AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014136.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014136.01.T01 MTR_3g051270 97.101 69 2 0 41 109 395 463 2.69e-41 141
MsG0380014136.01.T01 MTR_3g051270 97.101 69 2 0 41 109 411 479 3.32e-41 141
MsG0380014136.01.T01 MTR_3g051270 97.101 69 2 0 41 109 420 488 3.49e-41 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGGCAATTGAACTTAAA+TGG 0.180160 3:+50250679 MsG0380014136.01.T01:three_prime_UTR
GAAAAGCCAGGTTGCAAAAT+TGG 0.267671 3:-50250312 None:intergenic
GGGTTATGCTGGGCTGTCTA+TGG 0.275555 3:+50249096 None:intergenic
ATATAACCCTAAAATTTCTA+TGG 0.329326 3:-50250540 None:intergenic
CCAGGACCAAATGGTTTCTA+TGG 0.368413 3:+50250357 MsG0380014136.01.T01:CDS
GATACTTGATATTGTACGTT+TGG 0.373845 3:+50250662 MsG0380014136.01.T01:three_prime_UTR
TAAGGTTTCAATTCTTGTCT+TGG 0.375265 3:+50250608 MsG0380014136.01.T01:three_prime_UTR
ACTATACACTTCTCACATAA+AGG 0.392767 3:-50250502 None:intergenic
AAGGTTTCAATTCTTGTCTT+GGG 0.394254 3:+50250609 MsG0380014136.01.T01:three_prime_UTR
TTTGGCAATTGAACTTAAAT+GGG 0.403670 3:+50250680 MsG0380014136.01.T01:three_prime_UTR
AATGTGGCTTTGAACTTCAT+AGG 0.417556 3:-50250289 None:intergenic
TTTCATTGGGCCACTGAGAA+AGG 0.427026 3:-50249148 None:intergenic
GAAATTGTATGTGATTCAAC+GGG 0.428840 3:-50249928 None:intergenic
CTGAACTTTAACTCGGAGAA+AGG 0.442542 3:-50250425 None:intergenic
TTAGTGCCATAGAAACCATT+TGG 0.463379 3:-50250363 None:intergenic
TGATTGAAGGATATGGTTCA+TGG 0.473132 3:+50249879 MsG0380014136.01.T01:intron
CCATAGAAACCATTTGGTCC+TGG 0.484815 3:-50250357 None:intergenic
ATTTCAGTCCCAGGACCAAA+TGG 0.496523 3:+50250348 MsG0380014136.01.T01:CDS
TGCAAGCTTGTTATGACAGA+TGG 0.498794 3:-50250258 None:intergenic
CAACGGGGACGAGTTGAGAA+TGG 0.500401 3:-50249912 None:intergenic
CATAGAAACCATTTGGTCCT+GGG 0.505205 3:-50250356 None:intergenic
TGAAATTGTATGTGATTCAA+CGG 0.506107 3:-50249929 None:intergenic
TTATGCTGGGCTGTCTATGG+TGG 0.518400 3:+50249099 None:intergenic
CATGTGAAGATAAGGTACTA+AGG 0.521497 3:+50250590 MsG0380014136.01.T01:three_prime_UTR
TGAGTCATCATGTGAAGATA+AGG 0.526786 3:+50250582 MsG0380014136.01.T01:three_prime_UTR
GCAAGCTTGTTATGACAGAT+GGG 0.527962 3:-50250257 None:intergenic
TGAACTTTAACTCGGAGAAA+GGG 0.529295 3:-50250424 None:intergenic
AGTGTATAGTAGCTTTGTGC+TGG 0.541179 3:+50250515 MsG0380014136.01.T01:three_prime_UTR
CTGTCTATGGTGGTTTCCGT+TGG 0.543011 3:+50249109 MsG0380014136.01.T01:CDS
ATGTGGCTTTGAACTTCATA+GGG 0.544634 3:-50250288 None:intergenic
GCTCTAGGTGCCGAAAAGCC+AGG 0.551621 3:-50250324 None:intergenic
CCTAGAGCTATTTCAGTCCC+AGG 0.559587 3:+50250339 MsG0380014136.01.T01:CDS
CCTGGGACTGAAATAGCTCT+AGG 0.566185 3:-50250339 None:intergenic
CCGTTGGTTTACTCACAGCA+TGG 0.577593 3:+50249125 MsG0380014136.01.T01:CDS
GGATATGGTTCATGGTGTAA+CGG 0.597289 3:+50249887 MsG0380014136.01.T01:intron
CACAGCATGGCCTTTCTCAG+TGG 0.603762 3:+50249138 MsG0380014136.01.T01:CDS
CAGGTTGCAAAATTGGAATG+TGG 0.615532 3:-50250305 None:intergenic
CAAGCTTGTTATGACAGATG+GGG 0.636114 3:-50250256 None:intergenic
ATAGAGACTGAACTTTAACT+CGG 0.640192 3:-50250432 None:intergenic
AAGCTTGTTATGACAGATGG+GGG 0.644197 3:-50250255 None:intergenic
CCATGCTGTGAGTAAACCAA+CGG 0.667874 3:-50249125 None:intergenic
ATACAATTTCAAAAGCAGCA+AGG 0.675012 3:+50249941 MsG0380014136.01.T01:CDS
AGCTTGTTATGACAGATGGG+GGG 0.732233 3:-50250254 None:intergenic
AAATTGTATGTGATTCAACG+GGG 0.737306 3:-50249927 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATATTTCATATTTTCA+TGG + Chr3:50249688-50249707 MsG0380014136.01.T01:intron 10.0%
!!! TTTTGATATCAATTAAAAAA+TGG - Chr3:50250460-50250479 None:intergenic 10.0%
!! AACAAAAATTTCATTATGTA+AGG - Chr3:50250781-50250800 None:intergenic 15.0%
!!! CATAATGAAATTTTTGTTTA+AGG + Chr3:50250783-50250802 MsG0380014136.01.T01:three_prime_UTR 15.0%
!!! TTTTATATTTCATATTTCCA+TGG + Chr3:50249750-50249769 MsG0380014136.01.T01:intron 15.0%
!! AATTTGGATGTCAAAATTAT+TGG - Chr3:50250142-50250161 None:intergenic 20.0%
!! ATATAACCCTAAAATTTCTA+TGG - Chr3:50250543-50250562 None:intergenic 20.0%
!! ATTTAAAGAGATGGAAAATT+TGG + Chr3:50250723-50250742 MsG0380014136.01.T01:intron 20.0%
!! GTTCATATTCTTATTCAATT+TGG - Chr3:50250158-50250177 None:intergenic 20.0%
!! TTTACTAATTTCCTAACTTA+CGG + Chr3:50249374-50249393 MsG0380014136.01.T01:intron 20.0%
!!! AGAAAATAATCACTTTCTTT+TGG - Chr3:50250033-50250052 None:intergenic 20.0%
! AATTATGCTTCATATCGAAA+GGG - Chr3:50250106-50250125 None:intergenic 25.0%
! AGGAAATTAGTAAAAGAGAT+TGG - Chr3:50249368-50249387 None:intergenic 25.0%
! ATGAACAAGCTGTAATAATA+GGG + Chr3:50249182-50249201 MsG0380014136.01.T01:intron 25.0%
! ATGAAGCATAATTGAATCTT+GGG + Chr3:50250113-50250132 MsG0380014136.01.T01:intron 25.0%
! TATGAACAAGCTGTAATAAT+AGG + Chr3:50249181-50249200 MsG0380014136.01.T01:intron 25.0%
! TATGAAGCATAATTGAATCT+TGG + Chr3:50250112-50250131 MsG0380014136.01.T01:intron 25.0%
! TGAAATTGTATGTGATTCAA+CGG - Chr3:50249932-50249951 None:intergenic 25.0%
! TTCCATCTCTTTAAATAGTA+TGG - Chr3:50250719-50250738 None:intergenic 25.0%
! TTTGGCAATTGAACTTAAAT+GGG + Chr3:50250680-50250699 MsG0380014136.01.T01:three_prime_UTR 25.0%
!!! TTGTTCCATTTTTCAAAAAC+AGG + Chr3:50250198-50250217 MsG0380014136.01.T01:intron 25.0%
AAATTGTATGTGATTCAACG+GGG - Chr3:50249930-50249949 None:intergenic 30.0%
AAGGTTTCAATTCTTGTCTT+GGG + Chr3:50250609-50250628 MsG0380014136.01.T01:three_prime_UTR 30.0%
AATTAGCCAAAAAGATATGC+AGG - Chr3:50250180-50250199 None:intergenic 30.0%
ACTATACACTTCTCACATAA+AGG - Chr3:50250505-50250524 None:intergenic 30.0%
ATACAATTTCAAAAGCAGCA+AGG + Chr3:50249941-50249960 MsG0380014136.01.T01:CDS 30.0%
ATAGAGACTGAACTTTAACT+CGG - Chr3:50250435-50250454 None:intergenic 30.0%
ATCCTATGGATCCTTATAAA+GGG + Chr3:50249596-50249615 MsG0380014136.01.T01:intron 30.0%
ATGATAGTTGTAGTATCCTA+TGG + Chr3:50249582-50249601 MsG0380014136.01.T01:intron 30.0%
CAATTATGCTTCATATCGAA+AGG - Chr3:50250107-50250126 None:intergenic 30.0%
CTATGATGGTCAAAAAGATA+TGG - Chr3:50249842-50249861 None:intergenic 30.0%
CTCCATACTATTTAAAGAGA+TGG + Chr3:50250714-50250733 MsG0380014136.01.T01:intron 30.0%
GAAATTGTATGTGATTCAAC+GGG - Chr3:50249931-50249950 None:intergenic 30.0%
GATACTTGATATTGTACGTT+TGG + Chr3:50250662-50250681 MsG0380014136.01.T01:three_prime_UTR 30.0%
GTAGAAGTTATCTTTCTACT+TGG - Chr3:50249308-50249327 None:intergenic 30.0%
GTTTGGCAATTGAACTTAAA+TGG + Chr3:50250679-50250698 MsG0380014136.01.T01:three_prime_UTR 30.0%
TAAGGTTTCAATTCTTGTCT+TGG + Chr3:50250608-50250627 MsG0380014136.01.T01:three_prime_UTR 30.0%
TATCCTATGGATCCTTATAA+AGG + Chr3:50249595-50249614 MsG0380014136.01.T01:intron 30.0%
! ATCATTCCATGTACAGTTTT+TGG - Chr3:50249426-50249445 None:intergenic 30.0%
! TATGAACCTGCATATCTTTT+TGG + Chr3:50250171-50250190 MsG0380014136.01.T01:intron 30.0%
! TCATTCCATGTACAGTTTTT+GGG - Chr3:50249425-50249444 None:intergenic 30.0%
!! TTCCATTTTTCAAAAACAGG+AGG + Chr3:50250201-50250220 MsG0380014136.01.T01:intron 30.0%
!!! ATACCTTGCGTTTTTTCATT+GGG - Chr3:50249164-50249183 None:intergenic 30.0%
!!! TTCCTCCTGTTTTTGAAAAA+TGG - Chr3:50250206-50250225 None:intergenic 30.0%
ATCTTTCTACTTGGTATCAG+AGG - Chr3:50249299-50249318 None:intergenic 35.0%
CAAAAAGATATGGTTGACCA+TGG - Chr3:50249832-50249851 None:intergenic 35.0%
CTACTTGTGATTGAAGGATA+TGG + Chr3:50249872-50249891 MsG0380014136.01.T01:intron 35.0%
CTCTTGATTCAGTTAGCAAA+TGG - Chr3:50249718-50249737 None:intergenic 35.0%
GCAATTGAACTTAAATGGGT+TGG + Chr3:50250684-50250703 MsG0380014136.01.T01:intron 35.0%
GTAGAAAGACTTAGCTATGA+TGG - Chr3:50249856-50249875 None:intergenic 35.0%
GTCTTTCTACTTGTGATTGA+AGG + Chr3:50249866-50249885 MsG0380014136.01.T01:intron 35.0%
GTGAAATAGAACCGTAAGTT+AGG - Chr3:50249388-50249407 None:intergenic 35.0%
TATCAGAGGTCTTTCGATTT+GGG - Chr3:50249285-50249304 None:intergenic 35.0%
TGAACTTTAACTCGGAGAAA+GGG - Chr3:50250427-50250446 None:intergenic 35.0%
TGAGTCATCATGTGAAGATA+AGG + Chr3:50250582-50250601 MsG0380014136.01.T01:three_prime_UTR 35.0%
TGATTGAAGGATATGGTTCA+TGG + Chr3:50249879-50249898 MsG0380014136.01.T01:intron 35.0%
TTAGTGCCATAGAAACCATT+TGG - Chr3:50250366-50250385 None:intergenic 35.0%
TTCCCTTTATAAGGATCCAT+AGG - Chr3:50249601-50249620 None:intergenic 35.0%
! CATGTGAAGATAAGGTACTA+AGG + Chr3:50250590-50250609 MsG0380014136.01.T01:three_prime_UTR 35.0%
! CTGGCTCCATAGAAATTTTA+GGG + Chr3:50250534-50250553 MsG0380014136.01.T01:three_prime_UTR 35.0%
!! AATGTGGCTTTGAACTTCAT+AGG - Chr3:50250292-50250311 None:intergenic 35.0%
!! AATTTTGCAACCTGGCTTTT+CGG + Chr3:50250314-50250333 MsG0380014136.01.T01:CDS 35.0%
!! ATGTGGCTTTGAACTTCATA+GGG - Chr3:50250291-50250310 None:intergenic 35.0%
!!! CATACCTTGCGTTTTTTCAT+TGG - Chr3:50249165-50249184 None:intergenic 35.0%
!!! TTTTTGGGACAGATTTACAC+AGG - Chr3:50249410-50249429 None:intergenic 35.0%
AGTTAGCAAATGGTTGACCA+TGG - Chr3:50249708-50249727 None:intergenic 40.0%
CAGGTTGCAAAATTGGAATG+TGG - Chr3:50250308-50250327 None:intergenic 40.0%
CATAGAAACCATTTGGTCCT+GGG - Chr3:50250359-50250378 None:intergenic 40.0%
CTGAACTTTAACTCGGAGAA+AGG - Chr3:50250428-50250447 None:intergenic 40.0%
GAAAAGCCAGGTTGCAAAAT+TGG - Chr3:50250315-50250334 None:intergenic 40.0%
GAAGTCGCATTCCCTTTATA+AGG - Chr3:50249610-50249629 None:intergenic 40.0%
GGATATGGTTCATGGTGTAA+CGG + Chr3:50249887-50249906 MsG0380014136.01.T01:intron 40.0%
GTATCAGAGGTCTTTCGATT+TGG - Chr3:50249286-50249305 None:intergenic 40.0%
TAATAGGGCAGCAGCAATAA+AGG + Chr3:50249197-50249216 MsG0380014136.01.T01:intron 40.0%
TCAAAAACAGGAGGAACACA+TGG + Chr3:50250210-50250229 MsG0380014136.01.T01:intron 40.0%
TCTGTCCCAAAAACTGTACA+TGG + Chr3:50249417-50249436 MsG0380014136.01.T01:intron 40.0%
! CACATTCCAATTTTGCAACC+TGG + Chr3:50250306-50250325 MsG0380014136.01.T01:CDS 40.0%
!! AAGCTTGTTATGACAGATGG+GGG - Chr3:50250258-50250277 None:intergenic 40.0%
!! AGTGTATAGTAGCTTTGTGC+TGG + Chr3:50250515-50250534 MsG0380014136.01.T01:three_prime_UTR 40.0%
!! CAAGCTTGTTATGACAGATG+GGG - Chr3:50250259-50250278 None:intergenic 40.0%
!! GCAAGCTTGTTATGACAGAT+GGG - Chr3:50250260-50250279 None:intergenic 40.0%
!! GCTGGCTCCATAGAAATTTT+AGG + Chr3:50250533-50250552 MsG0380014136.01.T01:three_prime_UTR 40.0%
!! TGCAAGCTTGTTATGACAGA+TGG - Chr3:50250261-50250280 None:intergenic 40.0%
ATGGATGCAATGAAGCGACT+AGG + Chr3:50249235-50249254 MsG0380014136.01.T01:intron 45.0%
ATTTCAGTCCCAGGACCAAA+TGG + Chr3:50250348-50250367 MsG0380014136.01.T01:CDS 45.0%
CCAGGACCAAATGGTTTCTA+TGG + Chr3:50250357-50250376 MsG0380014136.01.T01:CDS 45.0%
CCATAGAAACCATTTGGTCC+TGG - Chr3:50250360-50250379 None:intergenic 45.0%
CCATGCTGTGAGTAAACCAA+CGG - Chr3:50249128-50249147 None:intergenic 45.0%
TGGATGCAATGAAGCGACTA+GGG + Chr3:50249236-50249255 MsG0380014136.01.T01:intron 45.0%
TGGCCCAATGAAAAAACGCA+AGG + Chr3:50249158-50249177 MsG0380014136.01.T01:CDS 45.0%
TTTCATTGGGCCACTGAGAA+AGG - Chr3:50249151-50249170 None:intergenic 45.0%
!! AGCTTGTTATGACAGATGGG+GGG - Chr3:50250257-50250276 None:intergenic 45.0%
ACAGATGGGGGGATAACAAC+TGG - Chr3:50250246-50250265 None:intergenic 50.0%
CCTGGGACTGAAATAGCTCT+AGG - Chr3:50250342-50250361 None:intergenic 50.0%
CTGTCTATGGTGGTTTCCGT+TGG + Chr3:50249109-50249128 MsG0380014136.01.T01:CDS 50.0%
GATGCAATGAAGCGACTAGG+GGG + Chr3:50249238-50249257 MsG0380014136.01.T01:intron 50.0%
GGATGCAATGAAGCGACTAG+GGG + Chr3:50249237-50249256 MsG0380014136.01.T01:intron 50.0%
! CCTAGAGCTATTTCAGTCCC+AGG + Chr3:50250339-50250358 MsG0380014136.01.T01:CDS 50.0%
!! CCGTTGGTTTACTCACAGCA+TGG + Chr3:50249125-50249144 MsG0380014136.01.T01:CDS 50.0%
AAGGCAGCTGCTGTCAGACA+TGG + Chr3:50249216-50249235 MsG0380014136.01.T01:intron 55.0%
CACAGCATGGCCTTTCTCAG+TGG + Chr3:50249138-50249157 MsG0380014136.01.T01:CDS 55.0%
! CAACGGGGACGAGTTGAGAA+TGG - Chr3:50249915-50249934 None:intergenic 55.0%
!! GCGACTAGGGGGTTTTGATG+CGG + Chr3:50249249-50249268 MsG0380014136.01.T01:intron 55.0%
!! GGGGGTTTTGATGCGGAAAC+AGG + Chr3:50249256-50249275 MsG0380014136.01.T01:intron 55.0%
!! GCTCTAGGTGCCGAAAAGCC+AGG - Chr3:50250327-50250346 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 50249101 50250806 50249101 ID=MsG0380014136.01;Name=MsG0380014136.01
Chr3 mRNA 50249101 50250806 50249101 ID=MsG0380014136.01.T01;Parent=MsG0380014136.01;Name=MsG0380014136.01.T01;_AED=0.48;_eAED=0.54;_QI=0|0.66|0.75|1|0|0|4|368|109
Chr3 exon 50249101 50249179 50249101 ID=MsG0380014136.01.T01:exon:9600;Parent=MsG0380014136.01.T01
Chr3 exon 50249888 50249962 50249888 ID=MsG0380014136.01.T01:exon:9601;Parent=MsG0380014136.01.T01
Chr3 exon 50250220 50250701 50250220 ID=MsG0380014136.01.T01:exon:9602;Parent=MsG0380014136.01.T01
Chr3 exon 50250745 50250806 50250745 ID=MsG0380014136.01.T01:exon:9603;Parent=MsG0380014136.01.T01
Chr3 CDS 50249101 50249179 50249101 ID=MsG0380014136.01.T01:cds;Parent=MsG0380014136.01.T01
Chr3 CDS 50249888 50249962 50249888 ID=MsG0380014136.01.T01:cds;Parent=MsG0380014136.01.T01
Chr3 CDS 50250220 50250395 50250220 ID=MsG0380014136.01.T01:cds;Parent=MsG0380014136.01.T01
Chr3 three_prime_UTR 50250396 50250701 50250396 ID=MsG0380014136.01.T01:three_prime_utr;Parent=MsG0380014136.01.T01
Chr3 three_prime_UTR 50250745 50250806 50250745 ID=MsG0380014136.01.T01:three_prime_utr;Parent=MsG0380014136.01.T01
Gene Sequence

>MsG0380014136.01.T01

ATGCTGGGCTGTCTATGGTGGTTTCCGTTGGTTTACTCACAGCATGGCCTTTCTCAGTGGCCCAATGAAAAAACGCAAGGATATGGTTCATGGTGTAACGGCTCCATTCTCAACTCGTCCCCGTTGAATCACATACAATTTCAAAAGCAGCAAGGAGGAACACATGGTCAAGCAATACCAGTTGTTATCCCCCCATCTGTCATAACAAGCTTGCAGCAACAACCCTATGAAGTTCAAAGCCACATTCCAATTTTGCAACCTGGCTTTTCGGCACCTAGAGCTATTTCAGTCCCAGGACCAAATGGTTTCTATGGCACTAAGTTTTCATGA
Protein sequence

>MsG0380014136.01.T01

MLGCLWWFPLVYSQHGLSQWPNEKTQGYGSWCNGSILNSSPLNHIQFQKQQGGTHGQAIPVVIPPSVITSLQQQPYEVQSHIPILQPGFSAPRAISVPGPNGFYGTKFS*