AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180005856.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005856.01.T01 MTR_1g108440 78.472 144 6 2 1 119 1 144 6.18e-57 179
MsG0180005856.01.T01 MTR_1g108440 73.846 65 14 1 99 163 207 268 1.25e-21 88.6
MsG0180005856.01.T01 MTR_7g114900 55.085 118 28 2 31 123 44 161 2.27e-31 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005856.01.T01 AT1G71100 63.063 111 16 1 34 119 27 137 3.13e-38 131
MsG0180005856.01.T01 AT1G71100 68.889 45 14 0 119 163 221 265 2.11e-13 66.2
MsG0180005856.01.T01 AT2G01290 54.676 139 34 4 6 119 7 141 6.89e-38 130
MsG0180005856.01.T01 AT2G01290 68.889 45 14 0 119 163 220 264 8.88e-14 67.4
MsG0180005856.01.T01 AT3G04790 53.030 132 30 2 24 123 26 157 1.13e-31 115

Find 50 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTGATCCTTATCTGAATT+TGG 0.242966 1:+96914923 MsG0180005856.01.T01:CDS
CACAGCTTGTTCATGGGTTA+TGG 0.303703 1:-96914829 None:intergenic
GCCACTACTGTTATTGTTGC+AGG 0.337617 1:+96915309 MsG0180005856.01.T01:CDS
GTTATTGATCTGGCTATTGA+TGG 0.345990 1:+96914891 MsG0180005856.01.T01:CDS
AAGATGGGGAGGAAGGGATT+AGG 0.355908 1:-96914618 None:intergenic
ACGGAGGAAGATGGGGAGGA+AGG 0.357599 1:-96914625 None:intergenic
TCAATAGCCAGATCAATAAC+AGG 0.377911 1:-96914888 None:intergenic
CAAGAGTATTGGTGATTTGA+GGG 0.386542 1:+96915224 MsG0180005856.01.T01:intron
CAAGCGACACAGCTTGTTCA+TGG 0.392562 1:-96914836 None:intergenic
TTCTCACCCTGTTATTGATC+TGG 0.396611 1:+96914881 MsG0180005856.01.T01:CDS
CGGAGGAAGATGGGGAGGAA+GGG 0.412061 1:-96914624 None:intergenic
ACAAGAGTATTGGTGATTTG+AGG 0.434810 1:+96915223 MsG0180005856.01.T01:intron
GTTATTGTTGCAGGTGAACT+TGG 0.447603 1:+96915318 MsG0180005856.01.T01:CDS
ATGACGGAGACGGAGGAAGA+TGG 0.454411 1:-96914634 None:intergenic
TGACGGAGACGGAGGAAGAT+GGG 0.457977 1:-96914633 None:intergenic
GACGTATTCGACGGCTTTGT+AGG 0.458278 1:-96914689 None:intergenic
CATGAACAAGCTGTGTCGCT+TGG 0.459092 1:+96914837 MsG0180005856.01.T01:CDS
TGCAGGTGAACTTGGATTAA+CGG 0.466113 1:+96915326 MsG0180005856.01.T01:CDS
GCCGTCGAATACGTCGAATC+CGG 0.469325 1:+96914697 MsG0180005856.01.T01:CDS
TCTTCAAATCGTCTTGGGAT+AGG 0.470931 1:-96914657 None:intergenic
ATGAACAAGCTGTGTCGCTT+GGG 0.481615 1:+96914838 MsG0180005856.01.T01:CDS
CTGAATTTGGTCAAAGGTCG+TGG 0.491213 1:+96914936 MsG0180005856.01.T01:CDS
CCTTTGACCAAATTCAGATA+AGG 0.499030 1:-96914930 None:intergenic
TCATGGGTTATGGTTGAAGT+GGG 0.501448 1:-96914819 None:intergenic
GCAAAAGCCGCCATGGAAGC+CGG 0.505670 1:+96914592 MsG0180005856.01.T01:CDS
GATTAGGAGACCGGCTTCCA+TGG 0.507400 1:-96914602 None:intergenic
CTCCTCCGCAAAAGCCGCCA+TGG 0.525693 1:+96914585 MsG0180005856.01.T01:CDS
ACCGGATTCGACGTATTCGA+CGG 0.531735 1:-96914698 None:intergenic
TTTGAATATTGCTGGAGTTG+TGG 0.542330 1:+96915263 MsG0180005856.01.T01:CDS
TTCATGGGTTATGGTTGAAG+TGG 0.548920 1:-96914820 None:intergenic
CCTTATCTGAATTTGGTCAA+AGG 0.562344 1:+96914930 MsG0180005856.01.T01:CDS
AAGCGACACAGCTTGTTCAT+GGG 0.563565 1:-96914835 None:intergenic
GGAGGAAGGGATTAGGAGAC+CGG 0.572887 1:-96914611 None:intergenic
GACGGAGACGGAGGAAGATG+GGG 0.575809 1:-96914632 None:intergenic
GGAAAACTCAAGAACATCAT+CGG 0.579574 1:+96914793 MsG0180005856.01.T01:CDS
ATTGCTGGAGTTGTGGAGCA+TGG 0.586645 1:+96915270 MsG0180005856.01.T01:CDS
TTTGCGGAGGAGATGAAATG+GGG 0.606219 1:-96914574 None:intergenic
ATCGTCTTGGGATAGGATGA+CGG 0.613450 1:-96914650 None:intergenic
TTTGAGAGAGAAAATGGTGA+AGG 0.618307 1:+96914968 MsG0180005856.01.T01:CDS
TTGGGATAGGATGACGGAGA+CGG 0.622137 1:-96914644 None:intergenic
ACCTGCAACAATAACAGTAG+TGG 0.628479 1:-96915310 None:intergenic
GTATTCGACGGCTTTGTAGG+CGG 0.629732 1:-96914686 None:intergenic
AACAGGGTGAGAATCTAGAT+CGG 0.631505 1:-96914871 None:intergenic
TGAGAATCTAGATCGGAGAG+AGG 0.637710 1:-96914864 None:intergenic
CAATAGCCAGATCAATAACA+GGG 0.638511 1:-96914887 None:intergenic
GGAGACGGAGGAAGATGGGG+AGG 0.656258 1:-96914629 None:intergenic
GGATAGGATGACGGAGACGG+AGG 0.661730 1:-96914641 None:intergenic
TAGGAGACCGGCTTCCATGG+CGG 0.675735 1:-96914599 None:intergenic
AATTTGGTCAAAGGTCGTGG+TGG 0.690593 1:+96914939 MsG0180005856.01.T01:CDS
TTGCGGAGGAGATGAAATGG+GGG 0.700075 1:-96914573 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCAAAACTTGTTAACTATT+TGG + Chr1:96915024-96915043 MsG0180005856.01.T01:intron 20.0%
!!! TCAAAACTTGTTAACTATTT+GGG + Chr1:96915025-96915044 MsG0180005856.01.T01:intron 20.0%
!!! TTGTATTTTAACAAGAGTAT+TGG + Chr1:96915213-96915232 MsG0180005856.01.T01:intron 20.0%
! AACCTTATGTTACTGATAAT+GGG + Chr1:96915175-96915194 MsG0180005856.01.T01:intron 25.0%
!!! TGATAATGGGAATTATATAG+TGG + Chr1:96915188-96915207 MsG0180005856.01.T01:intron 25.0%
AGTTGATCCTTATCTGAATT+TGG + Chr1:96914923-96914942 MsG0180005856.01.T01:CDS 30.0%
GAACCTTATGTTACTGATAA+TGG + Chr1:96915174-96915193 MsG0180005856.01.T01:intron 30.0%
TTCCCATTATCAGTAACATA+AGG - Chr1:96915180-96915199 None:intergenic 30.0%
! GATTTTCTTCAAATCGTCTT+GGG - Chr1:96914665-96914684 None:intergenic 30.0%
!! AAACTTGTTAACTATTTGGG+TGG + Chr1:96915028-96915047 MsG0180005856.01.T01:intron 30.0%
!! TTCACTTTTGAGAGAGAAAA+TGG + Chr1:96914962-96914981 MsG0180005856.01.T01:CDS 30.0%
!! TTGAAGTTATTCGCTTTTGT+TGG + Chr1:96915071-96915090 MsG0180005856.01.T01:intron 30.0%
!!! GATGCTATTTTGAATATTGC+TGG + Chr1:96915255-96915274 MsG0180005856.01.T01:CDS 30.0%
CAAAAGCGAATAACTTCAAC+AGG - Chr1:96915070-96915089 None:intergenic 35.0%
CAATAGCCAGATCAATAACA+GGG - Chr1:96914890-96914909 None:intergenic 35.0%
CCTTATCTGAATTTGGTCAA+AGG + Chr1:96914930-96914949 MsG0180005856.01.T01:CDS 35.0%
CCTTTGACCAAATTCAGATA+AGG - Chr1:96914933-96914952 None:intergenic 35.0%
GGAAAACTCAAGAACATCAT+CGG + Chr1:96914793-96914812 MsG0180005856.01.T01:CDS 35.0%
GTTATTGATCTGGCTATTGA+TGG + Chr1:96914891-96914910 MsG0180005856.01.T01:CDS 35.0%
GTTGCAAAGCTTAGAACTTT+CGG + Chr1:96915142-96915161 MsG0180005856.01.T01:intron 35.0%
TCAATAGCCAGATCAATAAC+AGG - Chr1:96914891-96914910 None:intergenic 35.0%
TTTGAATATTGCTGGAGTTG+TGG + Chr1:96915263-96915282 MsG0180005856.01.T01:CDS 35.0%
TTTGAGAGAGAAAATGGTGA+AGG + Chr1:96914968-96914987 MsG0180005856.01.T01:CDS 35.0%
! CGATTTTCTTCAAATCGTCT+TGG - Chr1:96914666-96914685 None:intergenic 35.0%
! TTTTGTTGGAAATTCACTGC+TGG + Chr1:96915085-96915104 MsG0180005856.01.T01:intron 35.0%
!! ACAAGAGTATTGGTGATTTG+AGG + Chr1:96915223-96915242 MsG0180005856.01.T01:intron 35.0%
!! CAAGAGTATTGGTGATTTGA+GGG + Chr1:96915224-96915243 MsG0180005856.01.T01:intron 35.0%
!!! GCATGGAATGTTTTTGGATA+TGG + Chr1:96915287-96915306 MsG0180005856.01.T01:CDS 35.0%
AACAGGGTGAGAATCTAGAT+CGG - Chr1:96914874-96914893 None:intergenic 40.0%
ACCTGCAACAATAACAGTAG+TGG - Chr1:96915313-96915332 None:intergenic 40.0%
CAGAATCTGTTTGAGGAATC+TGG + Chr1:96915115-96915134 MsG0180005856.01.T01:intron 40.0%
GCTTAGAACTTTCGGTGAAA+AGG + Chr1:96915150-96915169 MsG0180005856.01.T01:intron 40.0%
GTTAACTATTTGGGTGGTAG+TGG + Chr1:96915034-96915053 MsG0180005856.01.T01:intron 40.0%
GTTATTGTTGCAGGTGAACT+TGG + Chr1:96915318-96915337 MsG0180005856.01.T01:CDS 40.0%
TAGGCTTCAGAATCTGTTTG+AGG + Chr1:96915108-96915127 MsG0180005856.01.T01:intron 40.0%
TCTTCAAATCGTCTTGGGAT+AGG - Chr1:96914660-96914679 None:intergenic 40.0%
TGCAGGTGAACTTGGATTAA+CGG + Chr1:96915326-96915345 MsG0180005856.01.T01:CDS 40.0%
TTCTCACCCTGTTATTGATC+TGG + Chr1:96914881-96914900 MsG0180005856.01.T01:CDS 40.0%
! TCATGGGTTATGGTTGAAGT+GGG - Chr1:96914822-96914841 None:intergenic 40.0%
! TGTGGAGCATGGAATGTTTT+TGG + Chr1:96915281-96915300 MsG0180005856.01.T01:CDS 40.0%
! TGTTCTTGAGTTTTCCCTGA+CGG - Chr1:96914789-96914808 None:intergenic 40.0%
! TTCATGGGTTATGGTTGAAG+TGG - Chr1:96914823-96914842 None:intergenic 40.0%
! TTTTGCGGAGGAGATGAAAT+GGG - Chr1:96914578-96914597 None:intergenic 40.0%
AATTTGGTCAAAGGTCGTGG+TGG + Chr1:96914939-96914958 MsG0180005856.01.T01:CDS 45.0%
ATCGTCTTGGGATAGGATGA+CGG - Chr1:96914653-96914672 None:intergenic 45.0%
CTGAATTTGGTCAAAGGTCG+TGG + Chr1:96914936-96914955 MsG0180005856.01.T01:CDS 45.0%
GCCACTACTGTTATTGTTGC+AGG + Chr1:96915309-96915328 MsG0180005856.01.T01:CDS 45.0%
GTTGGAAATTCACTGCTGGT+AGG + Chr1:96915089-96915108 MsG0180005856.01.T01:intron 45.0%
TGAGAATCTAGATCGGAGAG+AGG - Chr1:96914867-96914886 None:intergenic 45.0%
TTTGCGGAGGAGATGAAATG+GGG - Chr1:96914577-96914596 None:intergenic 45.0%
! AAGCGACACAGCTTGTTCAT+GGG - Chr1:96914838-96914857 None:intergenic 45.0%
! CACAGCTTGTTCATGGGTTA+TGG - Chr1:96914832-96914851 None:intergenic 45.0%
! CTTTTGCGGAGGAGATGAAA+TGG - Chr1:96914579-96914598 None:intergenic 45.0%
!! ATGAACAAGCTGTGTCGCTT+GGG + Chr1:96914838-96914857 MsG0180005856.01.T01:CDS 45.0%
AAGATGGGGAGGAAGGGATT+AGG - Chr1:96914621-96914640 None:intergenic 50.0%
AAGCTCTCCAATTCTGGCGA+CGG - Chr1:96914764-96914783 None:intergenic 50.0%
AATTGGAGAGCTTCTCCGTC+AGG + Chr1:96914771-96914790 MsG0180005856.01.T01:intron 50.0%
ACCGGATTCGACGTATTCGA+CGG - Chr1:96914701-96914720 None:intergenic 50.0%
ACGGAGAAGCTCTCCAATTC+TGG - Chr1:96914770-96914789 None:intergenic 50.0%
ATTGCTGGAGTTGTGGAGCA+TGG + Chr1:96915270-96915289 MsG0180005856.01.T01:CDS 50.0%
ATTGGAGAGCTTCTCCGTCA+GGG + Chr1:96914772-96914791 MsG0180005856.01.T01:intron 50.0%
CGAATACGTCGAATCCGGTA+TGG + Chr1:96914702-96914721 MsG0180005856.01.T01:intron 50.0%
GTCGAATCCGGTATGGTTCT+AGG + Chr1:96914709-96914728 MsG0180005856.01.T01:intron 50.0%
TTGCGGAGGAGATGAAATGG+GGG - Chr1:96914576-96914595 None:intergenic 50.0%
! CAAGCGACACAGCTTGTTCA+TGG - Chr1:96914839-96914858 None:intergenic 50.0%
! CATGAACAAGCTGTGTCGCT+TGG + Chr1:96914837-96914856 MsG0180005856.01.T01:CDS 50.0%
! GACGTATTCGACGGCTTTGT+AGG - Chr1:96914692-96914711 None:intergenic 50.0%
! GTATTCGACGGCTTTGTAGG+CGG - Chr1:96914689-96914708 None:intergenic 50.0%
!! TTGGGATAGGATGACGGAGA+CGG - Chr1:96914647-96914666 None:intergenic 50.0%
AAACACGCCGTCGCCAGAAT+TGG + Chr1:96914754-96914773 MsG0180005856.01.T01:intron 55.0%
AATTCTGGCGACGGCGTGTT+TGG - Chr1:96914755-96914774 None:intergenic 55.0%
GAGGAGATGAAATGGGGGCA+AGG - Chr1:96914571-96914590 None:intergenic 55.0%
GCCGTCGAATACGTCGAATC+CGG + Chr1:96914697-96914716 MsG0180005856.01.T01:CDS 55.0%
GGAGGAAGGGATTAGGAGAC+CGG - Chr1:96914614-96914633 None:intergenic 55.0%
TCCGAGGCCTAGAACCATAC+CGG - Chr1:96914719-96914738 None:intergenic 55.0%
TGACGGAGACGGAGGAAGAT+GGG - Chr1:96914636-96914655 None:intergenic 55.0%
! ATGACGGAGACGGAGGAAGA+TGG - Chr1:96914637-96914656 None:intergenic 55.0%
! GATTAGGAGACCGGCTTCCA+TGG - Chr1:96914605-96914624 None:intergenic 55.0%
!! ATGGTTCTAGGCCTCGGAAC+CGG + Chr1:96914721-96914740 MsG0180005856.01.T01:intron 55.0%
!! TCCGGTATGGTTCTAGGCCT+CGG + Chr1:96914715-96914734 MsG0180005856.01.T01:intron 55.0%
ACGGAGGAAGATGGGGAGGA+AGG - Chr1:96914628-96914647 None:intergenic 60.0%
CGGAGGAAGATGGGGAGGAA+GGG - Chr1:96914627-96914646 None:intergenic 60.0%
GACGGAGACGGAGGAAGATG+GGG - Chr1:96914635-96914654 None:intergenic 60.0%
GCAAAAGCCGCCATGGAAGC+CGG + Chr1:96914592-96914611 MsG0180005856.01.T01:CDS 60.0%
! GGCTTCCATGGCGGCTTTTG+CGG - Chr1:96914593-96914612 None:intergenic 60.0%
! TAGGAGACCGGCTTCCATGG+CGG - Chr1:96914602-96914621 None:intergenic 60.0%
! TTCCATGGCGGCTTTTGCGG+AGG - Chr1:96914590-96914609 None:intergenic 60.0%
!! GGATAGGATGACGGAGACGG+AGG - Chr1:96914644-96914663 None:intergenic 60.0%
CTCCTCCGCAAAAGCCGCCA+TGG + Chr1:96914585-96914604 MsG0180005856.01.T01:CDS 65.0%
GGAGACGGAGGAAGATGGGG+AGG - Chr1:96914632-96914651 None:intergenic 65.0%
GGCGTGTTTGGCGGTTGAGC+CGG - Chr1:96914743-96914762 None:intergenic 65.0%
TCTGGCGACGGCGTGTTTGG+CGG - Chr1:96914752-96914771 None:intergenic 65.0%
! TGGCGGTTGAGCCGGTTCCG+AGG - Chr1:96914735-96914754 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr1 gene 96914559 96915362 96914559 ID=MsG0180005856.01;Name=MsG0180005856.01
Chr1 mRNA 96914559 96915362 96914559 ID=MsG0180005856.01.T01;Parent=MsG0180005856.01;Name=MsG0180005856.01.T01;_AED=0.47;_eAED=0.47;_QI=0|0|0|1|1|1|3|0|163
Chr1 exon 96914559 96914718 96914559 ID=MsG0180005856.01.T01:exon:16243;Parent=MsG0180005856.01.T01
Chr1 exon 96914793 96914989 96914793 ID=MsG0180005856.01.T01:exon:16244;Parent=MsG0180005856.01.T01
Chr1 exon 96915228 96915362 96915228 ID=MsG0180005856.01.T01:exon:16245;Parent=MsG0180005856.01.T01
Chr1 CDS 96914559 96914718 96914559 ID=MsG0180005856.01.T01:cds;Parent=MsG0180005856.01.T01
Chr1 CDS 96914793 96914989 96914793 ID=MsG0180005856.01.T01:cds;Parent=MsG0180005856.01.T01
Chr1 CDS 96915228 96915362 96915228 ID=MsG0180005856.01.T01:cds;Parent=MsG0180005856.01.T01
Gene Sequence

>MsG0180005856.01.T01

ATGGCAATTCCTTGCCCCCATTTCATCTCCTCCGCAAAAGCCGCCATGGAAGCCGGTCTCCTAATCCCTTCCTCCCCATCTTCCTCCGTCTCCGTCATCCTATCCCAAGACGATTTGAAGAAAATCGCCGCCTACAAAGCCGTCGAATACGTCGAATCCGGGAAAACTCAAGAACATCATCGGATACCCACTTCAACCATAACCCATGAACAAGCTGTGTCGCTTGGGATTCCTCTCTCCGATCTAGATTCTCACCCTGTTATTGATCTGGCTATTGATGGTGCTGATGAAGTTGATCCTTATCTGAATTTGGTCAAAGGTCGTGGTGGTTCACTTTTGAGAGAGAAAATGGTGAAGAGTATTGGTGATTTGAGGGTTGCAAGTGATGCTATTTTGAATATTGCTGGAGTTGTGGAGCATGGAATGTTTTTGGATATGGCCACTACTGTTATTGTTGCAGGTGAACTTGGATTAACGGTGAAGAATAAGTAG
Protein sequence

>MsG0180005856.01.T01

MAIPCPHFISSAKAAMEAGLLIPSSPSSSVSVILSQDDLKKIAAYKAVEYVESGKTQEHHRIPTSTITHEQAVSLGIPLSDLDSHPVIDLAIDGADEVDPYLNLVKGRGGSLLREKMVKSIGDLRVASDAILNIAGVVEHGMFLDMATTVIVAGELGLTVKNK*