t/data/genewise.out

   1 genewise $Name: not supported by cvs2svn $ (unreleased release)
   2 This program is freely distributed under a GPL. See source directory
   3 Copyright (c) GRL limited: portions of the code are from separate copyright
   4
   5 Query protein:       SINFRUP00000067802
   6 Comp Matrix:         blosum62.bla
   7 Gap open:            12
   8 Gap extension:       2
   9 Start/End            default
  10 Target Sequence      Scaffold_2042.1
  11 Strand:              forward
  12 Start/End (protein)  default
  13 Gene Paras:          human.gf
  14 Codon Table:         codon.table
  15 Subs error:          1e-05
  16 Indel error:         1e-05
  17 Model splice?        model
  18 Model codon bias?    flat
  19 Model intron bias?   tied
  20 Null model           syn
  21 Algorithm            623
  22
  23 genewise output
  24 Score 2054.68 bits over entire alignment
  25 Scores as bits over a synchronous coding model
  26
  27 Warning: The bits scores is not probablistically correct for single seqs
  28 See WWW help for more info
  29
  30 SINFRUP00000067    1 LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVE
  31                      LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVE
  32                      LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVE
  33 Scaffold_2042.122265 cgggcttcaaacctatccaggaagaaactagatcgatgtaaggg
  34                      taaaatcaggggtcgcctagtaacattagatcttaacaactata
  35                      gcgcgactccttccgtcgaacgaggaggtacaggcccccattag
  36
  37
  38 SINFRUP00000067   45                            KGARGQMLFDKVCEHLNLLERD
  39                                                 KGARGQMLFDKVCEHLNLLERD
  40                                                 KGARGQMLFDKVCEHLNLLERD
  41 Scaffold_2042.122397 GTGAGCA  Intron 1       CAGaggagcactgagtgccatcgag
  42                      <0-----[22397  :  24223]-0>agcggatttaatgaatattaga
  43                                                 aacgcagcttaatgtatacgac
  44
  45
  46 SINFRUP00000067   67 YFGITYRDVENQK                           NWLDPSKEL
  47                      YFGITYRDVENQK                           NWLDPSKEL
  48                      YFGITYRDVENQK                           NWLDPSKEL
  49 Scaffold_2042.124290 ttgaatagggacaGTAAATA  Intron 2       CAGatcgctagc
  50                      atgtcagataaaa<0-----[24329  :  24470]-0>agtaccaat
  51                      ctccatactgtgg                           tggtttagg
  52
  53
  54 SINFRUP00000067   89 KKQIR                              GPWNFAFNVKFYPP
  55                      KKQIR                              GPWNFAFNVKFYPP
  56                      KKQIR          T:T[act]            GPWNFAFNVKFYPP
  57 Scaffold_2042.124498 aacacAGTAAGCA  Intron 3       CAGCTgctatgtagattcc
  58                      aaatg <1-----[24514  :  24586]-1>  gcgatctatatacc
  59                      aggcg                              tcgctcctcgtcta
  60
  61
  62 SINFRUP00000067  109 DPVQLAEDIT                              YYLCLQLRD
  63                      DPVQLAEDIT                              YYLCLQLRD
  64                      DPVQLAEDIT           R:R[agg]           YYLCLQLRD
  65 Scaffold_2042.124631 gcgccgggaaAGGTAAGAG  Intron 4       CAGGttttcccag
  66                      actatcaatc  <2-----[24663  :  24816]-2> aatgtatga
  67                      ttcggtgcca                              ctgtgggat
  68
  69
  70 SINFRUP00000067  129 DVVSGRLPCSFATHTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQT
  71                      DVVSGRLPCSFATHTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQT
  72                      DVVSGRLPCSFATHTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQT
  73 Scaffold_2042.124845 gggtgccctttgacagcgttagctgcggtgcggcgagtcagcccgcaca
  74                      attcggtcgctccacttgcactacatgaaaaaatggaatgatgtccaac
  75                      tgtgctgccttcccatactcgggtagactctgggccccctggctaccgc
  76
  77
  78 SINFRUP00000067  178 KELEEKVMELHKSY                              GMTPG
  79                      KELEEKVMELHKSY                              GMTPG
  80                      KELEEKVMELHKSY           K:K[aag]           GMTPG
  81 Scaffold_2042.124992 agcggagagccaatAAGTTGGTT  Intron 5       CAGGgaacg
  82                      aataaattataaga  <2-----[25036  :  25161]-2> gtccg
  83                      agtgagcgaccgcc                              ggatg
  84
  85
  86 SINFRUP00000067  198 EAEMHFLENAKKLSMYGVDLHHAK
  87                      EAEMHFLENAKKLSMYGVDLHHAK
  88                      EAEMHFLENAKKLSMYGVDLHHAK
  89 Scaffold_2042.125178 gggactcgagaactatgggcccgaGTAATAA  Intron 6
  90                      acatattaacaatctagtataaca<0-----[25250  :  26185]
  91                      aaggccgatcgggcgccttccctg
  92
  93
  94 SINFRUP00000067  222    DSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIK
  95                         DSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIK
  96                         DSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIK
  97 Scaffold_2042.126183 TAGgtggggaacggttagccatagatcaaatgtcaacaattaaaattaa
  98                      -0>acagtatttgtgcggtttagagtgtagtcgcattatcaagaatata
  99                         ctgatgcggatcgccgtccacgggccgttgtaacgttcggtcccca
 100
 101
 102 SINFRUP00000067  268 IRPGE                           FEQFESTIGFKLPNHRA
 103                      IRPGE                           FEQFESTIGFKLPNHRA
 104                      IRPGE                           FEQFESTIGFKLPNHRA
 105 Scaffold_2042.126324 accggGTAATTA  Intron 7       CAGtgctgaaagtaccaccg
 106                      tgcga<0-----[26339  :  26457]-0>taatagctgtatcaagc
 107                      ctgcg                           tggtgcgctcgtctttt
 108
 109
 110 SINFRUP00000067  290 AKRLWKVCVEHHTFFRQVMKEVL
 111                      AKRLWKVCVEHHTFFRQVMKEVL
 112                      AKRLWKVCVEHHTFFRQVMKEVL           G:G[ggg]
 113 Scaffold_2042.126509 gaactagtggccattacgaaggcGGGTTGCCA  Intron 8
 114                      cagtgatgtaaacttgattaatt  <2-----[26580  :  26864]
 115                      cagcggctggtccccgacggggg
 116
 117
 118 SINFRUP00000067  313     LVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIRPAPFFERS
 119                          LVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIRPAPFFERS
 120                          LVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIRPAPFFERS
 121 Scaffold_2042.126862 CAGGcgtcggccaatcacgtatctagaacgcaccgatcaaacgcttgct
 122                      -2> ttccacccaattgtgcatgagggcacacggcgcattgcccttagc
 123                          agttggtaggcgttctgtcctcaggtgcagcctgctattgctgtc
 124
 125
 126 SINFRUP00000067  359 SSKRYNMSRSLDG                              SSADGV
 127                      SSKRYNMSRSLDG                              SSADGV
 128                      SSKRYNMSRSLDG          D:D[gac]            SSADGV
 129 Scaffold_2042.127001 taactaatcatggGGTAGGAT  Intron 9       AAGACatgggg
 130                      cgagaatcggtag <1-----[27041  :  27314]-1>  gccagt
 131                      ccacccgcttata                              ctttag
 132
 133
 134 SINFRUP00000067  379 ARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSPLHQETKV
 135                      ARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSPLHQETKV
 136                      ARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSPLHQETKV
 137 Scaffold_2042.127335 gcgagaaaaagacgaaggggaggcgggaaggggacgcggtaccccgaag
 138                      cgtagattcctccagacaaaagaaaacaaaccaacaccccgctaaacat
 139                      tatgatccctatagaaaaagcagggtcgctgacgactttcctccaaaga
 140
 141
 142 SINFRUP00000067  428 TL                              DPLRSELSLPSSPISFT
 143                      TL                              DPLRSELSLPSSPISFT
 144                      TL          D:D[gac]            DPLRSELSLPSSPISFT
 145 Scaffold_2042.127482 acGGTCAACC  Intron 10      CAGACgccctgctccttcatta
 146                      ct <1-----[27489  :  28576]-1>  actgcatctcccctctc
 147                      aa                              tccctgctccattcact
 148
 149
 150 SINFRUP00000067  448 KIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQALLLVA
 151                      KIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQALLLVA
 152                      KIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQALLLVA
 153 Scaffold_2042.128630 aaccacagagcacgttgacgaaaagctcccgcggcaggccggcgtccgg
 154                      atgggggaacaagccctgcgaggcgggggactcagaccttaaacttttc
 155                      aagggcggcatgaccactacgccagtcctgctttcatggatgacggcga
 156
 157
 158 SINFRUP00000067  497 RKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPEC
 159                      RKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPEC
 160                      RKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPEC
 161 Scaffold_2042.128777 cacacgcgaacggacttttccccgcttgtggggtaatcgctaactccgt
 162                      gaagtaaggaaggcttctctatcatccttaaagatctcatcatgttcag
 163                      aggagggcgttccacccccgcgccgctcgcactccccctgcagccctgt
 164
 165
 166 SINFRUP00000067  546 AQNFLPIKS                              YLCSLLLFTL
 167                      AQNFLPIKS                              YLCSLLLFTL
 168                      AQNFLPIKS           P:P[cct]           YLCSLLLFTL
 169 Scaffold_2042.128924 gcatccaatCCGTCACTC  Intron 11      CAGTtcttccctac
 170                      caattctac  <2-----[28953  :  30816]-2> atgcttttct
 171                      ggccgccga                              ttcggatctc
 172
 173
 174 SINFRUP00000067  566 FTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQIL
 175                      FTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQIL
 176                      FTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQIL
 177 Scaffold_2042.130848 tatttctccatccctttggacacaaacatacatagcatagccttaccac
 178                      tcttttgttactatcctctggaacgataagtgacgtcttagcgctaatt
 179                      cccttttaatttccctctctgggggtgacacgctgcttctgccggtact
 180
 181
 182 SINFRUP00000067  615 DILTRCPEPSASTISHFAVSILAYCF
 183                      DILTRCPEPSASTISHFAVSILAYCF
 184                      DILTRCPEPSASTISHFAVSILAYCF
 185 Scaffold_2042.130995 gacaatcgctgtaaactggtatgttt
 186                      attcggcaccccctgatctcttcagt
 187                      cccaaccgagaccctcttcccgtccc
 188
 189
 190 SINFRUP00000067  641                               EVVKHQTNISELKRSFLET
 191                                                    EVVKHQTNISELKRSFLET
 192                                S:S[tct]            EVVKHQTNISELKRSFLET
 193 Scaffold_2042.131073 TGTTGTCA  Intron 12      CAGCTgggaccaaaagcacttcga
 194                       <1-----[31074  :  31980]-1>  attaaacatgatagcttac
 195                                                    ggcacgccccaggcccggg
 196
 197
 198 SINFRUP00000067  661 GDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSV
 199                      GDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSV
 200                      GDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSV
 201 Scaffold_2042.132040 gggacgcagtgaactttcattcatgggcaagccggag
 202                      gagcagccagaagtcccctgccgtaaccttactatgt
 203                      ttcgacgcagggggcgtcgcaaattgaggtgggtacc
 204
 205
 206 SINFRUP00000067  698                               ERTSDSQEDVSERSMLKVS
 207                                                    ERTSDSQEDVSERSMLKVS
 208                                D:D[gat]            ERTSDSQEDVSERSMLKVS
 209 Scaffold_2042.132151 GGTCTGCA  Intron 13      CAGATgcatgtcgggtgatataga
 210                       <1-----[32152  :  33223]-1>  agccacaaatcagcttatg
 211                                                    gactccggcggggagggcc
 212
 213
 214 SINFRUP00000067  718 PRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKE
 215                      PRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKE
 216                      PRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKE
 217 Scaffold_2042.133283 caggacggtcgaagaagacaatagggcagggggcgggggggagtcctag
 218                      cgctcaatcactgaaaggttttaacaaaaaaaacgacagtaaatcccaa
 219                      cattagagggcctcggagttcgattataggcaacagtacgggagtaaag
 220
 221
 222 SINFRUP00000067  767 KEMVKEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSW
 223                      KEMVKEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSW
 224                      KEMVKEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSW
 225 Scaffold_2042.133430 agagaggggggcgtaaagaaacccaggaaaagaccaagagtcaagagtt
 226                      aattaaaccattcctcgataaaacatatacagcaataggaccaacttcg
 227                      aagtaacctttgctaagacgggtgggaaatccgagtcttcgtagcgggg
 228
 229
 230 SINFRUP00000067  816 ISEEVKTVATKEVSEGESVEAPQQTAEIFTFEEEQSKSSPTQITVSESS
 231                      ISEEVKTVATKEVSEGESVEAPQQTAEIFTFEEEQSKSSPTQITVSESS
 232                      ISEEVKTVATKEVSEGESVEAPQQTAEIFTFEEEQSKSSPTQITVSESS
 233 Scaffold_2042.133577 atgggaaggaaggagggagggcccaggatatgggctatacacaagtgtt
 234                      tcaatactccaatgagagtaccaaccattctaaaacacgccatctcacc
 235                      ctggggtcgagaatgagctagggagggccctagggagccgcgcattata
 236
 237
 238 SINFRUP00000067  865 ASFAVV                              LDTTDAGTKEMPV
 239                      ASFAVV                              LDTTDAGTKEMPV
 240                      ASFAVV           H:H[cat]           LDTTDAGTKEMPV
 241 Scaffold_2042.133724 gttgggCAGTATAAA  Intron 14      GAGTcgaagggaagacg
 242                      cctctt  <2-----[33744  :  35243]-2> taccacgcaatct
 243                      tttgga                              tcctttacaggcg
 244
 245
 246 SINFRUP00000067  885 IHTETKTITYESAE                           VDTNGDLD
 247                      IHTETKTITYESAE                           VDTNGDLD
 248                      IHTETKTITYESAE                           VDTNGDLD
 249 Scaffold_2042.135284 acagaaaaatgtggGTACACA  Intron 15      CAGggaaggtg
 250                      tacacactcaacca<0-----[35326  :  36271]-0>tacagata
 251                      ccagaatcccgtag                           tctttcgc
 252
 253
 254 SINFRUP00000067  907 PGVLLSAQTITSEITSTTTTTHITK
 255                      PGVLLSAQTITSEITSTTTTTHITK
 256                      PGVLLSAQTITSEITSTTTTTHITK
 257 Scaffold_2042.136296 cggccagcaaatgaaaaaaaacaaaGTCAGTT  Intron 16
 258                      cgtttgcactccatcgcccccatca<0-----[36371  :  36567]
 259                      cttcgttgcctaatccccacaccag
 260
 261
 262 SINFRUP00000067  932    MVKGGISETRIEKRIVISGDADIDHDQ
 263                         MVKGGISETRIEKRIVISGDADIDHDQ
 264                         MVKGGISETRIEKRIVISGDADIDHDQ
 265 Scaffold_2042.136565 CAGagaggatgaaagaaagatggggagcgc
 266                      -0>ttaggtcacgtaagtttcgacataaaa
 267                         ggaagtaaaacgagcccaatacctctg
 268
 269
 270 SINFRUP00000067  959                            ALAQAIKEAKEQHPDMSVTKVV
 271                                                 ALAQAIKEAKEQHPDMSVTKVV
 272                                                 ALAQAIKEAKEQHPDMSVTKVV
 273 Scaffold_2042.136649 GTCTCTT  Intron 17      CAGgcgcgaaggagcccgatgaagg
 274                      <0-----[36649  :  36954]-0>ctcactaacaaaacatctcatt
 275                                                 tgtgcaagtaagttcgagcaag
 276
 277
 278 SINFRUP00000067  981 VHKETEITPEEGED
 279                      VHKETEITPEEGED
 280                      VHKETEITPEEGED
 281 Scaffold_2042.137021 gcagagaacggggg
 282                      taaacatccaagaa
 283                      atagagcgaagggc
 284
 285
 286 //
 287 Gene 1
 288 Gene 22265 37062
 289   Exon 22265 22396 phase 0
 290      Supporting 22265 22396 1 44
 291   Exon 24224 24328 phase 0
 292      Supporting 24224 24328 45 79
 293   Exon 24471 24513 phase 0
 294      Supporting 24471 24512 80 93
 295   Exon 24587 24662 phase 1
 296      Supporting 24589 24660 95 118
 297   Exon 24817 25035 phase 2
 298      Supporting 24818 25033 120 191
 299   Exon 25162 25249 phase 2
 300      Supporting 25163 25249 193 221
 301   Exon 26186 26338 phase 0
 302      Supporting 26186 26338 222 272
 303   Exon 26458 26579 phase 0
 304      Supporting 26458 26577 273 312
 305   Exon 26865 27040 phase 2
 306      Supporting 26866 27039 314 371
 307   Exon 27315 27488 phase 1
 308      Supporting 27317 27487 373 429
 309   Exon 28577 28952 phase 1
 310      Supporting 28579 28950 431 554
 311   Exon 30817 31073 phase 2
 312      Supporting 30818 31072 556 640
 313   Exon 31981 32151 phase 1
 314      Supporting 31983 32150 642 697
 315   Exon 33224 33743 phase 1
 316      Supporting 33226 33741 699 870
 317   Exon 35244 35325 phase 2
 318      Supporting 35245 35325 872 898
 319   Exon 36272 36370 phase 0
 320      Supporting 36272 36370 899 931
 321   Exon 36568 36648 phase 0
 322      Supporting 36568 36648 932 958
 323   Exon 36955 37062 phase 0
 324      Supporting 36955 37062 959 994
 325 //