
C4 Alignment:
------------
         Query: NZ874 multi_hit_stitched_contig_comprising_2_hits
        Target: NZ874 Joins between unique SPAdes contigs are separated by 10 "N" characters
         Model: protein2genome:local
     Raw score: 2261
   Query range: 0 -> 437
  Target range: 2 -> 1779

    1 : IleLysTyrAlaGlnTrpGluGluSerGlnLysAspPheAsnArgAlaArgSerValTrpGl :   21
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        IleLysTyrAlaGlnTrpGluGluSerGlnLysAspPheAsnArgAlaArgSerValTrpGl
    3 : ATCAAGTACGCCCAATGGGAGGAGTCTCAGAAGGACTTCAACCGCGCCAGGTCGGTCTGGGA :   63

   22 : uArgAlaLeuGluValAspTyrArgAsnHisThrLeuTrpLeuLysTyrAlaGluValGluM :   42
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        uArgAlaLeuGluValAspTyrArgAsnHisThrLeuTrpLeuLysTyrAlaGluValGluM
   64 : GAGAGCTCTCGAAGTCGATTACCGGAACCACACGCTTTGGCTGAAGTACGCAGAGGTCGAGA :  126

   43 : etLysAsnLysPheIleAsnHisAlaArgAsnValTrpAspArgAlaValThrLeuLeuPro :   62
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        etLysAsnLysPheIleAsnHisAlaArgAsnValTrpAspArgAlaValThrLeuLeuPro
  127 : TGAAGAACAAGTTCATCAACCACGCCAGGAATGTGTGGGATAGGGCCGTCACGCTCTTGCCT :  186

   63 : ArgValAspGlnLeuTrpTyrLysTyrIleHisMetGluGluMetLeuGlyAsnValAlaGl :   83
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ArgValAspGlnLeuTrpTyrLysTyrIleHisMetGluGluMetLeuGlyAsnValAlaGl
  187 : AGGGTTGACCAGCTCTGGTACAAATACATCCACATGGAAGAGATGCTCGGGAATGTTGCCGG :  249

   84 : yAlaArgGlnIlePheGluArgTrpMetAsnTrpMetProAspGlnGlnGlyTrpLeuSerT :  104
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        yAlaArgGlnIlePheGluArgTrpMetAsnTrpMetProAspGlnGlnGlyTrpLeuSerT
  250 : AGCCAGACAGATTTTCGAGAGATGGATGAATTGGATGCCCGACCAGCAAGGTTGGCTTTCCT :  312

  105 : yrIleLysPheGluLeuArgTyrAsnGluValGluArgAlaArgLysIlePheGluArgPhe :  124
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        yrIleLysPheGluLeuArgTyrAsnGluValGluArgAlaArgLysIlePheGluArgPhe
  313 : ACATCAAGTTCGAGCTTAGATATAACGAGGTCGAGCGCGCGAGGAAGATTTTCGAGCGATTC :  372

  125 : ValGlnCysHisProThrIleGlyAlaTrpIleArgPheAlaLysPheGluMetLysAsnGl :  145
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ValGlnCysHisProThrIleGlyAlaTrpIleArgPheAlaLysPheGluMetLysAsnGl
  373 : GTGCAGTGCCACCCCACTATAGGGGCTTGGATTCGGTTCGCCAAGTTCGAGATGAAGAACGG :  435

  146 : yGluValGlyArgAlaArgAspValTyrGluArgAlaValLeuLysLeuGlyAspAspGluG :  166
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        yGluValGlyArgAlaArgAspValTyrGluArgAlaValLeuLysLeuGlyAspAspGluG
  436 : CGAGGTTGGCAGGGCCAGGGATGTGTATGAGAGGGCTGTGCTGAAATTGGGCGATGACGAAG :  498

  167 : luAlaGluHisLeuPheValAlaPheAlaGluPheGluGluArgCysLysGluThrGluArg :  186
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        luAlaGluHisLeuPheValAlaPheAlaGluPheGluGluArgCysLysGluThrGluArg
  499 : AGGCGGAGCATCTGTTTGTGGCTTTCGCTGAGTTCGAAGAGCGGTGTAAGGAGACGGAGCGA :  558

  187 : AlaArgAlaIleTyrLysPheAlaLeuAspHisIleProLysGlyArgAlaGluAspLeuTy :  207
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        AlaArgAlaIleTyrLysPheAlaLeuAspHisIleProLysGlyArgAlaGluAspLeuTy
  559 : GCCAGGGCTATATATAAGTTCGCTCTTGATCACATTCCCAAAGGGAGGGCTGAAGACTTGTA :  621

  208 : rArgArgPheValAlaPheGluLysGlnPheGlyAspArgGluGlyIleGluAspAlaIleV :  228
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        rArgArgPheValAlaPheGluLysGlnPheGlyAspArgGluGlyIleGluAspAlaIleV
  622 : TAGAAGATTCGTTGCCTTCGAGAAGCAGTTCGGAGATAGAGAGGGGATTGAGGATGCCATAG :  684

  229 : alGlyLysArgArgPheGlnTyrGluAspGluValArgLysSerProLeuAsnTyrAspThr :  248
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        alGlyLysArgArgPheGlnTyrGluAspGluValArgLysSerProLeuAsnTyrAspThr
  685 : TGGGGAAGAGGAGGTTTCAGTATGAGGATGAGGTGAGGAAGAGTCCTCTCAATTACGACACC :  744

  249 : TrpPheAspTyrIleArgLeuGluGluSerValGlyIleLysGluArgIleArgGluValTy :  269
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        TrpPheAspTyrIleArgLeuGluGluSerValGlyIleLysGluArgIleArgGluValTy
  745 : TGGTTCGATTACATTAGACTTGAGGAGAGTGTTGGAATTAAGGAGAGGATAAGAGAGGTTTA :  807

  270 : rGluArgAlaIleAlaAsnValProProAlaGluGluLysArgTyrTrpGlnArgTyrIleT :  290
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        rGluArgAlaIleAlaAsnValProProAlaGluGluLysArgTyrTrpGlnArgTyrIleT
  808 : TGAGCGAGCCATTGCTAATGTTCCTCCGGCTGAGGAGAAGCGGTATTGGCAGAGATATATCT :  870

  291 : yrLeu{Tr}  >>>> Target Intron 1 >>>>  {p}AlaTyrIleAspPheGluIle :  299
        |||||{||}            248 bp           {|}|||||||||||||||||||||
        yrLeu{Tr}++                         --{p}AlaTyrIleAspPheGluIle
  871 : ATTTA{TG}gt.........................ta{G}GCATACATCGACTTTGAAATT : 1145

  300 : SerGluSerGluPheGluArgThrArgGluLeuTyrGluArgLeuLeuGlyArgThrLysHi :  320
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        SerGluSerGluPheGluArgThrArgGluLeuTyrGluArgLeuLeuGlyArgThrLysHi
 1146 : TCAGAGAGTGAATTTGAGAGAACAAGAGAACTTTATGAGAGACTGTTGGGCCGGACAAAGCA : 1208

  321 : sLeuLysValTrpLeuSerTyrAlaGlnPheGluAlaThrAlaMetGluAlaSerAspProA :  341
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        sLeuLysValTrpLeuSerTyrAlaGlnPheGluAlaThrAlaMetGluAlaSerAspProA
 1209 : CCTGAAGGTGTGGCTTAGCTATGCACAGTTTGAGGCCACTGCCATGGAGGCAAGTGATCCAG : 1271

  342 : spLeuAlaGluGluAspIleGluArgGluGlnLysLysProCysIleGlnArgAlaArg{A} :  361
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||{|}
        spLeuAlaGluGluAspIleGluArgGluGlnLysLysProCysIleGlnArgAlaArg{A}
 1272 : ATTTGGCAGAAGAAGATATCGAACGTGAACAGAAGAAACCCTGTATTCAGCGTGCGAGA{A} : 1331

  362 :   >>>> Target Intron 2 >>>>  {rg}ValPheGluLysAlaValAsnTyrPheAr :  371
                    92 bp            {||}|||||||||||||||||||||||||||||
        ++                         ++{rg}ValPheGluLysAlaValAsnTyrPheAr
 1332 : gt.........................ag{GG}GTTTTCGAGAAAGCAGTCAACTATTTCAG : 1453

  372 : gThrSerAlaProGluLeuLysGluGluArgAlaMetLeuLeuGluGluTrpLeuAsnMetG :  392
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        gThrSerAlaProGluLeuLysGluGluArgAlaMetLeuLeuGluGluTrpLeuAsnMetG
 1454 : AACATCAGCACCTGAACTGAAGGAAGAAAGGGCTATGCTACTAGAAGAGTGGCTGAACATGG : 1516

  393 : luAlaSerPheGlyGluLeuGlyAspValSerIleValGlnSerLysLeuProLysLysLeu :  412
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        luAlaSerPheGlyGluLeuGlyAspValSerIleValGlnSerLysLeuProLysLysLeu
 1517 : AGGCTAGTTTCGGTGAACTAGGTGACGTTAGCATTGTGCAGTCAAAGCTGCCAAAGAAGCTA : 1576

  413 : LysLysArgArgGlnIleValThrGluAspGlyProAla{Gl}  >>>> Target Intro :  426
        |||||||||||||||||||||||||||||||||||||||{||}            126 bp 
        LysLysArgArgGlnIleValThrGluAspGlyProAla{Gl}++                 
 1577 : AAGAAAAGGAGACAAATAGTAACGGAGGATGGTCCTGCT{GG}gt................. : 1622

  427 : n 3 >>>>  {y}TyrGluGluTyrIleAspTyrLeuPheProGlu :  437
                  {|}|||||||||||||||||||||||||||||||||
                ++{y}TyrGluGluTyrIleAspTyrLeuPheProGlu
 1623 : ........ag{G}TACGAGGAGTACATAGATTACCTGTTCCCAGAG : 1779

# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.4.0
##date 2023-09-06
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
NZ874	exonerate:protein2genome:local	gene	3	1779	2261	+	.	gene_id 1 ; sequence NZ874 ; gene_orientation + ; identity 100.00 ; similarity 100.00
NZ874	exonerate:protein2genome:local	cds	3	877	.	+	.	
NZ874	exonerate:protein2genome:local	exon	3	877	.	+	.	insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
NZ874	exonerate:protein2genome:local	splice5	878	879	.	+	.	intron_id 1 ; splice_site "GT"
NZ874	exonerate:protein2genome:local	intron	878	1125	.	+	.	intron_id 1
NZ874	exonerate:protein2genome:local	splice3	1124	1125	.	+	.	intron_id 0 ; splice_site "TA"
NZ874	exonerate:protein2genome:local	cds	1126	1331	.	+	.	
NZ874	exonerate:protein2genome:local	exon	1126	1331	.	+	.	insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
NZ874	exonerate:protein2genome:local	splice5	1332	1333	.	+	.	intron_id 2 ; splice_site "GT"
NZ874	exonerate:protein2genome:local	intron	1332	1423	.	+	.	intron_id 2
NZ874	exonerate:protein2genome:local	splice3	1422	1423	.	+	.	intron_id 1 ; splice_site "AG"
NZ874	exonerate:protein2genome:local	cds	1424	1619	.	+	.	
NZ874	exonerate:protein2genome:local	exon	1424	1619	.	+	.	insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
NZ874	exonerate:protein2genome:local	splice5	1620	1621	.	+	.	intron_id 3 ; splice_site "GT"
NZ874	exonerate:protein2genome:local	intron	1620	1745	.	+	.	intron_id 3
NZ874	exonerate:protein2genome:local	splice3	1744	1745	.	+	.	intron_id 2 ; splice_site "AG"
NZ874	exonerate:protein2genome:local	cds	1746	1779	.	+	.	
NZ874	exonerate:protein2genome:local	exon	1746	1779	.	+	.	insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
NZ874	exonerate:protein2genome:local	similarity	3	1779	2261	+	.	alignment_id 1 ; Query NZ874 ; Align 3 1 873 ; Align 1127 293 204 ; Align 1426 362 192 ; Align 1747 427 33
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: NZ874 multi_hit_stitched_contig_comprising_2_hits
        Target: NZ874 Joins between unique SPAdes contigs are separated by 10 "N" characters
         Model: protein2genome:local
     Raw score: 211
   Query range: 0 -> 211
  Target range: 104 -> 869

   1 : IleLysTyrAlaGlnTrpGluGluSerGlnLysAspPheAsnArgAlaArgSerValTrpGluA :  22
       :!:|||||||||:!!   |||  !!.!.!.|||  !.!!|||!.!||||||!:!||||||!!:|
       LeuLysTyrAlaGluValGluMetLysAsnLysPheIleAsnHisAlaArgAsnValTrpAspA
 105 : CTGAAGTACGCAGAGGTCGAGATGAAGAACAAGTTCATCAACCACGCCAGGAATGTGTGGGATA : 168

  23 : rgAlaLeuGluValAspTyrArgAsnHisThrLeuTrpLeuLysTyrAlaGluValGluMetLy :  43
       |||||:!!  !:!!     !|||  ! !!  !||||||! !||||||  !.!.:!!|||  !! 
       rgAlaValThrLeuLeuProArgValAspGlnLeuTrpTyrLysTyrIleHisMetGluGluMe
 169 : GGGCCGTCACGCTCTTGCCTAGGGTTGACCAGCTCTGGTACAAATACATCCACATGGAAGAGAT : 231

  44 : sAsnLysPheIleAsnHisAlaArgAsnValTrpAspArgAlaValThrLeuLeuProArgVal :  64
       !  !  !  !:!!  !   ||||||.!.:!!!::!!:|||  !:!!!.!! !:!!|||  !   
       tLeuGlyAsnValAlaGlyAlaArgGlnIlePheGluArgTrpMetAsnTrpMetProAsp---
 232 : GCTCGGGAATGTTGCCGGAGCCAGACAGATTTTCGAGAGATGGATGAATTGGATGCCCGAC--- : 294

  65 : AspGlnLeuTrpTyrLysTyrIleHisMetGluGluMetLeuGlyAsnValAlaGlyAlaArgG :  86
       .!.|||  !|||  !...|||||| ! .!.|||   !  ! !..!.!.|||! ! !!||||||:
       GlnGlnGlyTrpLeuSerTyrIleLysPheGluLeuArgTyrAsnGluValGluArgAlaArgL
 295 : CAGCAAGGTTGGCTTTCCTACATCAAGTTCGAGCTTAGATATAACGAGGTCGAGCGCGCGAGGA : 357

  87 : lnIlePheGluArgTrpMetAsnTrpMetProAspGlnGlnGlyTrpLeuSerTyrIleLysPh : 107
       !!||||||||||||!:::!!.!.!!    |||  !  !  !!.!|||:!! !!!:!  !|||||
       ysIlePheGluArgPheValGlnCysHisProThrIleGlyAlaTrpIleArgPheAlaLysPh
 358 : AGATTTTCGAGCGATTCGTGCAGTGCCACCCCACTATAGGGGCTTGGATTCGGTTCGCCAAGTT : 420

 108 : eGluLeuArgTyrAsnGluValGluArgAlaArgLysIlePheGluArgPheVal<-><-><-> : 126
       ||||:!!!:! !!..!||||||!  ||||||||| ! :!:!:!||||||  !|||         
       eGluMetLysAsnGlyGluValGlyArgAlaArgAspValTyrGluArgAlaValLeuLysLeu
 421 : CGAGATGAAGAACGGCGAGGTTGGCAGGGCCAGGGATGTGTATGAGAGGGCTGTGCTGAAATTG : 483

 127 : <->GlnCysHisProThrIleGlyAlaTrpIleArgPheAlaLysPheGluMetLysAsnGlyG : 146
          .!.  !.!.  !.!!     !  !!:::!:  !||||||:!!||||||  !::!  !  !|
       GlyAspAspGluGluAlaGluHisLeuPheValAlaPheAlaGluPheGluGluArgCysLysG
 484 : GGCGATGACGAAGAGGCGGAGCATCTGTTTGTGGCTTTCGCTGAGTTCGAAGAGCGGTGTAAGG : 549

 147 : luValGlyArgAlaArgAspValTyrGluArgAlaVal<-><->LeuLysLeuGlyAspAspGl : 165
       ||..!! !|||||||||! !:!!|||:!!  !|||:!!      :!!     !|||   ! !||
       luThrGluArgAlaArgAlaIleTyrLysPheAlaLeuAspHisIleProLysGlyArgAlaGl
 550 : AGACGGAGCGAGCCAGGGCTATATATAAGTTCGCTCTTGATCACATTCCCAAAGGGAGGGCTGA : 612

 166 : uGluAlaGluHisLeuPheValAlaPheAla{Gl}  >>>> Target Intron 1 >>>>   : 176
       |!!:  ! ! ...  !||||||||||||! !{:!}            117 bp           
       uAspLeuTyrArgArgPheValAlaPheGlu{Ly}+-                         ++
 613 : AGACTTGTATAGAAGATTCGTTGCCTTCGAG{AA}gc.........................ag : 762

 177 : {u}PheGluGluArgCysLysGluThrGluArgAlaArgAlaIleTyrLysPheAlaLeuAspH : 197
       {!}.!!||||||!!!  !  !   ! !||||||  !|||! !:!!|||:!!   |||:!!! !:
       {s}LeuGluGluSerValGlyIleLysGluArgIleArgGluValTyrGluArgAlaIleAlaA
 763 : {A}CTTGAGGAGAGTGTTGGAATTAAGGAGAGGATAAGAGAGGTTTATGAGCGAGCCATTGCTA : 825

 198 : isIleProLysGlyArgAlaGluAspLeuTyrArgArgPheVal : 211
       !!:!!|||  !!.!..!! !:!!   ! !!::!:!|||!:!:!!
       snValProProAlaGluGluLysArgTyrTrpGlnArgTyrIle
 826 : ATGTTCCTCCGGCTGAGGAGAAGCGGTATTGGCAGAGATATATC : 869

# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.4.0
##date 2023-09-06
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
NZ874	exonerate:protein2genome:local	gene	105	869	211	+	.	gene_id 2 ; sequence NZ874 ; gene_orientation + ; identity 34.45 ; similarity 54.07
NZ874	exonerate:protein2genome:local	cds	105	646	.	+	.	
NZ874	exonerate:protein2genome:local	exon	105	646	.	+	.	insertions 18 ; deletions 1 ; identity 36.21 ; similarity 54.02
NZ874	exonerate:protein2genome:local	splice5	647	648	.	+	.	intron_id 1 ; splice_site "GC"
NZ874	exonerate:protein2genome:local	intron	647	763	.	+	.	intron_id 1
NZ874	exonerate:protein2genome:local	splice3	762	763	.	+	.	intron_id 0 ; splice_site "AG"
NZ874	exonerate:protein2genome:local	cds	764	869	.	+	.	
NZ874	exonerate:protein2genome:local	exon	764	869	.	+	.	insertions 0 ; deletions 0 ; identity 25.71 ; similarity 54.29
NZ874	exonerate:protein2genome:local	similarity	105	869	211	+	.	alignment_id 2 ; Query NZ874 ; Align 105 1 189 ; Align 294 65 183 ; Align 489 126 99 ; Align 594 159 51 ; Align 765 177 105
# --- END OF GFF DUMP ---
#
