File: algn-5_Wildtype.ape

Comments
>H43I07.3 unspliced + UTR + 2000 upstream + 2000 downstream; +ive
 strand; Sequence: 7823 bp
>Deletion size = 1325 bp
>algn-5 sgRNA #1, Chr V, GACTTTCCTACGCAACACCA; cut=4195777;
 strand=+1; GC=50; 3'GG=no; folding=0.0
>algn-5 sgRNA #2, Chr V, ATTCTCTTCGCAGATGCCGA; cut=4197082;
 strand=+1; GC=50; 3'GG=no; folding=-1.5


Features
algn-5-1 SV F	primer_bind	forward	1354..1374
AGCATGCTTAGTACCTGCTGC

algn-5 Upstream Homology arm	misc_feature	forward	1834..2183
GTTTTAAAATATTATTAATACAAAAATTCGTTTTTTTTGCTCCTTAAATTGAAACAATTGAGCAACTGATGGTTTTCGTTGCGAGACCCGGGCTTAAATTTCTATAACGCGCCTTTAAAAGTCCTACGGTTTGCTTTTTTTTCGTTAAATTTTTATTTTCGAAAACCAAAGCTTATTCCGATTTAATCTCGATTTTAATTCCAGAAATGTGGGATTTAATTTCGCCGGAAATTTTCTCAATACAAAATCTTTGCCTGCTGGGATTTCTCGTCGCCTCAATCGCCGTGAGCAGCCTCTTCACGTAAGTTTTTCGATTTTTCTCCAAAAAATCAATATCTTCACCATTTTCA

Left Deletion Flank	misc_structure	forward	2154..2183
TCCAAAAAATCAATATCTTCACCATTTTCA

algn-5 sgRNA #1	protein_bind	forward	2184..2203
GACTTTCCTACGCAACACCA

algn-5-1 WT F	primer_bind	forward	2541..2562
CCGACGAAACGGCTGATATAGT

algn-5 sgRNA #2	protein_bind	forward	3489..3508
ATTCTCTTCGCAGATGCCGA

algn-5 Downstream Homology Arm	misc_feature	forward	3509..3858
TGGAGCTACAAAATTCGCCGATTTTGAAAATCTCGAGAAAGAAATGCTCCGAACTGCCGGCGGAGAGCCACTTGATGAATCATTTCCAGCAGTTATTGTTGCTTCTAGGTTTTTAATTGATTTTTATAGAAATTTTTAATAATTTTCCCATTTTCAGAGCGCATTTGGAAGCCGAATCTATGGCTGTTAGATCAGTTCCACGCACAATTTTAATGCTCGGTTTTCACTTACTCGTCTATACTTTTGCTGCAAGAACAATTAAAGATACACAGTGTGGATTCAAACTTTTTACTAGATCGATTGCTGCGAGGGTGAGATTTTAGCTTATTTTTAGCTAAAAATCTCCAATT

Right Deletion Flank	misc_structure	forward	3509..3538
TGGAGCTACAAAATTCGCCGATTTTGAAAA

algn-5-1 SV R	primer_bind	reverse	4745..4766
CGATGGACTGAAATCGAAGGGT


formatted sequence

        1 ctcaattatt tttgaaatct cgggcaatta agtcaggggg gggggggcgc caaattgatt
       61 tgtcgacaaa ttcggcaaat tgccggtttg ccgatttgcc ggaaattttc aattcctgca
      121 atttgccgat ttgccggaaa ttttaaattc ctgcaatttg ccagtttgcc agaaattttc
      181 aattccggca atttgccggt ttgtcggaaa ttttcaattc ccgcagtttg ccggtttgtc
      241 ggaaattttc aatttcggca aattgcctat ttgccggaat aaatcgtttg tcgcccaccc
      301 ctgaattaag tgacgccatt tttgtgtatt ccggcatatt agtaggtttt tcttcgtttt
      361 ttttttcaat ttttagatta aatttaagta tttatataac ttgaaacaca attttcaatt
      421 tttcatacat ttttccttaa agaaaactgg ctaccctgta tgaaaatcga caaaacgctt
      481 aaaaattggt ataaaaatcg ataactacac attcatttta ccttttcttt actgaaaaca
      541 gtcatttgta gttaaaatgt gctcaaattg tagttaaaaa atttgtagtt aaaatgtgct
      601 caaatcaata atttaaagcg agagaaacta ccaaaatttg cattaatcgg ggataattta
      661 attaataaaa actggatttt agttgagttg ctgcaacaag gaaaagctgg cgaaattcca
      721 aatttttgag gtctcgtttt gaaatccggt agttttgggc caattttagt caatttatgc
      781 tctaacacct attcaaaatt cacgatagtc tgtcaatttt ttgaaaaaaa aacccctatt
      841 ccaactgtga atttaatttt ctaaactata aagctataaa gtatgtttcc agccacgcgg
      901 caaaaaattc ttcatatgga aatgtgtttt ccttggaaac acgcatttct gagcgaattt
      961 tggcggaaaa aaatttgaaa aaaacgttat ttaccattta ccggcgtctt tgcgttgttc
     1021 atcggatttt tttcgacgac agaaacacat attcggattg aaaattgaat ttgaattgaa
     1081 aaacaaaatt tgaaaacagg aaacacgtgg aaaacagcca catttcacat ttcacgcctt
     1141 cgagatttca agttttcaat taaaaaggca cgaggaaaga ggaaaatcaa ttaaaaacta
     1201 tttaactaaa taggaaggaa aatgaacttt taaattaatt atttaaaaca aaataaaccg
     1261 ggcaataatt ctgcacacac aagaaaaacc agaattcttt ttcttggcgt tgtcgtggaa
     1321 taacaaaatg aacaaagaat gacatacacc ggaagcatgc ttagtacctg ctgccccccg
     1381 gcaactcgct tgtttggcct tcaatcgatt agcgccctgc cggtgagtgc tgacgcatct
     1441 ctcgtgtcac ttgcacccgc ttttctccca ccgatttttg cacattgaaa gtgccacggg
     1501 ggctcaatgc aaatagaaaa ttgaacaaga ttgagccttg ttttaattct tttgtgcatc
     1561 tttttttctg aattagtttt ttcttcattt ttattatttt aggctgtgat atttaaagtt
     1621 tctttagaaa atcgtcttga aattgaaggg aaaacgaata taaatcgaaa aaatcgaaaa
     1681 aaaaggaatt taatttaaaa atcaatttaa actgattttt gttttcccat gcgcctttaa
     1741 tttttacagt atcctttttt ccgaaaatga actatttttg cctattcaac attcaatttt
     1801 tgctaaaata ctttattttg cttatttcaa tgtgttttaa aatattatta atacaaaaat
     1861 tcgttttttt tgctccttaa attgaaacaa ttgagcaact gatggttttc gttgcgagac
     1921 ccgggcttaa atttctataa cgcgccttta aaagtcctac ggtttgcttt tttttcgtta
     1981 aatttttatt ttcgaaaacc aaagcttatt ccgatttaat ctcgatttta attccagaaA
     2041 TGTGGGATTT AATTTCGCCG GAAATTTTCT CAATACAAAA TCTTTGCCTG CTGGGATTTC
     2101 TCGTCGCCTC AATCGCCGTG AGCAGCCTCT TCACgtaagt ttttcgattt ttctccaaaa
     2161 aatcaatatc ttcaccattt tcagACTTTC CTACGCAACA CCATGGGTCC GCCGACGTCG
     2221 TGCCGAGTAC CTAGAACCGG AAATCGTCTA CAGAAGCTCG CCGGAGCAAA AATTCCCGGT
     2281 TTTGTTGCAA GAAGATCGGG ATGCTCCGAA AAGATATACG CCGTCGAGCT GCTATCTTTC
     2341 TGTGATTATT CCGGCTATGA ATGAAGTTgt tagtagtgct aaaagagcat taaaatgagc
     2401 attaaaattg aaaaaaaaaa cggatttttt ctagGAAAGA ATCGAAATTA TGCTCGATGA
     2461 TTGTTGTGAC TACTTGGAAG CTCGTGCTGA GAAGGATAAA GATTTCACCT ACGAAATTAT
     2521 CGTTGTTGAT GATGGATCCA CCGACGAAAC GGCTGATATA GTCGTTCAAA TCGGCGCTAG
     2581 GCGTCAGAAT TTACGAGTTT TGAAAATGAA AGCTAATCGG GGAAAAGgta aggcattttt
     2641 tagtccaaaa tgacttaaaa ttacctaatt ccttctaaaa atgtcatttt attttgcgtt
     2701 tttcgtttat ttaggttaat ttttaggcca aaattctgta gatttaggct ttttcggatc
     2761 tcaattccct tttaaagatg gactacactt tgtggggaaa ttgctttaaa acacgcccat
     2821 gtggtcacaa tgaccgaata tcatgataaa aaaattcaaa aaaaatttct aaattttata
     2881 tgattttttg aaaattgaaa aatctcagtt ttcccctaat tcctatttga attaccgcca
     2941 attgaactcg ttcgttggag cgcgcttgca tcattttgat taattaattt tatttattct
     3001 tattatttca ctgattttct tcattttttg ggggttttta atcggaaaac gaaagaaata
     3061 aacaagaata atgcaaatag ttcctgaaaa aattactgaa aatgcccaaa actctaaaat
     3121 tagtatttta tcagttttaa gcatcttcga atacttttta gcgcacattt tgcatttttc
     3181 ttgtttattt ctttcatttt ccgattaaaa aaccccaaaa aatgaagaaa atcagtgaaa
     3241 taataagaat aaattacaaa aaaattaacg aaaaaaaatg caagcgcgct ccaacgaacg
     3301 aattcaattg gcggtaattc aaataggaat aaggtgaaaa cagagatttt tttaattttc
     3361 aaaaaatcat ataaaataag ggaaatttcc atctttaata aatatgtttg atttaatttt
     3421 tcaaaaaagt tcaatttatt ccagGTGGCG CTGTAAAAAT GGGAGTCCTC CACTCATCAG
     3481 GAAAACTAAT TCTCTTCGCA GATGCCGATG GAGCTACAAA ATTCGCCGAT TTTGAAAATC
     3541 TCGAGAAAGA AATGCTCCGA ACTGCCGGCG GAGAGCCACT TGATGAATCA TTTCCAGCAG
     3601 TTATTGTTGC TTCTAGgttt ttaattgatt tttatagaaa tttttaataa ttttcccatt
     3661 ttcagAGCGC ATTTGGAAGC CGAATCTATG GCTGTTAGAT CAGTTCCACG CACAATTTTA
     3721 ATGCTCGGTT TTCACTTACT CGTCTATACT TTTGCTGCAA GAACAATTAA AGATACACAG
     3781 TGTGGATTCA AACTTTTTAC TAGATCGATT GCTGCGAGGg tgagatttta gcttattttt
     3841 agctaaaaat ctccaatttt ggcctacttt ttggggtcgt agtggtcgga aatcgactat
     3901 tatatatata tatatatgtt cgaatttttt tttctttttg ggagaaaatg tttaaaaaat
     3961 tggcagactt ttttgtcgac aaattcggca agtcggcaag ttgccggttt gccgatttgc
     4021 cggaaatttt aaattctcga aaattgccgg attccaattt gccgcaagtt tttacaggga
     4081 tttttcttaa cctctgaaat ttccaaaaat gtgcaaaacc acaatttgcc gaaaattttc
     4141 ggcaattgcc gtgtttcagg cgaattcgtc aaatcgacaa tttgtcggtt tgccattttt
     4201 cctgaaattt taaattcagc aaaattgccg atttgccgga aatttcaatt ccggcaattt
     4261 gccgatttgc cggaaatttt caattccgga agtttgccga tttgccggaa attttcaatt
     4321 ccggcaattt gccgatttgc cagaaatttt caattccggc aatttgctga tttgccggaa
     4381 attttcaatt ccggaagttt gccgatttgc cggaaatttt caattccgga aatttgccga
     4441 tttgtcgatt tgccggaaat tttcaataac ggcaatttgt caatttaccg gatatttcaa
     4501 ttccggcaaa ttgctgattt tcctgaaatt ttcaattccg gcaaattgcc gatttgccga
     4561 aaattttcaa ttcctgattt aagattttag ctaaaattcg tcaaattaaa gtaaaaaaaa
     4621 ccaaaaaaaa aaaacgtttt tttttcagAT TTTCCCAGTA CTTCACATTG AGCGCTGGGC
     4681 TTTTGACGTT GAGCTCATCT TCCTTTGCGA AAGATGGACG GTCCCTGTGA AAGAAGTTTC
     4741 AGTTCGATGG ACTGAAATCG AAGGGTCTAA GATTACTCCA ATTTGGTCTT GGCTTCAAAT
     4801 GGGCCGAGAT CTTGTGCTCA TTTGGTTCAG ATATACGgta aaattgcagt tttttaggcc
     4861 ttttttgaag tggtgtcagg atgtcccatc gctctactgc acacgaaaat ggcgggaaaa
     4921 tatttttttt ttaatttgtg acgtcacagc gtatcttgaa taattttctt aattttaagc
     4981 gccgattttt gtcaaactta aaaaaaaaat aaataaataa tatctttctc attttaattt
     5041 ataaaatttg atattttacc aaaattctta aaatttagtg gaaaaattga agcaaaatac
     5101 acaataaaaa tgaataattt caattgaaac gaattttttt tttcgaaaaa ccatttaaac
     5161 cgttcattta ccaagtttcc gtgaattttt taaaaatgat tttccaaata aatttttgtt
     5221 taaattgaaa ttattcattt ttattgtatt ttgcttcaat ttctccacta aattttagaa
     5281 tttttgtaaa atatcaaatt ttataaatta aaatgagcca gtttttaaaa aaatttcacg
     5341 aaaatcggcg cttaaattga acaaaagcaa ttattcaaaa tgcgctgtgt gacgtcacaa
     5401 attttcaaaa aatattttcc cgccattttc gtgtgcggta gagcgacctg acaatatttt
     5461 tgacattaaa attttatttt cagATCGGAA TTTGGACGGA TGACCAGCCT CGCTAAatgc
     5521 tccacaaaaa atcgatacga gattttcaaa aaatcttgcc caaaaatttc ctttttcttc
     5581 tagtaatatc tatgctttaa tcactttttt tccctgcttt ttcctgattt tttttccaat
     5641 ttatggctgg ttgtaaatat ccatgattcc ttgaaaatgt gattctattc ttttttcttt
     5701 tcgcattttt attatttatt tatttacttg ttggtttttc ttttttttct ctcttgttct
     5761 ggggactctg ggtttatttt taatgctaaa ttcaaaaaaa tatcgattta aatgtttttt
     5821 tccatttttt tgtttttttt ttcgttttcc cagcgatttt atatctttcc atagagtttt
     5881 caggcgaaaa aaatcaaaaa atttccaggc aaaaatggtc aaaaaagcgg cggcaactag
     5941 caagcaggct acctatcaca gtgatgagat cgagatgaaa gaggaagttg tgctcaatgt
     6001 aggatttttt gaatatttca aggatgcaat cgcgctccat tgggaaacga gagcgctccg
     6061 cccccaaacg ttgggtctcg ttaggaaatc aggcggcaaa agcattttcc gtattttttt
     6121 aaaatttcgt ccagaaaaat tttaaaaaat tccaattttt tattgaaaat cgttattttt
     6181 ccgaaaaaaa ttgttataca aatttacgaa aaaaggcggc gatttatcaa ctgccggaaa
     6241 ttagtgaaag attacttttt ttcaaaaaaa attgaaaaaa tttaaaattg tgagataaac
     6301 caagaaaaaa ttaactttcg attttttcaa ctttttggaa aaaaaaaaca caaaccaaag
     6361 aaaaaatgaa caaaaaaaaa gcggattgcg tgtatttttc accacgcgta acgtcgttgt
     6421 cgcgatgtcc tccggaccga agagcaagaa gctaaaaacg cccacgcttg aacagcaaat
     6481 cgaagatgga gtcaatgctt atattcactc gcagcagttt gagttcaact ctccaccacg
     6541 ggaaaatttt tttgccaatt ttttcgtctc aaaaaaaaaa ggaaaaaaaa accaaaaaac
     6601 cgacatttct ggtcaatatt tttttttgtt tttttttttt gaagaaattc gattttttgc
     6661 ttttcggccg aaatttttat ttttttaaat tttccaaaaa ttcttcttca attccagacc
     6721 tacgacgaat gcaccgatta tgtcgaatac gacgatacaa aacaattcga tatcaacgag
     6781 tattgcgatc aaatccaagt ggcaatggtc aatgaatccg acgatggaat gacattggaa
     6841 tttgatatta ctcgcattga agctccaatt gcaaatgctc ttcgccgtgt gctcatcgcc
     6901 gaagtgccaa cgatggctct cgagaagatt tatctctatc agaatacttc tgtaattcaa
     6961 gatgaagtac tctgccatcg tttgggtctt ctgccgcttc gtgtggatcc acgtggattt
     7021 cagtttccaa aggaaaaagt cgttggaatc aatgagaagg gagtggattg tgacgaggag
     7081 cccgagggag atcccgcgaa aaatttgatc ttcaagatta atgtttcgtg tacgaagaat
     7141 cgaaatgcgg tgccgacggc taccgatccg aagcagcttt atcacaatag ctcggtctac
     7201 tcacgtgctt ttgaatgggt accgattgct gatcagaaga cgcaattcac cgaagaagcc
     7261 catccacgta tggtttctga tgatattctc gttgccaagc ttcgtcctgg acaggaaatt
     7321 gaagccagtt gccatgcggt caagggaatc ggacgggatc atgcaaagtt ctcaccggtt
     7381 gctactgcgt cctataggtg tgaattttga agctgctgaa atattttctt ttgatttttg
     7441 cggttttccg gaaaattgaa aatttttcgt ttttcgattt tctcggaaaa agtgaaaaat
     7501 tggggggaaa aaaattataa ttcatataat atattttcgg ttttacggga ccccaaattc
     7561 tgagaatgcg tattacacaa aatttttgac gcgcaaaata tctcgtagcg aaaactacag
     7621 taattcttta aatgactact gtagctttta aagagttact gtagttttcg ctacgagata
     7681 ttttggggaa gttaaataat ttttgtacat ctacctatat tcagtatatt tagactgttt
     7741 tctgtaattt tgtggaaaaa aaagttcgaa aatttcaagc cagaggtgaa tttttttgtc
     7801 gacaaatttg acaaattgcc aat   
//

plain sequence
 
