Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/DI1.fa -t gi|397456552|gb|JH738948.1|subseq.fa -E]
Hostname: [ws101062]
** (process:3183): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW
C4 Alignment:
------------
Query: SPP00000002_2.0 # Protein # Iodothyronine deiodinase 1 (DI1) # Human (Homo sapiens)
Target: gi|397456552|gb|JH738948.1|:subseq(11286,101000) Alligator mississippiensis unplaced genomic scaffold scaffold-13070, whole genome shotgun sequence
Model: protein2genome:local
Raw score: 392
Query range: 25 -> 246
Target range: 7156 -> 50482
26 : GlyLysValLeuLeuIleLeuPheProAspArgValLysArgAsnIleLeuAlaMetGly : 45
!.!|||:!!!!!|||:!::!! ! ! !!|||..!!:!!!!||| !||| !:!! !
AlaLysLeuPheLeuValValValAspHisArgThrArgSerAsnAspLeuLysLeuGln
7157 : GCTAAACTATTCTTAGTGGTGGTAGATCATAGAACAAGGAGCAATGATCTCAAGCTGCAG : 7214
46 : Glu{L} >>>> Target Intron 1 >>>> {ys}Thr{G} >>>> Target I : 49
:!!{ } 437 bp { !}|||{|} 1301
Gln{V}+- ++{al}Thr{G}++
7215 : CAA{G}gg.........................ag{TG}ACA{G}gt............. : 7666
50 : ntron 2 >>>> {ly}MetThrArgAsnProHisPheSerHis{A} >>>> Targe : 59
7 bp {||}! ! !!:!||| !||||||..!...{ } 5
++{ly}LysPheGlnAsnPheHisPheGlnArg{A}++
7667 : ............ag{GA}AAGTTTCAAAACTTTCATTTTCAAAGA{A}gt.......... : 20713
60 : t Intron 3 >>>> {sp}AsnTrpIleProThrPhePheSerThrGlnTyrPheTrp : 72
105 bp { }||| :!!||| !|||!:!!!! !.!.! !.!.!::
++{rg}AsnIleValProLeuPheTyrCysLeuAspCysLeuTyr
20714 : ...............ag{GA}AATATAGTTCCTCTATTTTATTGCTTAGACTGCCTATAC : 25854
73 : {Ph} >>>> Target Intron 4 >>>> {e}ValLeuLysValArgTrpGlnArg : 81
{!:} 23260 bp {:} !! ! ! !! !||| |||
{Tr}++ ++{p}Arg***AlaGlyProTrpGlyArg
25855 : {TG}gt.........................ag{G}CGGTGAGCCGGTCCCTGGGGCCGT : 49141
82 : LeuGluAspThr{T} >>>> Target Intron 5 >>>> {hr}GluLeuGlyGly : 90
! ! !!{.} 838 bp {!!}.!.:!!|||!.!
AlaProArgPro{A}++ -+{la}HisValGlyAla
49142 : GCCCCGAGGCCA{G}gt.........................gg{CG}CACGTGGGCGCG : 50006
91 : LeuAlaProAsnCysProValValArgLeuSerGlyGln<->ArgCysAsnIleTrpGlu : 109
! !||||||||| ! !|||:!!||||||..!|||||| ||| ..!:!! !!!:
ArgAlaProAsnProGluValIleArgLeuAspGlyGlnLysArgLeuArgLeuLeuAsp
50007 : CGGGCGCCCAACCCCGAGGTCATCCGGCTGGACGGGCAGAAGCGGCTGCGCCTCCTGGAC : 50066
110 : PheMetGlnGlyAsnArgProLeuValLeuAsnPheGlySerCysThrUnkProSerPhe : 129
||| !::|||!!.||||||||||||||||||||||||||||||||| ||| !!|||
PheAlaArgGlyLysArgProLeuValLeuAsnPheGlySerCysThr***ProProPhe
50067 : TTCGCCCGCGGCAAGCGGCCGCTCGTGCTCAACTTCGGCAGCTGCACCTGACCGCCCTTC : 50126
130 : MetPheLysPheAspGlnPheLysArgLeuIleGluAspPheSerSerIleAlaAspPhe : 149
||| !:::.!. ! |||:!!|||||| !! ! !!||| !..!||||||||||||
MetAlaArgLeuArgAlaPheGlnArgLeuAlaAlaHisPheLeuAspIleAlaAspPhe
50127 : ATGGCCCGCCTGCGCGCCTTCCAGCGCCTGGCCGCGCACTTCCTGGACATCGCCGACTTC : 50186
150 : LeuValIleTyrIleGluGluAlaHisAlaSerAspGlyTrpAlaPheLysAsn<->Asn : 168
|||:!!:!:|||||||||||||||||| !!||||||||||||!.! !..!:!! !
LeuLeuValTyrIleGluGluAlaHisProSerAspGlyTrpValSerSerAspAlaAla
50187 : CTGCTGGTGTACATCGAGGAGGCGCACCCCTCCGACGGCTGGGTCAGCTCGGACGCCGCC : 50246
169 : MetAspIleArgAsnHisGlnAsnLeuGlnAspArgLeuGlnAlaAlaHisLeuLeuLeu : 188
! |||! !!!.|||||| !|||||||||||||||!:!||||||!!.|||:!!! !
TyrLysIleProLysHisGlnCysLeuGlnAspArgLeuArgAlaAlaGlnLeuMetArg
50247 : TACAAGATCCCCAAGCACCAGTGCCTGCAGGACCGGCTGCGGGCGGCGCAGCTCATGCGG : 50306
189 : AlaArgSerProGlnCysProValValValAspThrMetGlnAsnGlnSerSerGlnLeu : 208
! ! !!:!!||| !||||||:!!!.!||||||||||||.!.||| |||||| !
GluGlyAlaProGlyCysProLeuAlaValAspThrMetAspAsnAlaSerSerAlaAla
50307 : GAAGGCGCCCCCGGGTGCCCGCTGGCGGTGGACACCATGGACAACGCCTCCAGCGCCGCC : 50366
209 : TyrAlaAlaLeuProGluArgLeuTyrIleIleGlnGluGlyArgIleLeuTyrLysGly : 228
|||!.!|||! ! !|||||||||||||||:!!||||||! !|||:!!:!!|||:!!|||
TyrGlyAlaTyrPheGluArgLeuTyrIleValGlnGluGluArgValMetTyrGlnGly
50367 : TACGGAGCCTACTTCGAGCGGCTGTACATCGTCCAGGAGGAGCGCGTCATGTACCAGGGC : 50426
229 : LysSerGlyProTrpAsnTyrAsnProGluGluValArgAlaValLeuGluLys : 246
!!|||||| !..!|||!!. !..!|||:!!|||::! !|||!!::!!
GlyArgGlyProGluGlyTyrLysIleSerGluLeuArgSerTrpLeuAspGln
50427 : GGCCGCGGCCCCGAGGGCTACAAGATCTCGGAGCTGCGCAGCTGGCTCGACCAG : 50482
vulgar: SPP00000002_2.0 25 246 . gi|397456552|gb|JH738948.1|:subseq(11286,101000) 7156 50482 + 392 M 21 63 S 0 1 5 0 2 I 0 433 3 0 2 S 1 2 M 1 3 S 0 1 5 0 2 I 0 13013 3 0 2 S 1 2 M 9 27 S 0 1 5 0 2 I 0 5101 3 0 2 S 1 2 M 13 39 S 0 2 5 0 2 I 0 23256 3 0 2 S 1 1 M 12 36 S 0 1 5 0 2 I 0 834 3 0 2 S 1 2 M 17 51 G 0 3 M 64 192 G 0 3 M 79 237
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local gene 7157 50482 392 + . gene_id 1 ; sequence SPP00000002_2.0 ; gene_orientation +
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local cds 7157 7220 . + .
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local exon 7157 7220 . + . insertions 0 ; deletions 0
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice5 7221 7222 . + . intron_id 1 ; splice_site "GG"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local intron 7221 7657 . + . intron_id 1
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice3 7656 7657 . + . intron_id 0 ; splice_site "AG"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local cds 7658 7663 . + .
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local exon 7658 7663 . + . insertions 0 ; deletions 0
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice5 7664 7665 . + . intron_id 2 ; splice_site "GT"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local intron 7664 20680 . + . intron_id 2
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice3 20679 20680 . + . intron_id 1 ; splice_site "AG"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local cds 20681 20710 . + .
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local exon 20681 20710 . + . insertions 0 ; deletions 0
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice5 20711 20712 . + . intron_id 3 ; splice_site "GT"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local intron 20711 25815 . + . intron_id 3
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice3 25814 25815 . + . intron_id 2 ; splice_site "AG"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local cds 25816 25858 . + .
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local exon 25816 25858 . + . insertions 0 ; deletions 0
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice5 25859 25860 . + . intron_id 4 ; splice_site "GT"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local intron 25859 49118 . + . intron_id 4
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice3 49117 49118 . + . intron_id 3 ; splice_site "AG"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local cds 49119 49156 . + .
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local exon 49119 49156 . + . insertions 0 ; deletions 0
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice5 49157 49158 . + . intron_id 5 ; splice_site "GT"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local intron 49157 49994 . + . intron_id 5
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local splice3 49993 49994 . + . intron_id 4 ; splice_site "GG"
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local cds 49995 50482 . + .
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local exon 49995 50482 . + . insertions 6 ; deletions 0
gi|397456552|gb|JH738948.1|:subseq(11286,101000) exonerate:protein2genome:local similarity 7157 50482 392 + . alignment_id 1 ; Query SPP00000002_2.0 ; Align 7157 26 63 ; Align 7660 48 3 ; Align 20683 50 27 ; Align 25818 60 39 ; Align 49120 74 36 ; Align 49997 87 51 ; Align 50051 104 192 ; Align 50246 168 237
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis