Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/DI2.fa -t gi|397463745|gb|JH731756.1|subseq.fa -E]
Hostname: [ws101062]
** (process:3203): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW
C4 Alignment:
------------
Query: SPP00000011_2.0 # Protein # Iodothyronine deiodinase 2 (DI2) # Human (Homo sapiens)
Target: gi|397463745|gb|JH731756.1|:subseq(1130000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-1225, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 1056
Query range: 0 -> 301
Target range: 64210 -> 52117
1 : MetGlyIleLeuSerValAspLeuLeuIleThrLeuGlnIleLeuProValPhePheSer : 20
||||||:!:|||||||||||||||||||||||||||||||||||||||||||||||||||
MetGlyLeuLeuSerValAspLeuLeuIleThrLeuGlnIleLeuProValPhePheSer
64210 : ATGGGTCTGTTAAGCGTGGATTTGCTGATCACGCTTCAGATCTTGCCAGTTTTTTTCTCC : 64153
21 : AsnCysLeuPheLeuAlaLeuTyrAspSerValIleLeuLeuLysHisValValLeuLeu : 40
||||||||||||||||||||||||||||||||||||||||||||||||:!!||||||!!!
AsnCysLeuPheLeuAlaLeuTyrAspSerValIleLeuLeuLysHisMetValLeuPhe
64152 : AATTGCCTCTTCCTTGCACTCTATGATTCTGTGATCCTCCTGAAGCACATGGTGCTGTTT : 64093
41 : LeuSerArgSerLysSerThrArgGlyGluTrpArgArgMetLeuThrSerGluGlyLeu : 60
||||||||||||||||||.!!|||||||||||||||||||||||||||||||||||||||
LeuSerArgSerLysSerAlaArgGlyGluTrpArgArgMetLeuThrSerGluGlyLeu
64092 : CTGAGTCGGTCTAAGTCTGCGCGTGGTGAGTGGCGAAGGATGCTGACCTCAGAGGGGCTG : 64033
61 : ArgCysValTrpLysSerPheLeuLeuAspAlaTyrLysGln >>>> Target Intr : 75
||||||||||||!!.||||||||||||||||||||||||||| 2355 bp
ArgCysValTrpAsnSerPheLeuLeuAspAlaTyrLysGln++
64032 : CGTTGCGTCTGGAATAGCTTCCTCCTAGATGCTTACAAACAGgt................ : 63986
76 : on 1 >>>> LeuAsnCysProProSerGlyPheSerLysAsp >>>> Target In : 86
:!!..!! !||| !|||||| ! ..! !! 3036
++ValGlyPheProLysSerGlyValGluLeuTyr++
63985 : .........agGTAGGTTTTCCCAAGTCTGGAGTGGAACTTTATgt.............. : 61598
87 : tron 2 >>>> GlyHisIleLeuUnkLeuValTyrGluAlaTyrLysSerArgLeuLe : 101
bp ! :!!||| |||:!! ! ! !! !||| !!!!||||||||
++HisSerValLeuProLeuLeuGluAlaGluTyrTrpThrArgLeuLe
61597 : ...........agCATTCAGTCCTGCCACTGTTAGAGGCAGAATACTGGACAAGACTGTT : 58519
102 : uValTyrSerHisLeu >>>> Target Intron 3 >>>> AspLeuTrpMet > : 111
||||! !! !:!! 4634 bp !!:||||||
uVal***ProSerMet++ +-GluLeuTrpAsp++
58518 : GGTCTGACCCAGTATGgt.........................atGAACTTTGGGATgt. : 53853
112 : >>> Target Intron 4 >>>> ValLysLeuGlyGluAspAlaProAsnSerSerV : 122
1168 bp ||||||||||||! !!!:||||||||||||!!!|
++ValLysLeuGlyGlyGluAlaProAsnSerArgV
53852 : ........................agGTGAAACTGGGTGGAGAAGCCCCAAACTCCAGAG : 52654
123 : alValHisValSerSerThrGluGlyGlyAspAsnSerGlyAsnGlyThrGlnGluLysI : 142
||:!!|||:!!!!!!:! ! .!!||| ..!||| !!.. !!! !.!.!
alIleHisIleThrAsnGlyIleSerGly---GlySerThrArgCysLysAsnValGlyG
52653 : TGATTCACATAACCAATGGCATCAGTGGT---GGCAGTACCAGATGCAAGAATGTTGGTG : 52597
143 : leAlaGluGlyAlaThrCysHisLeuLeuAspPheAlaSerProGluArgProLeuValV : 162
! ! !|||::!! !|||||||||||||||||||||!:! !!||||||||||||||||
lyLysLeuGlySerLysCysHisLeuLeuAspPheAlaAsnSerGluArgProLeuValV
52596 : GAAAGTTGGGGAGCAAGTGTCATCTCTTGGATTTTGCCAACTCTGAGCGTCCCCTGGTGG : 52537
163 : alAsnPheGlySerAlaThrUnkProProPheThrSerGlnLeuProAlaPheArgLysL : 182
|||||||||||||||||||| ||||||||||||||||||||| !!||||||!!!||||
alAsnPheGlySerAlaThr***ProProPheThrSerGlnLeuSerAlaPheSerLysL
52536 : TCAACTTTGGTTCAGCTACCTGACCTCCATTCACGAGCCAGCTGTCAGCCTTCAGCAAGC : 52477
183 : euValGluGluPheSerSerValAlaAspPheLeuLeuValTyrIleAspGluAlaHisP : 202
|||||||||||||||||.!!||||||||||||||||||||||||||||||||||||||||
euValGluGluPheSerGlyValAlaAspPheLeuLeuValTyrIleAspGluAlaHisP
52476 : TGGTGGAGGAGTTTTCAGGTGTGGCCGACTTCCTGTTGGTCTACATTGACGAGGCTCACC : 52417
203 : roSerAspGlyTrpAlaIleProGlyAspSerSerLeuSerPheGluValLysLysHisG : 222
||||||||||||||||| !|||||| !||| !!! !|||||||||||||||||||||:
roSerAspGlyTrpAlaAlaProGlyIleSerProSerSerPheGluValLysLysHisL
52416 : CATCGGATGGTTGGGCTGCTCCTGGAATCTCGCCCTCTTCATTTGAGGTGAAGAAGCACA : 52357
223 : lnAsnGlnGluAspArgCysAlaAlaAlaGlnGlnLeuLeuGluArgPheSerLeuProP : 242
!!|||||||||||||||||||||||||||!!.|||||||||:!!||||||||||||||||
ysAsnGlnGluAspArgCysAlaAlaAlaHisGlnLeuLeuGlnArgPheSerLeuProP
52356 : AGAACCAGGAAGACCGATGTGCAGCTGCTCACCAGCTCCTGCAGAGGTTTTCCTTGCCCC : 52297
243 : roGlnCysArgValValAlaAspArgMetAspAsnAsnAlaAsnIleAlaTyrGlyValA : 262
||||||||!:!|||||||||||| !!||||||||||||||||||:!!||||||||||||:
roGlnCysGlnValValAlaAspCysMetAspAsnAsnAlaAsnValAlaTyrGlyValS
52296 : CCCAGTGCCAAGTAGTGGCTGACTGCATGGATAATAATGCCAATGTAGCCTATGGGGTCT : 52237
263 : laPheGluArgValCysIleValGlnArgGlnLysIleAlaTyrLeuGlyGlyLysGlyP : 282
!!||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
erPheGluArgValCysIleValGlnArgGlnLysIleAlaTyrLeuGlyGlyLysGlyP
52236 : CCTTTGAGCGCGTGTGTATCGTGCAGCGACAGAAAATTGCTTACCTGGGGGGCAAGGGCC : 52177
283 : roPheSerTyrAsnLeuGlnGluValArgHisTrpLeuGluLysAsnPheSerLysArg : 301
|||||! !||||||||||||||||||!:!! !|||||||||:!!|||! !|||||||||
roPhePheTyrAsnLeuGlnGluValGlnLeuTrpLeuGluGlnAsnCysSerLysArg
52176 : CCTTTTTCTACAACCTCCAGGAAGTTCAGCTTTGGCTTGAACAAAACTGCAGCAAGAGA : 52118
vulgar: SPP00000011_2.0 0 301 . gi|397463745|gb|JH731756.1|:subseq(1130000,100000) 64210 52117 - 1056 M 74 222 5 0 2 I 0 2351 3 0 2 M 11 33 5 0 2 I 0 3032 3 0 2 M 21 63 5 0 2 I 0 4630 3 0 2 M 4 12 5 0 2 I 0 1164 3 0 2 M 21 63 G 1 0 M 169 507
# --- 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|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local gene 52118 64210 1056 - . gene_id 1 ; sequence SPP00000011_2.0 ; gene_orientation +
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local cds 63989 64210 . - .
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local exon 63989 64210 . - . insertions 0 ; deletions 0
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice5 63987 63988 . - . intron_id 1 ; splice_site "GT"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local intron 61634 63988 . - . intron_id 1
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice3 61634 61635 . - . intron_id 0 ; splice_site "AG"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local cds 61601 61633 . - .
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local exon 61601 61633 . - . insertions 0 ; deletions 0
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice5 61599 61600 . - . intron_id 2 ; splice_site "GT"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local intron 58565 61600 . - . intron_id 2
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice3 58565 58566 . - . intron_id 1 ; splice_site "AG"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local cds 58502 58564 . - .
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local exon 58502 58564 . - . insertions 0 ; deletions 0
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice5 58500 58501 . - . intron_id 3 ; splice_site "GT"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local intron 53868 58501 . - . intron_id 3
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice3 53868 53869 . - . intron_id 2 ; splice_site "AT"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local cds 53856 53867 . - .
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local exon 53856 53867 . - . insertions 0 ; deletions 0
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice5 53854 53855 . - . intron_id 4 ; splice_site "GT"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local intron 52688 53855 . - . intron_id 4
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local splice3 52688 52689 . - . intron_id 3 ; splice_site "AG"
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local cds 52118 52687 . - .
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local exon 52118 52687 . - . insertions 0 ; deletions 1
gi|397463745|gb|JH731756.1|:subseq(1130000,100000) exonerate:protein2genome:local similarity 52118 64210 1056 - . alignment_id 1 ; Query SPP00000011_2.0 ; Align 64211 1 222 ; Align 61634 75 33 ; Align 58565 86 63 ; Align 53868 107 12 ; Align 52688 111 63 ; Align 52625 133 507
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis