AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051720


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051720.t1 MTR_7g055747 95.938 320 13 0 27 346 110 429 0.0 540
MS.gene051720.t1 MTR_7g055560 95.938 320 13 0 27 346 110 429 0.0 540
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051720.t1 AT3G25130 45.902 183 73 5 182 343 228 405 3.37e-35 132

Find 56 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATATCTTCAATTGATTT+TGG 0.170861 7.3:-49932372 None:intergenic
CAAAGACTAAATGAAGATTT+TGG 0.193613 7.3:+49932756 MS.gene051720:CDS
AAATGAGTTGGAAGCATATT+TGG 0.211168 7.3:+49932314 MS.gene051720:CDS
TCAACAGGGAAGATGAATTT+AGG 0.246896 7.3:+49933110 MS.gene051720:CDS
TGTTCTAATCTTGGAAGTTT+TGG 0.255756 7.3:+49932837 MS.gene051720:CDS
ACACTATGGTCCATTGAAAA+TGG 0.271896 7.3:+49932678 MS.gene051720:CDS
GTTTAGTGAGGATGAGTTAG+AGG 0.283368 7.3:+49933040 MS.gene051720:CDS
GATGATAAAGATGAGGAAAT+TGG 0.284728 7.3:+49932285 MS.gene051720:CDS
TCCAATACCTTTCAAAGCTT+TGG 0.297202 7.3:-49933162 None:intergenic
TCCAAAGCTTTGAAAGGTAT+TGG 0.299212 7.3:+49933161 MS.gene051720:CDS
GAAGAAGTTTGTTCTAATCT+TGG 0.301550 7.3:+49932828 MS.gene051720:CDS
AAAATATGGAGAAACATAAA+TGG 0.320936 7.3:-49932014 None:intergenic
AGAAGTAGTCAAGCCTATAT+TGG 0.332436 7.3:+49932620 MS.gene051720:CDS
TGAGGATGAGTTAGAGGAAG+AGG 0.350921 7.3:+49933046 MS.gene051720:CDS
TTGAATTTAGTATCCAATAT+AGG 0.358936 7.3:-49932633 None:intergenic
CAAGCTTTGAAATTCTCAAC+AGG 0.378595 7.3:+49933095 MS.gene051720:CDS
GTGAAGGAATGGATATGCTT+TGG 0.388433 7.3:+49932940 MS.gene051720:CDS
AGAGAACTCATTGTTCTTGT+TGG 0.389427 7.3:-49931968 None:intergenic
GGACGTAGTTGAATCCATTA+AGG 0.402615 7.3:+49932509 MS.gene051720:CDS
GAGTATGGTGGAAAAGGTAT+AGG 0.411829 7.3:+49932798 MS.gene051720:CDS
AAAAGAGGTTTATTGTCAAA+TGG 0.412280 7.3:+49932437 MS.gene051720:CDS
AGTATGGTGGAAAAGGTATA+GGG 0.423952 7.3:+49932799 MS.gene051720:CDS
TTGGAGAATTTGACAAGGTT+AGG 0.431973 7.3:-49933143 None:intergenic
TGAAGGAATGGATATGCTTT+GGG 0.440242 7.3:+49932941 MS.gene051720:CDS
AAGAAAAGTAACACAAAGAA+AGG 0.440269 7.3:+49932996 MS.gene051720:CDS
AATTGGTTTGCTAAATGAGT+TGG 0.447975 7.3:+49932302 MS.gene051720:CDS
AGAAAATGTGTCTTGTGAAA+AGG 0.452614 7.3:+49932590 MS.gene051720:CDS
GTCTCTATTACCCTTCACTT+TGG 0.467195 7.3:-49932703 None:intergenic
GAGTTAGAGGAAGAGGAGGT+AGG 0.471390 7.3:+49933053 MS.gene051720:CDS
TTGCATCATGTAGGCAAGAA+TGG 0.480234 7.3:+49933188 MS.gene051720:CDS
AATTGGGAGTATGGTGGAAA+AGG 0.481166 7.3:+49932792 MS.gene051720:CDS
GAGAGACATAATAATAGTGA+TGG 0.502040 7.3:+49932915 MS.gene051720:CDS
AGAAAACAAAGTTGAGAAAG+TGG 0.508967 7.3:+49932488 MS.gene051720:CDS
GGATACTAAATTCAATAAAG+TGG 0.514253 7.3:+49932641 MS.gene051720:CDS
AGGGAAGATGAATTTAGGAA+TGG 0.516981 7.3:+49933115 MS.gene051720:CDS
GAACTTCAAAGATTGAAGCT+TGG 0.517540 7.3:-49932344 None:intergenic
AAGCTTTGAAAGGTATTGGA+TGG 0.532498 7.3:+49933165 MS.gene051720:CDS
TAGTGATGGAAGTGAAGGAA+TGG 0.536155 7.3:+49932929 MS.gene051720:CDS
GGGAAGATGAATTTAGGAAT+GGG 0.537973 7.3:+49933116 MS.gene051720:CDS
GGATGAGTTAGAGGAAGAGG+AGG 0.538629 7.3:+49933049 MS.gene051720:CDS
AAGTGAAGTTGAGTTTAGTG+AGG 0.546215 7.3:+49933028 MS.gene051720:CDS
AATAATAGTGATGGAAGTGA+AGG 0.548220 7.3:+49932924 MS.gene051720:CDS
AAGAAAGCAAAGAAACACTA+TGG 0.554986 7.3:+49932664 MS.gene051720:CDS
AGAAAAGTAACACAAAGAAA+GGG 0.575353 7.3:+49932997 MS.gene051720:CDS
AAATTCTCCAAAGCTTTGAA+AGG 0.585068 7.3:+49933155 MS.gene051720:CDS
TGAAAATGGATCCAAAGTGA+AGG 0.588660 7.3:+49932692 MS.gene051720:CDS
AAAAGAGTGGAGAAGGACAT+TGG 0.588797 7.3:+49932875 MS.gene051720:CDS
GAAAATGGATCCAAAGTGAA+GGG 0.600047 7.3:+49932693 MS.gene051720:CDS
AAAAGCAATTGGGAGTATGG+TGG 0.613321 7.3:+49932786 MS.gene051720:CDS
TGAAGCTGATGATAAAGATG+AGG 0.620705 7.3:+49932278 MS.gene051720:CDS
ATTGGATGGTTGCATCATGT+AGG 0.636955 7.3:+49933179 MS.gene051720:CDS
AGATGAATTTAGGAATGGGA+AGG 0.640076 7.3:+49933120 MS.gene051720:CDS
AAGCTTTGAAATTCTCAACA+GGG 0.664595 7.3:+49933096 MS.gene051720:CDS
AATGGAACAAGACAGTGAAG+AGG 0.664688 7.3:-49931996 None:intergenic
AAGCTTTGGAGAATTTGACA+AGG 0.677569 7.3:-49933148 None:intergenic
ATATGAGAAAGAATCAAACA+AGG 0.721458 7.3:+49932968 MS.gene051720:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAATAGGAAAAATATAA+AGG - chr7.3:49932045-49932064 None:intergenic 15.0%
!! GAAAATAGGAAAAATATAAA+GGG - chr7.3:49932044-49932063 None:intergenic 15.0%
!! AAAATATGGAGAAACATAAA+TGG - chr7.3:49932017-49932036 None:intergenic 20.0%
!! TTGAATTTAGTATCCAATAT+AGG - chr7.3:49932636-49932655 None:intergenic 20.0%
!!! GAAATATCTTCAATTGATTT+TGG - chr7.3:49932375-49932394 None:intergenic 20.0%
! AAAAGAGGTTTATTGTCAAA+TGG + chr7.3:49932437-49932456 MS.gene051720:CDS 25.0%
! AAAGAAAAGATAGGAGTTTA+AGG - chr7.3:49932086-49932105 None:intergenic 25.0%
! AAGAAAAGTAACACAAAGAA+AGG + chr7.3:49932996-49933015 MS.gene051720:CDS 25.0%
! AGAAAAGTAACACAAAGAAA+GGG + chr7.3:49932997-49933016 MS.gene051720:CDS 25.0%
! AGAAAGAAAAAAACACCATT+TGG - chr7.3:49932232-49932251 None:intergenic 25.0%
! ATATAAAGGGTGAGAAAATA+TGG - chr7.3:49932031-49932050 None:intergenic 25.0%
! ATATGAGAAAGAATCAAACA+AGG + chr7.3:49932968-49932987 MS.gene051720:CDS 25.0%
! GGATACTAAATTCAATAAAG+TGG + chr7.3:49932641-49932660 MS.gene051720:CDS 25.0%
!! CAAAGACTAAATGAAGATTT+TGG + chr7.3:49932756-49932775 MS.gene051720:CDS 25.0%
!!! TAACACTTTTTCTTCCTTAA+TGG - chr7.3:49932526-49932545 None:intergenic 25.0%
AAGAAAGCAAAGAAACACTA+TGG + chr7.3:49932664-49932683 MS.gene051720:CDS 30.0%
ACAAAGGAGAAAGAAAAGAT+AGG - chr7.3:49932095-49932114 None:intergenic 30.0%
AGAAAACAAAGTTGAGAAAG+TGG + chr7.3:49932488-49932507 MS.gene051720:CDS 30.0%
AGAAAATGTGTCTTGTGAAA+AGG + chr7.3:49932590-49932609 MS.gene051720:CDS 30.0%
GAGAGACATAATAATAGTGA+TGG + chr7.3:49932915-49932934 MS.gene051720:CDS 30.0%
GATAGGAGTTTAAGGATATA+TGG - chr7.3:49932078-49932097 None:intergenic 30.0%
GATGATAAAGATGAGGAAAT+TGG + chr7.3:49932285-49932304 MS.gene051720:CDS 30.0%
TGAAAGTAAGAAAAGCAACA+AGG - chr7.3:49932140-49932159 None:intergenic 30.0%
TGAAGAGAAAAAAGTGAACT+TGG + chr7.3:49932461-49932480 MS.gene051720:CDS 30.0%
TGGAGAAAAGAAGAGAAAAT+AGG - chr7.3:49932058-49932077 None:intergenic 30.0%
! AAATGAGTTGGAAGCATATT+TGG + chr7.3:49932314-49932333 MS.gene051720:CDS 30.0%
! AATAATAGTGATGGAAGTGA+AGG + chr7.3:49932924-49932943 MS.gene051720:CDS 30.0%
! GAAGAAGTTTGTTCTAATCT+TGG + chr7.3:49932828-49932847 MS.gene051720:CDS 30.0%
! GTTTTCAGTTGAAGAAAAAG+AGG + chr7.3:49932422-49932441 MS.gene051720:CDS 30.0%
! TGTTCTAATCTTGGAAGTTT+TGG + chr7.3:49932837-49932856 MS.gene051720:CDS 30.0%
!! AAATTCTCCAAAGCTTTGAA+AGG + chr7.3:49933155-49933174 MS.gene051720:CDS 30.0%
!! AAGCTTTGAAATTCTCAACA+GGG + chr7.3:49933096-49933115 MS.gene051720:CDS 30.0%
!! AATTGGTTTGCTAAATGAGT+TGG + chr7.3:49932302-49932321 MS.gene051720:CDS 30.0%
!! TTTTGCAAACTTTTCTAGCA+TGG + chr7.3:49932253-49932272 MS.gene051720:intron 30.0%
AAGTGAAGTTGAGTTTAGTG+AGG + chr7.3:49933028-49933047 MS.gene051720:CDS 35.0%
ACACTATGGTCCATTGAAAA+TGG + chr7.3:49932678-49932697 MS.gene051720:CDS 35.0%
AGAAGTAGTCAAGCCTATAT+TGG + chr7.3:49932620-49932639 MS.gene051720:CDS 35.0%
AGAGAACTCATTGTTCTTGT+TGG - chr7.3:49931971-49931990 None:intergenic 35.0%
AGATGAATTTAGGAATGGGA+AGG + chr7.3:49933120-49933139 MS.gene051720:CDS 35.0%
AGGGAAGATGAATTTAGGAA+TGG + chr7.3:49933115-49933134 MS.gene051720:CDS 35.0%
CCAAACCTTGTTCATCATAA+GGG + chr7.3:49932162-49932181 MS.gene051720:intron 35.0%
GAAAATGGATCCAAAGTGAA+GGG + chr7.3:49932693-49932712 MS.gene051720:CDS 35.0%
GAACTTCAAAGATTGAAGCT+TGG - chr7.3:49932347-49932366 None:intergenic 35.0%
GGGAAGATGAATTTAGGAAT+GGG + chr7.3:49933116-49933135 MS.gene051720:CDS 35.0%
TACTACCCTTATGATGAACA+AGG - chr7.3:49932170-49932189 None:intergenic 35.0%
TCAACAGGGAAGATGAATTT+AGG + chr7.3:49933110-49933129 MS.gene051720:CDS 35.0%
TCCAAACCTTGTTCATCATA+AGG + chr7.3:49932161-49932180 MS.gene051720:intron 35.0%
TCCAATACCTTTCAAAGCTT+TGG - chr7.3:49933165-49933184 None:intergenic 35.0%
TGAAAATGGATCCAAAGTGA+AGG + chr7.3:49932692-49932711 MS.gene051720:CDS 35.0%
TGAAGCTGATGATAAAGATG+AGG + chr7.3:49932278-49932297 MS.gene051720:CDS 35.0%
TGAAGGAATGGATATGCTTT+GGG + chr7.3:49932941-49932960 MS.gene051720:CDS 35.0%
TGGAAGTCCAAAAAGCAATT+GGG + chr7.3:49932776-49932795 MS.gene051720:CDS 35.0%
TTGAGAGTTATGAGTCCAAA+TGG + chr7.3:49932214-49932233 MS.gene051720:intron 35.0%
TTGGAAGTCCAAAAAGCAAT+TGG + chr7.3:49932775-49932794 MS.gene051720:CDS 35.0%
TTGGAGAATTTGACAAGGTT+AGG - chr7.3:49933146-49933165 None:intergenic 35.0%
! AGAGTAGTGGTAATGAACAA+AGG - chr7.3:49932111-49932130 None:intergenic 35.0%
! AGTATGGTGGAAAAGGTATA+GGG + chr7.3:49932799-49932818 MS.gene051720:CDS 35.0%
! CACTTTGGATCCATTTTCAA+TGG - chr7.3:49932691-49932710 None:intergenic 35.0%
!! AAGCTTTGAAAGGTATTGGA+TGG + chr7.3:49933165-49933184 MS.gene051720:CDS 35.0%
!! AAGCTTTGGAGAATTTGACA+AGG - chr7.3:49933151-49933170 None:intergenic 35.0%
!! CAAGCTTTGAAATTCTCAAC+AGG + chr7.3:49933095-49933114 MS.gene051720:CDS 35.0%
!! TCCAAAGCTTTGAAAGGTAT+TGG + chr7.3:49933161-49933180 MS.gene051720:CDS 35.0%
!!! AAGTTTTGGTTCAATGAGAG+TGG + chr7.3:49932851-49932870 MS.gene051720:CDS 35.0%
AAAAGAGTGGAGAAGGACAT+TGG + chr7.3:49932875-49932894 MS.gene051720:CDS 40.0%
AACAAGGAGAAGAAGAGTAG+TGG - chr7.3:49932124-49932143 None:intergenic 40.0%
AATGGAACAAGACAGTGAAG+AGG - chr7.3:49931999-49932018 None:intergenic 40.0%
ATTGGATGGTTGCATCATGT+AGG + chr7.3:49933179-49933198 MS.gene051720:CDS 40.0%
CAATGAGAGTGGAAAAAGAG+TGG + chr7.3:49932862-49932881 MS.gene051720:CDS 40.0%
CCAAAAAGCAATTGGGAGTA+TGG + chr7.3:49932783-49932802 MS.gene051720:CDS 40.0%
CCCTTATGATGAACAAGGTT+TGG - chr7.3:49932165-49932184 None:intergenic 40.0%
GGACGTAGTTGAATCCATTA+AGG + chr7.3:49932509-49932528 MS.gene051720:CDS 40.0%
GTCTCTATTACCCTTCACTT+TGG - chr7.3:49932706-49932725 None:intergenic 40.0%
GTGAAGGAATGGATATGCTT+TGG + chr7.3:49932940-49932959 MS.gene051720:CDS 40.0%
GTTTAGTGAGGATGAGTTAG+AGG + chr7.3:49933040-49933059 MS.gene051720:CDS 40.0%
TTGCATCATGTAGGCAAGAA+TGG + chr7.3:49933188-49933207 MS.gene051720:CDS 40.0%
! AAAAGCAATTGGGAGTATGG+TGG + chr7.3:49932786-49932805 MS.gene051720:CDS 40.0%
! AATTGGGAGTATGGTGGAAA+AGG + chr7.3:49932792-49932811 MS.gene051720:CDS 40.0%
! GAGTATGGTGGAAAAGGTAT+AGG + chr7.3:49932798-49932817 MS.gene051720:CDS 40.0%
! TAGTGATGGAAGTGAAGGAA+TGG + chr7.3:49932929-49932948 MS.gene051720:CDS 40.0%
!! CCATACTCCCAATTGCTTTT+TGG - chr7.3:49932786-49932805 None:intergenic 40.0%
!!! ATTGGCTTGCAAGCTTTTTG+AGG + chr7.3:49932893-49932912 MS.gene051720:CDS 40.0%
GAGTGGAAAAAGAGTGGAGA+AGG + chr7.3:49932868-49932887 MS.gene051720:CDS 45.0%
TGAGGATGAGTTAGAGGAAG+AGG + chr7.3:49933046-49933065 MS.gene051720:CDS 45.0%
GAGTTAGAGGAAGAGGAGGT+AGG + chr7.3:49933053-49933072 MS.gene051720:CDS 50.0%
GGATGAGTTAGAGGAAGAGG+AGG + chr7.3:49933049-49933068 MS.gene051720:CDS 50.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 49931940 49933229 49931940 ID=MS.gene051720
chr7.3 mRNA 49931940 49933229 49931940 ID=MS.gene051720.t1;Parent=MS.gene051720
chr7.3 exon 49931940 49932021 49931940 ID=MS.gene051720.t1.exon1;Parent=MS.gene051720.t1
chr7.3 CDS 49931940 49932021 49931940 ID=cds.MS.gene051720.t1;Parent=MS.gene051720.t1
chr7.3 exon 49932271 49933229 49932271 ID=MS.gene051720.t1.exon2;Parent=MS.gene051720.t1
chr7.3 CDS 49932271 49933229 49932271 ID=cds.MS.gene051720.t1;Parent=MS.gene051720.t1
Gene Sequence

>MS.gene051720

ATGAGTGAGTTATCTTTCTCAAATGCTTCCAACAAGAACAATGAGTTCTCTAGTAACCTCTTCACTGTCTTGTTCCATTTATGTTTCTCCATATTTTCTCACCCTTTATATTTTTCCTATTTTCTCTTCTTTTCTCCATATATCCTTAAACTCCTATCTTTTCTTTCTCCTTTGTTCATTACCACTACTCTTCTTCTCCTTGTTGCTTTTCTTACTTTCACTCCAAACCTTGTTCATCATAAGGGTAGTAGCAAAAGTACTAGTACTAGTAGTGTTGAGAGTTATGAGTCCAAATGGTGTTTTTTTCTTTCTATTTTGCAAACTTTTCTAGCATGGTTTGAAGCTGATGATAAAGATGAGGAAATTGGTTTGCTAAATGAGTTGGAAGCATATTTGGTTATGTTCCAAGCTTCAATCTTTGAAGTTCATGAGCCAAAATCAATTGAAGATATTTCTGAAGAGTTTGAAGAAGCAGATGACGAGTTTTCAGTTGAAGAAAAAGAGGTTTATTGTCAAATGGATGAAGAGAAAAAAGTGAACTTGGATGAAGAAAACAAAGTTGAGAAAGTGGACGTAGTTGAATCCATTAAGGAAGAAAAAGTGTTAGATGTGAAAAGTTTAGTAACTTTGTTTCAAGAATATGCAGAGTTAGAAAATGTGTCTTGTGAAAAGGAAGAAAAAGAAGTAGTCAAGCCTATATTGGATACTAAATTCAATAAAGTGGAAGAAAGCAAAGAAACACTATGGTCCATTGAAAATGGATCCAAAGTGAAGGGTAATAGAGACATGTATGCAAATAAAGTGAAAGTGAAATCTCAAAGACTAAATGAAGATTTTGGAAGTCCAAAAAGCAATTGGGAGTATGGTGGAAAAGGTATAGGGAATAATGAAGAAGTTTGTTCTAATCTTGGAAGTTTTGGTTCAATGAGAGTGGAAAAAGAGTGGAGAAGGACATTGGCTTGCAAGCTTTTTGAGGAGAGACATAATAATAGTGATGGAAGTGAAGGAATGGATATGCTTTGGGAAACATATGAGAAAGAATCAAACAAGGTTGTGAAGAAAAGTAACACAAAGAAAGGGAAGAAATTAAGTGAAGTTGAGTTTAGTGAGGATGAGTTAGAGGAAGAGGAGGTAGGAGCTAAGTTATGTTGTTTACAAGCTTTGAAATTCTCAACAGGGAAGATGAATTTAGGAATGGGAAGGCCTAACCTTGTCAAATTCTCCAAAGCTTTGAAAGGTATTGGATGGTTGCATCATGTAGGCAAGAATGGAAAGAAGAATAACCACTGA

Protein sequence

>MS.gene051720.t1

MSELSFSNASNKNNEFSSNLFTVLFHLSWFEADDKDEEIGLLNELEAYLVMFQASIFEVHEPKSIEDISEEFEEADDEFSVEEKEVYCQMDEEKKVNLDEENKVEKVDVVESIKEEKVLDVKSLVTLFQEYAELENVSCEKEEKEVVKPILDTKFNKVEESKETLWSIENGSKVKGNRDMYANKVKVKSQRLNEDFGSPKSNWEYGGKGIGNNEEVCSNLGSFGSMRVEKEWRRTLACKLFEERHNNSDGSEGMDMLWETYEKESNKVVKKSNTKKGKKLSEVEFSEDELEEEEVGAKLCCLQALKFSTGKMNLGMGRPNLVKFSKALKGIGWLHHVGKNGKKNNH