AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene064743


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064743.t1 MTR_3g105990 67.093 313 38 4 1 248 131 443 1.32e-132 402
MS.gene064743.t1 MTR_0189s0050 55.873 315 70 7 1 248 129 441 2.55e-100 301
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064743.t1 AT3G18090 54.217 166 69 3 87 248 153 315 1.47e-55 191
MS.gene064743.t1 AT3G18090 50.000 96 43 1 6 96 3 98 1.00e-23 100
MS.gene064743.t1 AT3G18090 54.217 166 69 3 87 248 153 315 2.19e-55 191
MS.gene064743.t1 AT3G18090 50.000 96 43 1 6 96 3 98 1.18e-23 99.8
MS.gene064743.t1 AT3G18090 54.217 166 69 3 87 248 153 315 2.93e-55 191
MS.gene064743.t1 AT3G18090 50.000 96 43 1 6 96 3 98 1.16e-23 100
MS.gene064743.t1 AT3G23780 53.012 166 71 3 87 248 271 433 9.70e-54 186
MS.gene064743.t1 AT3G23780 53.465 101 42 1 1 96 116 216 2.09e-27 110
MS.gene064743.t1 AT3G23780 53.012 166 71 3 87 248 271 433 9.70e-54 186
MS.gene064743.t1 AT3G23780 53.465 101 42 1 1 96 116 216 2.09e-27 110

Find 50 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTATGTCTTTCCGAACATTA+AGG 0.230507 3.4:-97752209 MS.gene064743:CDS
CATGGTGAAGGTTCTCTTAC+TGG 0.253238 3.4:-97752155 MS.gene064743:CDS
GAGAAGAGAGAAATAACTAT+TGG 0.321428 3.4:-97753167 MS.gene064743:CDS
CAAAACTGATGTTCAAGTTC+AGG 0.334875 3.4:-97753555 MS.gene064743:intron
ATTGTTGATCTCATCGATTA+TGG 0.358647 3.4:-97752394 MS.gene064743:CDS
GTTCTCTTACTGGCTTATAC+TGG 0.359333 3.4:-97752145 MS.gene064743:CDS
TATGTCTTTCCGAACATTAA+GGG 0.378939 3.4:-97752208 MS.gene064743:CDS
AGACCTGACTTGACCATAAC+AGG 0.387165 3.4:+97753137 None:intergenic
TTATCACTCCGAACTTTCTT+CGG 0.390704 3.4:+97753239 None:intergenic
GGGATGACTTTCAAAATAAG+AGG 0.403829 3.4:-97752102 MS.gene064743:CDS
TGGTCAAGTCAGGTCTCTGC+TGG 0.429579 3.4:-97753130 MS.gene064743:CDS
AGAAGAGAGAAATAACTATT+GGG 0.437663 3.4:-97753166 MS.gene064743:CDS
ACGAAATGTATCACATTTGT+CGG 0.440086 3.4:+97752321 None:intergenic
TACATATTCCGAAGAAAGTT+CGG 0.448036 3.4:-97753247 MS.gene064743:CDS
CTGCCTGTTATGGTCAAGTC+AGG 0.458511 3.4:-97753140 MS.gene064743:CDS
TATTGGGAGACTGCCTGTTA+TGG 0.459953 3.4:-97753150 MS.gene064743:CDS
TCGGAAAGACATACAAGTTA+AGG 0.463583 3.4:+97752218 None:intergenic
AACAATCTCTTTATCTGAAG+TGG 0.475073 3.4:+97752411 None:intergenic
TGGAGGCTACTTTCTGATCA+AGG 0.477024 3.4:-97753069 MS.gene064743:CDS
AATAAGAGGCTTGAGTTGAC+TGG 0.485554 3.4:-97752088 MS.gene064743:CDS
GGCACGGTACCTGGCATACA+TGG 0.508318 3.4:-97752173 MS.gene064743:CDS
GCTCTGCAAAGAGACCTCTA+TGG 0.509833 3.4:-97752004 MS.gene064743:CDS
ACATTTGTCGGCTTCACGAA+TGG 0.519230 3.4:+97752333 None:intergenic
TTTCTTAGAGGAACGTGTCA+AGG 0.521437 3.4:-97752278 MS.gene064743:CDS
CGGAGTGATAAATTCAAGAC+AGG 0.527623 3.4:-97753227 MS.gene064743:CDS
TCTGATCAAGGGTGCTGAGA+AGG 0.528492 3.4:-97753057 MS.gene064743:intron
CACATGCTCGGAAGCGAATG+TGG 0.528935 3.4:-97752030 MS.gene064743:CDS
ATCGATTATGGAGAGGGAGA+TGG 0.529999 3.4:-97752382 MS.gene064743:CDS
CAAATGTGATACATTTCGTA+GGG 0.535115 3.4:-97752317 MS.gene064743:CDS
GAACCTTCACCATGTATGCC+AGG 0.538389 3.4:+97752164 None:intergenic
TAAATTCAAGACAGGAAAAG+AGG 0.540476 3.4:-97753219 MS.gene064743:CDS
CTCTGAAGACGAGCATGTCT+AGG 0.548315 3.4:+97753599 None:intergenic
AAGTGCACTTTGCACATGCT+CGG 0.551400 3.4:-97752042 MS.gene064743:CDS
GCACTCGTCAATAGATTCTG+AGG 0.566118 3.4:+97752240 None:intergenic
TGATCAGAAAGTAGCCTCCA+TGG 0.573050 3.4:+97753072 None:intergenic
TGCTCGGAAGCGAATGTGGA+AGG 0.573065 3.4:-97752026 MS.gene064743:CDS
GATCTCATCGATTATGGAGA+GGG 0.573846 3.4:-97752388 MS.gene064743:CDS
TTCTTAGAGGAACGTGTCAA+GGG 0.577874 3.4:-97752277 MS.gene064743:CDS
GGAGGCTACTTTCTGATCAA+GGG 0.578986 3.4:-97753068 MS.gene064743:CDS
GCATAAAATAGTATCCATAC+CGG 0.583912 3.4:+97752433 None:intergenic
ACAAATGTGATACATTTCGT+AGG 0.596270 3.4:-97752318 MS.gene064743:CDS
AAACATCTCAATCTCCATAG+AGG 0.600669 3.4:+97751990 None:intergenic
TGTCTGTTGAGATTCCGGTA+TGG 0.606023 3.4:-97752447 MS.gene064743:intron
CACTCGTCAATAGATTCTGA+GGG 0.638441 3.4:+97752241 None:intergenic
TGATCTCATCGATTATGGAG+AGG 0.644956 3.4:-97752389 MS.gene064743:CDS
AGTGATTGTGAATTTGACCA+TGG 0.651979 3.4:-97753089 MS.gene064743:CDS
GTACCTGGCATACATGGTGA+AGG 0.671158 3.4:-97752167 MS.gene064743:CDS
TCGTCAATAGATTCTGAGGG+CGG 0.676515 3.4:+97752244 None:intergenic
AAATGTGATACATTTCGTAG+GGG 0.709049 3.4:-97752316 MS.gene064743:CDS
GATTGTGAATTTGACCATGG+AGG 0.783133 3.4:-97753086 MS.gene064743:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGTATTCATAATAAATTA+AGG - chr3.4:97752117-97752136 MS.gene064743:CDS 10.0%
!!! TACAAAATCCTATTTTTATA+GGG - chr3.4:97752807-97752826 MS.gene064743:intron 15.0%
!!! TACATATTTTATACATCTTA+TGG - chr3.4:97752622-97752641 MS.gene064743:intron 15.0%
!!! TTACAAAATCCTATTTTTAT+AGG - chr3.4:97752806-97752825 MS.gene064743:intron 15.0%
!!! TTTTTAATCCCTATAAAAAT+AGG + chr3.4:97752818-97752837 None:intergenic 15.0%
!! AAGTTTAACAAAATTTATGC+AGG + chr3.4:97752687-97752706 None:intergenic 20.0%
!! AGTTTAACAAAATTTATGCA+GGG + chr3.4:97752686-97752705 None:intergenic 20.0%
!! ATTTGAGTAAAATTTATCCA+CGG - chr3.4:97752776-97752795 MS.gene064743:intron 20.0%
!!! AAAGTTTTCATATTTCTATG+TGG - chr3.4:97752093-97752112 MS.gene064743:CDS 20.0%
!!! AAGTTTTCATATTTCTATGT+GGG - chr3.4:97752094-97752113 MS.gene064743:CDS 20.0%
!!! TATTGTGTATTTTTGAAATG+TGG - chr3.4:97752235-97752254 MS.gene064743:CDS 20.0%
! AAATAGGATGGTTGTTAAAT+TGG - chr3.4:97753074-97753093 MS.gene064743:CDS 25.0%
! AACAAAAGCAATTTACAAAC+AGG + chr3.4:97752958-97752977 None:intergenic 25.0%
! AGAAGAGAGAAATAACTATT+GGG - chr3.4:97752436-97752455 MS.gene064743:CDS 25.0%
! CATTAAGGGATTAAAAAGAA+AGG - chr3.4:97753408-97753427 MS.gene064743:intron 25.0%
! TTAGTTCCTAATGCAAAATA+GGG + chr3.4:97752714-97752733 None:intergenic 25.0%
!! CTTTTTAATCCCTTAATGTT+CGG + chr3.4:97753406-97753425 None:intergenic 25.0%
!! TTTAGTTCCTAATGCAAAAT+AGG + chr3.4:97752715-97752734 None:intergenic 25.0%
!!! ATTTTTAATTCCTTCAATGC+TGG + chr3.4:97753109-97753128 None:intergenic 25.0%
!!! TTGAACATCAGTTTTGATTT+TGG + chr3.4:97752043-97752062 None:intergenic 25.0%
AAATGTGATACATTTCGTAG+GGG - chr3.4:97753286-97753305 MS.gene064743:intron 30.0%
AACAAAATTTATGCAGGGAA+CGG + chr3.4:97752681-97752700 None:intergenic 30.0%
AACAATCTCTTTATCTGAAG+TGG + chr3.4:97753194-97753213 None:intergenic 30.0%
ACAAATGTGATACATTTCGT+AGG - chr3.4:97753284-97753303 MS.gene064743:intron 30.0%
ACGAAATGTATCACATTTGT+CGG + chr3.4:97753284-97753303 None:intergenic 30.0%
CAAATGTGATACATTTCGTA+GGG - chr3.4:97753285-97753304 MS.gene064743:intron 30.0%
CACTGAATTAAAATGTAGAC+TGG + chr3.4:97752850-97752869 None:intergenic 30.0%
GAGAAGAGAGAAATAACTAT+TGG - chr3.4:97752435-97752454 MS.gene064743:CDS 30.0%
GAGATATAGATAAACACGTA+TGG - chr3.4:97752285-97752304 MS.gene064743:CDS 30.0%
GCATAAAATAGTATCCATAC+CGG + chr3.4:97753172-97753191 None:intergenic 30.0%
TAAATTCAAGACAGGAAAAG+AGG - chr3.4:97752383-97752402 MS.gene064743:CDS 30.0%
TACATATTCCGAAGAAAGTT+CGG - chr3.4:97752355-97752374 MS.gene064743:CDS 30.0%
TATGTCTTTCCGAACATTAA+GGG - chr3.4:97753394-97753413 MS.gene064743:intron 30.0%
! AAATATTTCTGAAGAGGCTT+TGG - chr3.4:97753001-97753020 MS.gene064743:intron 30.0%
! AAGAGCAAATATTTCTGAAG+AGG - chr3.4:97752995-97753014 MS.gene064743:intron 30.0%
! AATATTTCTGAAGAGGCTTT+GGG - chr3.4:97753002-97753021 MS.gene064743:intron 30.0%
! ATTGTTGATCTCATCGATTA+TGG - chr3.4:97753208-97753227 MS.gene064743:CDS 30.0%
! GATTTTGTAAGTTTAATCCG+TGG + chr3.4:97752796-97752815 None:intergenic 30.0%
! TTTAGTCCCTATTTTGCATT+AGG - chr3.4:97752705-97752724 MS.gene064743:intron 30.0%
!!! ACTTTTTTACTTCTGCAACT+TGG + chr3.4:97752261-97752280 None:intergenic 30.0%
!!! TTTTTTGTCTGTTGAGATTC+CGG - chr3.4:97753150-97753169 MS.gene064743:CDS 30.0%
AAATGAAGAGAAGTTGCTCA+CGG - chr3.4:97753125-97753144 MS.gene064743:CDS 35.0%
ACAGATGAAGAGAAATAGGA+TGG - chr3.4:97753062-97753081 MS.gene064743:CDS 35.0%
ACTGTGTGTGTGTTAATTTC+AGG - chr3.4:97752332-97752351 MS.gene064743:CDS 35.0%
AGGGATTAAAAAGAAAGGCA+CGG - chr3.4:97753413-97753432 MS.gene064743:intron 35.0%
AGTGACAGATGAAGAGAAAT+AGG - chr3.4:97753058-97753077 MS.gene064743:CDS 35.0%
AGTGATTGTGAATTTGACCA+TGG - chr3.4:97752513-97752532 MS.gene064743:intron 35.0%
GGGATGACTTTCAAAATAAG+AGG - chr3.4:97753500-97753519 MS.gene064743:intron 35.0%
GGGTTTCAAATATTCCGTAT+TGG - chr3.4:97753022-97753041 MS.gene064743:intron 35.0%
GTATGTCTTTCCGAACATTA+AGG - chr3.4:97753393-97753412 MS.gene064743:intron 35.0%
TAGGATGGTTGTTAAATTGG+TGG - chr3.4:97753077-97753096 MS.gene064743:CDS 35.0%
TCGGAAAGACATACAAGTTA+AGG + chr3.4:97753387-97753406 None:intergenic 35.0%
TTATACTGGACGCCAAAAAA+CGG - chr3.4:97753471-97753490 MS.gene064743:intron 35.0%
TTATCACTCCGAACTTTCTT+CGG + chr3.4:97752366-97752385 None:intergenic 35.0%
TTGTATGCAACTGTCCAATA+CGG + chr3.4:97753039-97753058 None:intergenic 35.0%
! CAAAACTGATGTTCAAGTTC+AGG - chr3.4:97752047-97752066 MS.gene064743:CDS 35.0%
! GAATGCTGTTCTTTTCTTAG+AGG - chr3.4:97753312-97753331 MS.gene064743:intron 35.0%
ACGCCAAAAAACGGATAACA+GGG - chr3.4:97753480-97753499 MS.gene064743:intron 40.0%
CACTCGTCAATAGATTCTGA+GGG + chr3.4:97753364-97753383 None:intergenic 40.0%
CGGAGTGATAAATTCAAGAC+AGG - chr3.4:97752375-97752394 MS.gene064743:CDS 40.0%
CGTATGGTGTCTTTGATGTT+CGG - chr3.4:97752301-97752320 MS.gene064743:CDS 40.0%
GATTGTGAATTTGACCATGG+AGG - chr3.4:97752516-97752535 MS.gene064743:intron 40.0%
TTCTTAGAGGAACGTGTCAA+GGG - chr3.4:97753325-97753344 MS.gene064743:intron 40.0%
TTTCTTAGAGGAACGTGTCA+AGG - chr3.4:97753324-97753343 MS.gene064743:intron 40.0%
! GATCTCATCGATTATGGAGA+GGG - chr3.4:97753214-97753233 MS.gene064743:CDS 40.0%
! TGATCTCATCGATTATGGAG+AGG - chr3.4:97753213-97753232 MS.gene064743:CDS 40.0%
!! AATAAGAGGCTTGAGTTGAC+TGG - chr3.4:97753514-97753533 MS.gene064743:intron 40.0%
!! GTTCTCTTACTGGCTTATAC+TGG - chr3.4:97753457-97753476 MS.gene064743:intron 40.0%
!!! CATCCCTGTTATCCGTTTTT+TGG + chr3.4:97753486-97753505 None:intergenic 40.0%
AAGTGCACTTTGCACATGCT+CGG - chr3.4:97753560-97753579 MS.gene064743:CDS 45.0%
ATCGATTATGGAGAGGGAGA+TGG - chr3.4:97753220-97753239 MS.gene064743:CDS 45.0%
CATGGTGAAGGTTCTCTTAC+TGG - chr3.4:97753447-97753466 MS.gene064743:intron 45.0%
GACGCCAAAAAACGGATAAC+AGG - chr3.4:97753479-97753498 MS.gene064743:intron 45.0%
GCACTCGTCAATAGATTCTG+AGG + chr3.4:97753365-97753384 None:intergenic 45.0%
GGAACGGCTGTGAATTGTAT+AGG + chr3.4:97752665-97752684 None:intergenic 45.0%
TATTGGGAGACTGCCTGTTA+TGG - chr3.4:97752452-97752471 MS.gene064743:intron 45.0%
TGATCAGAAAGTAGCCTCCA+TGG + chr3.4:97752533-97752552 None:intergenic 45.0%
TGTCTGTTGAGATTCCGGTA+TGG - chr3.4:97753155-97753174 MS.gene064743:CDS 45.0%
! AAAAAGAAAGGCACGGTACC+TGG - chr3.4:97753420-97753439 MS.gene064743:intron 45.0%
! AGACCTGACTTGACCATAAC+AGG + chr3.4:97752468-97752487 None:intergenic 45.0%
! GGAGGCTACTTTCTGATCAA+GGG - chr3.4:97752534-97752553 MS.gene064743:intron 45.0%
! GTGGAGAATTCCAGCATTGA+AGG - chr3.4:97753096-97753115 MS.gene064743:CDS 45.0%
! TCGTCAATAGATTCTGAGGG+CGG + chr3.4:97753361-97753380 None:intergenic 45.0%
! TGGAGGCTACTTTCTGATCA+AGG - chr3.4:97752533-97752552 MS.gene064743:intron 45.0%
!! ACATTTGTCGGCTTCACGAA+TGG + chr3.4:97753272-97753291 None:intergenic 45.0%
CTGCCTGTTATGGTCAAGTC+AGG - chr3.4:97752462-97752481 MS.gene064743:intron 50.0%
GAACCTTCACCATGTATGCC+AGG + chr3.4:97753441-97753460 None:intergenic 50.0%
GCTCTGCAAAGAGACCTCTA+TGG - chr3.4:97753598-97753617 MS.gene064743:CDS 50.0%
GTACCTGGCATACATGGTGA+AGG - chr3.4:97753435-97753454 MS.gene064743:intron 50.0%
! CTCTGAAGACGAGCATGTCT+AGG + chr3.4:97752006-97752025 None:intergenic 50.0%
!! TCTGATCAAGGGTGCTGAGA+AGG - chr3.4:97752545-97752564 MS.gene064743:intron 50.0%
CACATGCTCGGAAGCGAATG+TGG - chr3.4:97753572-97753591 MS.gene064743:CDS 55.0%
TGCTCGGAAGCGAATGTGGA+AGG - chr3.4:97753576-97753595 MS.gene064743:CDS 55.0%
TGGTCAAGTCAGGTCTCTGC+TGG - chr3.4:97752472-97752491 MS.gene064743:intron 55.0%
GGCACGGTACCTGGCATACA+TGG - chr3.4:97753429-97753448 MS.gene064743:intron 60.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 97751997 97753627 97751997 ID=MS.gene064743
chr3.4 mRNA 97751997 97753627 97751997 ID=MS.gene064743.t1;Parent=MS.gene064743
chr3.4 exon 97753556 97753627 97753556 ID=MS.gene064743.t1.exon1;Parent=MS.gene064743.t1
chr3.4 CDS 97753556 97753627 97753556 ID=cds.MS.gene064743.t1;Parent=MS.gene064743.t1
chr3.4 exon 97753058 97753270 97753058 ID=MS.gene064743.t1.exon2;Parent=MS.gene064743.t1
chr3.4 CDS 97753058 97753270 97753058 ID=cds.MS.gene064743.t1;Parent=MS.gene064743.t1
chr3.4 exon 97751997 97752458 97751997 ID=MS.gene064743.t1.exon3;Parent=MS.gene064743.t1
chr3.4 CDS 97751997 97752458 97751997 ID=cds.MS.gene064743.t1;Parent=MS.gene064743.t1
Gene Sequence

>MS.gene064743

ATGCTTCCTAGACATGCTCGTCTTCAGAGAATGACTTATGCTTCCAAAATCAAAACTGATGTTCAAGTTCAGGTTAGAAATTTTGAATCATTTCTTAAAGTTTTCATATTTCTATGTGGGTTAGTATTCATAATAAATTAAGGTGTTGTTGTGATTTTGTTAAGAGTTACTATTTTTAATGCTTTGAAATTTGTGATATCTGTTTGTTGTTTTTGTGTTAATGAGAAATGCATTGTTTTATTGTGTATTTTTGAAATGTGGCCAAGTTGCAGAAGTAAAAAAGTAAGAGAGATATAGATAAACACGTATGGTGTCTTTGATGTTCGGATAACACAACTGTGTGTGTGTTAATTTCAGGTACATATTCCGAAGAAAGTTCGGAGTGATAAATTCAAGACAGGAAAAGAGGAGTATATTGATAGAGAGATAATCATGAATGAGAAGAGAGAAATAACTATTGGGAGACTGCCTGTTATGGTCAAGTCAGGTCTCTGCTGGATGAGTGATGTTGAAAAAAGTGATTGTGAATTTGACCATGGAGGCTACTTTCTGATCAAGGGTGCTGAGAAGGTTAGCTATAATTATGATTTCTTTATTTACTTACATGAATTTCTGTCTTGTTTGCTACATATTTTATACATCTTATGGTTGCATATATTTTTAGTCCTATACAATTCACAGCCGTTCCCTGCATAAATTTTGTTAAACTTTAGTCCCTATTTTGCATTAGGAACTAAAAGTACTCATTTTTTGTATGAAGTTTTCAAAATACAGACTAAATTTGAGTAAAATTTATCCACGGATTAAACTTACAAAATCCTATTTTTATAGGGATTAAAAACATGCGTCTCCAGTCTACATTTTAATTCAGTGCATTAATGTTGTATTTATATTATTGTGCTTTGTTTTTGTATGTCTATATTATTATTATTATATCTTCACAATGTCTTTCTTTGCTCCTGTTTGTAAATTGCTTTTGTTGCAGATTTTTATTGCACAAGAGCAAATATTTCTGAAGAGGCTTTGGGTTTCAAATATTCCGTATTGGACAGTTGCATACAAGTGACAGATGAAGAGAAATAGGATGGTTGTTAAATTGGTGGAGAATTCCAGCATTGAAGGAATTAAAAATGAAGAGAAGTTGCTCACGGTTTTTTTTGTCTGTTGAGATTCCGGTATGGATACTATTTTATGCCACTTCAGATAAAGAGATTGTTGATCTCATCGATTATGGAGAGGGAGATGGAAGAATTCATAACATTCTCTTTGCATCCATTCGTGAAGCCGACAAATGTGATACATTTCGTAGGGGAAAGAATGCTGTTCTTTTCTTAGAGGAACGTGTCAAGGGTGTTCAATATCCGCCCTCAGAATCTATTGACGAGTGCCTTAACTTGTATGTCTTTCCGAACATTAAGGGATTAAAAAGAAAGGCACGGTACCTGGCATACATGGTGAAGGTTCTCTTACTGGCTTATACTGGACGCCAAAAAACGGATAACAGGGATGACTTTCAAAATAAGAGGCTTGAGTTGACTGGTGAGCTGCGCGAGCACGAGATCAAAGTGCACTTTGCACATGCTCGGAAGCGAATGTGGAAGGCTCTGCAAAGAGACCTCTATGGAGATTGA

Protein sequence

>MS.gene064743.t1

MLPRHARLQRMTYASKIKTDVQVQVHIPKKVRSDKFKTGKEEYIDREIIMNEKREITIGRLPVMVKSGLCWMSDVEKSDCEFDHGGYFLIKGAEKIPVWILFYATSDKEIVDLIDYGEGDGRIHNILFASIREADKCDTFRRGKNAVLFLEERVKGVQYPPSESIDECLNLYVFPNIKGLKRKARYLAYMVKVLLLAYTGRQKTDNRDDFQNKRLELTGELREHEIKVHFAHARKRMWKALQRDLYGD