Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/GPX1.fa -t gi|397464367|gb|JH731134.1|.subseq.fa -E]
Hostname: [ws101062]
** (process:3219): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW
C4 Alignment:
------------
Query: SPP00000017_2.0 # Protein # Glutathione peroxidase 1 (GPx1) # Human (Homo sapiens)
Target: gi|397464367|gb|JH731134.1|:subseq(120000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-234, whole genome shotgun sequence
Model: protein2genome:local
Raw score: 752
Query range: 8 -> 203
Target range: 53942 -> 57315
9 : AlaAlaAlaAlaAlaGlnSerValTyrAlaPheSerAlaArgProLeuAlaGlyGlyGlu : 28
:!!||| !|||!.!!::.!!:!! !.!.!...!||||||||||||!.!|||||||||
SerAlaLeuAlaGlyArgGlyLeuAlaGlyLeuGluAlaArgProLeuGlyGlyGlyGlu
53943 : TCGGCGCTGGCCGGGCGCGGGCTCGCGGGGCTGGAGGCGCGGCCGCTGGGCGGGGGGGAG : 54000
29 : ProValSerLeuGlySerLeuArgGlyLysValLeuLeuIleGluAsnValAlaSerLeu : 48
|||:!!:!!||||||||||||! !|||::!|||||||||:!!...|||||||||||||||
ProLeuAlaLeuGlySerLeuLeuGlyArgValLeuLeuValSerAsnValAlaSerLeu
54001 : CCGCTGGCGCTGGGCTCGCTGCTGGGCCGGGTGCTCCTGGTCTCCAACGTGGCTTCGCTC : 54060
49 : UnkGlyThrThrValArgAspTyrThrGlnMetAsnGluLeuGlnArgArgLeuGlyPro : 68
|||||||||!.!||||||!:!||||||:!:||||||||||||..!|||! !||||||
***GlyThrThrAlaArgAspPheThrGlnLeuAsnGluLeuGlnGluArgTyrGlyPro
54061 : TGAGGCACCACGGCCCGCGACTTCACGCAGCTCAACGAGCTGCAGGAGCGGTACGGGCCT : 54120
69 : ArgGlyLeuValValLeuGlyPheProCysAsnGlnPheGlyHisGln >>>> Targe : 85
|||||||||:!!|||||||||||||||||||||||||||||||||||| 2
ArgGlyLeuLeuValLeuGlyPheProCysAsnGlnPheGlyHisGln++
54121 : CGCGGGCTGCTCGTCCTGGGCTTCCCCTGCAACCAGTTCGGACACCAGgt.......... : 54173
86 : t Intron 1 >>>> GluAsnAlaLysAsnGluGluIleLeuAsnSerLeuLysTyrV : 99
788 bp |||||||||! |||!!:||||||||| !|||||||||||||
++GluAsnAlaThrAsnAspGluIleLeuLeuSerLeuLysTyrV
54174 : ...............agGAGAATGCCACCAATGATGAGATTCTGCTTTCCTTAAAGTATG : 57001
100 : alArgProGlyGlyGlyPheGluProAsnPheMetLeuPheGluLysCysGluValAsnG : 119
|||||||||||..!|||!:!||||||||||||! :!!||||||||||||!!:|||||||
alArgProGlyAsnGlyTyrGluProAsnPheThrMetPheGluLysCysAspValAsnG
57002 : TCCGTCCTGGCAATGGTTATGAGCCCAATTTTACCATGTTTGAGAAATGCGACGTGAATG : 57061
120 : lyAlaGlyAlaHisProLeuPheAlaPheLeuArgGluAlaLeuProAlaProSerAspA : 139
|||||..!|||||||||||||||.!!||||||!:!|||||||||||| !||| !||||
lyAlaAsnAlaHisProLeuPheThrPheLeuLysGluAlaLeuProPheProHisAspA
57062 : GAGCAAATGCTCACCCACTTTTCACATTTTTGAAAGAGGCATTGCCTTTCCCACATGATG : 57121
140 : spAlaThrAlaLeuMetThrAspProLysLeuIleThrTrpSerProValCysArgAsnA : 159
|| !!..!||||||||||||:!!|||:!!! !|||! !||||||||||||||||||||||
spProValAlaLeuMetThrAsnProGlnTyrIleIleTrpSerProValCysArgAsnA
57122 : ATCCAGTGGCACTGATGACCAATCCACAGTACATCATCTGGTCTCCAGTTTGCAGGAACG : 57181
160 : spValAlaTrpAsnPheGluLysPheLeuValGlyProAspGlyValProLeuArgArgT : 179
||:!!:!!|||||||||||||||||||||:!!||||||||||||:!!|||!!!!:!||||
spIleSerTrpAsnPheGluLysPheLeuIleGlyProAspGlyIleProPheLysArgT
57182 : ACATCTCCTGGAACTTTGAAAAGTTCCTCATTGGCCCTGATGGAATACCTTTCAAGCGTT : 57241
180 : yrSerArgArgPheGlnThrIleAspIleGluProAspIleGluAlaLeuLeuSerGlnG : 199
||||||||||||||:!!|||||| ! |||:!! !||||||||| !||||||..!|||
yrSerArgArgPheGluThrIleLysIleGlnAspAspIleGluLysLeuLeuGlnGlnI
57242 : ACAGCAGACGCTTTGAAACTATCAAGATCCAAGATGATATTGAAAAGCTCCTTCAGCAGA : 57301
200 : lyProSerCysAla : 203
!|||||| !|||
leProSerAsnAla
57302 : TTCCTTCAAATGCT : 57315
vulgar: SPP00000017_2.0 8 203 . gi|397464367|gb|JH731134.1|:subseq(120000,100000) 53942 57315 + 752 M 76 228 5 0 2 I 0 2784 3 0 2 M 119 357
# --- 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|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local gene 53943 57315 752 + . gene_id 1 ; sequence SPP00000017_2.0 ; gene_orientation +
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 53943 54170 . + .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 53943 54170 . + . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 54171 54172 . + . intron_id 1 ; splice_site "GT"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 54171 56958 . + . intron_id 1
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 56957 56958 . + . intron_id 0 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 56959 57315 . + .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 56959 57315 . + . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local similarity 53943 57315 752 + . alignment_id 1 ; Query SPP00000017_2.0 ; Align 53943 9 228 ; Align 56959 85 357
# --- END OF GFF DUMP ---
#
C4 Alignment:
------------
Query: SPP00000017_2.0 # Protein # Glutathione peroxidase 1 (GPx1) # Human (Homo sapiens)
Target: gi|397464367|gb|JH731134.1|:subseq(120000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-234, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 100
Query range: 6 -> 144
Target range: 80754 -> 4137
7 : AlaAlaAlaAlaAlaAlaAlaGlnSerValTyrAlaPheSerAlaArgProLeuAlaGly : 26
||||||||| !::! !! !! !:!! !||||||! !||| !!:!|||! !||||||
AlaAlaAlaArgSerProProGlyAlaSerTyrAlaCysSerArgGlnProArgAlaGly
80754 : GCAGCCGCTCGCAGCCCACCTGGGGCTTCCTATGCCTGCTCCAGACAGCCCCGCGCGGGC : 80697
27 : GlyGluProValSerLeuGlySerLeuArgGlyLysVal >>>> Target Intron : 40
!!|||! !:!! !!! !||| !||| ! ! ! ! 19153 bp
CysGluGlnLeuArgGlnGlyValLeuAlaThrGlyGln+-
80696 : TGCGAGCAGCTGCGGCAGGGAGTGCTAGCCACGGGGCAGgg................... : 80653
41 : 1 >>>> LeuLeuIleGluAsnValAlaSerLeuUnkGlyThrThr{V} >>>> Tar : 53
|||||| !.!...!||| !||| ! ||||||! !{.}
++LeuLeuSerHisGlyVal***SerAlaGlnGlyThrLys{T}++
80652 : ......agCTTCTTTCCCATGGTGTGTGAAGTGCCCAAGGAACGAAA{A}gt........ : 61460
54 : get Intron 2 >>>> {al}ArgAspTyrThrGlnMetAsnGluLeuGlnArgArgL : 66
62 bp {.!} !!! ! !!||| |||..!||||||!:!|||
++{hr}GlyValArgProGlnCysAsnArgLeuGlnGlnArgS
61459 : .................ag{CT}GGTGTCAGACCTCAATGCAACAGGCTACAGCAGAGAA : 61362
67 : euGlyProArg{Gl} >>>> Target Intron 3 >>>> {y}LeuValValLeuG : 75
! !||| !{||} 3574 bp {|}||| !!:!!||||
erGlnProSer{Gl}+- ++{y}LeuPheIleLeuG
61361 : GCCAACCTTCA{GG}gg.........................ag{G}CTGTTCATCCTGG : 57761
76 : lyPheProCysAsnGlnPheGlyHisGln >>>> Target Intron 4 >>>> Gl : 85
|||||||||||||||||||| !!:!!||| 36224 bp !!
lyPheProCysAsnGlnPheArgTyrGln++ ++As
57760 : GCTTCCCCTGCAACCAGTTCAGGTATCAGgt.........................agGA : 21507
86 : uAsnAlaLysAsnGluGluIleLeuAsnSerLeuLys{T} >>>> Target Intron : 98
: !! !:!!|||.!. !!::!!!:!:!! !:!!{ } 4824 bp
pProGluGlnAsnAsnLeuMetValSerAlaAlaGln{G}++
21506 : TCCTGAACAAAATAATCTCATGGTCAGTGCTGCCCAA{G}gt.................. : 21465
99 : 5 >>>> {yr}{V} >>>> Target Intron 6 >>>> {al}ArgProGlyGl : 103
{! }{!} 5523 bp {.!} ! !!..! !
++{lu}{A}++ ++{la}AspSerSerAr
21464 : .......ag{AA}{G}gt.........................ag{CA}GATTCATCAAG : 11106
104 : yGlyPheGluProAsnPheMetLeuPheGluLysCysGluValAsnGlyAlaGlyAlaHi : 123
!!.! ! !.!..!. |||||| ! !|||! ! ||| !!.!!.!..
gAlaSerThrSerGluLeuProLeuPheThrLeuLeuGluGluAlaGlyLeuAlaValAr
11105 : GGCCAGTACTAGTGAACTGCCACTGTTTACCTTGCTTGAGGAAGCAGGACTTGCAGTCAG : 11046
124 : sProLeuPhe{A} >>>> Target Intron 7 >>>> {la}PheLeuArgGluAl : 132
.||| !|||{!} 6843 bp {.!} :!!..!|||
gProThrPhe{G}++ ++{ly}GlnMetGluGluGl
11045 : ACCCACGTTT{G}gt.........................ag{GA}CAGATGGAGGAACA : 4176
133 : aLeuProAlaProSerAspAspAlaThrAlaLeuMet : 144
! !|||||| ! !! !.!.|||||| !|||:!:
nThrProAlaLeuProProGlnAlaThrArgLeuVal
4175 : AACCCCTGCCTTGCCCCCCCAAGCTACAAGGCTTGTA : 4138
vulgar: SPP00000017_2.0 6 144 . gi|397464367|gb|JH731134.1|:subseq(120000,100000) 80754 4137 - 100 M 33 99 5 0 2 I 0 19149 3 0 2 M 13 39 S 0 1 5 0 2 I 0 58 3 0 2 S 1 2 M 16 48 S 0 2 5 0 2 I 0 3570 3 0 2 S 1 1 M 14 42 5 0 2 I 0 36220 3 0 2 M 13 39 S 0 1 5 0 2 I 0 4820 3 0 2 S 1 3 5 0 2 I 0 5519 3 0 2 S 1 2 M 27 81 S 0 1 5 0 2 I 0 6839 3 0 2 S 1 2 M 17 51
# --- 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|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local gene 4138 80754 100 - . gene_id 1 ; sequence SPP00000017_2.0 ; gene_orientation +
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 80656 80754 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 80656 80754 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 80654 80655 . - . intron_id 1 ; splice_site "GG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 61503 80655 . - . intron_id 1
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 61503 61504 . - . intron_id 0 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 61463 61502 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 61463 61502 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 61461 61462 . - . intron_id 2 ; splice_site "GT"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 61401 61462 . - . intron_id 2
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 61401 61402 . - . intron_id 1 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 61349 61400 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 61349 61400 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 61347 61348 . - . intron_id 3 ; splice_site "GG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 57775 61348 . - . intron_id 3
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 57775 57776 . - . intron_id 2 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 57732 57774 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 57732 57774 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 57730 57731 . - . intron_id 4 ; splice_site "GT"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 21508 57731 . - . intron_id 4
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 21508 21509 . - . intron_id 3 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 21468 21507 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 21468 21507 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 21466 21467 . - . intron_id 5 ; splice_site "GT"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 16644 21467 . - . intron_id 5
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 16644 16645 . - . intron_id 4 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 16641 16643 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 16641 16643 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 16639 16640 . - . intron_id 6 ; splice_site "GT"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 11118 16640 . - . intron_id 6
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 11118 11119 . - . intron_id 5 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 11034 11117 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 11034 11117 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 11032 11033 . - . intron_id 7 ; splice_site "GT"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local intron 4191 11033 . - . intron_id 7
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 4191 4192 . - . intron_id 6 ; splice_site "AG"
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local cds 4138 4190 . - .
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local exon 4138 4190 . - . insertions 0 ; deletions 0
gi|397464367|gb|JH731134.1|:subseq(120000,100000) exonerate:protein2genome:local similarity 4138 80754 100 - . alignment_id 1 ; Query SPP00000017_2.0 ; Align 80755 7 99 ; Align 61503 40 39 ; Align 61399 54 48 ; Align 57774 71 42 ; Align 21508 85 39 ; Align 11116 100 81 ; Align 4189 128 51
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis