AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062999

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 51 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTAACTCTGTACTTGAATT+TGG 0.163739 4.2:-35273950 None:intergenic
TTGTTGCAGTTGTCTGATTT+TGG 0.183983 4.2:+35273095 MS.gene062999:intron
GTTATTACCTGATTAAATTT+AGG 0.189769 4.2:-35273652 None:intergenic
CAGATACTGAAGATCCTAAA+AGG 0.238779 4.2:+35273857 MS.gene062999:intron
CACTTAACTCTTGCATTACT+TGG 0.261108 4.2:+35273971 MS.gene062999:CDS
TTTCCATACATGAAGTATTC+AGG 0.263993 4.2:-35273194 None:intergenic
CCAATAATAGAGAGTGGTTT+TGG 0.270194 4.2:+35273591 MS.gene062999:intron
TACATCTTCTTGTGTCAAAA+AGG 0.287552 4.2:-35273147 None:intergenic
CGCAATACTTTAACTGCAAT+TGG 0.301742 4.2:-35272443 None:intergenic
TTCATTGCAGAAAATTTGAT+TGG 0.351745 4.2:+35272371 None:intergenic
ACTTCGTCCTAAATTTAATC+AGG 0.372511 4.2:+35273645 MS.gene062999:CDS
TTTCCCTAAAGGAAGCTTAG+AGG 0.382841 4.2:+35272595 MS.gene062999:CDS
TTTCCTCTAAGCTTCCTTTA+GGG 0.385756 4.2:-35272598 None:intergenic
TCCATCAGGGAGAATTCCTT+TGG 0.389177 4.2:-35272417 None:intergenic
GAAGATGTAGTAGGAACATT+TGG 0.393986 4.2:+35273161 MS.gene062999:CDS
GACGAGAGAGCTTGGTAGCT+TGG 0.396181 4.2:+35273309 MS.gene062999:CDS
GTACTACTTGAACTACTATC+AGG 0.424843 4.2:+35273254 MS.gene062999:CDS
TTGACACAAGAAGATGTAGT+AGG 0.432844 4.2:+35273152 MS.gene062999:CDS
GTGAGATTTAATGTAGCTGT+TGG 0.445725 4.2:+35272764 MS.gene062999:intron
CTTCTGTGTGTAGGTAATCA+AGG 0.446565 4.2:-35272799 None:intergenic
ACGAGAGAGCTTGGTAGCTT+GGG 0.455773 4.2:+35273310 MS.gene062999:CDS
TACTTGTGGCTCAAGCTCCT+TGG 0.457589 4.2:-35272873 None:intergenic
GCAGAAAATTTGATTGGGAA+AGG 0.464633 4.2:+35272377 None:intergenic
TTCAAACATTCTTCTTTCCA+AGG 0.467525 4.2:+35272856 MS.gene062999:CDS
TTGCAAGGTTCAGAGCTGAT+TGG 0.473617 4.2:-35273284 None:intergenic
TCATTGCAGAAAATTTGATT+GGG 0.474912 4.2:+35272372 None:intergenic
GCTCCTGAATACTTCATGTA+TGG 0.476094 4.2:+35273191 MS.gene062999:CDS
GTTTATGAGTATTTCCCTAA+AGG 0.477708 4.2:+35272584 MS.gene062999:CDS
AAGATAGATGTCTATGCCTT+TGG 0.486190 4.2:+35273227 MS.gene062999:CDS
CAGCATCTTTATGCATCGCA+CGG 0.490450 4.2:+35273614 MS.gene062999:CDS
AAAGTATTGCGATCATCAAA+AGG 0.500424 4.2:+35272455 MS.gene062999:CDS
GAAAATTTGATTGGGAAAGG+AGG 0.507785 4.2:+35272380 None:intergenic
GTGAGAATTTGAAAGATCAA+TGG 0.511673 4.2:+35274041 MS.gene062999:CDS
TTGCAAAGGACGAGAGAGCT+TGG 0.538082 4.2:+35273301 MS.gene062999:CDS
AGATACTGAAGATCCTAAAA+GGG 0.539548 4.2:+35273858 MS.gene062999:intron
ATTTGAAAGATCAATGGAGC+AGG 0.542261 4.2:+35274047 MS.gene062999:CDS
AAGCTCTCTCGTCCTTTGCA+AGG 0.545203 4.2:-35273299 None:intergenic
TCCAAAGGAATTCTCCCTGA+TGG 0.547063 4.2:+35272416 MS.gene062999:CDS
ACTTGAACTACTATCAGGTA+GGG 0.558129 4.2:+35273259 MS.gene062999:CDS
TGATATTATTTCCATCTCAA+AGG 0.559194 4.2:-35272495 None:intergenic
TGCGATCATCAAAAGGAGCA+TGG 0.559245 4.2:+35272462 MS.gene062999:CDS
GGAGAATTCCTTTGGACACA+CGG 0.560372 4.2:-35272409 None:intergenic
AGCATCTTTATGCATCGCAC+GGG 0.581862 4.2:+35273615 MS.gene062999:CDS
GGAAGCAACCGTGTGTCCAA+AGG 0.584769 4.2:+35272401 MS.gene062999:CDS
TTCTGTGTGTAGGTAATCAA+GGG 0.590326 4.2:-35272798 None:intergenic
GCTTCGAAGCTTCTGTGTGT+AGG 0.594575 4.2:-35272808 None:intergenic
ATCAGCTCTGAACCTTGCAA+AGG 0.618686 4.2:+35273287 MS.gene062999:CDS
TTCAAGTAGTACTACACCAA+AGG 0.624918 4.2:-35273243 None:intergenic
TACTTGAACTACTATCAGGT+AGG 0.626862 4.2:+35273258 MS.gene062999:CDS
TGTAGCTGTTGGAGTAGCTG+AGG 0.632490 4.2:+35272775 MS.gene062999:CDS
AGCTTAGAGGAAAATCTACA+TGG 0.638566 4.2:+35272608 MS.gene062999:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGTTTTCAAAATATATAAT+TGG - chr4.2:35273807-35273826 None:intergenic 10.0%
!! TCATATAAATTTCCTTTAAA+CGG + chr4.2:35272671-35272690 MS.gene062999:intron 15.0%
!! TTTAAAGGAAATTTATATGA+TGG - chr4.2:35272671-35272690 None:intergenic 15.0%
!! AAATTTATATGATGGTTGAA+AGG - chr4.2:35272663-35272682 None:intergenic 20.0%
!! AATCATTTCTCTTTACAAAA+TGG - chr4.2:35272933-35272952 None:intergenic 20.0%
!! AGCTTATATGAATCTATAAA+TGG + chr4.2:35272700-35272719 MS.gene062999:intron 20.0%
!! GTTATTACCTGATTAAATTT+AGG - chr4.2:35273655-35273674 None:intergenic 20.0%
!! TCAAAAAATTTGATTACTTG+TGG - chr4.2:35272890-35272909 None:intergenic 20.0%
!!! AATTTGTTCTAATTGAAGTT+AGG - chr4.2:35273341-35273360 None:intergenic 20.0%
!!! TGAAAAATGATTTCATTTTC+AGG + chr4.2:35273563-35273582 MS.gene062999:intron 20.0%
!!! TTGTAAAGAGAAATGATTTT+TGG + chr4.2:35272935-35272954 MS.gene062999:intron 20.0%
! AAAAACATTACTCAACTACT+TGG + chr4.2:35272530-35272549 MS.gene062999:CDS 25.0%
! AAATTGTGATTTCAACTATC+GGG + chr4.2:35273480-35273499 MS.gene062999:intron 25.0%
! AACTAAATCAGATATTGAAC+AGG + chr4.2:35273406-35273425 MS.gene062999:intron 25.0%
! AGTTGTAAGATGTCTAAATT+TGG - chr4.2:35272965-35272984 None:intergenic 25.0%
! ATGAATCTATAAATGGATGT+AGG + chr4.2:35272707-35272726 MS.gene062999:intron 25.0%
! CAATAATTTAATTGCAGTGA+TGG + chr4.2:35273693-35273712 MS.gene062999:intron 25.0%
! CATCACTGCAATTAAATTAT+TGG - chr4.2:35273695-35273714 None:intergenic 25.0%
! GAAATTGTGATTTCAACTAT+CGG + chr4.2:35273479-35273498 MS.gene062999:intron 25.0%
! TGATATTATTTCCATCTCAA+AGG - chr4.2:35272498-35272517 None:intergenic 25.0%
AAAGTTGTCGAGACTAAATT+TGG + chr4.2:35272990-35273009 MS.gene062999:intron 30.0%
ACTTCGTCCTAAATTTAATC+AGG + chr4.2:35273645-35273664 MS.gene062999:CDS 30.0%
AGATACTGAAGATCCTAAAA+GGG + chr4.2:35273858-35273877 MS.gene062999:intron 30.0%
GTGAGAATTTGAAAGATCAA+TGG + chr4.2:35274041-35274060 MS.gene062999:CDS 30.0%
GTTTATGAGTATTTCCCTAA+AGG + chr4.2:35272584-35272603 MS.gene062999:CDS 30.0%
TAAACAATTGAATCGTGACT+CGG - chr4.2:35273440-35273459 None:intergenic 30.0%
TACATCTTCTTGTGTCAAAA+AGG - chr4.2:35273150-35273169 None:intergenic 30.0%
TGTAACTCTGTACTTGAATT+TGG - chr4.2:35273953-35273972 None:intergenic 30.0%
TTCAAACATTCTTCTTTCCA+AGG + chr4.2:35272856-35272875 MS.gene062999:CDS 30.0%
! TGATTTTGGACTTGCAATAT+GGG + chr4.2:35273109-35273128 MS.gene062999:CDS 30.0%
! TTTCCATACATGAAGTATTC+AGG - chr4.2:35273197-35273216 None:intergenic 30.0%
!! AAAGTATTGCGATCATCAAA+AGG + chr4.2:35272455-35272474 MS.gene062999:CDS 30.0%
AAGATAGATGTCTATGCCTT+TGG + chr4.2:35273227-35273246 MS.gene062999:CDS 35.0%
AATGGATGTAGGAAAGAACA+AGG + chr4.2:35272718-35272737 MS.gene062999:intron 35.0%
ACTTGAACTACTATCAGGTA+GGG + chr4.2:35273259-35273278 MS.gene062999:CDS 35.0%
AGCTTAGAGGAAAATCTACA+TGG + chr4.2:35272608-35272627 MS.gene062999:CDS 35.0%
ATCAGACAACTGCAACAAAA+AGG - chr4.2:35273093-35273112 None:intergenic 35.0%
ATTTGAAAGATCAATGGAGC+AGG + chr4.2:35274047-35274066 MS.gene062999:CDS 35.0%
CACTTAACTCTTGCATTACT+TGG + chr4.2:35273971-35273990 MS.gene062999:CDS 35.0%
CAGATACTGAAGATCCTAAA+AGG + chr4.2:35273857-35273876 MS.gene062999:intron 35.0%
CCAAAACCACTCTCTATTAT+TGG - chr4.2:35273594-35273613 None:intergenic 35.0%
CGCAATACTTTAACTGCAAT+TGG - chr4.2:35272446-35272465 None:intergenic 35.0%
GAAGATGTAGTAGGAACATT+TGG + chr4.2:35273161-35273180 MS.gene062999:CDS 35.0%
GATCTTCAGTATCTGTACAT+AGG - chr4.2:35273852-35273871 None:intergenic 35.0%
GCAAAACCAATAATAGAGAG+TGG + chr4.2:35273585-35273604 MS.gene062999:intron 35.0%
GTACTACTTGAACTACTATC+AGG + chr4.2:35273254-35273273 MS.gene062999:CDS 35.0%
GTCAAAAAGGATGTTGTTGT+TGG - chr4.2:35273137-35273156 None:intergenic 35.0%
GTGAGATTTAATGTAGCTGT+TGG + chr4.2:35272764-35272783 MS.gene062999:intron 35.0%
TAAGCTTTGCTTCCGTTTAA+AGG - chr4.2:35272686-35272705 None:intergenic 35.0%
TACTTGAACTACTATCAGGT+AGG + chr4.2:35273258-35273277 MS.gene062999:CDS 35.0%
TTCAAGTAGTACTACACCAA+AGG - chr4.2:35273246-35273265 None:intergenic 35.0%
TTCTGTGTGTAGGTAATCAA+GGG - chr4.2:35272801-35272820 None:intergenic 35.0%
TTGACACAAGAAGATGTAGT+AGG + chr4.2:35273152-35273171 MS.gene062999:CDS 35.0%
TTTCCTCTAAGCTTCCTTTA+GGG - chr4.2:35272601-35272620 None:intergenic 35.0%
! CCAATAATAGAGAGTGGTTT+TGG + chr4.2:35273591-35273610 MS.gene062999:intron 35.0%
! CTGATTTTGGACTTGCAATA+TGG + chr4.2:35273108-35273127 MS.gene062999:CDS 35.0%
! GATTTTGGACTTGCAATATG+GGG + chr4.2:35273110-35273129 MS.gene062999:CDS 35.0%
! TTGTTGCAGTTGTCTGATTT+TGG + chr4.2:35273095-35273114 MS.gene062999:intron 35.0%
! TTTTCCTCTAAGCTTCCTTT+AGG - chr4.2:35272602-35272621 None:intergenic 35.0%
!! GAAAGATTTTGCCTTTGAGA+TGG + chr4.2:35272484-35272503 MS.gene062999:CDS 35.0%
CTTCTGTGTGTAGGTAATCA+AGG - chr4.2:35272802-35272821 None:intergenic 40.0%
GATGTAGGAAAGAACAAGGA+TGG + chr4.2:35272722-35272741 MS.gene062999:intron 40.0%
GCTCCTGAATACTTCATGTA+TGG + chr4.2:35273191-35273210 MS.gene062999:CDS 40.0%
TTTCCCTAAAGGAAGCTTAG+AGG + chr4.2:35272595-35272614 MS.gene062999:CDS 40.0%
! CATCGTCATTGTTCCCTTTT+AGG - chr4.2:35273874-35273893 None:intergenic 40.0%
!!! ACTGCAATTGGTTTTCCATC+AGG - chr4.2:35272434-35272453 None:intergenic 40.0%
!!! CTGCAATTGGTTTTCCATCA+GGG - chr4.2:35272433-35272452 None:intergenic 40.0%
AGCATCTTTATGCATCGCAC+GGG + chr4.2:35273615-35273634 MS.gene062999:CDS 45.0%
CAGCATCTTTATGCATCGCA+CGG + chr4.2:35273614-35273633 MS.gene062999:CDS 45.0%
GGAGAATTCCTTTGGACACA+CGG - chr4.2:35272412-35272431 None:intergenic 45.0%
TCCAAAGGAATTCTCCCTGA+TGG + chr4.2:35272416-35272435 MS.gene062999:CDS 45.0%
TCCATCAGGGAGAATTCCTT+TGG - chr4.2:35272420-35272439 None:intergenic 45.0%
TGCGATCATCAAAAGGAGCA+TGG + chr4.2:35272462-35272481 MS.gene062999:CDS 45.0%
TTGCAAGGTTCAGAGCTGAT+TGG - chr4.2:35273287-35273306 None:intergenic 45.0%
!! ATCAGCTCTGAACCTTGCAA+AGG + chr4.2:35273287-35273306 MS.gene062999:CDS 45.0%
AAGCTCTCTCGTCCTTTGCA+AGG - chr4.2:35273302-35273321 None:intergenic 50.0%
GCTTCGAAGCTTCTGTGTGT+AGG - chr4.2:35272811-35272830 None:intergenic 50.0%
TACTTGTGGCTCAAGCTCCT+TGG - chr4.2:35272876-35272895 None:intergenic 50.0%
TGTAGCTGTTGGAGTAGCTG+AGG + chr4.2:35272775-35272794 MS.gene062999:CDS 50.0%
TTGCAAAGGACGAGAGAGCT+TGG + chr4.2:35273301-35273320 MS.gene062999:CDS 50.0%
! ACGAGAGAGCTTGGTAGCTT+GGG + chr4.2:35273310-35273329 MS.gene062999:CDS 50.0%
GGAAGCAACCGTGTGTCCAA+AGG + chr4.2:35272401-35272420 MS.gene062999:CDS 55.0%
! GACGAGAGAGCTTGGTAGCT+TGG + chr4.2:35273309-35273328 MS.gene062999:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 35272381 35274087 35272381 ID=MS.gene062999
chr4.2 mRNA 35272381 35274087 35272381 ID=MS.gene062999.t1;Parent=MS.gene062999
chr4.2 exon 35272381 35272629 35272381 ID=MS.gene062999.t1.exon1;Parent=MS.gene062999.t1
chr4.2 CDS 35272381 35272629 35272381 ID=cds.MS.gene062999.t1;Parent=MS.gene062999.t1
chr4.2 exon 35272765 35272892 35272765 ID=MS.gene062999.t1.exon2;Parent=MS.gene062999.t1
chr4.2 CDS 35272765 35272892 35272765 ID=cds.MS.gene062999.t1;Parent=MS.gene062999.t1
chr4.2 exon 35273104 35273331 35273104 ID=MS.gene062999.t1.exon3;Parent=MS.gene062999.t1
chr4.2 CDS 35273104 35273331 35273104 ID=cds.MS.gene062999.t1;Parent=MS.gene062999.t1
chr4.2 exon 35273601 35273666 35273601 ID=MS.gene062999.t1.exon4;Parent=MS.gene062999.t1
chr4.2 CDS 35273601 35273666 35273601 ID=cds.MS.gene062999.t1;Parent=MS.gene062999.t1
chr4.2 exon 35273860 35274087 35273860 ID=MS.gene062999.t1.exon5;Parent=MS.gene062999.t1
chr4.2 CDS 35273860 35274087 35273860 ID=cds.MS.gene062999.t1;Parent=MS.gene062999.t1
Gene Sequence

>MS.gene062999

AAAATTTGATTGGGAAAGGAGGAAGCAACCGTGTGTCCAAAGGAATTCTCCCTGATGGAAAACCAATTGCAGTTAAAGTATTGCGATCATCAAAAGGAGCATGGAAAGATTTTGCCTTTGAGATGGAAATAATATCATCATTGAATCACAAAAACATTACTCAACTACTTGGAATTTGCATAGAGAACAATACTTTAATATCTGTTTATGAGTATTTCCCTAAAGGAAGCTTAGAGGAAAATCTACATGGTAAAAGTTTGAGTTCATTTTCTGTTTTCACCTTTCAACCATCATATAAATTTCCTTTAAACGGAAGCAAAGCTTATATGAATCTATAAATGGATGTAGGAAAGAACAAGGATGGATCTCTTTTGTCATGAGAAGTGAGATTTAATGTAGCTGTTGGAGTAGCTGAGGCCCTTGATTACCTACACACAGAAGCTTCGAAGCATGTCATACATAGAGATGTCAAGTCTTCAAACATTCTTCTTTCCAAGGAGCTTGAGCCACAAGTAATCAAATTTTTTGACATCGTTAACATTGAAATAACCATTTTGTAAAGAGAAATGATTTTTGGACAACCAAATTTAGACATCTTACAACTTTTTGAAAGTTGTCGAGACTAAATTTGGTTGATACGATTTTCAGTCAATCAAAGTAAAACATTATGTAGAAAATTGACTTTATCACTCATGAACGATAATTTTGTCCTTTTTGTTGCAGTTGTCTGATTTTGGACTTGCAATATGGGGACCAACAACAACATCCTTTTTGACACAAGAAGATGTAGTAGGAACATTTGGTTATCTTGCTCCTGAATACTTCATGTATGGAAAAGTTAGTGACAAGATAGATGTCTATGCCTTTGGTGTAGTACTACTTGAACTACTATCAGGTAGGGAACCAATCAGCTCTGAACCTTGCAAAGGACGAGAGAGCTTGGTAGCTTGGGTAAGACCTAACTTCAATTAGAACAAATTTTGACTAATATGAATTATATTTGACATAAACATCAATGTCTTAAAAACTAAATCAGATATTGAACAGGTAAAATCTCCGAGTCACGATTCAATTGTTTAAAATTGTTCGAACTAATATGAAATTGTGATTTCAACTATCGGGTTCGACTTTTGAAATATTGATAAATATGCTTTTATCGTAGAATATATAAAATTTGAATGATGAAAAATGATTTCATTTTCAGGCAAAACCAATAATAGAGAGTGGTTTTGGCAGCATCTTTATGCATCGCACGGGCTGCTAGACTTCGTCCTAAATTTAATCAGGTAATAACATTTTTTACACATGCATCCAATAATTTAATTGCAGTGATGGATATGTAAAACTTGCTTATGTAAATACTAATTAAATCTAATAATAAATGACAGTGAAGTTGTCAAATTCTCAATATGAAGTCACATTACCAATTATATATTTTGAAAACTTTCAGCTCTTAAAGTTTATCATTCCTATGTACAGATACTGAAGATCCTAAAAGGGAACAATGACGATGAATATTGCTTCAATGAGTATTCAGAAAATGAAGAAAACATTGATGATGAAGTATATCCAAATTCAAGTACAGAGTTACACTTAACTCTTGCATTACTTGGCGTTGATGATGACAGTACATCATGTAATAGTACAGACAACAACTATAGTGAGAATTTGAAAGATCAATGGAGCAGGTCTTTGCGTTTTAACTAG
Protein sequence

>MS.gene062999.t1

KIULGKEEATVCPKEFSLMENQLQLKYCDHQKEHGKILPLRWKUYHHUITKTLLNYLEFAURTILUYLFMSISLKEAURKIYMUDLMULLEULRPLITYTQKLRSMSYIEMSSLQTFFFPRSLSHNCLILDLQYGDQQQHPFUHKKMUUEHLVILLLNTSCMEKLVTRUMSMPLVUYYLNYYQVGNQSALNLAKDERAWULGEWFWQHLYASHGLLDFVLNLIRYURSUKGTMTMNIASMSIQKMKKTLMMKYIQIQVQSYTULLHYLALMMTVHHVIVQTTTIVRIUKINGAGLCVLT