AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0102880

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATTAGAATGACATATAAT+TGG 0.218390 1_3:-9776358 None:intergenic
TCATCATGTAAGCCCTCTTT+TGG 0.256450 1_3:-9775815 None:intergenic
ATTAACTTCGATCTCATTCA+TGG 0.296896 1_3:-9775861 None:intergenic
GCCGCCGCTCCTTCTCCTTC+TGG 0.315411 1_3:-9776037 None:intergenic
GTAGATGTGGTGTGAGTTGA+AGG 0.397913 1_3:+9776136 Msa0102880:three_prime_UTR
TAAGATTGTTAGTGTTGTAA+TGG 0.398843 1_3:+9775973 Msa0102880:three_prime_UTR
CTGCACCACAAGGCGACATC+TGG 0.433355 1_3:+9772917 Msa0102880:CDS
TGTTCTTATCCATGTGTTGA+AGG 0.437532 1_3:+9773804 Msa0102880:CDS
AATGGAAATTGAAAACTATA+TGG 0.441067 1_3:+9775991 Msa0102880:three_prime_UTR
TGTTGTGATTCTTATGTTGA+AGG 0.449563 1_3:+9774173 Msa0102880:CDS
GCTCCTTCTCCTTCTGGTTG+CGG 0.498102 1_3:-9776031 None:intergenic
AGGAGAAGGAGCGGCGGCTA+TGG 0.498537 1_3:+9776042 Msa0102880:three_prime_UTR
GTGAAAGAAGTCCTGCGATT+TGG 0.504851 1_3:+9775777 Msa0102880:three_prime_UTR
TGTAATCTTTGATTTGCTGT+TGG 0.505943 1_3:+9775738 Msa0102880:three_prime_UTR
ATATGACATGATTTAGATCA+AGG 0.507574 1_3:+9774235 Msa0102880:three_prime_UTR
CCACCGCAACCAGAAGGAGA+AGG 0.537496 1_3:+9776028 Msa0102880:three_prime_UTR
AAATGAAATGTTTGTAGATG+TGG 0.537685 1_3:+9776123 Msa0102880:three_prime_UTR
GGTGATACAGTGTCAGTATG+AGG 0.540392 1_3:+9775906 Msa0102880:three_prime_UTR
TCATGTCATATTGATTTCGC+CGG 0.549696 1_3:-9774223 None:intergenic
AAAGAAGTCCTGCGATTTGG+TGG 0.561416 1_3:+9775780 Msa0102880:three_prime_UTR
AGTTCATCCCACCAAATCGC+AGG 0.565089 1_3:-9775788 None:intergenic
GTGCGGCCACCGCAACCAGA+AGG 0.569602 1_3:+9776022 Msa0102880:three_prime_UTR
TCTTTGATTTGCTGTTGGTG+TGG 0.571367 1_3:+9775743 Msa0102880:three_prime_UTR
CCTTCTCCTTCTGGTTGCGG+TGG 0.584742 1_3:-9776028 None:intergenic
AATTGAAAACTATATGGTGG+TGG 0.600622 1_3:+9775997 Msa0102880:three_prime_UTR
GGATGAACTAGATCCAAAAG+AGG 0.603004 1_3:+9775802 Msa0102880:three_prime_UTR
TGAAAACTATATGGTGGTGG+AGG 0.605543 1_3:+9776000 Msa0102880:three_prime_UTR
TATCTTCAACCTTCAACACA+TGG 0.606912 1_3:-9773813 None:intergenic
GGAGTGCACGCTGCACCACA+AGG 0.613329 1_3:+9772907 Msa0102880:CDS
ACTATATGGTGGTGGAGGTG+CGG 0.615339 1_3:+9776005 Msa0102880:three_prime_UTR
CGCTGCCAGATGTCGCCTTG+TGG 0.622280 1_3:-9772922 None:intergenic
GCAACCAGAAGGAGAAGGAG+CGG 0.630733 1_3:+9776033 Msa0102880:three_prime_UTR
ACCAGAAGGAGAAGGAGCGG+CGG 0.633155 1_3:+9776036 Msa0102880:three_prime_UTR
TCATTCATGGAGTTTAGCAG+CGG 0.648637 1_3:-9775848 None:intergenic
GGAAATTGAAAACTATATGG+TGG 0.682928 1_3:+9775994 Msa0102880:three_prime_UTR
GATGAACTAGATCCAAAAGA+GGG 0.688786 1_3:+9775803 Msa0102880:three_prime_UTR
AAGAAGTCCTGCGATTTGGT+GGG 0.691563 1_3:+9775781 Msa0102880:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATACAAAAATAAAAATA+AGG - chr1_3:9773729-9773748 None:intergenic 10.0%
!! AGAAAATAATAAGAAATATA+AGG - chr1_3:9774090-9774109 None:intergenic 10.0%
!! CAAAAAAAAAAATAAACAAA+AGG - chr1_3:9774437-9774456 None:intergenic 10.0%
!! TTGTAAAAACAAATTATTAA+TGG - chr1_3:9774653-9774672 None:intergenic 10.0%
!!! GGTAATTTTGTAAAAAAAAT+CGG - chr1_3:9773261-9773280 None:intergenic 15.0%
!! ATAAAATAAACTTGAAGAAA+TGG - chr1_3:9773438-9773457 None:intergenic 15.0%
!! AATAAAAATAAGGAATTGAA+TGG - chr1_3:9773719-9773738 None:intergenic 15.0%
!!! AATTTTTTTCAATCAAAAGA+AGG - chr1_3:9774307-9774326 None:intergenic 15.0%
!! CAAAATTCAAATTTAGAAGA+GGG - chr1_3:9773052-9773071 None:intergenic 20.0%
!! TCAAAATTCAAATTTAGAAG+AGG - chr1_3:9773053-9773072 None:intergenic 20.0%
!!! ATACTGATTTAACATTAGTT+GGG - chr1_3:9773125-9773144 None:intergenic 20.0%
!!! TATACTGATTTAACATTAGT+TGG - chr1_3:9773126-9773145 None:intergenic 20.0%
!! ATATATGTGTAGAAAACAAA+AGG - chr1_3:9773282-9773301 None:intergenic 20.0%
!!! GTTTCATACCTTTTTTTTTT+TGG - chr1_3:9773878-9773897 None:intergenic 20.0%
!!! TTAATTTTGTAAGTCAATCA+TGG - chr1_3:9774114-9774133 None:intergenic 20.0%
!! AAAGAAATACACAATATGAA+TGG - chr1_3:9774271-9774290 None:intergenic 20.0%
!!! TTTTTCCAATTACAATTTGT+TGG - chr1_3:9774342-9774361 None:intergenic 20.0%
!!! TGTCATTCTTTATTTCTAAA+AGG + chr1_3:9774764-9774783 Msa0102880:intron 20.0%
!! TTCTTCTGATAAAACAAAAT+TGG - chr1_3:9775118-9775137 None:intergenic 20.0%
!!! TCTTTTGATAATACTTCTAT+TGG - chr1_3:9775416-9775435 None:intergenic 20.0%
!!! AGTCAAGAAGTTTTTTTTAA+TGG - chr1_3:9775462-9775481 None:intergenic 20.0%
!!! TTAATATCACTTTTCTTGTT+CGG - chr1_3:9775485-9775504 None:intergenic 20.0%
!! ATGATTATGCAAAAAGAAAA+AGG + chr1_3:9775528-9775547 Msa0102880:intron 20.0%
!!! TTTTATAGATCTGATACTAA+TGG - chr1_3:9775599-9775618 None:intergenic 20.0%
!! AATGGAAATTGAAAACTATA+TGG + chr1_3:9775991-9776010 Msa0102880:three_prime_UTR 20.0%
!!! ACATGCTTACTTTTTTTTGA+GGG - chr1_3:9773396-9773415 None:intergenic 25.0%
! TCAACAAAATCAGAAATGAA+AGG - chr1_3:9773908-9773927 None:intergenic 25.0%
!!! TGTTGTGATTCTTATTTTGA+AGG + chr1_3:9773989-9774008 Msa0102880:intron 25.0%
!!! ATTCTTATTTTGAAGGTTGA+AGG + chr1_3:9773996-9774015 Msa0102880:intron 25.0%
! CTATAGAAACAAAAGAGATT+GGG - chr1_3:9774038-9774057 None:intergenic 25.0%
! ACTATAGAAACAAAAGAGAT+TGG - chr1_3:9774039-9774058 None:intergenic 25.0%
!! AAATGAGACATTTTTGTAAC+CGG + chr1_3:9774204-9774223 Msa0102880:exon 25.0%
! ATATGACATGATTTAGATCA+AGG + chr1_3:9774235-9774254 Msa0102880:three_prime_UTR 25.0%
! AAAAAAAAAATCAACAGCCA+CGG + chr1_3:9774358-9774377 Msa0102880:intron 25.0%
! AAAAATGAAAACAACCATGA+AGG + chr1_3:9774528-9774547 Msa0102880:intron 25.0%
!!! TAATTTGTTTTTACAACCTG+TGG + chr1_3:9774657-9774676 Msa0102880:intron 25.0%
!!! GAATATTTTTAAATAGCCAC+AGG - chr1_3:9774676-9774695 None:intergenic 25.0%
!! CTTACTGCTATTGATTAAAA+AGG - chr1_3:9775154-9775173 None:intergenic 25.0%
!! AATAAAATCCAAGAAAGTGT+AGG + chr1_3:9775199-9775218 Msa0102880:intron 25.0%
!!! ATTTTTTTCCTACACTTTCT+TGG - chr1_3:9775210-9775229 None:intergenic 25.0%
! CTAATAGAAGAATTACCAAA+AGG + chr1_3:9775570-9775589 Msa0102880:intron 25.0%
! AGATCGAAGTTAATCAAAAA+TGG + chr1_3:9775870-9775889 Msa0102880:three_prime_UTR 25.0%
!!! ATCAAAAATGGTGTTTTTAG+TGG + chr1_3:9775882-9775901 Msa0102880:three_prime_UTR 25.0%
! TAAGATTGTTAGTGTTGTAA+TGG + chr1_3:9775973-9775992 Msa0102880:three_prime_UTR 25.0%
! AAATGAAATGTTTGTAGATG+TGG + chr1_3:9776123-9776142 Msa0102880:three_prime_UTR 25.0%
! AAATAAAAAATATGTGGGTG+TGG + chr1_3:9776179-9776198 Msa0102880:three_prime_UTR 25.0%
AGAACATTGAGATCTGAATA+GGG - chr1_3:9773339-9773358 None:intergenic 30.0%
!!! GACATGCTTACTTTTTTTTG+AGG - chr1_3:9773397-9773416 None:intergenic 30.0%
TTTATCTTCTATCTTCACCA+TGG - chr1_3:9773628-9773647 None:intergenic 30.0%
ATGGTGAAGATAGAAGATAA+AGG + chr1_3:9773627-9773646 Msa0102880:intron 30.0%
! AAGGAATTGAATGGTTAGTT+TGG - chr1_3:9773710-9773729 None:intergenic 30.0%
AGAACAACATAGATCTAACA+TGG - chr1_3:9773790-9773809 None:intergenic 30.0%
CTACGATGCCAAAAAAAAAA+AGG + chr1_3:9773867-9773886 Msa0102880:CDS 30.0%
TGTTGTGATTCTTATGTTGA+AGG + chr1_3:9774173-9774192 Msa0102880:CDS 30.0%
TAGAGCCAACAAATTGTAAT+TGG + chr1_3:9774334-9774353 Msa0102880:intron 30.0%
TTCTTGTTCATAATCCTTCA+TGG - chr1_3:9774545-9774564 None:intergenic 30.0%
! TGCTAACAAGAAAAGTTTTC+AGG + chr1_3:9775286-9775305 Msa0102880:intron 30.0%
!! TGTAATCTTTGATTTGCTGT+TGG + chr1_3:9775738-9775757 Msa0102880:three_prime_UTR 30.0%
ATTAACTTCGATCTCATTCA+TGG - chr1_3:9775864-9775883 None:intergenic 30.0%
!!! AAAAATGGTGTTTTTAGTGG+CGG + chr1_3:9775885-9775904 Msa0102880:three_prime_UTR 30.0%
GGAAATTGAAAACTATATGG+TGG + chr1_3:9775994-9776013 Msa0102880:three_prime_UTR 30.0%
AATTGAAAACTATATGGTGG+TGG + chr1_3:9775997-9776016 Msa0102880:three_prime_UTR 30.0%
! AAAGTGTGGGAAAAGGTTTT+GGG - chr1_3:9773026-9773045 None:intergenic 35.0%
TTAGAGAGAGAAGCTTACTT+GGG - chr1_3:9773218-9773237 None:intergenic 35.0%
ATTAGAGAGAGAAGCTTACT+TGG - chr1_3:9773219-9773238 None:intergenic 35.0%
GAGAACATTGAGATCTGAAT+AGG - chr1_3:9773340-9773359 None:intergenic 35.0%
AAAGAAAGTTCACTTCTCCA+TGG + chr1_3:9773608-9773627 Msa0102880:intron 35.0%
TGTTCTTATCCATGTGTTGA+AGG + chr1_3:9773804-9773823 Msa0102880:CDS 35.0%
TATCTTCAACCTTCAACACA+TGG - chr1_3:9773816-9773835 None:intergenic 35.0%
!! TCATGTCATATTGATTTCGC+CGG - chr1_3:9774226-9774245 None:intergenic 35.0%
! GTCATCTTCAATGATTTTGC+AGG + chr1_3:9775354-9775373 Msa0102880:intron 35.0%
! TGGAGTCAATGAATCTGTTT+TGG - chr1_3:9775442-9775461 None:intergenic 35.0%
! TGATACTAATGGTAGCCTTT+TGG - chr1_3:9775588-9775607 None:intergenic 35.0%
GATGAACTAGATCCAAAAGA+GGG + chr1_3:9775803-9775822 Msa0102880:three_prime_UTR 35.0%
!! GAAAGTGTGGGAAAAGGTTT+TGG - chr1_3:9773027-9773046 None:intergenic 40.0%
! TAGAAGAGGGAAGAAAGTGT+GGG - chr1_3:9773039-9773058 None:intergenic 40.0%
TTAGAAGAGGGAAGAAAGTG+TGG - chr1_3:9773040-9773059 None:intergenic 40.0%
!! TCTTTGATTTGCTGTTGGTG+TGG + chr1_3:9775743-9775762 Msa0102880:three_prime_UTR 40.0%
GGATGAACTAGATCCAAAAG+AGG + chr1_3:9775802-9775821 Msa0102880:three_prime_UTR 40.0%
! TCATCATGTAAGCCCTCTTT+TGG - chr1_3:9775818-9775837 None:intergenic 40.0%
TCATTCATGGAGTTTAGCAG+CGG - chr1_3:9775851-9775870 None:intergenic 40.0%
!! TGAAAACTATATGGTGGTGG+AGG + chr1_3:9776000-9776019 Msa0102880:three_prime_UTR 40.0%
TGCAGCTTTGCTTGACAAGT+GGG + chr1_3:9772964-9772983 Msa0102880:intron 45.0%
GCAGTTGCTGAATTGACAAG+TGG + chr1_3:9772986-9773005 Msa0102880:intron 45.0%
! AGGGAAGAAAGTGTGGGAAA+AGG - chr1_3:9773033-9773052 None:intergenic 45.0%
GAGAGAAGCTTACTTGGGTA+TGG - chr1_3:9773213-9773232 None:intergenic 45.0%
TGAACAAACACACTCTACCG+TGG - chr1_3:9774378-9774397 None:intergenic 45.0%
GTGAAAGAAGTCCTGCGATT+TGG + chr1_3:9775777-9775796 Msa0102880:three_prime_UTR 45.0%
! AAAGAAGTCCTGCGATTTGG+TGG + chr1_3:9775780-9775799 Msa0102880:three_prime_UTR 45.0%
!! AAGAAGTCCTGCGATTTGGT+GGG + chr1_3:9775781-9775800 Msa0102880:three_prime_UTR 45.0%
GGTGATACAGTGTCAGTATG+AGG + chr1_3:9775906-9775925 Msa0102880:three_prime_UTR 45.0%
!!! CGGCGGCTATGGTTTTTTAA+GGG + chr1_3:9776053-9776072 Msa0102880:three_prime_UTR 45.0%
! GTAGATGTGGTGTGAGTTGA+AGG + chr1_3:9776136-9776155 Msa0102880:three_prime_UTR 45.0%
!! TAAAATAAATAAAAAATATG+TGG + chr1_3:9776173-9776192 Msa0102880:three_prime_UTR 5.0%
!! AAAATAAATAAAAAATATGT+GGG + chr1_3:9776174-9776193 Msa0102880:three_prime_UTR 5.0%
! CAGCGTGTATGTGTGCCATT+TGG + chr1_3:9772940-9772959 Msa0102880:intron 50.0%
CAAGCAAAGCTGCAGCCAAA+TGG - chr1_3:9772958-9772977 None:intergenic 50.0%
CTGCAGCTTTGCTTGACAAG+TGG + chr1_3:9772963-9772982 Msa0102880:intron 50.0%
AGTTCATCCCACCAAATCGC+AGG - chr1_3:9775791-9775810 None:intergenic 50.0%
!! ACTATATGGTGGTGGAGGTG+CGG + chr1_3:9776005-9776024 Msa0102880:three_prime_UTR 50.0%
!!! GCGGCGGCTATGGTTTTTTA+AGG + chr1_3:9776052-9776071 Msa0102880:three_prime_UTR 50.0%
! GCTCCTTCTCCTTCTGGTTG+CGG - chr1_3:9776034-9776053 None:intergenic 55.0%
GCAACCAGAAGGAGAAGGAG+CGG + chr1_3:9776033-9776052 Msa0102880:three_prime_UTR 55.0%
CTGCACCACAAGGCGACATC+TGG + chr1_3:9772917-9772936 Msa0102880:CDS 60.0%
! CCTTCTCCTTCTGGTTGCGG+TGG - chr1_3:9776031-9776050 None:intergenic 60.0%
CCACCGCAACCAGAAGGAGA+AGG + chr1_3:9776028-9776047 Msa0102880:three_prime_UTR 60.0%
ACCAGAAGGAGAAGGAGCGG+CGG + chr1_3:9776036-9776055 Msa0102880:three_prime_UTR 60.0%
GGAGTGCACGCTGCACCACA+AGG + chr1_3:9772907-9772926 Msa0102880:CDS 65.0%
CGCTGCCAGATGTCGCCTTG+TGG - chr1_3:9772925-9772944 None:intergenic 65.0%
AGGAGAAGGAGCGGCGGCTA+TGG + chr1_3:9776042-9776061 Msa0102880:three_prime_UTR 65.0%
GTGCGGCCACCGCAACCAGA+AGG + chr1_3:9776022-9776041 Msa0102880:three_prime_UTR 70.0%
GCCGCCGCTCCTTCTCCTTC+TGG - chr1_3:9776040-9776059 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 9772904 9776367 9772904 ID=Msa0102880;Name=Msa0102880
chr1_3 mRNA 9772904 9776367 9772904 ID=Msa0102880-mRNA-1;Parent=Msa0102880;Name=Msa0102880-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0.5|0.6|0.8|0|0|5|680|61
chr1_3 exon 9772904 9772945 9772904 ID=Msa0102880-mRNA-1:exon:4007;Parent=Msa0102880-mRNA-1
chr1_3 exon 9773694 9773699 9773694 ID=Msa0102880-mRNA-1:exon:4008;Parent=Msa0102880-mRNA-1
chr1_3 exon 9773796 9773888 9773796 ID=Msa0102880-mRNA-1:exon:4009;Parent=Msa0102880-mRNA-1
chr1_3 exon 9774165 9774256 9774165 ID=Msa0102880-mRNA-1:exon:4010;Parent=Msa0102880-mRNA-1
chr1_3 exon 9775735 9776367 9775735 ID=Msa0102880-mRNA-1:exon:4011;Parent=Msa0102880-mRNA-1
chr1_3 CDS 9772904 9772945 9772904 ID=Msa0102880-mRNA-1:cds;Parent=Msa0102880-mRNA-1
chr1_3 CDS 9773694 9773699 9773694 ID=Msa0102880-mRNA-1:cds;Parent=Msa0102880-mRNA-1
chr1_3 CDS 9773796 9773888 9773796 ID=Msa0102880-mRNA-1:cds;Parent=Msa0102880-mRNA-1
chr1_3 CDS 9774165 9774209 9774165 ID=Msa0102880-mRNA-1:cds;Parent=Msa0102880-mRNA-1
chr1_3 three_prime_UTR 9774210 9774256 9774210 ID=Msa0102880-mRNA-1:three_prime_utr;Parent=Msa0102880-mRNA-1
chr1_3 three_prime_UTR 9775735 9776367 9775735 ID=Msa0102880-mRNA-1:three_prime_utr;Parent=Msa0102880-mRNA-1
Gene Sequence

>Msa0102880

AAAGGAGTGCACGCTGCACCACAAGGCGACATCTGGCAGCGTAAAAATATCTATGTTGTTCTTATCCATGTGTTGAAGGTTGAAGATAAATCTTACATTTTTACTAATCTCATTTGTTTCTACGATGCCAAAAAAAAAAAGATCTATGATGTTGTGATTCTTATGTTGAAGGCTAAAGATAAATGA
Protein sequence

>Msa0102880

KGVHAAPQGDIWQRKNIYVVLIHVLKVEDKSYIFTNLICFYDAKKKKIYDVVILMLKAKDK*