147   16.17     55956 -     56147    192
       2 +    9 CDSi     56247 -     56346    4.35     56247 -     56345     99
       2 +   10 CDSi     56578 -     56712    0.91     56580 -     56711    132
       2 +   11 CDSi     56802 -     56933   13.63     56804 -     56932    129
       2 +   12 CDSl     57040 -     57416   10.97     57042 -     57416    375
       2 +      PolA     57628               -2.36
    
       3 +      TSS     107897               -6.98
       3 +    1 CDSf    107993 -    108484   19.07    107993 -    108484    492
       3 +    2 CDSi    108566 -    108663    2.49    108566 -    108661     96
       3 +    3 CDSl    108694 -    108748   -2.80    108695 -    108748     54
       3 +      PolA    108956               -1.06
    
       4 -      PolA    178270                0.44
       4 -    1 CDSo    178653 -    179015   36.39    178653 -    179015    363
       4 -      TSS     179462               -8.28
    
       5 +      TSS     179643               -7.18
       5 +    1 CDSf    179830 -    179905   -7.66    179830 -    179904     75
       5 +    2 CDSi    181494 -    181552    9.94    181496 -    181552     57
       5 +    3 CDSi    181988 -    182069   13.89    181988 -    182068     81
       5 +    4 CDSi    182581 -    182643    8.17    182583 -    182642     60
       5 +    5 CDSl    182724 -    182842    4.74    182726 -    182842    117
       5 +      PolA    182865               -1.06
    
       6 -      PolA    212437               -1.06
       6 -    1 CDSl    212793 -    212885    3.81    212793 -    212885     93
       6 -    2 CDSi    212986 -    213048    5.89    212986 -    213048     63
       6 -    3 CDSf    213132 -    213251    9.07    213132 -    213251    120
       6 -      TSS     213777               -5.68
    
       7 +      TSS     214267               -6.18
       7 +    1 CDSo    214695 -    214856    6.68    214695 -    214856    162
       7 +      PolA    214937                0.44
    
       8 -      PolA    285882               -4.96
       8 -    1 CDSl    285982 -    286251   21.26    285982 -    286251    270
       8 -    2 CDSi    286335 -    286629   27.59    286335 -    286628    294
       8 -    3 CDSi    286717 -    286846    6.27    286719 -    286844    126
       8 -    4 CDSi    286945 -    287344   19.44    286946 -    287344    399
       8 -    5 CDSi    287551 -    287655    8.17    287551 -    287655    105
       8 -    6 CDSi    287859 -    287984   20.77    287859 -    287984    126
       8 -    7 CDSf    289166 -    289309   21.72    289166 -    289309    144
       8 -      TSS     290753               -4.28
    
       9 +      TSS     337237               -4.98
       9 +    1 CDSo    337665 -    338435   19.89    337665 -    338435    771
       9 +      PolA    338706                0.44
    
      10 -      PolA    395592                0.44
      10 -    1 CDSl    396506 -    396786   11.23    396506 -    396784    279
      10 -    2 CDSi    397623 -    397734   11.93    397624 -    397734    111
      10 -    3 CDSi    397818 -    397859    0.80    397818 -    397859     42
      10 -    4 CDSi    398824 -    398920   -4.97    398824 -    398919     96
      10 -    5 CDSf    399697 -    399962   23.38    399699 -    399962    264
    
    


     

     Table S6: Genemark Gene Prediction

       Program: Eukaryotic GeneMark.hmm

       Input: repeat masked sequence

      

    GeneMark.hmm (Version 2.2a)
    Sequence name: Sun Nov 21 16:23:28 EST 2010
    Sequence length: 240000 bp
    G+C content: 88.26%
    Matrix: corn
    Sun Nov 21 16:23:30 2010

    Predicted genes/exons

    Gene Exon Strand Exon           Exon Range     Exon      Start/End
      #    #         Type                         Length       Frame

      1     4   -  Terminal     49638     49749     112          3 3
      1     3   -  Internal     50239     50349     111          2 3
      1     2   -  Internal     50423     50878     456          2 3
      1     1   -  Initial      51833     51951     119          2 1

      2     2   -  Terminal     52005     52053      49          3 3
      2     1   -  Initial      52143     52339     197          2 1

      3     2   -  Terminal     54017     54175     159          3 1
      3     1   -  Initial      54411     54455      45          3 1

      4     1   +  Initial      56885     56933      49          1 1
      4     2   +  Terminal     57040     57416     377          2 3

      5     4   -  Terminal    101066    101173     108          3 1
      5     3   -  Internal    101218    101620     403          3 3
      5     2   -  Internal    107979    108048      70          2 2
      5     1   -  Initial     108181    108256      76          1 1

      6     1   +  Initial     108281    108484     204          1 3
      6     2   +  Internal    108566    108646      81          1 3
      6     3   +  Terminal    113605    113925     321          1 3

      7     1   +  Initial     150541    150608      68          1 2
      7     2   +  Terminal    150767    150773       7          3 3
      8     1   -  Single      178653    179015     363          3 1

      9     1   -  Terminal    214448    214564     117          3 1

     

    GeneMark.hmm Protein Translations
    Go to: GeneMark.hmm Listing
    Go to: Job Submission

     

    >Sun Nov 21 16:23:28 EST 2010_1|GeneMark.hmm|gene 1|265_aa
    MAILYCTRASGLGMEIVPTVAFALAPRERASCAMAPAAGNHKHGKDGRVESTTNGVFNTL
    SGFEAADRQNSWQYFKMLLSDKESLLDDLEGENSDQSDSDHVTLAISIEDTGVGIPLQAQ
    DRVFTPFMQADSSTSRNYGGTGIGLSISKCLAELMGGQISFVSRPFVGSTFTFSATLKRS
    YKDTSVDSSRSFAVTRYHLKRLGIIVQVVNNLSAVAKAFPGQNGATVSREKATILFIESD
    FWRPETDVQLLNHLRENKNRQLSDG

    >Sun Nov 21 16:23:28 EST 2010_2|GeneMark.hmm|gene 2|81_aa
    MNRPRLETQYAVNGCGGEQVRRDSQLMRKVLSFGGGILQWQMEAPKEHNLDGNLSATMEL
    TPNSMWEGVRKKARKQKEDSA

    >Sun Nov 21 16:23:28 EST 2010_3|GeneMark.hmm|gene 3|67_aa
    MVIAHHYATAYVKSHVTIENLLRANKDPQPIFLCHEFHSMQQGDTSINCYQRIKTTTDTL
    RDVGHPV

    >Sun Nov 21 16:23:28 EST 2010_4|GeneMark.hmm|gene 4|141_aa
    MASDKEHLAFAEQLLSGQTPDVVLLTEASVAGGTSRAMPASSLKEVWIAAARDRGIEYVD
    IGGVSGAETPEHISDLLDCSPSSNSGRKPMVIGCQDVAPFSSNLIVAASQLLESRGTAPG
    LICVTGSLHLVGAVLQQMGRH

    >Sun Nov 21 16:23:28 EST 2010_5|GeneMark.hmm|gene 5|218_aa
    MWEAEGGREAVAEHPSRPCGGGGRRPEDEREETTDDEEGAEEEHTNGNGQIQGAAPSDAI
    SSRLGLNLNGFRLDFRSVAASSGDRAPLNVKLRLNLESLCRPRHQSAVSSSPRPATRPCS
    PSTYRTAQSSGFALETSLRGRKVLPRIRVTPRAGQSGNSSPVLAPNLSPHPVVACFRHSS
    ARSVVSVGEISRQRAILAVTGKLAAAEALWRRLGAVIG

    >Sun Nov 21 16:23:28 EST 2010_6|GeneMark.hmm|gene 6|201_aa
    MARRGLTIMAGGEAEGPLAGFFDYMERLRNYERSGVPRGAGTDSDDGFDLGRMRRLLRRL
    GDPHTHFPAVHIAGTKGKGSTAAFLSNIMRAQGYNLSYHGTEAAPQCFCGGELAGDGQNG
    PLATNLPDRDNLNSESTMVNTIMWLTERAELWRKQATTGCGERLGASTGEEFPDCPARGV
    TLMRGNTFLPRSDVSRAKPEL

    >Sun Nov 21 16:23:28 EST 2010_7|GeneMark.hmm|gene 7|24_aa
    MAMADRHGGQQNSNSIDNQRSMRS

    >Sun Nov 21 16:23:28 EST 2010_8|GeneMark.hmm|gene 8|120_aa
    MGQKPSYLLLLVGLLAIAMLCAGPGHALRQLNDANGGGLELSLGSKAATAGAKTEPLDPS
    LSDDYEVCAVMGYGDGCFVAGGGRMAMALRWGCALLSGAGCGSCRRARGWVAGALWTLMF


    >Sun Nov 21 16:23:28 EST 2010_9|GeneMark.hmm|gene 9|38_aa
    EGTSSSALKARKDRRSRHKRRRHERERRRSASDDDSYR

     

    GeneMark.hmm (Version 2.2a)
    Sequence name: Sun Nov 21 16:29:02 EST 2010
    Sequence length: 160000 bp
    G+C content: 89.07%
    Matrix: corn
    Sun Nov 21 16:29:03 2010

    Predicted genes/exons

    Gene Exon Strand Exon           Exon Range     Exon      Start/End
      #    #         Type                         Length       Frame

      1     6   -  Terminal     45982     46251     270          3 1
      1     5   -  Internal     46335     46629     295          3 3
      1     4   -  Internal     46717     46838     122          2 1
      1     3   -  Internal     47859     47984     126          3 1
      1     2   -  Internal     49166     49450     285          3 1
      1     1   -  Initial      49694     49822     129          3 1

      2     1   +  Initial      97665     97960     296          1 2
      2     2   +  Terminal     98049     98556     508          3 3

      3     1   +  Initial     121821    122045     225          1 3
      3     2   +  Internal    122135    122192      58          1 1
      3     3   +  Internal    122323    122431     109          2 2
      3     4   +  Terminal    122461    122584     124          3 3

      4     2   -  Terminal    159547    159586      40          3 3
      4     1   -  Internal    159697    159953     257          2 1

     

    GeneMark.hmm Protein Translations
    Go to: GeneMark.hmm Listing
    Go to: Job Submission

     

    >Sun Nov 21 16:29:02 EST 2010_1|GeneMark.hmm|gene 1|408_aa
    MSREAQKLDCAAGAGGIGVLSLDLLGQVLEHLREPRDRKTCRLALVAACPKLAAVDLSHC
    VTAGDREAAALAAASELRDLRLDKCLAVTDMGLAKVAVGCPKLEKLSLKWCREISDIGID
    LLAKKCPELRSLNISYLKVGNGSLGSISSLERLEELAMVCCSGIDDEGLELLSKGSDSLQ
    HLAKCSELRILKLGLCSSISDRGIAFISSNCGKLVELDLYRCNSITDDGLAALANGCKRI
    KLLNLCYCNKITDTGLGHLGSLEELTNLELRCLVRVTGIGISSVAIGCKNLIELDLKRCY
    SVDDAGLWALARYALNLRQLTISYCQVTGLGLCHLLSSLRCLQDIKMVHLSWVSIEGFEM
    ALRAACGRLKKLKMLCGLKTVLSPELLQMLQACGCRIRWVNKPLVYKD

    >Sun Nov 21 16:29:02 EST 2010_2|GeneMark.hmm|gene 2|267_aa
    MEAGAPWRLLPLLGVLEGGLLCAMEIAKGNSTGWLGQQAWCCAARGWLLAGKPGIGHGRR
    RPHLLELGSEGVPHHGWNRGEDGRRAQGWMAGALGTSPRERGNRELGHGAAGGWVPLERG
    PGVGSSASEQRGPADRACRAQLGAALRSSGWSKREGAQGEEPWTVLELKRRWGRRPPAAA
    ARQRRSRELGGQGEGCWRPAGKKLHGEEALCWKKIWAPWSCCSPAGSREEGAMVAEGSAQ
    SWRFFCAMHREEESCACGGEEEEGCGG

    >Sun Nov 21 16:29:02 EST 2010_3|GeneMark.hmm|gene 3|171_aa
    MDVVTSMVPTRFTFFLWILPSHDILVSRASQTPPPLLLPLATAEARFCGGALHIFADPTI
    TRDLSVARGPGEDNEAATVKRTQVKTGEHVACEDEIQTRPLVDPLHVEPLLKLSNTDIDE
    FIAFDPVYEPKPNEFITLYLSHNSLEANLGWETQSRLLEATPGQETQLGLA

    >Sun Nov 21 16:29:02 EST 2010_4|GeneMark.hmm|gene 4|98_aa
    EARAPEERLWLGEEHTIAQTLTSLDFWLMFASFLMGVGTGLAVMNNLGQMDVAMGYIDVS
    LFVSMTSIWGFFGRIASGTISEHFIKTRAILRPLPTPR

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