AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000241.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000241.01.T01 MTR_1g019800 90.323 124 12 0 1 124 1 124 8.05e-79 232
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 61 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGAGCATTCCGTCCTTTA+AGG 0.089873 1:+3291564 None:intergenic
CCCTAAAATAATACACTTTA+TGG 0.093718 1:+3291606 None:intergenic
TTAACTTAACTTTACCTTAA+AGG 0.134585 1:-3291578 MsG0180000241.01.T01:five_prime_UTR
AGTTCTGATTCTTACATTTC+TGG 0.208989 1:+3290579 None:intergenic
CAAAGTTACTTGAATTTATA+TGG 0.221019 1:-3290637 MsG0180000241.01.T01:three_prime_UTR
TCTTCATCAAGATCACTAAT+TGG 0.271099 1:+3291258 None:intergenic
TATACAAGATGTTTATATAT+TGG 0.271828 1:+3291460 None:intergenic
ATTATGTGTTACTGGGAAAA+TGG 0.272982 1:-3290969 MsG0180000241.01.T01:CDS
TGGTTGAACATTATTGAATA+AGG 0.278431 1:-3290557 MsG0180000241.01.T01:three_prime_UTR
TTGGAAGCGTTCTATAATTC+AGG 0.285690 1:-3290775 MsG0180000241.01.T01:three_prime_UTR
CATTGTGAAGGATGGCCTTT+TGG 0.301790 1:-3290744 MsG0180000241.01.T01:three_prime_UTR
ACAAGAGAATTATGTGTTAC+TGG 0.321124 1:-3290977 MsG0180000241.01.T01:CDS
CAATGAAGCAGGTCAATTAA+AGG 0.321544 1:-3291510 MsG0180000241.01.T01:five_prime_UTR
TTACCTCCCTCCTTTGCCTT+TGG 0.326286 1:+3290944 None:intergenic
GTGTATTCTTCTAGTGCTAA+TGG 0.339241 1:-3290870 MsG0180000241.01.T01:CDS
TGCAAAGCATTTGCATCTCT+TGG 0.342800 1:+3291365 None:intergenic
TTGACCTGCTTCATTGATAG+TGG 0.371174 1:+3291517 None:intergenic
ACACATAATTCTCTTGTTGC+AGG 0.374763 1:+3290983 None:intergenic
TGTATTCTTCTAGTGCTAAT+GGG 0.374850 1:-3290869 MsG0180000241.01.T01:CDS
TTGCATCTCTTGGAATGGTT+TGG 0.387372 1:+3291375 None:intergenic
CATATAAATTCAAGTAACTT+TGG 0.429792 1:+3290638 None:intergenic
TAGTGATCTTGATGAAGAAC+AGG 0.434961 1:-3291253 MsG0180000241.01.T01:CDS
TTTCTGGCTTTAATCAGAAT+AGG 0.450498 1:+3290595 None:intergenic
ATTCAAGTAACTTTGGTACT+TGG 0.457278 1:+3290645 None:intergenic
TTTACTTTCAGTTTCACAAT+GGG 0.475858 1:-3291423 MsG0180000241.01.T01:exon
ATGCTTTGCAGCTGCTCTGA+AGG 0.476673 1:-3291352 MsG0180000241.01.T01:CDS
TAATTGGAAACTCCTCTTCA+AGG 0.478540 1:+3291274 None:intergenic
AAACTCTCTCTCAGTAGGAT+TGG 0.486208 1:+3291022 None:intergenic
GGTTTGGTTGCTCCTCCTCA+TGG 0.490726 1:+3291391 None:intergenic
GGCGGTTAGAAGCCGAGCTA+TGG 0.496315 1:-3291062 MsG0180000241.01.T01:CDS
AGAAATGTAAGAATCAGAAC+TGG 0.513218 1:-3290577 MsG0180000241.01.T01:three_prime_UTR
CTAAGTCACCATCTGAATCA+TGG 0.518553 1:-3290686 MsG0180000241.01.T01:three_prime_UTR
GCTTTACGACAGAGACCAAA+AGG 0.525795 1:+3290729 None:intergenic
AGCATTTGCATCTCTTGGAA+TGG 0.526952 1:+3291370 None:intergenic
CAAGAGAATTATGTGTTACT+GGG 0.534810 1:-3290976 MsG0180000241.01.T01:CDS
TTCGACCAAAAGTTTGACAC+TGG 0.545482 1:+3291319 None:intergenic
TCTTCTAGTGCTAATGGGGA+AGG 0.547226 1:-3290864 MsG0180000241.01.T01:CDS
CTTAACTTTACCTTAAAGGA+CGG 0.549608 1:-3291574 MsG0180000241.01.T01:five_prime_UTR
TAAAGGACGGAATGCTCTAG+TGG 0.550594 1:-3291561 MsG0180000241.01.T01:five_prime_UTR
TCAAGCTTGAACATCTTGAA+AGG 0.551732 1:+3290820 None:intergenic
AATGGAACCAAAGGCAAAGG+AGG 0.558037 1:-3290951 MsG0180000241.01.T01:CDS
TTCGACTACAAGCCTTGAAG+AGG 0.565475 1:-3291286 MsG0180000241.01.T01:CDS
TACTGGGAAAATGGAACCAA+AGG 0.569555 1:-3290960 MsG0180000241.01.T01:CDS
CGATACAACCATGATTCAGA+TGG 0.575454 1:+3290678 None:intergenic
AAGGCCACTATCAATGAAGC+AGG 0.578192 1:-3291521 MsG0180000241.01.T01:five_prime_UTR
AAAGGACGGAATGCTCTAGT+GGG 0.578314 1:-3291560 MsG0180000241.01.T01:five_prime_UTR
CATGATTCAGATGGTGACTT+AGG 0.584417 1:+3290687 None:intergenic
ATTTACTTTCAGTTTCACAA+TGG 0.590773 1:-3291424 MsG0180000241.01.T01:exon
TCGACCAAAAGTTTGACACT+GGG 0.608137 1:+3291320 None:intergenic
GTATTCTTCTAGTGCTAATG+GGG 0.608962 1:-3290868 MsG0180000241.01.T01:CDS
GATGGTGACTTAGGCAGTGG+TGG 0.623202 1:+3290696 None:intergenic
GGGGTTTCAATATTGCTGCA+AGG 0.632160 1:-3291540 MsG0180000241.01.T01:five_prime_UTR
GAAAATGGAACCAAAGGCAA+AGG 0.636908 1:-3290954 MsG0180000241.01.T01:CDS
ATGGAACCAAAGGCAAAGGA+GGG 0.641016 1:-3290950 MsG0180000241.01.T01:CDS
TTATTTCTATGCATAAGTTG+CGG 0.643978 1:+3291715 None:intergenic
GAGGGAGGTAATGAAGAACA+AGG 0.652290 1:-3290932 MsG0180000241.01.T01:CDS
TCAGATGGTGACTTAGGCAG+TGG 0.663320 1:+3290693 None:intergenic
GAACCAAAGGCAAAGGAGGG+AGG 0.663364 1:-3290947 MsG0180000241.01.T01:CDS
TCTTCAGGTGATTGTCTCGG+CGG 0.664433 1:-3291080 MsG0180000241.01.T01:intron
AAGGACGGAATGCTCTAGTG+GGG 0.669921 1:-3291559 MsG0180000241.01.T01:five_prime_UTR
TGTTGCAGGAGAATATACCC+AGG 0.714302 1:+3290997 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATACAAGATGTTTATATAT+TGG + Chr1:3290840-3290859 None:intergenic 15.0%
!!! TCAAAAATAGTTTGATTTTA+AGG + Chr1:3291101-3291120 None:intergenic 15.0%
!! CAAAGTTACTTGAATTTATA+TGG - Chr1:3291660-3291679 MsG0180000241.01.T01:five_prime_UTR 20.0%
!! CATATAAATTCAAGTAACTT+TGG + Chr1:3291662-3291681 None:intergenic 20.0%
!! TTAACTTAACTTTACCTTAA+AGG - Chr1:3290719-3290738 MsG0180000241.01.T01:three_prime_UTR 20.0%
!!! AATTAGTTATTGTTCTTTTG+TGG - Chr1:3291191-3291210 MsG0180000241.01.T01:intron 20.0%
!!! CCATAAAGTGTATTATTTTA+GGG - Chr1:3290691-3290710 MsG0180000241.01.T01:three_prime_UTR 20.0%
!!! TGCATCAATTAAATTTTCTT+AGG - Chr1:3290612-3290631 MsG0180000241.01.T01:three_prime_UTR 20.0%
! ATTTACTTTCAGTTTCACAA+TGG - Chr1:3290873-3290892 MsG0180000241.01.T01:CDS 25.0%
! CCCTAAAATAATACACTTTA+TGG + Chr1:3290694-3290713 None:intergenic 25.0%
! TGGTTGAACATTATTGAATA+AGG - Chr1:3291740-3291759 MsG0180000241.01.T01:five_prime_UTR 25.0%
! TTTACTTTCAGTTTCACAAT+GGG - Chr1:3290874-3290893 MsG0180000241.01.T01:CDS 25.0%
!! GCCATAAAGTGTATTATTTT+AGG - Chr1:3290690-3290709 MsG0180000241.01.T01:three_prime_UTR 25.0%
!!! ATTTTGATTTGTCGGAATAT+TGG - Chr1:3291503-3291522 MsG0180000241.01.T01:five_prime_UTR 25.0%
!!! CTTGAATGATTTTGATTTGT+CGG - Chr1:3291495-3291514 MsG0180000241.01.T01:five_prime_UTR 25.0%
!!! TAGTTTGATTTTAAGGTTGA+AGG + Chr1:3291094-3291113 None:intergenic 25.0%
!!! TTATTTCTATGCATAAGTTG+CGG + Chr1:3290585-3290604 None:intergenic 25.0%
ACAAGAGAATTATGTGTTAC+TGG - Chr1:3291320-3291339 MsG0180000241.01.T01:CDS 30.0%
AGAAATGTAAGAATCAGAAC+TGG - Chr1:3291720-3291739 MsG0180000241.01.T01:five_prime_UTR 30.0%
ATTCAAGTAACTTTGGTACT+TGG + Chr1:3291655-3291674 None:intergenic 30.0%
CTTAACTTTACCTTAAAGGA+CGG - Chr1:3290723-3290742 MsG0180000241.01.T01:three_prime_UTR 30.0%
TCTTCATCAAGATCACTAAT+TGG + Chr1:3291042-3291061 None:intergenic 30.0%
TGTATTCTTCTAGTGCTAAT+GGG - Chr1:3291428-3291447 MsG0180000241.01.T01:five_prime_UTR 30.0%
! AGTTCTGATTCTTACATTTC+TGG + Chr1:3291721-3291740 None:intergenic 30.0%
! ATTATGTGTTACTGGGAAAA+TGG - Chr1:3291328-3291347 MsG0180000241.01.T01:CDS 30.0%
! CAAGAGAATTATGTGTTACT+GGG - Chr1:3291321-3291340 MsG0180000241.01.T01:CDS 30.0%
!! TTTCTGGCTTTAATCAGAAT+AGG + Chr1:3291705-3291724 None:intergenic 30.0%
ACACATAATTCTCTTGTTGC+AGG + Chr1:3291317-3291336 None:intergenic 35.0%
CAATGAAGCAGGTCAATTAA+AGG - Chr1:3290787-3290806 MsG0180000241.01.T01:three_prime_UTR 35.0%
GTATTCTTCTAGTGCTAATG+GGG - Chr1:3291429-3291448 MsG0180000241.01.T01:five_prime_UTR 35.0%
GTGTATTCTTCTAGTGCTAA+TGG - Chr1:3291427-3291446 MsG0180000241.01.T01:exon 35.0%
TAATTGGAAACTCCTCTTCA+AGG + Chr1:3291026-3291045 None:intergenic 35.0%
TAGTGATCTTGATGAAGAAC+AGG - Chr1:3291044-3291063 MsG0180000241.01.T01:CDS 35.0%
TCAAGCTTGAACATCTTGAA+AGG + Chr1:3291480-3291499 None:intergenic 35.0%
! GTTCTTTTGTGGTTTTCTTC+AGG - Chr1:3291202-3291221 MsG0180000241.01.T01:intron 35.0%
! TTTTCCCAGTGTCAAACTTT+TGG - Chr1:3290973-3290992 MsG0180000241.01.T01:CDS 35.0%
! TTTTCTTCAGGTGATTGTCT+CGG - Chr1:3291214-3291233 MsG0180000241.01.T01:intron 35.0%
!! AGTTTTGTCATTGTGAAGGA+TGG - Chr1:3291545-3291564 MsG0180000241.01.T01:five_prime_UTR 35.0%
!! GTGAAAGAGAAGAGTTTTGT+CGG - Chr1:3291387-3291406 MsG0180000241.01.T01:CDS 35.0%
!! TCTTTTGTTTCTCCATAGCT+CGG + Chr1:3291250-3291269 None:intergenic 35.0%
!! TTGGAAGCGTTCTATAATTC+AGG - Chr1:3291522-3291541 MsG0180000241.01.T01:five_prime_UTR 35.0%
AAACTCTCTCTCAGTAGGAT+TGG + Chr1:3291278-3291297 None:intergenic 40.0%
AGCATTTGCATCTCTTGGAA+TGG + Chr1:3290930-3290949 None:intergenic 40.0%
AGGAAAAACTCTCTCTCAGT+AGG + Chr1:3291283-3291302 None:intergenic 40.0%
CATGATTCAGATGGTGACTT+AGG + Chr1:3291613-3291632 None:intergenic 40.0%
CGATACAACCATGATTCAGA+TGG + Chr1:3291622-3291641 None:intergenic 40.0%
CTAAGTCACCATCTGAATCA+TGG - Chr1:3291611-3291630 MsG0180000241.01.T01:five_prime_UTR 40.0%
GAAAATGGAACCAAAGGCAA+AGG - Chr1:3291343-3291362 MsG0180000241.01.T01:CDS 40.0%
TACTGGGAAAATGGAACCAA+AGG - Chr1:3291337-3291356 MsG0180000241.01.T01:CDS 40.0%
TCGACCAAAAGTTTGACACT+GGG + Chr1:3290980-3290999 None:intergenic 40.0%
TTCGACCAAAAGTTTGACAC+TGG + Chr1:3290981-3291000 None:intergenic 40.0%
TTGACCTGCTTCATTGATAG+TGG + Chr1:3290783-3290802 None:intergenic 40.0%
TTGCATCTCTTGGAATGGTT+TGG + Chr1:3290925-3290944 None:intergenic 40.0%
! AAACTTTTGGTCGAAGTCGA+AGG - Chr1:3290986-3291005 MsG0180000241.01.T01:CDS 40.0%
! AATGGGTGTTTTCTACCATG+AGG - Chr1:3290891-3290910 MsG0180000241.01.T01:CDS 40.0%
! ACTGAGAGAGAGTTTTTCCT+GGG - Chr1:3291283-3291302 MsG0180000241.01.T01:CDS 40.0%
! TACTGAGAGAGAGTTTTTCC+TGG - Chr1:3291282-3291301 MsG0180000241.01.T01:CDS 40.0%
! TGCAAAGCATTTGCATCTCT+TGG + Chr1:3290935-3290954 None:intergenic 40.0%
!! CAGGAGTTTTGTCATTGTGA+AGG - Chr1:3291541-3291560 MsG0180000241.01.T01:five_prime_UTR 40.0%
AAAGGACGGAATGCTCTAGT+GGG - Chr1:3290737-3290756 MsG0180000241.01.T01:three_prime_UTR 45.0%
AAGGCCACTATCAATGAAGC+AGG - Chr1:3290776-3290795 MsG0180000241.01.T01:three_prime_UTR 45.0%
AATGGAACCAAAGGCAAAGG+AGG - Chr1:3291346-3291365 MsG0180000241.01.T01:CDS 45.0%
ATGGAACCAAAGGCAAAGGA+GGG - Chr1:3291347-3291366 MsG0180000241.01.T01:CDS 45.0%
GAGGGAGGTAATGAAGAACA+AGG - Chr1:3291365-3291384 MsG0180000241.01.T01:CDS 45.0%
GCTTTACGACAGAGACCAAA+AGG + Chr1:3291571-3291590 None:intergenic 45.0%
GGGGTTTCAATATTGCTGCA+AGG - Chr1:3290757-3290776 MsG0180000241.01.T01:three_prime_UTR 45.0%
TAAAGGACGGAATGCTCTAG+TGG - Chr1:3290736-3290755 MsG0180000241.01.T01:three_prime_UTR 45.0%
TCTTCTAGTGCTAATGGGGA+AGG - Chr1:3291433-3291452 MsG0180000241.01.T01:five_prime_UTR 45.0%
TGTTGCAGGAGAATATACCC+AGG + Chr1:3291303-3291322 None:intergenic 45.0%
TTCGACTACAAGCCTTGAAG+AGG - Chr1:3291011-3291030 MsG0180000241.01.T01:CDS 45.0%
! CATTGTGAAGGATGGCCTTT+TGG - Chr1:3291553-3291572 MsG0180000241.01.T01:five_prime_UTR 45.0%
! CTAGAGCATTCCGTCCTTTA+AGG + Chr1:3290736-3290755 None:intergenic 45.0%
AAGGACGGAATGCTCTAGTG+GGG - Chr1:3290738-3290757 MsG0180000241.01.T01:three_prime_UTR 50.0%
ATGCTTTGCAGCTGCTCTGA+AGG - Chr1:3290945-3290964 MsG0180000241.01.T01:CDS 50.0%
TCAGATGGTGACTTAGGCAG+TGG + Chr1:3291607-3291626 None:intergenic 50.0%
TCTTCAGGTGATTGTCTCGG+CGG - Chr1:3291217-3291236 MsG0180000241.01.T01:intron 50.0%
TTACCTCCCTCCTTTGCCTT+TGG + Chr1:3291356-3291375 None:intergenic 50.0%
! GGGTGTTTTCTACCATGAGG+AGG - Chr1:3290894-3290913 MsG0180000241.01.T01:CDS 50.0%
GAACCAAAGGCAAAGGAGGG+AGG - Chr1:3291350-3291369 MsG0180000241.01.T01:CDS 55.0%
GATGGTGACTTAGGCAGTGG+TGG + Chr1:3291604-3291623 None:intergenic 55.0%
! GGTTTGGTTGCTCCTCCTCA+TGG + Chr1:3290909-3290928 None:intergenic 55.0%
GGCGGTTAGAAGCCGAGCTA+TGG - Chr1:3291235-3291254 MsG0180000241.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 3290543 3291776 3290543 ID=MsG0180000241.01;Name=MsG0180000241.01
Chr1 mRNA 3290543 3291776 3290543 ID=MsG0180000241.01.T01;Parent=MsG0180000241.01;Name=MsG0180000241.01.T01;_AED=0.09;_eAED=0.09;_QI=349|1|1|1|1|1|2|307|140
Chr1 exon 3291251 3291776 3291251 ID=MsG0180000241.01.T01:exon:6171;Parent=MsG0180000241.01.T01
Chr1 exon 3290543 3291095 3290543 ID=MsG0180000241.01.T01:exon:6172;Parent=MsG0180000241.01.T01
Chr1 five_prime_UTR 3291428 3291776 3291428 ID=MsG0180000241.01.T01:five_prime_utr;Parent=MsG0180000241.01.T01
Chr1 CDS 3291251 3291427 3291251 ID=MsG0180000241.01.T01:cds;Parent=MsG0180000241.01.T01
Chr1 CDS 3290850 3291095 3290850 ID=MsG0180000241.01.T01:cds;Parent=MsG0180000241.01.T01
Chr1 three_prime_UTR 3290543 3290849 3290543 ID=MsG0180000241.01.T01:three_prime_utr;Parent=MsG0180000241.01.T01
Gene Sequence

>MsG0180000241.01.T01

ATGGGTGTTTTCTACCATGAGGAGGAGCAACCAAACCATTCCAAGAGATGCAAATGCTTTGCAGCTGCTCTGAAGGAAGTTTTTTCCCAGTGTCAAACTTTTGGTCGAAGTCGAAGGTTTTCGACTACAAGCCTTGAAGAGGAGTTTCCAATTAGTGATCTTGATGAAGAACAGGAAGTGATTGTCTCGGCGGTTAGAAGCCGAGCTATGGAGAAACAAAAGAACAAGCCAATCCTACTGAGAGAGAGTTTTTCCTGGGTATATTCTCCTGCAACAAGAGAATTATGTGTTACTGGGAAAATGGAACCAAAGGCAAAGGAGGGAGGTAATGAAGAACAAGGTGAAAGAGAAGAGTTTTGTCGGTTAAAAGCTGTTTCTCAGTGTATTCTTCTAGTGCTAATGGGGAAGGATTTTATTCTGTGA

Protein sequence

>MsG0180000241.01.T01

MGVFYHEEEQPNHSKRCKCFAAALKEVFSQCQTFGRSRRFSTTSLEEEFPISDLDEEQEVIVSAVRSRAMEKQKNKPILLRESFSWVYSPATRELCVTGKMEPKAKEGGNEEQGEREEFCRLKAVSQCILLVLMGKDFIL*