AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080048306.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048306.01.T01 MTR_2g009390 65.179 112 22 2 1 95 1 112 6.96e-41 130
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048306.01.T01 AT5G64350 58.929 112 29 2 1 95 1 112 5.64e-38 123

Find 52 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTCTCCAATATTAATATT+TGG 0.175040 contig271end:+81470 MsG0080048306.01.T01:three_prime_UTR
ATTTGTTAATCAATATTATT+TGG 0.178121 contig271end:+81529 MsG0080048306.01.T01:three_prime_UTR
CGCTAGTGGCTTTCCTGCTT+GGG 0.208113 contig271end:+81238 MsG0080048306.01.T01:CDS
GAAATAAAAGAACAATCTTT+AGG 0.287880 contig271end:-81615 None:intergenic
TGCTCTCCTGATTATGCTTA+TGG 0.301017 contig271end:+81215 MsG0080048306.01.T01:CDS
TACCGAAGGACAAACTAAAA+AGG 0.318636 contig271end:-81320 None:intergenic
TCGGAGAAGTTGCTCGTCTT+CGG 0.329775 contig271end:+80634 MsG0080048306.01.T01:CDS
AATACAACCCAACTCTGTTT+TGG 0.332199 contig271end:+81262 MsG0080048306.01.T01:CDS
TAACAAATTGATAAAGAAAC+AGG 0.335116 contig271end:-81514 None:intergenic
GCGCTAGTGGCTTTCCTGCT+TGG 0.337892 contig271end:+81237 MsG0080048306.01.T01:CDS
CGGAGAAGTTGCTCGTCTTC+GGG 0.345948 contig271end:+80635 MsG0080048306.01.T01:CDS
ACACTACCAAATATTAATAT+TGG 0.352985 contig271end:-81476 None:intergenic
AATCCATTCACTTTCAAAAT+CGG 0.376739 contig271end:+80218 MsG0080048306.01.T01:CDS
TATAAATCCATTAACAAATA+CGG 0.383450 contig271end:-81670 None:intergenic
GAAAGAAGGAAGAAGAAAGA+TGG 0.415250 contig271end:+79811 MsG0080048306.01.T01:exon
AAAGAAGGAAGAAGAAAGAT+GGG 0.430314 contig271end:+79812 MsG0080048306.01.T01:exon
GTTGGCTTAGGACCGTTTCC+AGG 0.435084 contig271end:-79857 None:intergenic
TATTTGGCAATGCATGGTCT+TGG 0.437640 contig271end:+81545 MsG0080048306.01.T01:three_prime_UTR
GAGAGAGTGCTCACCGTATC+CGG 0.441515 contig271end:-79908 None:intergenic
ATAAATCCATTAACAAATAC+GGG 0.444663 contig271end:-81669 None:intergenic
CTAGCGCCATAAGCATAATC+AGG 0.449393 contig271end:-81221 None:intergenic
TCAAACTCCAAAACAGAGTT+GGG 0.461799 contig271end:-81269 None:intergenic
CTCAAACTCCAAAACAGAGT+TGG 0.473985 contig271end:-81270 None:intergenic
GGTGTCATTGGCATGCAAAT+CGG 0.478078 contig271end:+80615 MsG0080048306.01.T01:CDS
GTTTGACCAGGAGTTGGCTT+AGG 0.482531 contig271end:-79869 None:intergenic
CAAATCGTTCGTCCTGGAAA+CGG 0.494067 contig271end:+79845 MsG0080048306.01.T01:CDS
AAAGTGAATGGATTCTGGCC+AGG 0.495829 contig271end:-80209 None:intergenic
GCAGATATCACTCAAAGTGC+AGG 0.504337 contig271end:-81397 None:intergenic
ACTGTCCACTGCACCGGATA+CGG 0.518197 contig271end:+79895 MsG0080048306.01.T01:CDS
TTCACTTTCAAAATCGGCAA+AGG 0.528436 contig271end:+80224 MsG0080048306.01.T01:CDS
CAATATTATTTGGCAATGCA+TGG 0.531070 contig271end:+81539 MsG0080048306.01.T01:three_prime_UTR
GCATAAGATCGAGTGAAAGA+AGG 0.537335 contig271end:+79797 MsG0080048306.01.T01:five_prime_UTR
GTGGACAGTGACGTTTGACC+AGG 0.538868 contig271end:-79881 None:intergenic
ATACATGTCCACAGAGATGT+AGG 0.540488 contig271end:-81365 None:intergenic
TATTACAGTACAAAAGATCC+TGG 0.543772 contig271end:+80191 MsG0080048306.01.T01:intron
ATTGGAGAGTTTGAGATCAG+TGG 0.545467 contig271end:-81458 None:intergenic
GATTATGCTTATGGCGCTAG+TGG 0.545830 contig271end:+81224 MsG0080048306.01.T01:CDS
AACGGTCCTAAGCCAACTCC+TGG 0.550713 contig271end:+79863 MsG0080048306.01.T01:CDS
AACGTCACTGTCCACTGCAC+CGG 0.551030 contig271end:+79889 MsG0080048306.01.T01:CDS
AGGATGGATGAAGGTGTCAT+TGG 0.552787 contig271end:+80603 MsG0080048306.01.T01:intron
TTGGGTTGTATTCCCCAAGC+AGG 0.558631 contig271end:-81251 None:intergenic
GAGAAGCAAATCGTTCGTCC+TGG 0.559322 contig271end:+79839 MsG0080048306.01.T01:CDS
CAGATATCACTCAAAGTGCA+GGG 0.569024 contig271end:-81396 None:intergenic
GCTAGTGGCTTTCCTGCTTG+GGG 0.575669 contig271end:+81239 MsG0080048306.01.T01:CDS
GCTCACCGTATCCGGTGCAG+TGG 0.596990 contig271end:-79900 None:intergenic
AGTGACGTTTGACCAGGAGT+TGG 0.612752 contig271end:-79875 None:intergenic
GTTGTGTGTAGGATGGATGA+AGG 0.630209 contig271end:+80594 MsG0080048306.01.T01:intron
CTCATAATAATAATTACCGA+AGG 0.641075 contig271end:-81334 None:intergenic
TTGAGTATCCTACATCTCTG+TGG 0.668816 contig271end:+81357 MsG0080048306.01.T01:three_prime_UTR
AACAAATTGATAAAGAAACA+GGG 0.676496 contig271end:-81513 None:intergenic
AGATATCACTCAAAGTGCAG+GGG 0.704961 contig271end:-81395 None:intergenic
TAAATCCATTAACAAATACG+GGG 0.738816 contig271end:-81668 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAATATTAAAAACAAAAAA+TGG - contig271end:80149-80168 None:intergenic 10.0%
!! CTAATTTAATTCAATATAAA+GGG - contig271end:79981-80000 None:intergenic 10.0%
!! TCTAATTTAATTCAATATAA+AGG - contig271end:79982-80001 None:intergenic 10.0%
!!! ATTTGTTAATCAATATTATT+TGG + contig271end:81529-81548 MsG0080048306.01.T01:three_prime_UTR 10.0%
!! ATATAAGCTAAAATAGTTTA+TGG - contig271end:80802-80821 None:intergenic 15.0%
!! TAAAATGAAAGATAAGAAAT+GGG - contig271end:79954-79973 None:intergenic 15.0%
!! TTAAAATGAAAGATAAGAAA+TGG - contig271end:79955-79974 None:intergenic 15.0%
!! AAAATGAAAGATAAGAAATG+GGG - contig271end:79953-79972 None:intergenic 20.0%
!! AACAAATTGATAAAGAAACA+GGG - contig271end:81516-81535 None:intergenic 20.0%
!! AACTCTCCAATATTAATATT+TGG + contig271end:81470-81489 MsG0080048306.01.T01:three_prime_UTR 20.0%
!! AATGGAAATTCAACATATTA+AGG - contig271end:80980-80999 None:intergenic 20.0%
!! ACACTACCAAATATTAATAT+TGG - contig271end:81479-81498 None:intergenic 20.0%
!! ATTTCTATGATAAGTGTTTA+TGG + contig271end:80918-80937 MsG0080048306.01.T01:intron 20.0%
!! GAAATAAAAGAACAATCTTT+AGG - contig271end:81618-81637 None:intergenic 20.0%
!! GTTGATACTTTGTTAAATAA+TGG + contig271end:81146-81165 MsG0080048306.01.T01:intron 20.0%
!! TAACAAATTGATAAAGAAAC+AGG - contig271end:81517-81536 None:intergenic 20.0%
!!! TACTACTTTTACTTTATTTC+TGG + contig271end:80490-80509 MsG0080048306.01.T01:intron 20.0%
! AAACAAAAAATGGAATGACA+AGG - contig271end:80139-80158 None:intergenic 25.0%
! AACAAAAAATGGAATGACAA+GGG - contig271end:80138-80157 None:intergenic 25.0%
! AATCCATTCACTTTCAAAAT+CGG + contig271end:80218-80237 MsG0080048306.01.T01:CDS 25.0%
! CTCATAATAATAATTACCGA+AGG - contig271end:81337-81356 None:intergenic 25.0%
!!! AAATGGGGTTTTTAGTTTTA+GGG - contig271end:79938-79957 None:intergenic 25.0%
!!! TTCAGTTTATATCGTTTTTG+TGG + contig271end:81590-81609 MsG0080048306.01.T01:three_prime_UTR 25.0%
AAAGAAGGAAGAAGAAAGAT+GGG + contig271end:79812-79831 MsG0080048306.01.T01:exon 30.0%
CAACATATTAAGGTCATGTT+TGG - contig271end:80970-80989 None:intergenic 30.0%
CAATATTATTTGGCAATGCA+TGG + contig271end:81539-81558 MsG0080048306.01.T01:three_prime_UTR 30.0%
TATTACAGTACAAAAGATCC+TGG + contig271end:80191-80210 MsG0080048306.01.T01:intron 30.0%
TGAGTAAAAACAAACAGCAA+TGG - contig271end:80998-81017 None:intergenic 30.0%
! GTGTAGAGTTTTTACACTAT+CGG + contig271end:80310-80329 MsG0080048306.01.T01:intron 30.0%
! TTTTTACTCACACACATACA+AGG + contig271end:81008-81027 MsG0080048306.01.T01:intron 30.0%
!! TTATAACTTGTTGCCACTTT+GGG + contig271end:80686-80705 MsG0080048306.01.T01:intron 30.0%
!! TTTATAACTTGTTGCCACTT+TGG + contig271end:80685-80704 MsG0080048306.01.T01:intron 30.0%
!! TTTTGAAAGTGAATGGATTC+TGG - contig271end:80217-80236 None:intergenic 30.0%
!!! AACCTTTTTAGTTTGTCCTT+CGG + contig271end:81318-81337 MsG0080048306.01.T01:three_prime_UTR 30.0%
!!! GAAATGGGGTTTTTAGTTTT+AGG - contig271end:79939-79958 None:intergenic 30.0%
AATTATCTTGTCCCCGTATT+TGG + contig271end:81657-81676 MsG0080048306.01.T01:three_prime_UTR 35.0%
CAATGTACATTCAGATGTGT+TGG + contig271end:80536-80555 MsG0080048306.01.T01:intron 35.0%
CAATTCAATAAAGCCCAAAG+TGG - contig271end:80702-80721 None:intergenic 35.0%
GAAAGAAGGAAGAAGAAAGA+TGG + contig271end:79811-79830 MsG0080048306.01.T01:exon 35.0%
TACCGAAGGACAAACTAAAA+AGG - contig271end:81323-81342 None:intergenic 35.0%
TATCAACAAGGTCAATGACA+GGG - contig271end:81186-81205 None:intergenic 35.0%
TCAAACTCCAAAACAGAGTT+GGG - contig271end:81272-81291 None:intergenic 35.0%
TTACACACTTGCGAAACTTT+AGG - contig271end:80401-80420 None:intergenic 35.0%
TTATCAACAAGGTCAATGAC+AGG - contig271end:81187-81206 None:intergenic 35.0%
TTCACTTTCAAAATCGGCAA+AGG + contig271end:80224-80243 MsG0080048306.01.T01:CDS 35.0%
! AATACAACCCAACTCTGTTT+TGG + contig271end:81262-81281 MsG0080048306.01.T01:CDS 35.0%
! TGATGATGATCAGGCAAAAA+CGG + contig271end:80067-80086 MsG0080048306.01.T01:intron 35.0%
!! CACTTTGGGCTTTATTGAAT+TGG + contig271end:80700-80719 MsG0080048306.01.T01:intron 35.0%
!! TGATTGTGTTGATGATGATC+AGG + contig271end:80058-80077 MsG0080048306.01.T01:intron 35.0%
!!! TGTTTTGGAGTTTGAGATTG+AGG + contig271end:81277-81296 MsG0080048306.01.T01:CDS 35.0%
!!! TTGCCGATTTTGAAAGTGAA+TGG - contig271end:80224-80243 None:intergenic 35.0%
ACTATCTGTTGTGTGTAGGA+TGG + contig271end:80587-80606 MsG0080048306.01.T01:intron 40.0%
AGATATCACTCAAAGTGCAG+GGG - contig271end:81398-81417 None:intergenic 40.0%
ATACATGTCCACAGAGATGT+AGG - contig271end:81368-81387 None:intergenic 40.0%
CAGATATCACTCAAAGTGCA+GGG - contig271end:81399-81418 None:intergenic 40.0%
CTCAAACTCCAAAACAGAGT+TGG - contig271end:81273-81292 None:intergenic 40.0%
GCACTGCAAGATTATCAACA+AGG - contig271end:81198-81217 None:intergenic 40.0%
GCATAAGATCGAGTGAAAGA+AGG + contig271end:79797-79816 MsG0080048306.01.T01:five_prime_UTR 40.0%
TATTTGGCAATGCATGGTCT+TGG + contig271end:81545-81564 MsG0080048306.01.T01:three_prime_UTR 40.0%
TCCAACTATCTGTTGTGTGT+AGG + contig271end:80583-80602 MsG0080048306.01.T01:intron 40.0%
TCCTACACACAACAGATAGT+TGG - contig271end:80587-80606 None:intergenic 40.0%
TGCTCTCCTGATTATGCTTA+TGG + contig271end:81215-81234 MsG0080048306.01.T01:CDS 40.0%
TTGAGTATCCTACATCTCTG+TGG + contig271end:81357-81376 MsG0080048306.01.T01:three_prime_UTR 40.0%
! AACCTCCAGAATTCTGAGAA+AGG - contig271end:80096-80115 None:intergenic 40.0%
! ATTGGAGAGTTTGAGATCAG+TGG - contig271end:81461-81480 None:intergenic 40.0%
! TTTCTCAGAATTCTGGAGGT+TGG + contig271end:80095-80114 MsG0080048306.01.T01:intron 40.0%
!! CTTGCGAAACTTTAGGACTT+AGG - contig271end:80394-80413 None:intergenic 40.0%
!! GAAACTTTAGGACTTAGGAG+TGG - contig271end:80389-80408 None:intergenic 40.0%
ATACACGCGACTCGATTAAG+TGG - contig271end:81041-81060 None:intergenic 45.0%
CAAATCGTTCGTCCTGGAAA+CGG + contig271end:79845-79864 MsG0080048306.01.T01:CDS 45.0%
CTAGCGCCATAAGCATAATC+AGG - contig271end:81224-81243 None:intergenic 45.0%
GACCTTTCTCAGAATTCTGG+AGG + contig271end:80091-80110 MsG0080048306.01.T01:intron 45.0%
GATTATGCTTATGGCGCTAG+TGG + contig271end:81224-81243 MsG0080048306.01.T01:CDS 45.0%
GCAGATATCACTCAAAGTGC+AGG - contig271end:81400-81419 None:intergenic 45.0%
GGTGACCTTTCTCAGAATTC+TGG + contig271end:80088-80107 MsG0080048306.01.T01:intron 45.0%
GTTGTGTGTAGGATGGATGA+AGG + contig271end:80594-80613 MsG0080048306.01.T01:intron 45.0%
TGGATGCGCAGGTCAATTAA+GGG - contig271end:80950-80969 None:intergenic 45.0%
TTGGATGCGCAGGTCAATTA+AGG - contig271end:80951-80970 None:intergenic 45.0%
! AAAGTGAATGGATTCTGGCC+AGG - contig271end:80212-80231 None:intergenic 45.0%
!! AGGATGGATGAAGGTGTCAT+TGG + contig271end:80603-80622 MsG0080048306.01.T01:intron 45.0%
!! GGTGTCATTGGCATGCAAAT+CGG + contig271end:80615-80634 MsG0080048306.01.T01:CDS 45.0%
AAGGTCATGTTTGGATGCGC+AGG - contig271end:80961-80980 None:intergenic 50.0%
AGTGACGTTTGACCAGGAGT+TGG - contig271end:79878-79897 None:intergenic 50.0%
GAGAAGCAAATCGTTCGTCC+TGG + contig271end:79839-79858 MsG0080048306.01.T01:CDS 50.0%
TCGGAGAAGTTGCTCGTCTT+CGG + contig271end:80634-80653 MsG0080048306.01.T01:CDS 50.0%
! GTTTGACCAGGAGTTGGCTT+AGG - contig271end:79872-79891 None:intergenic 50.0%
! TTGGGTTGTATTCCCCAAGC+AGG - contig271end:81254-81273 None:intergenic 50.0%
AACGGTCCTAAGCCAACTCC+TGG + contig271end:79863-79882 MsG0080048306.01.T01:CDS 55.0%
AACGTCACTGTCCACTGCAC+CGG + contig271end:79889-79908 MsG0080048306.01.T01:CDS 55.0%
ACTGTCCACTGCACCGGATA+CGG + contig271end:79895-79914 MsG0080048306.01.T01:CDS 55.0%
CGCTAGTGGCTTTCCTGCTT+GGG + contig271end:81238-81257 MsG0080048306.01.T01:CDS 55.0%
CGGAGAAGTTGCTCGTCTTC+GGG + contig271end:80635-80654 MsG0080048306.01.T01:CDS 55.0%
GCTAGTGGCTTTCCTGCTTG+GGG + contig271end:81239-81258 MsG0080048306.01.T01:CDS 55.0%
GTGGACAGTGACGTTTGACC+AGG - contig271end:79884-79903 None:intergenic 55.0%
! GTTGGCTTAGGACCGTTTCC+AGG - contig271end:79860-79879 None:intergenic 55.0%
!! GAGAGAGTGCTCACCGTATC+CGG - contig271end:79911-79930 None:intergenic 55.0%
GCGCTAGTGGCTTTCCTGCT+TGG + contig271end:81237-81256 MsG0080048306.01.T01:CDS 60.0%
GCTCACCGTATCCGGTGCAG+TGG - contig271end:79903-79922 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
contig271end gene 79759 81678 79759 ID=MsG0080048306.01;Name=MsG0080048306.01
contig271end mRNA 79759 81678 79759 ID=MsG0080048306.01.T01;Parent=MsG0080048306.01;Name=MsG0080048306.01.T01;_AED=0.50;_eAED=0.50;_QI=71|0.33|0.75|1|1|1|4|362|95
contig271end exon 81215 81678 81215 ID=MsG0080048306.01.T01:exon:2238;Parent=MsG0080048306.01.T01
contig271end exon 80605 80656 80605 ID=MsG0080048306.01.T01:exon:2237;Parent=MsG0080048306.01.T01
contig271end exon 80199 80245 80199 ID=MsG0080048306.01.T01:exon:2236;Parent=MsG0080048306.01.T01
contig271end exon 79759 79916 79759 ID=MsG0080048306.01.T01:exon:2235;Parent=MsG0080048306.01.T01
contig271end five_prime_UTR 79759 79829 79759 ID=MsG0080048306.01.T01:five_prime_utr;Parent=MsG0080048306.01.T01
contig271end CDS 79830 79916 79830 ID=MsG0080048306.01.T01:cds;Parent=MsG0080048306.01.T01
contig271end CDS 80199 80245 80199 ID=MsG0080048306.01.T01:cds;Parent=MsG0080048306.01.T01
contig271end CDS 80605 80656 80605 ID=MsG0080048306.01.T01:cds;Parent=MsG0080048306.01.T01
contig271end CDS 81215 81316 81215 ID=MsG0080048306.01.T01:cds;Parent=MsG0080048306.01.T01
contig271end three_prime_UTR 81317 81678 81317 ID=MsG0080048306.01.T01:three_prime_utr;Parent=MsG0080048306.01.T01
Gene Sequence

>MsG0080048306.01.T01

ATGGGAGTTGAGAAGCAAATCGTTCGTCCTGGAAACGGTCCTAAGCCAACTCCTGGTCAAACGTCACTGTCCACTGCACCGGATACGTACAAAAGATCCTGGCCAGAATCCATTCACTTTCAAAATCGGCAAAGGATGGATGAAGGTGTCATTGGCATGCAAATCGGAGAAGTTGCTCGTCTTCGGTGCTCTCCTGATTATGCTTATGGCGCTAGTGGCTTTCCTGCTTGGGGAATACAACCCAACTCTGTTTTGGAGTTTGAGATTGAGGTCTTGAGTGTAGAATGA
Protein sequence

>MsG0080048306.01.T01

MGVEKQIVRPGNGPKPTPGQTSLSTAPDTYKRSWPESIHFQNRQRMDEGVIGMQIGEVARLRCSPDYAYGASGFPAWGIQPNSVLEFEIEVLSVE*