AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0880042903.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880042903.01.T01 MTR_4g123470 82.677 127 16 1 7 133 105 225 6.62e-75 222
MsG0880042903.01.T01 MTR_7g113060 84.211 38 6 0 95 132 3 40 1.03e-16 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCCTATCGTTGGATA+TGG 0.258835 8:-15709609 MsG0880042903.01.T01:CDS
CCAAATGTGATGTTCGAAAA+AGG 0.275905 8:-15709364 MsG0880042903.01.T01:CDS
AATCGTGATGTTTCACTCTA+AGG 0.341127 8:+15709455 None:intergenic
TTCGAACATCACATTTGGTA+TGG 0.409212 8:+15709369 None:intergenic
ACCTTTGAAGTTCCTATCGT+TGG 0.439777 8:-15709615 MsG0880042903.01.T01:CDS
TGCCGCACTCATGGAATGAT+AGG 0.462626 8:+15709653 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 8:-15709329 MsG0880042903.01.T01:CDS
TCGAACATCACATTTGGTAT+GGG 0.469875 8:+15709370 None:intergenic
GTCATGTGTTTATCAACGCT+TGG 0.483566 8:+15709246 None:intergenic
ACATGATGCTGCCGCACTCA+TGG 0.492689 8:+15709644 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 8:-15709328 MsG0880042903.01.T01:CDS
ACAGGAATTATATTGTCATA+AGG 0.502590 8:+15709415 None:intergenic
GAATGATAGGGTGGATATGA+AGG 0.532152 8:+15709666 None:intergenic
CGAACATCACATTTGGTATG+GGG 0.552019 8:+15709371 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 8:+15709397 None:intergenic
TTTCAAGTGCAAATGCGTCA+TGG 0.564910 8:-15709290 MsG0880042903.01.T01:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 8:+15709321 None:intergenic
CACGATTACGTCATGTTGTG+CGG 0.590860 8:-15709439 MsG0880042903.01.T01:CDS
TCCAACGATAGGAACTTCAA+AGG 0.611311 8:+15709614 None:intergenic
GCCGCACTCATGGAATGATA+GGG 0.629158 8:+15709654 None:intergenic
GTCGATCCATATCCAACGAT+AGG 0.629633 8:+15709603 None:intergenic
ACCCTATCATTCCATGAGTG+CGG 0.640367 8:-15709655 MsG0880042903.01.T01:CDS
GCACTCATGGAATGATAGGG+TGG 0.649652 8:+15709657 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 8:-15709589 MsG0880042903.01.T01:intron
GCTGCCAATGGTATTGAGGG+CGG 0.739556 8:-15709325 MsG0880042903.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAACAATAAACAACCTT+CGG + Chr8:15709411-15709430 None:intergenic 20.0%
!!! TGTCATTAACAGTTTTTTTT+AGG - Chr8:15709478-15709497 MsG0880042903.01.T01:CDS 20.0%
! ACAGGAATTATATTGTCATA+AGG + Chr8:15709569-15709588 None:intergenic 25.0%
AGGAATTTGCCAAAAATATC+AGG + Chr8:15709509-15709528 None:intergenic 30.0%
! TAGGAACTACCTGATATTTT+TGG - Chr8:15709497-15709516 MsG0880042903.01.T01:intron 30.0%
AAGGTGAGAAAAACACAAGA+AGG + Chr8:15709299-15709318 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG + Chr8:15709529-15709548 None:intergenic 35.0%
AGGTGAGAAAAACACAAGAA+GGG + Chr8:15709298-15709317 None:intergenic 35.0%
ATGTGATGTTCGAAAAAGGT+TGG - Chr8:15709621-15709640 MsG0880042903.01.T01:CDS 35.0%
CCAAATGTGATGTTCGAAAA+AGG - Chr8:15709617-15709636 MsG0880042903.01.T01:CDS 35.0%
TCGAACATCACATTTGGTAT+GGG + Chr8:15709614-15709633 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + Chr8:15709587-15709606 None:intergenic 35.0%
TTCGAACATCACATTTGGTA+TGG + Chr8:15709615-15709634 None:intergenic 35.0%
!!! CCTTTTTCGAACATCACATT+TGG + Chr8:15709620-15709639 None:intergenic 35.0%
CGAACATCACATTTGGTATG+GGG + Chr8:15709613-15709632 None:intergenic 40.0%
GAAGTTCCTATCGTTGGATA+TGG - Chr8:15709372-15709391 MsG0880042903.01.T01:CDS 40.0%
GAATGATAGGGTGGATATGA+AGG + Chr8:15709318-15709337 None:intergenic 40.0%
GGTGAGAAAAACACAAGAAG+GGG + Chr8:15709297-15709316 None:intergenic 40.0%
GTGAGAAAAACACAAGAAGG+GGG + Chr8:15709296-15709315 None:intergenic 40.0%
TCCAACGATAGGAACTTCAA+AGG + Chr8:15709370-15709389 None:intergenic 40.0%
TGAGAAAAACACAAGAAGGG+GGG + Chr8:15709295-15709314 None:intergenic 40.0%
! TTTCAAGTGCAAATGCGTCA+TGG - Chr8:15709691-15709710 MsG0880042903.01.T01:CDS 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG - Chr8:15709366-15709385 MsG0880042903.01.T01:CDS 40.0%
ACCCTATCATTCCATGAGTG+CGG - Chr8:15709326-15709345 MsG0880042903.01.T01:CDS 45.0%
CACGATTACGTCATGTTGTG+CGG - Chr8:15709542-15709561 MsG0880042903.01.T01:intron 45.0%
GTCGATCCATATCCAACGAT+AGG + Chr8:15709381-15709400 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG - Chr8:15709652-15709671 MsG0880042903.01.T01:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - Chr8:15709644-15709663 MsG0880042903.01.T01:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - Chr8:15709653-15709672 MsG0880042903.01.T01:CDS 45.0%
GCACTCATGGAATGATAGGG+TGG + Chr8:15709327-15709346 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + Chr8:15709330-15709349 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + Chr8:15709331-15709350 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - Chr8:15709392-15709411 MsG0880042903.01.T01:CDS 50.0%
ACATGATGCTGCCGCACTCA+TGG + Chr8:15709340-15709359 None:intergenic 55.0%
GTCTCCGCCCTCAATACCAT+TGG + Chr8:15709663-15709682 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - Chr8:15709656-15709675 MsG0880042903.01.T01:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr8 gene 15709258 15709745 15709258 ID=MsG0880042903.01;Name=MsG0880042903.01
Chr8 mRNA 15709258 15709745 15709258 ID=MsG0880042903.01.T01;Parent=MsG0880042903.01;Name=MsG0880042903.01.T01;_AED=0.47;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|133
Chr8 exon 15709590 15709745 15709590 ID=MsG0880042903.01.T01:exon:1068;Parent=MsG0880042903.01.T01
Chr8 exon 15709258 15709503 15709258 ID=MsG0880042903.01.T01:exon:1067;Parent=MsG0880042903.01.T01
Chr8 CDS 15709590 15709745 15709590 ID=MsG0880042903.01.T01:cds;Parent=MsG0880042903.01.T01
Chr8 CDS 15709258 15709503 15709258 ID=MsG0880042903.01.T01:cds;Parent=MsG0880042903.01.T01
Gene Sequence

>MsG0880042903.01.T01

GAGAAACGAAGAATTTTTCTAAAACACAATTCAACCCCCCTTCTTGTGTTTTTCTCACCTTCATATCCACCCTATCATTCCATGAGTGCGGCAGCATCATGTTATTGTACCTTTGAAGTTCCTATCGTTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATATTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATAATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGAAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAATGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>MsG0880042903.01.T01

EKRRIFLKHNSTPLLVFFSPSYPPYHSMSAAASCYCTFEVPIVGYGSTKSPKELPDIFGKFLRVKHHDYVMLCGPYDNIIPVRLKYTDDPIPNVMFEKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*