AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580029300.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580029300.01.T01 MTR_5g084060 60.714 56 22 0 1 56 1 56 2.39e-17 68.9
MsG0580029300.01.T01 MTR_4g127150 60.714 56 22 0 1 56 1 56 2.39e-17 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580029300.01.T01 AT5G50460 57.143 56 24 0 1 56 1 56 4.87e-16 65.9
MsG0580029300.01.T01 AT4G24920 57.143 56 24 0 1 56 1 56 4.87e-16 65.9
MsG0580029300.01.T01 AT3G48570 51.786 56 27 0 1 56 1 56 4.88e-14 60.5

Find 26 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGAAGAGAAAATCGATTT+AGG 0.188712 5:+94947546 None:intergenic
CACTGAATGTTCTATTGAAA+TGG 0.278559 5:+94945841 None:intergenic
GTGAAGAGAAAATCGATTTA+GGG 0.287423 5:+94947547 None:intergenic
AACGAGCCTAACGCTGTCTT+TGG 0.352610 5:+94947605 None:intergenic
AAGTTGTTGGTTGTACAATT+TGG 0.363808 5:+94945571 None:intergenic
CACCTTTGCGATCGGGTTTG+TGG 0.390413 5:+94947574 None:intergenic
TTATCTATATTTCTTATCTT+CGG 0.410507 5:-94945787 MsG0580029300.01.T01:three_prime_UTR
GGGGTTACACCTTTGCGATC+GGG 0.438874 5:+94947567 None:intergenic
ACATGTTACATAAAACTGTA+AGG 0.442953 5:+94945757 None:intergenic
ACTGAATGTTCTATTGAAAT+GGG 0.454214 5:+94945842 None:intergenic
AGGGGTTACACCTTTGCGAT+CGG 0.459137 5:+94947566 None:intergenic
TCAGTTAGTAAATTTCTAAG+AGG 0.462491 5:-94945610 MsG0580029300.01.T01:three_prime_UTR
TGGATCGAAGACGGAATCAA+TGG 0.467824 5:+94947641 None:intergenic
GATTATTTCTGCAGGATGAC+GGG 0.476757 5:-94945915 MsG0580029300.01.T01:intron
TGATTATTTCTGCAGGATGA+CGG 0.511253 5:-94945916 MsG0580029300.01.T01:intron
TTCTCTGAGTGGATCGAAGA+CGG 0.515282 5:+94947632 None:intergenic
CCTCAGGAAAGTTGTGAAGC+AGG 0.527193 5:-94945881 MsG0580029300.01.T01:CDS
GAAAGTTGTGAAGCAGGAGG+AGG 0.550624 5:-94945875 MsG0580029300.01.T01:CDS
ACGGGAATTACAATCGCCTC+AGG 0.556837 5:-94945897 MsG0580029300.01.T01:CDS
AATTCGCCAAAGACAGCGTT+AGG 0.569841 5:-94947611 MsG0580029300.01.T01:CDS
TGAAGAGAAAATCGATTTAG+GGG 0.612420 5:+94947548 None:intergenic
CCTGCTTCACAACTTTCCTG+AGG 0.626602 5:+94945881 None:intergenic
TGCCACAAACCCGATCGCAA+AGG 0.641778 5:-94947576 MsG0580029300.01.T01:CDS
AGGTCAAAAGTCTCAACACA+TGG 0.662789 5:+94945720 None:intergenic
CAGGAAAGTTGTGAAGCAGG+AGG 0.667526 5:-94945878 MsG0580029300.01.T01:CDS
TCTTTGGCGAATTCTCTGAG+TGG 0.681670 5:+94947621 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGAAAGAAAAAAAAAAA+TGG - Chr5:94946201-94946220 MsG0580029300.01.T01:intron 10.0%
!! ACAAAATAAACATTATATTG+AGG + Chr5:94947082-94947101 None:intergenic 15.0%
!! TTATCTATATTTCTTATCTT+CGG - Chr5:94947399-94947418 MsG0580029300.01.T01:intron 15.0%
!!! ATAATGTTTATTTTGTCTTT+TGG - Chr5:94947086-94947105 MsG0580029300.01.T01:intron 15.0%
!!! TTGATTTGAATGAAATATTT+TGG - Chr5:94945914-94945933 MsG0580029300.01.T01:intron 15.0%
!!! TTTTATAATGTTCATCTAAA+TGG - Chr5:94946530-94946549 MsG0580029300.01.T01:intron 15.0%
!! AAAAATAGCAAATAAGTTGT+TGG + Chr5:94947631-94947650 None:intergenic 20.0%
!! AAACATATTTGTGACAATAA+GGG - Chr5:94946666-94946685 MsG0580029300.01.T01:intron 20.0%
!! TAAACATATTTGTGACAATA+AGG - Chr5:94946665-94946684 MsG0580029300.01.T01:intron 20.0%
!!! ATTTGAATGAAATATTTTGG+TGG - Chr5:94945917-94945936 MsG0580029300.01.T01:intron 20.0%
!!! ATTTTTTGTATGATTTGCAA+TGG - Chr5:94946408-94946427 MsG0580029300.01.T01:intron 20.0%
! ACAAGTAAATCCATTATGTT+AGG + Chr5:94946384-94946403 None:intergenic 25.0%
! ACATGTTACATAAAACTGTA+AGG + Chr5:94947432-94947451 None:intergenic 25.0%
! ACTGAATGTTCTATTGAAAT+GGG + Chr5:94947347-94947366 None:intergenic 25.0%
! ATTGAAAACAACTTTGCAAT+TGG + Chr5:94946716-94946735 None:intergenic 25.0%
! GAAACAATTTGATTGAATCA+AGG - Chr5:94945980-94945999 MsG0580029300.01.T01:intron 25.0%
! GAGAATTTAGTATTTACACT+AGG - Chr5:94947012-94947031 MsG0580029300.01.T01:intron 25.0%
! TCAGTTAGTAAATTTCTAAG+AGG - Chr5:94947576-94947595 MsG0580029300.01.T01:CDS 25.0%
! TGAGATCTTAATATGAATCA+GGG - Chr5:94946311-94946330 MsG0580029300.01.T01:intron 25.0%
! TTGAGATCTTAATATGAATC+AGG - Chr5:94946310-94946329 MsG0580029300.01.T01:intron 25.0%
!! GGTTTTTGTAAGATTTACAA+TGG - Chr5:94946064-94946083 MsG0580029300.01.T01:intron 25.0%
!!! AATGAAATATTTTGGTGGAA+TGG - Chr5:94945922-94945941 MsG0580029300.01.T01:intron 25.0%
!!! TGAATCAAGGATATTTTGAA+GGG - Chr5:94945993-94946012 MsG0580029300.01.T01:intron 25.0%
!!! TTGAATCAAGGATATTTTGA+AGG - Chr5:94945992-94946011 MsG0580029300.01.T01:intron 25.0%
AGGAGGAAAAAGTTTAGATA+AGG - Chr5:94947497-94947516 MsG0580029300.01.T01:intron 30.0%
CACTGAATGTTCTATTGAAA+TGG + Chr5:94947348-94947367 None:intergenic 30.0%
CATAGGTAGTAAAAACAGAT+AGG + Chr5:94946953-94946972 None:intergenic 30.0%
GAGATCTTAATATGAATCAG+GGG - Chr5:94946312-94946331 MsG0580029300.01.T01:intron 30.0%
TGAATTGCTGATGTAAATGT+TGG - Chr5:94945951-94945970 MsG0580029300.01.T01:intron 30.0%
TGTTCGTAGTTATGATTGAT+TGG - Chr5:94946483-94946502 MsG0580029300.01.T01:intron 30.0%
TTTAATGTGATCACATGTGT+TGG - Chr5:94946229-94946248 MsG0580029300.01.T01:intron 30.0%
! AAGTTGTTGGTTGTACAATT+TGG + Chr5:94947618-94947637 None:intergenic 30.0%
! AGTGAAGAGAAAATCGATTT+AGG + Chr5:94945643-94945662 None:intergenic 30.0%
! CTTATGTCAAAGGATGTTTT+TGG - Chr5:94947044-94947063 MsG0580029300.01.T01:intron 30.0%
! GATTTTCATGCCTAACATAA+TGG - Chr5:94946371-94946390 MsG0580029300.01.T01:intron 30.0%
! GTGAAGAGAAAATCGATTTA+GGG + Chr5:94945642-94945661 None:intergenic 30.0%
! TGAAGAGAAAATCGATTTAG+GGG + Chr5:94945641-94945660 None:intergenic 30.0%
! TTAGTATTGTGTTACTCATG+TGG - Chr5:94946122-94946141 MsG0580029300.01.T01:intron 30.0%
! TTGAATGTAATCAGAAGTGT+CGG + Chr5:94946839-94946858 None:intergenic 30.0%
!! AATCAAGGATATTTTGAAGG+GGG - Chr5:94945995-94946014 MsG0580029300.01.T01:intron 30.0%
!! GAATCAAGGATATTTTGAAG+GGG - Chr5:94945994-94946013 MsG0580029300.01.T01:intron 30.0%
!! TAACTCTTGATTATTTCTGC+AGG - Chr5:94947263-94947282 MsG0580029300.01.T01:intron 30.0%
!! TTGTTTTGTAGAATTCTCCA+AGG - Chr5:94945710-94945729 MsG0580029300.01.T01:three_prime_UTR 30.0%
!!! TGGTTGTTTTTATGCATAGT+GGG - Chr5:94946027-94946046 MsG0580029300.01.T01:intron 30.0%
!!! TTGGTTGTTTTTATGCATAG+TGG - Chr5:94946026-94946045 MsG0580029300.01.T01:intron 30.0%
ACCAACACTAACACTTCTAA+CGG + Chr5:94946271-94946290 None:intergenic 35.0%
ACTGTCAATTTGTGATGCTA+CGG + Chr5:94946579-94946598 None:intergenic 35.0%
ATGAACAACTCAAACTGACA+TGG + Chr5:94946890-94946909 None:intergenic 35.0%
CTCAAATCAAATTGACGATG+AGG + Chr5:94946295-94946314 None:intergenic 35.0%
GATTGTTCTTTCCATTGAGT+TGG - Chr5:94947144-94947163 MsG0580029300.01.T01:intron 35.0%
TGAATCCTGTAAGACATATG+AGG + Chr5:94947199-94947218 None:intergenic 35.0%
!! ATTGGTGATTTTCTCTGCAT+TGG - Chr5:94946501-94946520 MsG0580029300.01.T01:intron 35.0%
!! TGATTATTTCTGCAGGATGA+CGG - Chr5:94947270-94947289 MsG0580029300.01.T01:intron 35.0%
!!! AATCAGGGGATTTTTGAAGT+GGG - Chr5:94946326-94946345 MsG0580029300.01.T01:intron 35.0%
AACAACATCATCGTTGGATC+TGG - Chr5:94945810-94945829 MsG0580029300.01.T01:three_prime_UTR 40.0%
AACTGCCTCATATGTCTTAC+AGG - Chr5:94947191-94947210 MsG0580029300.01.T01:intron 40.0%
AATCACAGCAACCAACTCAA+TGG + Chr5:94947158-94947177 None:intergenic 40.0%
ACACAAGACACAACACTGAA+TGG + Chr5:94946867-94946886 None:intergenic 40.0%
AGGTCAAAAGTCTCAACACA+TGG + Chr5:94947469-94947488 None:intergenic 40.0%
CCAACGATGATGTTGTTGAT+TGG + Chr5:94945807-94945826 None:intergenic 40.0%
CCAATCAACAACATCATCGT+TGG - Chr5:94945804-94945823 MsG0580029300.01.T01:three_prime_UTR 40.0%
CTTCACAGAAATAGTTCCAC+GGG + Chr5:94946986-94947005 None:intergenic 40.0%
GCTGTAGCAACTTATGTCAA+AGG - Chr5:94947034-94947053 MsG0580029300.01.T01:intron 40.0%
GCTTCACAGAAATAGTTCCA+CGG + Chr5:94946987-94947006 None:intergenic 40.0%
! TGCATGTTTGCTACAATGCA+TGG - Chr5:94946097-94946116 MsG0580029300.01.T01:intron 40.0%
! TTTGAAGTGGGTGATCTGTT+TGG - Chr5:94946338-94946357 MsG0580029300.01.T01:intron 40.0%
!! GAATCAGGGGATTTTTGAAG+TGG - Chr5:94946325-94946344 MsG0580029300.01.T01:intron 40.0%
!! GATTATTTCTGCAGGATGAC+GGG - Chr5:94947271-94947290 MsG0580029300.01.T01:intron 40.0%
!! TCCGTTAGAAGTGTTAGTGT+TGG - Chr5:94946267-94946286 MsG0580029300.01.T01:intron 40.0%
!! TTTGAAGGGGGTATTCTGTT+TGG - Chr5:94946007-94946026 MsG0580029300.01.T01:intron 40.0%
!!! GATTTTCTCTGCATTGGTTG+TGG - Chr5:94946507-94946526 MsG0580029300.01.T01:intron 40.0%
!!! GCATAGTGGGTTTTAGTTGT+TGG - Chr5:94946040-94946059 MsG0580029300.01.T01:intron 40.0%
!!! TAGTGGGTTTTAGTTGTTGG+AGG - Chr5:94946043-94946062 MsG0580029300.01.T01:intron 40.0%
AATTCGCCAAAGACAGCGTT+AGG - Chr5:94945575-94945594 MsG0580029300.01.T01:three_prime_UTR 45.0%
CATCACAACGAAACCAATCG+CGG + Chr5:94945748-94945767 None:intergenic 45.0%
CATCATCGTTGGATCTGGTT+AGG - Chr5:94945815-94945834 MsG0580029300.01.T01:three_prime_UTR 45.0%
CTTCTAACGGAAGATGTGTC+TGG + Chr5:94946258-94946277 None:intergenic 45.0%
TCTTTGGCGAATTCTCTGAG+TGG + Chr5:94945568-94945587 None:intergenic 45.0%
TGGATCGAAGACGGAATCAA+TGG + Chr5:94945548-94945567 None:intergenic 45.0%
TTCTCTGAGTGGATCGAAGA+CGG + Chr5:94945557-94945576 None:intergenic 45.0%
! CTTTTTCCTCCTTGAGCAAC+AGG + Chr5:94947489-94947508 None:intergenic 45.0%
! GACTTTTGACCTGTTGCTCA+AGG - Chr5:94947477-94947496 MsG0580029300.01.T01:intron 45.0%
! TCGTTGTGATGGGATTCGTT+GGG - Chr5:94945757-94945776 MsG0580029300.01.T01:three_prime_UTR 45.0%
! TTCGTTGTGATGGGATTCGT+TGG - Chr5:94945756-94945775 MsG0580029300.01.T01:three_prime_UTR 45.0%
! TTTTGACCTGTTGCTCAAGG+AGG - Chr5:94947480-94947499 MsG0580029300.01.T01:intron 45.0%
!! GCGATTGGTTTCGTTGTGAT+GGG - Chr5:94945747-94945766 MsG0580029300.01.T01:three_prime_UTR 45.0%
AACGAGCCTAACGCTGTCTT+TGG + Chr5:94945584-94945603 None:intergenic 50.0%
AATAGTTCCACGGGCTCTTG+AGG + Chr5:94946977-94946996 None:intergenic 50.0%
ACATATGAGGCAGTTCCGCT+CGG + Chr5:94947186-94947205 None:intergenic 50.0%
ACGGGAATTACAATCGCCTC+AGG - Chr5:94947289-94947308 MsG0580029300.01.T01:intron 50.0%
AGGGGTTACACCTTTGCGAT+CGG + Chr5:94945623-94945642 None:intergenic 50.0%
ATAGTTCCACGGGCTCTTGA+GGG + Chr5:94946976-94946995 None:intergenic 50.0%
CAGGAAAGTTGTGAAGCAGG+AGG - Chr5:94947308-94947327 MsG0580029300.01.T01:intron 50.0%
CCTCAGGAAAGTTGTGAAGC+AGG - Chr5:94947305-94947324 MsG0580029300.01.T01:intron 50.0%
CCTGCTTCACAACTTTCCTG+AGG + Chr5:94947308-94947327 None:intergenic 50.0%
GAAAGTTGTGAAGCAGGAGG+AGG - Chr5:94947311-94947330 MsG0580029300.01.T01:intron 50.0%
TGCTGTGATTGATTGCCGAG+CGG - Chr5:94947168-94947187 MsG0580029300.01.T01:intron 50.0%
!! CGCGATTGGTTTCGTTGTGA+TGG - Chr5:94945746-94945765 MsG0580029300.01.T01:three_prime_UTR 50.0%
CACCTTTGCGATCGGGTTTG+TGG + Chr5:94945615-94945634 None:intergenic 55.0%
GGGGTTACACCTTTGCGATC+GGG + Chr5:94945622-94945641 None:intergenic 55.0%
TGCCACAAACCCGATCGCAA+AGG - Chr5:94945610-94945629 MsG0580029300.01.T01:three_prime_UTR 55.0%
! GTTGCTGTTCGTACCGCGAT+TGG - Chr5:94945732-94945751 MsG0580029300.01.T01:three_prime_UTR 55.0%
CGCGGTACGAACAGCAACCT+TGG + Chr5:94945730-94945749 None:intergenic 60.0%
CCTATGCCCTCAAGAGCCCG+TGG - Chr5:94946967-94946986 MsG0580029300.01.T01:intron 65.0%
! CCACGGGCTCTTGAGGGCAT+AGG + Chr5:94946970-94946989 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr5 gene 94945538 94947670 94945538 ID=MsG0580029300.01;Name=MsG0580029300.01
Chr5 mRNA 94945538 94947670 94945538 ID=MsG0580029300.01.T01;Parent=MsG0580029300.01;Name=MsG0580029300.01.T01;_AED=0.50;_eAED=0.51;_QI=0|0|0.5|1|0|0|2|314|71
Chr5 exon 94945538 94945923 94945538 ID=MsG0580029300.01.T01:exon:49974;Parent=MsG0580029300.01.T01
Chr5 exon 94947527 94947670 94947527 ID=MsG0580029300.01.T01:exon:49973;Parent=MsG0580029300.01.T01
Chr5 CDS 94947527 94947670 94947527 ID=MsG0580029300.01.T01:cds;Parent=MsG0580029300.01.T01
Chr5 CDS 94945852 94945923 94945852 ID=MsG0580029300.01.T01:cds;Parent=MsG0580029300.01.T01
Chr5 three_prime_UTR 94945538 94945851 94945538 ID=MsG0580029300.01.T01:three_prime_utr;Parent=MsG0580029300.01.T01
Gene Sequence

>MsG0580029300.01.T01

ATGGACGCCATTGATTCCGTCTTCGATCCACTCAGAGAATTCGCCAAAGACAGCGTTAGGCTCGTTAAGCGTTGCCACAAACCCGATCGCAAAGGTGTAACCCCTAAATCGATTTTCTCTTCACTTGATTTCAATCTCTATATTGATGACGGGAATTACAATCGCCTCAGGAAAGTTGTGAAGCAGGAGGAGGCAAAAGTGTTCCCATTTCAATAG

Protein sequence

>MsG0580029300.01.T01

MDAIDSVFDPLREFAKDSVRLVKRCHKPDRKGVTPKSIFSSLDFNLYIDDGNYNRLRKVVKQEEAKVFPFQ*