AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0780040020.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0780040020.01.T01 MTR_7g085180 96.364 110 4 0 17 126 346 455 9.78e-75 229
MsG0780040020.01.T01 MTR_7g085160 80.357 112 14 1 15 126 116 219 1.63e-60 185
MsG0780040020.01.T01 MTR_4g036220 69.027 113 34 1 15 126 321 433 1.24e-50 166
MsG0780040020.01.T01 MTR_7g085150 66.964 112 35 2 17 126 367 478 3.07e-46 155
MsG0780040020.01.T01 MTR_7g085120 65.766 111 37 1 17 126 346 456 5.65e-46 154
MsG0780040020.01.T01 MTR_7g085200 49.091 110 56 0 17 126 345 454 1.87e-35 126
MsG0780040020.01.T01 MTR_7g085200 49.091 110 56 0 17 126 347 456 1.90e-35 126
MsG0780040020.01.T01 MTR_7g085090 50.485 103 51 0 13 115 364 466 1.88e-34 124
MsG0780040020.01.T01 MTR_6g033000 49.038 104 53 0 13 116 379 482 4.76e-33 120
MsG0780040020.01.T01 MTR_7g085150 62.121 66 23 2 17 80 367 432 4.72e-20 84.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0780040020.01.T01 AT5G18280 45.631 103 56 0 13 115 369 471 1.39e-30 114
MsG0780040020.01.T01 AT3G04080 45.631 103 56 0 13 115 368 470 1.10e-29 111

Find 25 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTATGGAATTAGGTTTATT+TGG 0.217073 7:+72117275 None:intergenic
ACTGGATGAAGTATGGAATT+AGG 0.275392 7:+72117266 None:intergenic
AAACTTAGGTAACGCTGATA+TGG 0.305974 7:+72116728 None:intergenic
CAACATGTGTTGCTTGTTCA+TGG 0.317545 7:-72117128 MsG0780040020.01.T01:CDS
GAAATCTACTGGATGAAGTA+TGG 0.326285 7:+72117259 None:intergenic
GCTTCAATTTCGAAATCTAC+TGG 0.387215 7:+72117248 None:intergenic
TACATTAATCGCTTAAACTT+AGG 0.392460 7:+72116714 None:intergenic
GTGTTGCTTGTTCATGGATT+TGG 0.395528 7:-72117122 MsG0780040020.01.T01:intron
TACCTCTTTGTGATCTCTCA+AGG 0.442729 7:+72118196 None:intergenic
AGCTTGTGCATTAAACTTTG+AGG 0.451748 7:-72117219 MsG0780040020.01.T01:CDS
AAGAGATCCATGCATACATA+TGG 0.457084 7:+72117155 None:intergenic
GTGGAAGCTGCATGGCCTCT+AGG 0.468068 7:-72116765 MsG0780040020.01.T01:CDS
ATCCACTTATCCTCGACTTA+CGG 0.480369 7:-72117189 MsG0780040020.01.T01:CDS
TCAATATCAGAATTCTGTTG+TGG 0.555684 7:-72116784 MsG0780040020.01.T01:CDS
ATCCGTAAGTCGAGGATAAG+TGG 0.562884 7:+72117187 None:intergenic
AAAGAGATTACAGTAGGTGA+GGG 0.573833 7:-72116810 MsG0780040020.01.T01:CDS
AAAAGAGATTACAGTAGGTG+AGG 0.588180 7:-72116811 MsG0780040020.01.T01:CDS
CATGAACAAGCAACACATGT+TGG 0.594494 7:+72117129 None:intergenic
TAACGCTGATATGGCTTCCA+CGG 0.618228 7:+72116737 None:intergenic
CACCTTGAGAGATCACAAAG+AGG 0.632231 7:-72118198 MsG0780040020.01.T01:CDS
ATTCTGTTGTGGAAGCTGCA+TGG 0.638309 7:-72116773 MsG0780040020.01.T01:CDS
CCACGAAAAGAGATTACAGT+AGG 0.642945 7:-72116816 MsG0780040020.01.T01:CDS
AAAACGTCCATATGTATGCA+TGG 0.646148 7:-72117162 MsG0780040020.01.T01:CDS
ATGGCCTCTAGGTACTGCCG+TGG 0.707657 7:-72116754 MsG0780040020.01.T01:CDS
GCTTCCACGGCAGTACCTAG+AGG 0.713599 7:+72116750 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTTATTTTATTTTTTT+AGG - Chr7:72117601-72117620 MsG0780040020.01.T01:intron 0.0%
!!! TTTATTTTATTTTTTTAGGT+TGG - Chr7:72117605-72117624 MsG0780040020.01.T01:intron 10.0%
!!! TTTTTTTTTTTAAGCAAATA+GGG - Chr7:72117079-72117098 MsG0780040020.01.T01:intron 10.0%
!!! TTTTTTTTTTTTAAGCAAAT+AGG - Chr7:72117078-72117097 MsG0780040020.01.T01:intron 10.0%
!!! AAAAATTGATTTGTAACATA+AGG - Chr7:72117853-72117872 MsG0780040020.01.T01:intron 15.0%
!!! TTTAGTACACTTTTTTTATT+GGG - Chr7:72116888-72116907 MsG0780040020.01.T01:intron 15.0%
!!! TTTTAGTACACTTTTTTTAT+TGG - Chr7:72116887-72116906 MsG0780040020.01.T01:intron 15.0%
!! ACAAAACATTCGATATATTA+AGG - Chr7:72117896-72117915 MsG0780040020.01.T01:intron 20.0%
!! TTGCAAAGAAATAATTCTTA+AGG - Chr7:72117376-72117395 MsG0780040020.01.T01:intron 20.0%
!! TTTGATCTATATATACTTTG+AGG + Chr7:72116988-72117007 None:intergenic 20.0%
!!! AAAAGTAGTTACTTTGTTAT+TGG + Chr7:72117273-72117292 None:intergenic 20.0%
!!! AAATATTTGAGTTACTAGTT+TGG - Chr7:72116940-72116959 MsG0780040020.01.T01:intron 20.0%
!!! TTTATTTTTTTAGGTTGGTA+TGG - Chr7:72117610-72117629 MsG0780040020.01.T01:intron 20.0%
! AGTATGGAATTAGGTTTATT+TGG + Chr7:72117641-72117660 None:intergenic 25.0%
! TACATTAATCGCTTAAACTT+AGG + Chr7:72118202-72118221 None:intergenic 25.0%
!! AACCAAAAAGCAATTTTACA+TGG - Chr7:72117993-72118012 MsG0780040020.01.T01:intron 25.0%
!!! ACTTTTTTTTCCTTCTTCAA+AGG - Chr7:72117287-72117306 MsG0780040020.01.T01:CDS 25.0%
!!! ATCCATGTAAAATTGCTTTT+TGG + Chr7:72117998-72118017 None:intergenic 25.0%
!!! CTTTTTTTTCCTTCTTCAAA+GGG - Chr7:72117288-72117307 MsG0780040020.01.T01:CDS 25.0%
!!! TGACAATTTTGTTGTTGTTT+CGG + Chr7:72117017-72117036 None:intergenic 25.0%
AGATAGAGTAGTAGTAGTAA+GGG + Chr7:72117934-72117953 None:intergenic 30.0%
ATTGTCTTGTATTTGTTTGC+AGG - Chr7:72118067-72118086 MsG0780040020.01.T01:intron 30.0%
CTTTCTCAACGAAAGATATA+CGG + Chr7:72116856-72116875 None:intergenic 30.0%
GTAACATAAGGACATTCAAA+TGG - Chr7:72117865-72117884 MsG0780040020.01.T01:intron 30.0%
TCAATATCAGAATTCTGTTG+TGG - Chr7:72118129-72118148 MsG0780040020.01.T01:intron 30.0%
TTCTTTGCAATCATCAAAGT+TGG + Chr7:72117366-72117385 None:intergenic 30.0%
AAAACGTCCATATGTATGCA+TGG - Chr7:72117751-72117770 MsG0780040020.01.T01:intron 35.0%
AAAAGAGATTACAGTAGGTG+AGG - Chr7:72118102-72118121 MsG0780040020.01.T01:intron 35.0%
AAACTTAGGTAACGCTGATA+TGG + Chr7:72118188-72118207 None:intergenic 35.0%
AAAGAGATTACAGTAGGTGA+GGG - Chr7:72118103-72118122 MsG0780040020.01.T01:intron 35.0%
AAAGGGACCTTTACATATTC+AGG - Chr7:72117305-72117324 MsG0780040020.01.T01:intron 35.0%
AAGAGATCCATGCATACATA+TGG + Chr7:72117761-72117780 None:intergenic 35.0%
ACTGGATGAAGTATGGAATT+AGG + Chr7:72117650-72117669 None:intergenic 35.0%
AGCTTGTGCATTAAACTTTG+AGG - Chr7:72117694-72117713 MsG0780040020.01.T01:intron 35.0%
ATATTCAGGAGTGGAGTATA+AGG - Chr7:72117319-72117338 MsG0780040020.01.T01:intron 35.0%
CAGATAGAGTAGTAGTAGTA+AGG + Chr7:72117935-72117954 None:intergenic 35.0%
GAAATCTACTGGATGAAGTA+TGG + Chr7:72117657-72117676 None:intergenic 35.0%
GCTTCAATTTCGAAATCTAC+TGG + Chr7:72117668-72117687 None:intergenic 35.0%
TGATGTGTTGAACAAGTGTA+AGG - Chr7:72116804-72116823 MsG0780040020.01.T01:CDS 35.0%
TTGTATTTGTTTGCAGGCTT+AGG - Chr7:72118073-72118092 MsG0780040020.01.T01:intron 35.0%
! ACTTTTGGTGGAATATGGAA+TGG - Chr7:72117437-72117456 MsG0780040020.01.T01:intron 35.0%
! AGTATTTTACATCTTCAGCC+AGG + Chr7:72117513-72117532 None:intergenic 35.0%
!! TTTGTTATTGGCATGCTTGA+TGG + Chr7:72117261-72117280 None:intergenic 35.0%
!!! CTTTTTGGTTTCAAATAGCC+TGG + Chr7:72117983-72118002 None:intergenic 35.0%
ATCCACTTATCCTCGACTTA+CGG - Chr7:72117724-72117743 MsG0780040020.01.T01:intron 40.0%
CATGAACAAGCAACACATGT+TGG + Chr7:72117787-72117806 None:intergenic 40.0%
CCACGAAAAGAGATTACAGT+AGG - Chr7:72118097-72118116 MsG0780040020.01.T01:intron 40.0%
CTCCACTCCTGAATATGTAA+AGG + Chr7:72117315-72117334 None:intergenic 40.0%
GACCTTTACATATTCAGGAG+TGG - Chr7:72117310-72117329 MsG0780040020.01.T01:intron 40.0%
TACCTCTTTGTGATCTCTCA+AGG + Chr7:72116720-72116739 None:intergenic 40.0%
TTTGGTGGAATATGGAATGG+TGG - Chr7:72117440-72117459 MsG0780040020.01.T01:intron 40.0%
! ATTCCACCAAAAGTGCAACT+CGG + Chr7:72117431-72117450 None:intergenic 40.0%
! CCTACTGTAATCTCTTTTCG+TGG + Chr7:72118100-72118119 None:intergenic 40.0%
! GTTGCACTTTTGGTGGAATA+TGG - Chr7:72117432-72117451 MsG0780040020.01.T01:intron 40.0%
! TGCTTGTTCATGGATTTGGT+AGG - Chr7:72117795-72117814 MsG0780040020.01.T01:intron 40.0%
! TGTAAAGGTCCCTTTGAAGA+AGG + Chr7:72117300-72117319 None:intergenic 40.0%
! TTTGGTTTCAAATAGCCTGG+CGG + Chr7:72117980-72117999 None:intergenic 40.0%
!! CAACATGTGTTGCTTGTTCA+TGG - Chr7:72117785-72117804 MsG0780040020.01.T01:intron 40.0%
!! GTGTTGCTTGTTCATGGATT+TGG - Chr7:72117791-72117810 MsG0780040020.01.T01:intron 40.0%
AAAGTTGGAGCCAGAAGAAG+GGG + Chr7:72117351-72117370 None:intergenic 45.0%
ATCCGTAAGTCGAGGATAAG+TGG + Chr7:72117729-72117748 None:intergenic 45.0%
ATTCTGTTGTGGAAGCTGCA+TGG - Chr7:72118140-72118159 MsG0780040020.01.T01:intron 45.0%
CAAAGTTGGAGCCAGAAGAA+GGG + Chr7:72117352-72117371 None:intergenic 45.0%
CACCTTGAGAGATCACAAAG+AGG - Chr7:72116715-72116734 MsG0780040020.01.T01:CDS 45.0%
TAACGCTGATATGGCTTCCA+CGG + Chr7:72118179-72118198 None:intergenic 45.0%
TACTTCAGCTTTCGCTTACC+TGG - Chr7:72117492-72117511 MsG0780040020.01.T01:intron 45.0%
TCAAAGTTGGAGCCAGAAGA+AGG + Chr7:72117353-72117372 None:intergenic 45.0%
! ACCAAAAGTGCAACTCGGAT+AGG + Chr7:72117426-72117445 None:intergenic 45.0%
! CCAAAAGTGCAACTCGGATA+GGG + Chr7:72117425-72117444 None:intergenic 45.0%
! GAATATGGAATGGTGGAGGA+GGG - Chr7:72117447-72117466 MsG0780040020.01.T01:intron 45.0%
! TATCCGAGTTGCACTTTTGG+TGG - Chr7:72117425-72117444 MsG0780040020.01.T01:intron 45.0%
!! AAGGCTTTTTCCCCTTCTTC+TGG - Chr7:72117338-72117357 MsG0780040020.01.T01:intron 45.0%
GGTGGAATATGGAATGGTGG+AGG - Chr7:72117443-72117462 MsG0780040020.01.T01:intron 50.0%
! CCCTATCCGAGTTGCACTTT+TGG - Chr7:72117422-72117441 MsG0780040020.01.T01:intron 50.0%
! CGTTTTGCATCCGTAAGTCG+AGG + Chr7:72117737-72117756 None:intergenic 50.0%
! GGAATATGGAATGGTGGAGG+AGG - Chr7:72117446-72117465 MsG0780040020.01.T01:intron 50.0%
! TATGTCTAAGTGTTGCCGCC+AGG - Chr7:72117962-72117981 MsG0780040020.01.T01:intron 50.0%
GTGCAACTCGGATAGGGACA+TGG + Chr7:72117419-72117438 None:intergenic 55.0%
GCTTCCACGGCAGTACCTAG+AGG + Chr7:72118166-72118185 None:intergenic 60.0%
GTGGAAGCTGCATGGCCTCT+AGG - Chr7:72118148-72118167 MsG0780040020.01.T01:intron 60.0%
! ATGGCCTCTAGGTACTGCCG+TGG - Chr7:72118159-72118178 MsG0780040020.01.T01:intron 60.0%
! TGGAATGGTGGAGGAGGGAG+TGG - Chr7:72117452-72117471 MsG0780040020.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr7 gene 72116704 72118231 72116704 ID=MsG0780040020.01;Name=MsG0780040020.01
Chr7 mRNA 72116704 72118231 72116704 ID=MsG0780040020.01.T01;Parent=MsG0780040020.01;Name=MsG0780040020.01.T01;_AED=0.49;_eAED=0.56;_QI=0|0|0|1|1|0.66|3|0|126
Chr7 exon 72118184 72118231 72118184 ID=MsG0780040020.01.T01:exon:34940;Parent=MsG0780040020.01.T01
Chr7 exon 72117123 72117312 72117123 ID=MsG0780040020.01.T01:exon:34941;Parent=MsG0780040020.01.T01
Chr7 exon 72116704 72116846 72116704 ID=MsG0780040020.01.T01:exon:34942;Parent=MsG0780040020.01.T01
Chr7 CDS 72118184 72118231 72118184 ID=MsG0780040020.01.T01:cds;Parent=MsG0780040020.01.T01
Chr7 CDS 72117123 72117312 72117123 ID=MsG0780040020.01.T01:cds;Parent=MsG0780040020.01.T01
Chr7 CDS 72116704 72116846 72116704 ID=MsG0780040020.01.T01:cds;Parent=MsG0780040020.01.T01
Gene Sequence

>MsG0780040020.01.T01

ATGGGTGTTTACACCTTGAGAGATCACAAAGAGGTAAAAGAGAGTCGTGTTGGTATGGTTGAGCCAAATAAACCTAATTCCATACTTCATCCAGTAGATTTCGAAATTGAAGCTAAGCGAGCTTGTGCATTAAACTTTGAGGATGTCAAATCCACTTATCCTCGACTTACGGATGCAAAACGTCCATATGTATGCATGGATCTCTTATACCAACATGTGTTGCTTGTTCATGGATTTGGCTTAGGTCCACGAAAAGAGATTACAGTAGGTGAGGGAATTCAATATCAGAATTCTGTTGTGGAAGCTGCATGGCCTCTAGGTACTGCCGTGGAAGCCATATCAGCGTTACCTAAGTTTAAGCGATTAATGTATTTTATTTAA
Protein sequence

>MsG0780040020.01.T01

MGVYTLRDHKEVKESRVGMVEPNKPNSILHPVDFEIEAKRACALNFEDVKSTYPRLTDAKRPYVCMDLLYQHVLLVHGFGLGPRKEITVGEGIQYQNSVVEAAWPLGTAVEAISALPKFKRLMYFI*