AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0878220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0878220 MtrunA17_Chr6g0460751 84.211 95 8 1 25 119 1 88 1.69e-53 162
Msa0878220 MtrunA17_Chr7g0254151 49.351 77 34 2 41 116 20 92 1.34e-14 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACCACTCCCAGGGGATTT+TGG 0.070443 6_1:-18882384 None:intergenic
TGAATTTGTAATATCAAATA+AGG 0.210050 6_1:+18882546 Msa0878220:three_prime_UTR
GATGGGAAGAAGGGTCAATT+TGG 0.296094 6_1:+18882317 Msa0878220:CDS
CCACTAACATATTAATATTC+TGG 0.317915 6_1:-18881262 None:intergenic
GCTACATCCTAAACTTTAGA+AGG 0.318376 6_1:+18882432 Msa0878220:three_prime_UTR
TCAAAACCCTTACTTGTTGC+AGG 0.325578 6_1:-18881419 None:intergenic
CACCAGGCCCTTCATAATCA+TGG 0.396641 6_1:-18882344 None:intergenic
ATATTCTGGCGTACTATACT+AGG 0.411234 6_1:-18881248 None:intergenic
CCAGAATATTAATATGTTAG+TGG 0.424217 6_1:+18881262 Msa0878220:exon
TGAGAAAATGATGGTACATA+TGG 0.459434 6_1:+18882284 Msa0878220:CDS
TTGGAACTCCATGATTATGA+AGG 0.463143 6_1:+18882336 Msa0878220:CDS
ATGAAAGATTGATGGGAAGA+AGG 0.472148 6_1:+18882307 Msa0878220:CDS
TGAAAGATTGATGGGAAGAA+GGG 0.490161 6_1:+18882308 Msa0878220:CDS
ACATATGGATGAAAGATTGA+TGG 0.490804 6_1:+18882299 Msa0878220:CDS
TTATGTTCTTTATTTGCACC+AGG 0.490997 6_1:-18882360 None:intergenic
GCACTAACCTTATATAAAGA+AGG 0.507798 6_1:-18881553 None:intergenic
CTCCATGATTATGAAGGGCC+TGG 0.512793 6_1:+18882342 Msa0878220:CDS
GGAACATGGTTCATTGATGT+TGG 0.518756 6_1:+18882254 Msa0878220:intron
CATATGGATGAAAGATTGAT+GGG 0.518975 6_1:+18882300 Msa0878220:CDS
GAACATAACCCAAAATCCCC+TGG 0.526511 6_1:+18882375 Msa0878220:CDS
AACCCAAAATCCCCTGGGAG+TGG 0.548305 6_1:+18882381 Msa0878220:CDS
CAAAACCCTTACTTGTTGCA+GGG 0.553598 6_1:-18881418 None:intergenic
TTTGCACATCAACCACTCCC+AGG 0.556615 6_1:-18882393 None:intergenic
TGGAACTCCATGATTATGAA+GGG 0.574524 6_1:+18882337 Msa0878220:CDS
TTGCACATCAACCACTCCCA+GGG 0.587694 6_1:-18882392 None:intergenic
AACATAACCCAAAATCCCCT+GGG 0.609618 6_1:+18882376 Msa0878220:CDS
TTTCATCTTGAATTGGATGG+TGG 0.617406 6_1:-18881330 None:intergenic
AATTAGAATCAAAGTATGTG+TGG 0.621826 6_1:+18882487 Msa0878220:three_prime_UTR
TTGCAGGGATAGCAAAGACA+TGG 0.624053 6_1:-18881403 None:intergenic
TGCACATCAACCACTCCCAG+GGG 0.679834 6_1:-18882391 None:intergenic
TGGATGGTGGAAGATAACAA+AGG 0.717266 6_1:-18881317 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTATTGAATTGATTTTTT+TGG + chr6_1:18881486-18881505 Msa0878220:intron 15.0%
!!! TTTACTTTTCAAATTTTTGT+TGG + chr6_1:18881829-18881848 Msa0878220:intron 15.0%
!!! TTTTTTATTCTTTTAAATCG+TGG - chr6_1:18881964-18881983 None:intergenic 15.0%
!!! TTAATTAGTCAAACTTTTTT+TGG - chr6_1:18882190-18882209 None:intergenic 15.0%
!! TGAATTTGTAATATCAAATA+AGG + chr6_1:18882546-18882565 Msa0878220:three_prime_UTR 15.0%
!!! TGATAAAAATATTAGTGTTT+TGG + chr6_1:18882589-18882608 Msa0878220:three_prime_UTR 15.0%
!!! ATGTATTGAATTGATTTTTT+TGG + chr6_1:18881486-18881505 Msa0878220:intron 15.0%
!!! TTTACTTTTCAAATTTTTGT+TGG + chr6_1:18881829-18881848 Msa0878220:intron 15.0%
!!! TTTTTTATTCTTTTAAATCG+TGG - chr6_1:18881964-18881983 None:intergenic 15.0%
!!! TTAATTAGTCAAACTTTTTT+TGG - chr6_1:18882190-18882209 None:intergenic 15.0%
!! TGAATTTGTAATATCAAATA+AGG + chr6_1:18882546-18882565 Msa0878220:three_prime_UTR 15.0%
!!! TGATAAAAATATTAGTGTTT+TGG + chr6_1:18882589-18882608 Msa0878220:three_prime_UTR 15.0%
!!! AGTTTTTTTTCATCTTGAAT+TGG - chr6_1:18881340-18881359 None:intergenic 20.0%
!!! AGTTTTTCCTTCTTTATATA+AGG + chr6_1:18881546-18881565 Msa0878220:CDS 20.0%
!!! CTTCTTAATTTTCATCTATT+TGG + chr6_1:18881575-18881594 Msa0878220:intron 20.0%
!!! ATTTTTTCATCCAATATCTA+AGG + chr6_1:18881640-18881659 Msa0878220:intron 20.0%
!!! ACTTTTTTTGGCAAAAATTA+AGG - chr6_1:18882178-18882197 None:intergenic 20.0%
!!! AAAAACTAATTAGTTTGAAC+TGG + chr6_1:18882623-18882642 Msa0878220:three_prime_UTR 20.0%
!!! AGTTTTTTTTCATCTTGAAT+TGG - chr6_1:18881340-18881359 None:intergenic 20.0%
!!! AGTTTTTCCTTCTTTATATA+AGG + chr6_1:18881546-18881565 Msa0878220:CDS 20.0%
!!! CTTCTTAATTTTCATCTATT+TGG + chr6_1:18881575-18881594 Msa0878220:intron 20.0%
!!! ATTTTTTCATCCAATATCTA+AGG + chr6_1:18881640-18881659 Msa0878220:intron 20.0%
!!! ACTTTTTTTGGCAAAAATTA+AGG - chr6_1:18882178-18882197 None:intergenic 20.0%
!!! AAAAACTAATTAGTTTGAAC+TGG + chr6_1:18882623-18882642 Msa0878220:three_prime_UTR 20.0%
! CCACTAACATATTAATATTC+TGG - chr6_1:18881265-18881284 None:intergenic 25.0%
! CCAGAATATTAATATGTTAG+TGG + chr6_1:18881262-18881281 Msa0878220:exon 25.0%
!!! TTTTTTCATCTTGAATTGGA+TGG - chr6_1:18881336-18881355 None:intergenic 25.0%
!!! GAATTGATTTTTTTGGTTGT+AGG + chr6_1:18881493-18881512 Msa0878220:intron 25.0%
!! ATCTTCACCATTCAAATTTT+TGG - chr6_1:18881521-18881540 None:intergenic 25.0%
!! AAAGTCATGGTTATGTATTT+TGG + chr6_1:18881615-18881634 Msa0878220:intron 25.0%
!! GTTCATTATTTGTGTTTTGT+AGG + chr6_1:18882233-18882252 Msa0878220:intron 25.0%
! AATTAGAATCAAAGTATGTG+TGG + chr6_1:18882487-18882506 Msa0878220:three_prime_UTR 25.0%
! CCACTAACATATTAATATTC+TGG - chr6_1:18881265-18881284 None:intergenic 25.0%
! CCAGAATATTAATATGTTAG+TGG + chr6_1:18881262-18881281 Msa0878220:exon 25.0%
!!! TTTTTTCATCTTGAATTGGA+TGG - chr6_1:18881336-18881355 None:intergenic 25.0%
!!! GAATTGATTTTTTTGGTTGT+AGG + chr6_1:18881493-18881512 Msa0878220:intron 25.0%
!! ATCTTCACCATTCAAATTTT+TGG - chr6_1:18881521-18881540 None:intergenic 25.0%
!! AAAGTCATGGTTATGTATTT+TGG + chr6_1:18881615-18881634 Msa0878220:intron 25.0%
!! GTTCATTATTTGTGTTTTGT+AGG + chr6_1:18882233-18882252 Msa0878220:intron 25.0%
! AATTAGAATCAAAGTATGTG+TGG + chr6_1:18882487-18882506 Msa0878220:three_prime_UTR 25.0%
GTAGGAACCAAAAATTTGAA+TGG + chr6_1:18881511-18881530 Msa0878220:intron 30.0%
GCACTAACCTTATATAAAGA+AGG - chr6_1:18881556-18881575 None:intergenic 30.0%
!! CCTCATTTTTCCTTAGATAT+TGG - chr6_1:18881653-18881672 None:intergenic 30.0%
CCAATATCTAAGGAAAAATG+AGG + chr6_1:18881650-18881669 Msa0878220:intron 30.0%
! ATTTGTGTTTTGTAGGAACA+TGG + chr6_1:18882240-18882259 Msa0878220:intron 30.0%
GGAAAAAAGTGAGAAAATGA+TGG + chr6_1:18882275-18882294 Msa0878220:CDS 30.0%
TGAGAAAATGATGGTACATA+TGG + chr6_1:18882284-18882303 Msa0878220:CDS 30.0%
ACATATGGATGAAAGATTGA+TGG + chr6_1:18882299-18882318 Msa0878220:CDS 30.0%
CATATGGATGAAAGATTGAT+GGG + chr6_1:18882300-18882319 Msa0878220:CDS 30.0%
! TTATGTTCTTTATTTGCACC+AGG - chr6_1:18882363-18882382 None:intergenic 30.0%
!!! GATTTTGCCTTCTAAAGTTT+AGG - chr6_1:18882442-18882461 None:intergenic 30.0%
!!! TGTGTGGTTTTTTGTTTCTT+TGG + chr6_1:18882503-18882522 Msa0878220:three_prime_UTR 30.0%
GTAGGAACCAAAAATTTGAA+TGG + chr6_1:18881511-18881530 Msa0878220:intron 30.0%
GCACTAACCTTATATAAAGA+AGG - chr6_1:18881556-18881575 None:intergenic 30.0%
!! CCTCATTTTTCCTTAGATAT+TGG - chr6_1:18881653-18881672 None:intergenic 30.0%
CCAATATCTAAGGAAAAATG+AGG + chr6_1:18881650-18881669 Msa0878220:intron 30.0%
! ATTTGTGTTTTGTAGGAACA+TGG + chr6_1:18882240-18882259 Msa0878220:intron 30.0%
GGAAAAAAGTGAGAAAATGA+TGG + chr6_1:18882275-18882294 Msa0878220:CDS 30.0%
TGAGAAAATGATGGTACATA+TGG + chr6_1:18882284-18882303 Msa0878220:CDS 30.0%
ACATATGGATGAAAGATTGA+TGG + chr6_1:18882299-18882318 Msa0878220:CDS 30.0%
CATATGGATGAAAGATTGAT+GGG + chr6_1:18882300-18882319 Msa0878220:CDS 30.0%
! TTATGTTCTTTATTTGCACC+AGG - chr6_1:18882363-18882382 None:intergenic 30.0%
!!! GATTTTGCCTTCTAAAGTTT+AGG - chr6_1:18882442-18882461 None:intergenic 30.0%
!!! TGTGTGGTTTTTTGTTTCTT+TGG + chr6_1:18882503-18882522 Msa0878220:three_prime_UTR 30.0%
ATATTCTGGCGTACTATACT+AGG - chr6_1:18881251-18881270 None:intergenic 35.0%
TTTCATCTTGAATTGGATGG+TGG - chr6_1:18881333-18881352 None:intergenic 35.0%
TTCCTATTCTTGCAAAGTCA+TGG + chr6_1:18881602-18881621 Msa0878220:intron 35.0%
AACCATGACTTTGCAAGAAT+AGG - chr6_1:18881607-18881626 None:intergenic 35.0%
ATGAAAGATTGATGGGAAGA+AGG + chr6_1:18882307-18882326 Msa0878220:CDS 35.0%
TGAAAGATTGATGGGAAGAA+GGG + chr6_1:18882308-18882327 Msa0878220:CDS 35.0%
TTGGAACTCCATGATTATGA+AGG + chr6_1:18882336-18882355 Msa0878220:CDS 35.0%
TGGAACTCCATGATTATGAA+GGG + chr6_1:18882337-18882356 Msa0878220:CDS 35.0%
GCTACATCCTAAACTTTAGA+AGG + chr6_1:18882432-18882451 Msa0878220:three_prime_UTR 35.0%
ATATTCTGGCGTACTATACT+AGG - chr6_1:18881251-18881270 None:intergenic 35.0%
TTTCATCTTGAATTGGATGG+TGG - chr6_1:18881333-18881352 None:intergenic 35.0%
TTCCTATTCTTGCAAAGTCA+TGG + chr6_1:18881602-18881621 Msa0878220:intron 35.0%
AACCATGACTTTGCAAGAAT+AGG - chr6_1:18881607-18881626 None:intergenic 35.0%
ATGAAAGATTGATGGGAAGA+AGG + chr6_1:18882307-18882326 Msa0878220:CDS 35.0%
TGAAAGATTGATGGGAAGAA+GGG + chr6_1:18882308-18882327 Msa0878220:CDS 35.0%
TTGGAACTCCATGATTATGA+AGG + chr6_1:18882336-18882355 Msa0878220:CDS 35.0%
TGGAACTCCATGATTATGAA+GGG + chr6_1:18882337-18882356 Msa0878220:CDS 35.0%
GCTACATCCTAAACTTTAGA+AGG + chr6_1:18882432-18882451 Msa0878220:three_prime_UTR 35.0%
!! TGGATGGTGGAAGATAACAA+AGG - chr6_1:18881320-18881339 None:intergenic 40.0%
! CAAAACCCTTACTTGTTGCA+GGG - chr6_1:18881421-18881440 None:intergenic 40.0%
! TCAAAACCCTTACTTGTTGC+AGG - chr6_1:18881422-18881441 None:intergenic 40.0%
CAACAATTGTGTCAAGCAGA+AGG + chr6_1:18881783-18881802 Msa0878220:intron 40.0%
GGAACATGGTTCATTGATGT+TGG + chr6_1:18882254-18882273 Msa0878220:intron 40.0%
AACATAACCCAAAATCCCCT+GGG + chr6_1:18882376-18882395 Msa0878220:CDS 40.0%
!! TGGATGGTGGAAGATAACAA+AGG - chr6_1:18881320-18881339 None:intergenic 40.0%
! CAAAACCCTTACTTGTTGCA+GGG - chr6_1:18881421-18881440 None:intergenic 40.0%
! TCAAAACCCTTACTTGTTGC+AGG - chr6_1:18881422-18881441 None:intergenic 40.0%
CAACAATTGTGTCAAGCAGA+AGG + chr6_1:18881783-18881802 Msa0878220:intron 40.0%
GGAACATGGTTCATTGATGT+TGG + chr6_1:18882254-18882273 Msa0878220:intron 40.0%
AACATAACCCAAAATCCCCT+GGG + chr6_1:18882376-18882395 Msa0878220:CDS 40.0%
TTGCAGGGATAGCAAAGACA+TGG - chr6_1:18881406-18881425 None:intergenic 45.0%
TGCTATCCCTGCAACAAGTA+AGG + chr6_1:18881412-18881431 Msa0878220:intron 45.0%
GCTATCCCTGCAACAAGTAA+GGG + chr6_1:18881413-18881432 Msa0878220:intron 45.0%
GATGGGAAGAAGGGTCAATT+TGG + chr6_1:18882317-18882336 Msa0878220:CDS 45.0%
GAACATAACCCAAAATCCCC+TGG + chr6_1:18882375-18882394 Msa0878220:CDS 45.0%
TTGCAGGGATAGCAAAGACA+TGG - chr6_1:18881406-18881425 None:intergenic 45.0%
TGCTATCCCTGCAACAAGTA+AGG + chr6_1:18881412-18881431 Msa0878220:intron 45.0%
GCTATCCCTGCAACAAGTAA+GGG + chr6_1:18881413-18881432 Msa0878220:intron 45.0%
GATGGGAAGAAGGGTCAATT+TGG + chr6_1:18882317-18882336 Msa0878220:CDS 45.0%
GAACATAACCCAAAATCCCC+TGG + chr6_1:18882375-18882394 Msa0878220:CDS 45.0%
!!! ATTAACTTTTTAATTTATTT+TGG + chr6_1:18882205-18882224 Msa0878220:intron 5.0%
!!! ATTAACTTTTTAATTTATTT+TGG + chr6_1:18882205-18882224 Msa0878220:intron 5.0%
CTCCATGATTATGAAGGGCC+TGG + chr6_1:18882342-18882361 Msa0878220:CDS 50.0%
CACCAGGCCCTTCATAATCA+TGG - chr6_1:18882347-18882366 None:intergenic 50.0%
! AACCACTCCCAGGGGATTTT+GGG - chr6_1:18882386-18882405 None:intergenic 50.0%
TTGCACATCAACCACTCCCA+GGG - chr6_1:18882395-18882414 None:intergenic 50.0%
TTTGCACATCAACCACTCCC+AGG - chr6_1:18882396-18882415 None:intergenic 50.0%
CTCCATGATTATGAAGGGCC+TGG + chr6_1:18882342-18882361 Msa0878220:CDS 50.0%
CACCAGGCCCTTCATAATCA+TGG - chr6_1:18882347-18882366 None:intergenic 50.0%
! AACCACTCCCAGGGGATTTT+GGG - chr6_1:18882386-18882405 None:intergenic 50.0%
TTGCACATCAACCACTCCCA+GGG - chr6_1:18882395-18882414 None:intergenic 50.0%
TTTGCACATCAACCACTCCC+AGG - chr6_1:18882396-18882415 None:intergenic 50.0%
AACCCAAAATCCCCTGGGAG+TGG + chr6_1:18882381-18882400 Msa0878220:CDS 55.0%
! CAACCACTCCCAGGGGATTT+TGG - chr6_1:18882387-18882406 None:intergenic 55.0%
TGCACATCAACCACTCCCAG+GGG - chr6_1:18882394-18882413 None:intergenic 55.0%
AACCCAAAATCCCCTGGGAG+TGG + chr6_1:18882381-18882400 Msa0878220:CDS 55.0%
! CAACCACTCCCAGGGGATTT+TGG - chr6_1:18882387-18882406 None:intergenic 55.0%
TGCACATCAACCACTCCCAG+GGG - chr6_1:18882394-18882413 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 18881218 18882752 18881218 ID=Msa0878220;Name=Msa0878220
chr6_1 mRNA 18881218 18882752 18881218 ID=Msa0878220-mRNA-1;Parent=Msa0878220;Name=Msa0878220-mRNA-1;_AED=0.02;_eAED=0.02;_QI=57|1|1|1|1|1|3|345|119
chr6_1 exon 18881218 18881428 18881218 ID=Msa0878220-mRNA-1:exon:5073;Parent=Msa0878220-mRNA-1
chr6_1 exon 18881515 18881567 18881515 ID=Msa0878220-mRNA-1:exon:5074;Parent=Msa0878220-mRNA-1
chr6_1 exon 18882255 18882752 18882255 ID=Msa0878220-mRNA-1:exon:5075;Parent=Msa0878220-mRNA-1
chr6_1 five_prime_UTR 18881218 18881274 18881218 ID=Msa0878220-mRNA-1:five_prime_utr;Parent=Msa0878220-mRNA-1
chr6_1 CDS 18881275 18881428 18881275 ID=Msa0878220-mRNA-1:cds;Parent=Msa0878220-mRNA-1
chr6_1 CDS 18881515 18881567 18881515 ID=Msa0878220-mRNA-1:cds;Parent=Msa0878220-mRNA-1
chr6_1 CDS 18882255 18882407 18882255 ID=Msa0878220-mRNA-1:cds;Parent=Msa0878220-mRNA-1
chr6_1 three_prime_UTR 18882408 18882752 18882408 ID=Msa0878220-mRNA-1:three_prime_utr;Parent=Msa0878220-mRNA-1
Gene Sequence

>Msa0878220

ATGTTAGTGGCACTATATAACAAGCATAAAGTATTCATACATCCTTTGTTATCTTCCACCATCCAATTCAAGATGAAAAAAAACTTTTTCATACTTTTTGTGATACTTCTGAGTTTCTCATATATTCTCCATGTCTTTGCTATCCCTGCAACAAGAACCAAAAATTTGAATGGTGAAGATGAATCAGTTTTTCCTTCTTTATATAAGGAACATGGTTCATTGATGTTGGAAAAAAGTGAGAAAATGATGGTACATATGGATGAAAGATTGATGGGAAGAAGGGTCAATTTGGAACTCCATGATTATGAAGGGCCTGGTGCAAATAAAGAACATAACCCAAAATCCCCTGGGAGTGGTTGA

Protein sequence

>Msa0878220

MLVALYNKHKVFIHPLLSSTIQFKMKKNFFILFVILLSFSYILHVFAIPATRTKNLNGEDESVFPSLYKEHGSLMLEKSEKMMVHMDERLMGRRVNLELHDYEGPGANKEHNPKSPGSG*