AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280006491.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006491.01.T01 MTR_8g102020 83.000 100 5 1 21 108 103 202 1.21e-36 124
MsG0280006491.01.T01 MTR_6g090515 62.245 98 24 1 24 108 120 217 1.93e-19 80.1
MsG0280006491.01.T01 MTR_8g102030 63.265 98 21 3 24 108 124 219 3.97e-15 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006491.01.T01 AT2G19830 52.041 98 28 3 24 108 100 191 8.04e-21 82.8
MsG0280006491.01.T01 AT2G19830 52.041 98 28 3 24 108 119 210 8.38e-21 83.2
MsG0280006491.01.T01 AT4G29160 52.525 99 33 3 24 108 91 189 6.40e-14 65.1
MsG0280006491.01.T01 AT4G29160 52.525 99 33 3 24 108 118 216 1.00e-13 64.7
MsG0280006491.01.T01 AT4G29160 52.525 99 33 3 24 108 118 216 1.00e-13 64.7

Find 38 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGTATGTTGCTGCCCAGC+TGG 0.279006 2:+2699526 None:intergenic
TGCCCAGCTGGGACATGAAC+CGG 0.324395 2:+2699538 None:intergenic
AATTCATCTTCCTCAGTTGT+TGG 0.363178 2:+2699487 None:intergenic
GGGACATGAACCGGGGCTGC+TGG 0.381712 2:+2699547 None:intergenic
AACAACTGAGGAAGATGAAT+TGG 0.385587 2:-2699485 MsG0280006491.01.T01:CDS
AGATGAATTGGCAAAGTTGC+AGG 0.389941 2:-2699473 MsG0280006491.01.T01:CDS
GCCCCGGTTCATGTCCCAGC+TGG 0.396844 2:-2699541 MsG0280006491.01.T01:CDS
GCCCAGCTGGGACATGAACC+GGG 0.405036 2:+2699539 None:intergenic
AGAAAAGATGAGTCAGGTTC+AGG 0.445663 2:-2699893 MsG0280006491.01.T01:CDS
GCTGCTGGAGTTGTAATTGT+AGG 0.455721 2:+2699562 None:intergenic
AGAGCTAGAGGGTGCTGAGT+TGG 0.470621 2:-2699602 MsG0280006491.01.T01:CDS
GGGTATGTTGCTGCCCAGCT+GGG 0.476183 2:+2699527 None:intergenic
GAGTGGTTGTTAACAACCGC+TGG 0.493918 2:+2700192 None:intergenic
CCCCGGTTCATGTCCCAGCT+GGG 0.508373 2:-2699540 MsG0280006491.01.T01:CDS
ACAGACAGAAAAGATGAGTC+AGG 0.510656 2:-2699899 MsG0280006491.01.T01:CDS
CGCCGGCAGTTAACTGCCGC+TGG 0.511992 2:-2700162 MsG0280006491.01.T01:CDS
GAAGCATTGTCAGCTCCAAT+TGG 0.513583 2:-2699871 MsG0280006491.01.T01:intron
TGATGATGTTGACAATATCA+TGG 0.524912 2:-2699935 MsG0280006491.01.T01:CDS
TGCCAGCGGCAGTTAACTGC+CGG 0.532657 2:+2700160 None:intergenic
TTGGCAAAGTTGCAGGCTGA+TGG 0.552083 2:-2699466 MsG0280006491.01.T01:CDS
CAAAGTTGCAGGCTGATGGA+AGG 0.552405 2:-2699462 MsG0280006491.01.T01:CDS
AATTACAACTCCAGCAGCCC+CGG 0.560878 2:-2699557 MsG0280006491.01.T01:CDS
GTTGTTGGTTTCACAGACAC+AGG 0.568504 2:+2699502 None:intergenic
AGCAGAACTTGAAGAGCTAG+AGG 0.569985 2:-2699614 MsG0280006491.01.T01:intron
AGTGGTTGTTAACAACCGCT+GGG 0.577164 2:+2700193 None:intergenic
CCCAGCTGGGACATGAACCG+GGG 0.594040 2:+2699540 None:intergenic
ACAACCACTCTGCAAATCGC+CGG 0.620346 2:-2700179 MsG0280006491.01.T01:CDS
AAAGTTGCAGGCTGATGGAA+GGG 0.626638 2:-2699461 MsG0280006491.01.T01:CDS
ACTGCCGGCGATTTGCAGAG+TGG 0.631031 2:+2700175 None:intergenic
TTGTTGGTTTCACAGACACA+GGG 0.635809 2:+2699503 None:intergenic
TTGGTTTCACAGACACAGGG+TGG 0.644268 2:+2699506 None:intergenic
GCAGAACTTGAAGAGCTAGA+GGG 0.656486 2:-2699613 MsG0280006491.01.T01:intron
TGGTTTCACAGACACAGGGT+GGG 0.666058 2:+2699507 None:intergenic
TAACTACCGCTGAGTGCCAG+CGG 0.669862 2:+2700146 None:intergenic
GTGGTTGTTAACAACCGCTG+GGG 0.674257 2:+2700194 None:intergenic
TGGTTGTTAACAACCGCTGG+GGG 0.692202 2:+2700195 None:intergenic
TAACTGCCGCTGGCACTCAG+CGG 0.705631 2:-2700152 MsG0280006491.01.T01:intron
GTCTGTGAAACCAACAACTG+AGG 0.717230 2:-2699497 MsG0280006491.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTGAATTTATTTTTTATTTC+AGG - Chr2:2699999-2700018 MsG0280006491.01.T01:intron 15.0%
!!! ATTTTTTATTTCAGGATGAT+TGG - Chr2:2700007-2700026 MsG0280006491.01.T01:intron 20.0%
! AATAAATTCAGTATGTTGCT+TGG + Chr2:2699990-2700009 None:intergenic 25.0%
!! ATAAATTCAGTATGTTGCTT+GGG + Chr2:2699989-2700008 None:intergenic 25.0%
TTCATGTTCTTGCTCTTAAT+CGG - Chr2:2699664-2699683 MsG0280006491.01.T01:intron 30.0%
TTTATTACTCTATGCTGAAG+AGG - Chr2:2699847-2699866 MsG0280006491.01.T01:intron 30.0%
! TGATGATGTTGACAATATCA+TGG - Chr2:2699710-2699729 MsG0280006491.01.T01:intron 30.0%
AAATGAATTGGCAAAGTTGC+AGG + Chr2:2699580-2699599 None:intergenic 35.0%
AACAACTGAGGAAGATGAAT+TGG - Chr2:2700160-2700179 MsG0280006491.01.T01:CDS 35.0%
AATTCATCTTCCTCAGTTGT+TGG + Chr2:2700161-2700180 None:intergenic 35.0%
AGTTAACTACCGGTGAAAAA+TGG - Chr2:2699517-2699536 MsG0280006491.01.T01:CDS 35.0%
!!! ACAGAAAAGCCATTTTTCAC+CGG + Chr2:2699529-2699548 None:intergenic 35.0%
ACAGACAGAAAAGATGAGTC+AGG - Chr2:2699746-2699765 MsG0280006491.01.T01:intron 40.0%
AGAAAAGATGAGTCAGGTTC+AGG - Chr2:2699752-2699771 MsG0280006491.01.T01:intron 40.0%
AGATGAATTGGCAAAGTTGC+AGG - Chr2:2700172-2700191 MsG0280006491.01.T01:CDS 40.0%
CCAACACTGAGGAAATGAAT+TGG + Chr2:2699592-2699611 None:intergenic 40.0%
CCAATTCATTTCCTCAGTGT+TGG - Chr2:2699589-2699608 MsG0280006491.01.T01:CDS 40.0%
GAAGACAACCTCATCATAGT+CGG + Chr2:2699805-2699824 None:intergenic 40.0%
!! TTGTTGGTTTCACAGACACA+GGG + Chr2:2700145-2700164 None:intergenic 40.0%
AAAGTTGCAGGCTGATGGAA+GGG - Chr2:2700184-2700203 MsG0280006491.01.T01:CDS 45.0%
AAAGTTGCAGGCTGATGGAA+GGG + Chr2:2700203-2700184 None:intergenic 45.0%
ACTCAGCGGTAGTTAACTAC+CGG - Chr2:2699507-2699526 MsG0280006491.01.T01:CDS 45.0%
AGCAGAACTTGAAGAGCTAG+AGG - Chr2:2700031-2700050 MsG0280006491.01.T01:intron 45.0%
AGTGGTTGTTAACAACCGCT+GGG + Chr2:2699455-2699474 None:intergenic 45.0%
GCAGAACTTGAAGAGCTAGA+GGG - Chr2:2700032-2700051 MsG0280006491.01.T01:intron 45.0%
GCTGCTGGAGTTGTAATTGT+AGG + Chr2:2700086-2700105 None:intergenic 45.0%
GTCTGTGAAACCAACAACTG+AGG - Chr2:2700148-2700167 MsG0280006491.01.T01:intron 45.0%
TGTCTGTGAAACCAACACTG+AGG + Chr2:2699603-2699622 None:intergenic 45.0%
!! AGTGTTGGTTTCACAGACAC+AGG - Chr2:2699604-2699623 MsG0280006491.01.T01:CDS 45.0%
!! GAAGCATTGTCAGCTCCAAT+TGG - Chr2:2699774-2699793 MsG0280006491.01.T01:intron 45.0%
!! GTTGTTGGTTTCACAGACAC+AGG + Chr2:2700146-2700165 None:intergenic 45.0%
AATTACAACTCCAGCAGCCC+CGG - Chr2:2700088-2700107 MsG0280006491.01.T01:intron 50.0%
ACAACCACTCTGCAAATCGC+CGG - Chr2:2699466-2699485 MsG0280006491.01.T01:CDS 50.0%
CAAAGTTGCAGGCTGATGGA+AGG - Chr2:2700183-2700202 MsG0280006491.01.T01:CDS 50.0%
CAAAGTTGCAGGCTGATGGA+AGG + Chr2:2700202-2700183 None:intergenic 50.0%
GAGTGGTTGTTAACAACCGC+TGG + Chr2:2699456-2699475 None:intergenic 50.0%
GTGGTTGTTAACAACCGCTG+GGG + Chr2:2699454-2699473 None:intergenic 50.0%
TCATAGTCGGCTGCACCAAT+TGG + Chr2:2699792-2699811 None:intergenic 50.0%
TGGTTGTTAACAACCGCTGG+GGG + Chr2:2699453-2699472 None:intergenic 50.0%
TGGTTTCACAGACACAGGGT+GGG + Chr2:2700141-2700160 None:intergenic 50.0%
TTGGCAAAGTTGCAGGCTGA+TGG - Chr2:2700179-2700198 MsG0280006491.01.T01:CDS 50.0%
TTGGCAAAGTTGCAGGCTGA+TGG + Chr2:2700198-2700179 None:intergenic 50.0%
TTGGTTTCACAGACACAGGG+TGG + Chr2:2700142-2700161 None:intergenic 50.0%
TAACTACCGCTGAGTGCCAG+CGG + Chr2:2699502-2699521 None:intergenic 55.0%
TGGTGCAGCCGACTATGATG+AGG - Chr2:2699794-2699813 MsG0280006491.01.T01:intron 55.0%
!! AGAGCTAGAGGGTGCTGAGT+TGG - Chr2:2700043-2700062 MsG0280006491.01.T01:intron 55.0%
ACTGCCGGCGATTTGCAGAG+TGG + Chr2:2699473-2699492 None:intergenic 60.0%
GGGTATGTTGCTGCCCAGCT+GGG + Chr2:2700121-2700140 None:intergenic 60.0%
TAACTGCCGCTGGCACTCAG+CGG - Chr2:2699493-2699512 MsG0280006491.01.T01:CDS 60.0%
TGCCAGCGGCAGTTAACTGC+CGG + Chr2:2699488-2699507 None:intergenic 60.0%
TGCCCAGCTGGGACATGAAC+CGG + Chr2:2700110-2700129 None:intergenic 60.0%
TGGGTATGTTGCTGCCCAGC+TGG + Chr2:2700122-2700141 None:intergenic 60.0%
CCCAGCTGGGACATGAACCG+GGG + Chr2:2700108-2700127 None:intergenic 65.0%
CCCCGGTTCATGTCCCAGCT+GGG - Chr2:2700105-2700124 MsG0280006491.01.T01:intron 65.0%
GCCCAGCTGGGACATGAACC+GGG + Chr2:2700109-2700128 None:intergenic 65.0%
CGCCGGCAGTTAACTGCCGC+TGG - Chr2:2699483-2699502 MsG0280006491.01.T01:CDS 70.0%
GCCCCGGTTCATGTCCCAGC+TGG - Chr2:2700104-2700123 MsG0280006491.01.T01:intron 70.0%
GGGACATGAACCGGGGCTGC+TGG + Chr2:2700101-2700120 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr2 gene 2699447 2700220 2699447 ID=MsG0280006491.01;Name=MsG0280006491.01
Chr2 mRNA 2699447 2700220 2699447 ID=MsG0280006491.01.T01;Parent=MsG0280006491.01;Name=MsG0280006491.01.T01;_AED=0.21;_eAED=0.21;_QI=0|0|0|0.66|1|1|3|0|114
Chr2 exon 2700153 2700220 2700153 ID=MsG0280006491.01.T01:exon:1491;Parent=MsG0280006491.01.T01
Chr2 exon 2699872 2699963 2699872 ID=MsG0280006491.01.T01:exon:1490;Parent=MsG0280006491.01.T01
Chr2 exon 2699447 2699631 2699447 ID=MsG0280006491.01.T01:exon:1489;Parent=MsG0280006491.01.T01
Chr2 CDS 2700153 2700220 2700153 ID=MsG0280006491.01.T01:cds;Parent=MsG0280006491.01.T01
Chr2 CDS 2699872 2699963 2699872 ID=MsG0280006491.01.T01:cds;Parent=MsG0280006491.01.T01
Chr2 CDS 2699447 2699631 2699447 ID=MsG0280006491.01.T01:cds;Parent=MsG0280006491.01.T01
Gene Sequence

>MsG0280006491.01.T01

ATGCCCCCAGCGGTTGTTAACAACCACTCTGCAAATCGCCGGCAGTTAACTGCCGCTGGCACTCAGCGCAATCTTGATGATGTTGACAATATCATGGATGAGATCACTGAACAGACAGAAAAGATGAGTCAGGTTCAGGAAGCATTGTCAGCTCCAATTGAACTTGAAGAGCTAGAGGGTGCTGAGTTGGAAGAACAGCTTCTTCAACCTACAATTACAACTCCAGCAGCCCCGGTTCATGTCCCAGCTGGGCAGCAACATACCCACCCTGTGTCTGTGAAACCAACAACTGAGGAAGATGAATTGGCAAAGTTGCAGGCTGATGGAAGGGATGAGAGAGAATAG

Protein sequence

>MsG0280006491.01.T01

MPPAVVNNHSANRRQLTAAGTQRNLDDVDNIMDEITEQTEKMSQVQEALSAPIELEELEGAELEEQLLQPTITTPAAPVHVPAGQQHTHPVSVKPTTEEDELAKLQADGRDERE*