Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/SECP43.fa -t gi|397461042|gb|JH734459.1|subseq.fa -E]
Hostname: [ws101066]
** (process:3891): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW
C4 Alignment:
------------
Query: SPP00000146_2.0 # Protein # tRNA Sec 1 associated protein 1 (SECp43) # Human (Homo sapiens)
Target: gi|397461042|gb|JH734459.1|:subseq(152395,112049) Alligator mississippiensis unplaced genomic scaffold scaffold-5587, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 1399
Query range: 0 -> 287
Target range: 62489 -> 49999
1 : MetAlaAlaSerLeuTrpMetGlyAsp >>>> Target Intron 1 >>>> LeuG : 11
||||||||||||||||||||||||||| 413 bp ||||
MetAlaAlaSerLeuTrpMetGlyAsp++ ++LeuG
62489 : ATGGCCGCCAGCCTCTGGATGGGAGACgt.........................agCTGG : 62046
12 : luProTyrMetAspGluAsnPheIleSerArgAlaPheAlaThrMetGlyGluThrValM : 31
|||||||||||||||||||||||:!!||||||||||||||||||||||||||| !|||:
luProTyrMetAspGluAsnPheValSerArgAlaPheAlaThrMetGlyGluLeuValL
62045 : AGCCGTACATGGACGAGAACTTTGTTTCGAGAGCCTTCGCCACCATGGGAGAGCTTGTGC : 61986
32 : etSerValLysIleIleArgAsnArgLeuThr{Gl} >>>> Target Intron 2 > : 42
!!||||||||||||||||||||||||||||||{||} 1086 bp
euSerValLysIleIleArgAsnArgLeuThr{Gl}++
61985 : TGAGCGTGAAAATCATCCGCAATCGATTGACG{GG}gt...................... : 61949
43 : >>> {y}IleProAlaGlyTyrCysPheValGluPheAlaAspLeuAlaThrAlaGluL : 60
{|}||||||||||||||||||||||||||||||||||||||||||||||||||||
++{y}IleProAlaGlyTyrCysPheValGluPheAlaAspLeuAlaThrAlaGluL
61948 : ...ag{A}ATTCCTGCGGGCTATTGCTTTGTGGAATTTGCAGATCTGGCTACTGCAGAGA : 60813
61 : ysCysLeuHisLysIleAsnGlyLysProLeuProGlyAlaThrPro >>>> Target : 76
||||||||||||||||||||||||||||||||||||||||||||||| 24
ysCysLeuHisLysIleAsnGlyLysProLeuProGlyAlaThrPro++
60812 : AATGTTTACACAAAATCAATGGAAAACCACTTCCTGGTGCCACACCAgt........... : 60763
77 : Intron 3 >>>> AlaLysArgPheLysLeuAsnTyrAlaThrTyrGlyLysGlnPr : 90
64 bp ||||||||||||||||||||||||||||||||||||||||||||
++AlaLysArgPheLysLeuAsnTyrAlaThrTyrGlyLysGlnPr
60762 : ..............agGCAAAACGATTTAAACTGAATTATGCAACATACGGAAAACAACC : 58259
91 : oAspAsn{Se} >>>> Target Intron 4 >>>> {r}ProGluTyrSerLeuPh : 99
|||||||{||} 1177 bp {|}|||||||||||||||||
oAspAsn{Se}++ ++{r}ProGluTyrSerLeuPh
58258 : TGATAAC{AG}gt.........................ag{T}CCGGAATACTCGCTTTT : 57055
100 : eValGlyAspLeuThrProAspValAspAspGlyMetLeuTyrGluPhePheValLysVa : 119
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
eValGlyAspLeuThrProAspValAspAspGlyMetLeuTyrGluPhePheValLysVa
57054 : TGTGGGAGATTTGACCCCTGATGTGGATGATGGCATGCTATATGAGTTTTTTGTTAAAGT : 56995
120 : lTyrProSerCysArgGlyGlyLysValValLeuAspGlnThrGlyValSer{Ly} >> : 137
||||||||||||||||||||||||||||||||||||||||:!!|||||||||{||}
lTyrProSerCysArgGlyGlyLysValValLeuAspGlnSerGlyValSer{Ly}++
56994 : TTACCCATCATGTAGAGGTGGTAAAGTTGTCTTGGACCAATCAGGAGTTTCC{AA}gt.. : 56937
138 : >> Target Intron 5 >>>> {s}GlyTyrGlyPheValLysPheThrAspGluLe : 148
1975 bp {|}||||||||||||||||||||||||||||||||
++{s}GlyTyrGlyPheValLysPheThrAspGluLe
56936 : .......................ag{A}GGCTATGGGTTTGTGAAATTCACAGATGAACT : 54933
149 : uGluGlnLysArgAlaLeuThrGluCysGlnGlyAlaValGlyLeuGlySerLysProVa : 168
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||:!
uGluGlnLysArgAlaLeuThrGluCysGlnGlyAlaValGlyLeuGlySerLysProIl
54932 : GGAACAGAAGAGAGCCCTGACAGAATGCCAAGGAGCTGTGGGGTTGGGCTCCAAACCTAT : 54873
169 : lArgLeuSerValAlaIleProLys{Al} >>>> Target Intron 6 >>>> {a : 177
!||||||||||||||||||||||||{||} 2233 bp {|
eArgLeuSerValAlaIleProLys{Al}++ ++{a
54872 : ACGTTTGAGCGTGGCCATACCAAAA{GC}gt.........................ag{G : 52611
178 : }SerArgValLysProValGluTyrSerGlnMetTyrSerTyrSerTyrAsnGlnTyrTy : 197
}!:!||||||||| !!!.!||||||!:!|||||||||!:!|||!:!||||||||||||||
}AsnArgValLysThrAlaGluTyrAsnGlnMetTyrAsnTyrAsnTyrAsnGlnTyrTy
52610 : }AACCGTGTGAAGACAGCCGAGTACAATCAGATGTACAACTATAATTATAACCAATATTA : 52553
198 : rGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpGlyTyrAspGlnAsnThrGlySerTyrSe : 217
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
rGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpGlyTyrAspGlnAsnThrGlySerTyrSe
52552 : CCAACAATATCAGAACTACTATGCGCAGTGGGGATATGACCAGAACACAGGCAGTTACAG : 52493
218 : rTyrSerTyrProGlnTyrGlyTyrThrGlnSerThrMetGln >>>> Target Int : 232
||||||||||||||||||||||||||||||||||||||||||| 609 b
rTyrSerTyrProGlnTyrGlyTyrThrGlnSerThrMetGln++
52492 : CTACAGCTACCCCCAGTATGGGTACACGCAGAGCACTATGCAGgt............... : 52446
233 : ron 7 >>>> ThrTyrGluGluValGlyAspAspAlaLeuGlu{A} >>>> Targe : 243
p ||||||||||||||||||!!:||||||||||||{|} 1
++ThrTyrGluGluValGlyGluAspAlaLeuGlu{A}++
52445 : ..........agACATATGAAGAAGTTGGTGAGGATGCATTGGAA{G}gt.......... : 51803
244 : t Intron 8 >>>> {sp}ProMetProGlnLeuAspValThrGluAlaAsnLysGlu : 256
672 bp {||}||| |||||||||||||||!:!||||||||||||:!!
++{sp}ProAlaProGlnLeuAspValSerGluAlaAsnLysGln
51802 : ...............ag{AT}CCAGCTCCTCAGTTAGATGTGAGTGAAGCAAACAAGCAG : 50095
257 : PheMetGluGlnSerGluGluLeuTyrAspAlaLeuMetAspCysHisTrpGlnProLeu : 276
|||:!:||||||||||||||||||||||||||||||! |||! !|||||||||||||||
PheValGluGlnSerGluGluLeuTyrAspAlaLeuThrAspSerHisTrpGlnProLeu
50094 : TTTGTAGAACAGAGTGAAGAGCTTTATGATGCCTTGACTGACTCTCACTGGCAGCCTTTG : 50035
277 : AspThrValSerSerGluIleProAlaMetMet : 287
|||||||||||||||||||||||||||!!::!:
AspThrValSerSerGluIleProAlaIleLeu
50034 : GACACCGTCTCTTCAGAGATTCCAGCCATCTTA : 50000
vulgar: SPP00000146_2.0 0 287 . gi|397461042|gb|JH734459.1|:subseq(152395,112049) 62489 49999 - 1399 M 9 27 5 0 2 I 0 409 3 0 2 M 32 96 S 0 2 5 0 2 I 0 1082 3 0 2 S 1 1 M 33 99 5 0 2 I 0 2460 3 0 2 M 17 51 S 0 2 5 0 2 I 0 1173 3 0 2 S 1 1 M 43 129 S 0 2 5 0 2 I 0 1971 3 0 2 S 1 1 M 39 117 S 0 2 5 0 2 I 0 2229 3 0 2 S 1 1 M 54 162 5 0 2 I 0 605 3 0 2 M 11 33 S 0 1 5 0 2 I 0 1668 3 0 2 S 1 2 M 44 132
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local gene 50000 62489 1399 - . gene_id 1 ; sequence SPP00000146_2.0 ; gene_orientation +
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 62463 62489 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 62463 62489 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 62461 62462 . - . intron_id 1 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 62050 62462 . - . intron_id 1
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 62050 62051 . - . intron_id 0 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 61952 62049 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 61952 62049 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 61950 61951 . - . intron_id 2 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 60866 61951 . - . intron_id 2
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 60866 60867 . - . intron_id 1 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 60766 60865 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 60766 60865 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 60764 60765 . - . intron_id 3 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 58302 60765 . - . intron_id 3
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 58302 58303 . - . intron_id 2 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 58249 58301 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 58249 58301 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 58247 58248 . - . intron_id 4 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 57072 58248 . - . intron_id 4
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 57072 57073 . - . intron_id 3 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 56940 57071 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 56940 57071 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 56938 56939 . - . intron_id 5 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 54965 56939 . - . intron_id 5
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 54965 54966 . - . intron_id 4 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 54845 54964 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 54845 54964 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 54843 54844 . - . intron_id 6 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 52612 54844 . - . intron_id 6
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 52612 52613 . - . intron_id 5 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 52449 52611 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 52449 52611 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 52447 52448 . - . intron_id 7 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 51840 52448 . - . intron_id 7
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 51840 51841 . - . intron_id 6 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 51806 51839 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 51806 51839 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice5 51804 51805 . - . intron_id 8 ; splice_site "GT"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local intron 50134 51805 . - . intron_id 8
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local splice3 50134 50135 . - . intron_id 7 ; splice_site "AG"
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local cds 50000 50133 . - .
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local exon 50000 50133 . - . insertions 0 ; deletions 0
gi|397461042|gb|JH734459.1|:subseq(152395,112049) exonerate:protein2genome:local similarity 50000 62489 1399 - . alignment_id 1 ; Query SPP00000146_2.0 ; Align 62490 1 27 ; Align 62050 10 96 ; Align 60865 43 99 ; Align 58302 76 51 ; Align 57071 94 129 ; Align 54964 138 117 ; Align 52611 178 162 ; Align 51840 232 33 ; Align 50132 244 132
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis