AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70080

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 70 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTCAAACGTACTGAAATT+TGG 0.113029 4.2:+85247515 None:intergenic
GTATCATACAACAACCTTTC+TGG 0.183710 4.2:-85246765 MS.gene70080:CDS
ATCTTACATAACAATATTAT+TGG 0.187533 4.2:-85246553 MS.gene70080:CDS
CTTTCTCAAAACAAGTTAAT+TGG 0.204622 4.2:-85247545 MS.gene70080:CDS
ATAAGTCAAGACTCTCTATT+TGG 0.215048 4.2:+85246856 None:intergenic
TTGAAGAAAGAATTTCTATT+TGG 0.238239 4.2:+85247140 None:intergenic
CTCAATAATAACAACTTTAG+TGG 0.269758 4.2:-85247764 MS.gene70080:CDS
TGTGATTGAGTTATTGGATA+TGG 0.270796 4.2:+85247691 None:intergenic
TCCACCGAAGCCTCATTAAA+TGG 0.297401 4.2:+85247095 None:intergenic
ATTCAAACGTACTGAAATTT+GGG 0.309690 4.2:+85247516 None:intergenic
TCAAAGCTCTAATTTGTTGT+AGG 0.313567 4.2:+85246934 None:intergenic
TTTAACCGACACAACTGAAT+TGG 0.327287 4.2:+85247302 None:intergenic
AACACTTGAAGATCTATTAA+TGG 0.330641 4.2:-85247741 MS.gene70080:CDS
TTCAACAGGGTCAGTTCATT+AGG 0.331630 4.2:+85246807 None:intergenic
TTGAGGGAGAACAAATTATC+AGG 0.360013 4.2:-85247404 MS.gene70080:CDS
GGTGTCATCCCTTCTCAAAT+TGG 0.379151 4.2:-85246960 MS.gene70080:CDS
TTGTCTCAAAATCAATTAGA+AGG 0.383463 4.2:-85247617 MS.gene70080:CDS
GAGAAGGGATGACACCTGTT+AGG 0.398982 4.2:+85246967 None:intergenic
ACACTTGAAGATCTATTAAT+GGG 0.411024 4.2:-85247740 MS.gene70080:CDS
TTATCATGCAATAACCTAAC+AGG 0.412231 4.2:-85246981 MS.gene70080:CDS
ACCTCCATTTAATGAGGCTT+CGG 0.416326 4.2:-85247099 MS.gene70080:CDS
AACTACAACTTCTAGATTTG+AGG 0.432468 4.2:-85247421 MS.gene70080:CDS
CCACCTAGTACAGGACAGTT+TGG 0.436656 4.2:-85246738 MS.gene70080:CDS
GACATGTTGGAAATCTCAAT+AGG 0.441108 4.2:+85247587 None:intergenic
CATTCAGCATGTTCCGTGAT+AGG 0.444855 4.2:+85247261 None:intergenic
CTATCACATAATTACTTGTC+AGG 0.449370 4.2:-85246909 MS.gene70080:CDS
ACTACAACTTCTAGATTTGA+GGG 0.458773 4.2:-85247420 MS.gene70080:CDS
TTGCAAGAGAATGGTCTCTC+TGG 0.460225 4.2:-85247476 MS.gene70080:CDS
ATCTTGTATTTGCAAGAGAA+TGG 0.463843 4.2:-85247485 MS.gene70080:CDS
TCTCCAAACTGTCCTGTACT+AGG 0.464805 4.2:+85246735 None:intergenic
ATCCAATGACAATGGAGAAA+AGG 0.468182 4.2:-85246619 MS.gene70080:CDS
GATAGTTTGTCCATCCAGTT+CGG 0.472461 4.2:+85247374 None:intergenic
TCTGGAGAATATGACTGGAT+TGG 0.476647 4.2:-85247006 MS.gene70080:CDS
TTATCATACAATAGCTTGAC+TGG 0.478155 4.2:-85246837 MS.gene70080:CDS
CATGTTCACACTTTCGATTG+AGG 0.479895 4.2:+85246664 None:intergenic
AATTGAACCTCCATTTAATG+AGG 0.485806 4.2:-85247105 MS.gene70080:CDS
TATCAGGTAAAATTCCGAAC+TGG 0.493884 4.2:-85247388 MS.gene70080:CDS
TAAGTCAAGACTCTCTATTT+GGG 0.500651 4.2:+85246857 None:intergenic
ACATGTTGGAAATCTCAATA+GGG 0.500697 4.2:+85247588 None:intergenic
TTTGAATTCTCAACGATCAT+GGG 0.505912 4.2:-85247167 MS.gene70080:CDS
ATTGAGATTTCCAACATGTC+CGG 0.506952 4.2:-85247584 MS.gene70080:CDS
AAGATCTAAAATTTGAAGAC+CGG 0.514668 4.2:+85247565 None:intergenic
AATTCCTAGTTCAATTGGGA+TGG 0.519621 4.2:-85247663 MS.gene70080:CDS
GAAACCATCCCAATTGAACT+AGG 0.523474 4.2:+85247659 None:intergenic
TCCATTTAATGAGGCTTCGG+TGG 0.527219 4.2:-85247096 MS.gene70080:CDS
GAGGAGTGGTCCACACAGAC+CGG 0.536434 4.2:+85246683 None:intergenic
GACAATTACAGAGGTAATCC+CGG 0.540467 4.2:-85246702 MS.gene70080:CDS
AAAGTTCTGGAGAATATGAC+TGG 0.541900 4.2:-85247011 MS.gene70080:CDS
GTTGTTGTATGATACATTGA+AGG 0.542204 4.2:+85246773 None:intergenic
TCTGGAACGCCACCTAGTAC+AGG 0.545680 4.2:-85246747 MS.gene70080:CDS
AATGCACAACACAGTTATGA+AGG 0.547405 4.2:+85246530 None:intergenic
ATATCCAATAACTCAATCAC+AGG 0.551252 4.2:-85247689 MS.gene70080:CDS
TACTAGGTGGCGTTCCAGAA+AGG 0.558767 4.2:+85246751 None:intergenic
TGTAGGTCTCCAATTTGAGA+AGG 0.559427 4.2:+85246951 None:intergenic
TTATTCCAATTCAGTTGTGT+CGG 0.561879 4.2:-85247307 MS.gene70080:CDS
AGGTAAAATTCCGAACTGGA+TGG 0.577263 4.2:-85247384 MS.gene70080:CDS
GAGTCTTCAGAGAGTTCAGA+TGG 0.588859 4.2:+85247446 None:intergenic
TAGACATAATGGACCTATCA+CGG 0.589629 4.2:-85247274 MS.gene70080:CDS
GTAGGTCTCCAATTTGAGAA+GGG 0.593269 4.2:+85246952 None:intergenic
AATTTGAAGACCGGACATGT+TGG 0.594271 4.2:+85247574 None:intergenic
AGGAGTGGTCCACACAGACC+GGG 0.596614 4.2:+85246684 None:intergenic
TGGAGAAAAGGAAACTGTTG+TGG 0.599113 4.2:-85246607 MS.gene70080:CDS
TGAATATGTACAATTTGAAG+TGG 0.600023 4.2:-85247072 MS.gene70080:CDS
AGAGGTAATCCCGGTCTGTG+TGG 0.620823 4.2:-85246693 MS.gene70080:CDS
TCATCACAATCCAATGACAA+TGG 0.625168 4.2:-85246627 MS.gene70080:CDS
ACAGTTTGGAGACTTTGATG+AGG 0.627652 4.2:-85246724 MS.gene70080:CDS
TCACACTTTCGATTGAGGAG+TGG 0.636047 4.2:+85246669 None:intergenic
ACCGAAGCCTCATTAAATGG+AGG 0.677214 4.2:+85247098 None:intergenic
CCAAACTGTCCTGTACTAGG+TGG 0.687098 4.2:+85246738 None:intergenic
TTTGATGAGGACAATTACAG+AGG 0.703420 4.2:-85246711 MS.gene70080:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTTACATAACAATATTAT+TGG - chr4.2:85247773-85247792 MS.gene70080:CDS 15.0%
!! GTTAAAAAAGATAGACATAA+TGG - chr4.2:85247041-85247060 MS.gene70080:CDS 20.0%
!! TTGAAGAAAGAATTTCTATT+TGG + chr4.2:85247189-85247208 None:intergenic 20.0%
!!! AAGTTACATGTTCTTTTATT+AGG - chr4.2:85246976-85246995 MS.gene70080:CDS 20.0%
! AACACTTGAAGATCTATTAA+TGG - chr4.2:85246585-85246604 MS.gene70080:CDS 25.0%
! ACACTTGAAGATCTATTAAT+GGG - chr4.2:85246586-85246605 MS.gene70080:CDS 25.0%
! ATTCAAACGTACTGAAATTT+GGG + chr4.2:85246813-85246832 None:intergenic 25.0%
! ATTTGAAAAAGTCATTGGAA+TGG + chr4.2:85247445-85247464 None:intergenic 25.0%
! CTCAATAATAACAACTTTAG+TGG - chr4.2:85246562-85246581 MS.gene70080:CDS 25.0%
! CTTTCTCAAAACAAGTTAAT+TGG - chr4.2:85246781-85246800 MS.gene70080:CDS 25.0%
! GAAAAATTCCTAGTTCAATT+GGG - chr4.2:85246659-85246678 MS.gene70080:CDS 25.0%
! GTAAGATTTGAAAAAGTCAT+TGG + chr4.2:85247450-85247469 None:intergenic 25.0%
! TGAATATGTACAATTTGAAG+TGG - chr4.2:85247254-85247273 MS.gene70080:CDS 25.0%
! TGCTTCAAAAATATGTCATT+TGG - chr4.2:85247102-85247121 MS.gene70080:CDS 25.0%
! TTGTCTCAAAATCAATTAGA+AGG - chr4.2:85246709-85246728 MS.gene70080:CDS 25.0%
! TTTGAAAAAGTCATTGGAAT+GGG + chr4.2:85247444-85247463 None:intergenic 25.0%
!! AAGATCTAAAATTTGAAGAC+CGG + chr4.2:85246764-85246783 None:intergenic 25.0%
!! CACAATGAATACTTTTACAA+GGG - chr4.2:85247291-85247310 MS.gene70080:CDS 25.0%
!! CTTGCAAATACAAGATTTTT+AGG + chr4.2:85246837-85246856 None:intergenic 25.0%
!! TACATGTTCTTTTATTAGGA+GGG - chr4.2:85246980-85246999 MS.gene70080:CDS 25.0%
!! TGGACATGATAACATTTTAT+TGG - chr4.2:85247739-85247758 MS.gene70080:CDS 25.0%
!! TTACATGTTCTTTTATTAGG+AGG - chr4.2:85246979-85246998 MS.gene70080:CDS 25.0%
!!! ATTGATTTTGAGACAAAAGA+AGG + chr4.2:85246705-85246724 None:intergenic 25.0%
!!! GACATATTTTTGAAGCAATA+TGG + chr4.2:85247099-85247118 None:intergenic 25.0%
AACTACAACTTCTAGATTTG+AGG - chr4.2:85246905-85246924 MS.gene70080:CDS 30.0%
AATTGAACCTCCATTTAATG+AGG - chr4.2:85247221-85247240 MS.gene70080:CDS 30.0%
ACATGTTGGAAATCTCAATA+GGG + chr4.2:85246741-85246760 None:intergenic 30.0%
ACTACAACTTCTAGATTTGA+GGG - chr4.2:85246906-85246925 MS.gene70080:CDS 30.0%
ATAAGTCAAGACTCTCTATT+TGG + chr4.2:85247473-85247492 None:intergenic 30.0%
ATATCCAATAACTCAATCAC+AGG - chr4.2:85246637-85246656 MS.gene70080:CDS 30.0%
ATCTTGTATTTGCAAGAGAA+TGG - chr4.2:85246841-85246860 MS.gene70080:CDS 30.0%
CATTCAAACGTACTGAAATT+TGG + chr4.2:85246814-85246833 None:intergenic 30.0%
CTATCACATAATTACTTGTC+AGG - chr4.2:85247417-85247436 MS.gene70080:CDS 30.0%
GGAAAAATTCCTAGTTCAAT+TGG - chr4.2:85246658-85246677 MS.gene70080:CDS 30.0%
GTTGTTGTATGATACATTGA+AGG + chr4.2:85247556-85247575 None:intergenic 30.0%
TAAGTCAAGACTCTCTATTT+GGG + chr4.2:85247472-85247491 None:intergenic 30.0%
TGTGATTGAGTTATTGGATA+TGG + chr4.2:85246638-85246657 None:intergenic 30.0%
TTATCATACAATAGCTTGAC+TGG - chr4.2:85247489-85247508 MS.gene70080:CDS 30.0%
TTATCATGCAATAACCTAAC+AGG - chr4.2:85247345-85247364 MS.gene70080:CDS 30.0%
TTATTCCAATTCAGTTGTGT+CGG - chr4.2:85247019-85247038 MS.gene70080:CDS 30.0%
TTTGAATTCTCAACGATCAT+GGG - chr4.2:85247159-85247178 MS.gene70080:CDS 30.0%
! GCACAATGAATACTTTTACA+AGG - chr4.2:85247290-85247309 MS.gene70080:CDS 30.0%
! TTAGGAGGGAATAATTTTGA+AGG - chr4.2:85246994-85247013 MS.gene70080:CDS 30.0%
! TTTTCCTGTGATTGAGTTAT+TGG + chr4.2:85246644-85246663 None:intergenic 30.0%
! TTTTGAATTCTCAACGATCA+TGG - chr4.2:85247158-85247177 MS.gene70080:CDS 30.0%
!! AGGTTGATAAAAAGTTCAAC+AGG + chr4.2:85247536-85247555 None:intergenic 30.0%
!! GGTTGATAAAAAGTTCAACA+GGG + chr4.2:85247535-85247554 None:intergenic 30.0%
!! TCAAAGCTCTAATTTGTTGT+AGG + chr4.2:85247395-85247414 None:intergenic 30.0%
AATTCCTAGTTCAATTGGGA+TGG - chr4.2:85246663-85246682 MS.gene70080:CDS 35.0%
ATCCAATGACAATGGAGAAA+AGG - chr4.2:85247707-85247726 MS.gene70080:CDS 35.0%
ATTGAGATTTCCAACATGTC+CGG - chr4.2:85246742-85246761 MS.gene70080:CDS 35.0%
GACATGTTGGAAATCTCAAT+AGG + chr4.2:85246742-85246761 None:intergenic 35.0%
GTATCATACAACAACCTTTC+TGG - chr4.2:85247561-85247580 MS.gene70080:CDS 35.0%
TATCAGGTAAAATTCCGAAC+TGG - chr4.2:85246938-85246957 MS.gene70080:CDS 35.0%
TCATCACAATCCAATGACAA+TGG - chr4.2:85247699-85247718 MS.gene70080:CDS 35.0%
TTGAGGGAGAACAAATTATC+AGG - chr4.2:85246922-85246941 MS.gene70080:CDS 35.0%
TTTAACCGACACAACTGAAT+TGG + chr4.2:85247027-85247046 None:intergenic 35.0%
TTTGATGAGGACAATTACAG+AGG - chr4.2:85247615-85247634 MS.gene70080:CDS 35.0%
! CTTTTACAAGGGTAAAGTTC+TGG - chr4.2:85247302-85247321 MS.gene70080:CDS 35.0%
! TTCCTTTTCTCCATTGTCAT+TGG + chr4.2:85247712-85247731 None:intergenic 35.0%
!! AAAGTTCTGGAGAATATGAC+TGG - chr4.2:85247315-85247334 MS.gene70080:CDS 35.0%
!! TAGACATAATGGACCTATCA+CGG - chr4.2:85247052-85247071 MS.gene70080:CDS 35.0%
AATTTGAAGACCGGACATGT+TGG + chr4.2:85246755-85246774 None:intergenic 40.0%
ACAGTTTGGAGACTTTGATG+AGG - chr4.2:85247602-85247621 MS.gene70080:CDS 40.0%
ACCTCCATTTAATGAGGCTT+CGG - chr4.2:85247227-85247246 MS.gene70080:CDS 40.0%
AGGTAAAATTCCGAACTGGA+TGG - chr4.2:85246942-85246961 MS.gene70080:CDS 40.0%
CATGTTCACACTTTCGATTG+AGG + chr4.2:85247665-85247684 None:intergenic 40.0%
GAAACCATCCCAATTGAACT+AGG + chr4.2:85246670-85246689 None:intergenic 40.0%
GACAATTACAGAGGTAATCC+CGG - chr4.2:85247624-85247643 MS.gene70080:CDS 40.0%
GTAGGTCTCCAATTTGAGAA+GGG + chr4.2:85247377-85247396 None:intergenic 40.0%
TCTGGAGAATATGACTGGAT+TGG - chr4.2:85247320-85247339 MS.gene70080:CDS 40.0%
TGGAGAAAAGGAAACTGTTG+TGG - chr4.2:85247719-85247738 MS.gene70080:CDS 40.0%
TGTAGGTCTCCAATTTGAGA+AGG + chr4.2:85247378-85247397 None:intergenic 40.0%
TTCAACAGGGTCAGTTCATT+AGG + chr4.2:85247522-85247541 None:intergenic 40.0%
! GATAGTTTGTCCATCCAGTT+CGG + chr4.2:85246955-85246974 None:intergenic 40.0%
ACCGAAGCCTCATTAAATGG+AGG + chr4.2:85247231-85247250 None:intergenic 45.0%
CATTCAGCATGTTCCGTGAT+AGG + chr4.2:85247068-85247087 None:intergenic 45.0%
GAGTCTTCAGAGAGTTCAGA+TGG + chr4.2:85246883-85246902 None:intergenic 45.0%
TCACACTTTCGATTGAGGAG+TGG + chr4.2:85247660-85247679 None:intergenic 45.0%
TCCACCGAAGCCTCATTAAA+TGG + chr4.2:85247234-85247253 None:intergenic 45.0%
TCCATTTAATGAGGCTTCGG+TGG - chr4.2:85247230-85247249 MS.gene70080:CDS 45.0%
TCTCCAAACTGTCCTGTACT+AGG + chr4.2:85247594-85247613 None:intergenic 45.0%
TTGCAAGAGAATGGTCTCTC+TGG - chr4.2:85246850-85246869 MS.gene70080:CDS 45.0%
! GGTGTCATCCCTTCTCAAAT+TGG - chr4.2:85247366-85247385 MS.gene70080:CDS 45.0%
CCAAACTGTCCTGTACTAGG+TGG + chr4.2:85247591-85247610 None:intergenic 50.0%
CCACCTAGTACAGGACAGTT+TGG - chr4.2:85247588-85247607 MS.gene70080:CDS 50.0%
GAGAAGGGATGACACCTGTT+AGG + chr4.2:85247362-85247381 None:intergenic 50.0%
TACTAGGTGGCGTTCCAGAA+AGG + chr4.2:85247578-85247597 None:intergenic 50.0%
AGAGGTAATCCCGGTCTGTG+TGG - chr4.2:85247633-85247652 MS.gene70080:CDS 55.0%
! TCTGGAACGCCACCTAGTAC+AGG - chr4.2:85247579-85247598 MS.gene70080:CDS 55.0%
AGGAGTGGTCCACACAGACC+GGG + chr4.2:85247645-85247664 None:intergenic 60.0%
GAGGAGTGGTCCACACAGAC+CGG + chr4.2:85247646-85247665 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 85246542 85247806 85246542 ID=MS.gene70080
chr4.2 mRNA 85246542 85247806 85246542 ID=MS.gene70080.t1;Parent=MS.gene70080
chr4.2 exon 85246542 85247806 85246542 ID=MS.gene70080.t1.exon1;Parent=MS.gene70080.t1
chr4.2 CDS 85246542 85247806 85246542 ID=cds.MS.gene70080.t1;Parent=MS.gene70080.t1
Gene Sequence

>MS.gene70080

TGAATATGATAGCTTTATTTCTCAATAATAACAACTTTAGTGGAACACTTGAAGATCTATTAATGGGAAACAGTACAAGATTATTAATTCTATCCATATCCAATAACTCAATCACAGGAAAAATTCCTAGTTCAATTGGGATGGTTTCTAACATGATTGTCCTTCTTTTGTCTCAAAATCAATTAGAAGGTCAGATCCCTATTGAGATTTCCAACATGTCCGGTCTTCAAATTTTAGATCTTTCTCAAAACAAGTTAATTGGATCAATCCCAAATTTCAGTACGTTTGAATGCCTAAAAATCTTGTATTTGCAAGAGAATGGTCTCTCTGGATCTATACCATCTGAACTCTCTGAAGACTCACAACTACAACTTCTAGATTTGAGGGAGAACAAATTATCAGGTAAAATTCCGAACTGGATGGACAAACTATCAAAGTTACATGTTCTTTTATTAGGAGGGAATAATTTTGAAGGAGTTATTCCAATTCAGTTGTGTCGGTTAAAAAAGATAGACATAATGGACCTATCACGGAACATGCTGAATGCTTCAATACCATATTGCTTCAAAAATATGTCATTTGGAATGAGACAATATGTTGATGATGACAGATATACTTTTGAATTCTCAACGATCATGGGAATACCAAATAGAAATTCTTTCTTCAATGCTAGTTTATCAATTGAACCTCCATTTAATGAGGCTTCGGTGGATGAATATGTACAATTTGAAGTGGAGTTTAGAACAAAGCACAATGAATACTTTTACAAGGGTAAAGTTCTGGAGAATATGACTGGATTGGATTTATCATGCAATAACCTAACAGGTGTCATCCCTTCTCAAATTGGAGACCTACAACAAATTAGAGCTTTGAATCTATCACATAATTACTTGTCAGGTCCCATTCCAATGACTTTTTCAAATCTTACCCAAATAGAGAGTCTTGACTTATCATACAATAGCTTGACTGGTAAAATTCCTAATGAACTGACCCTGTTGAACTTTTTATCAACCTTCAATGTATCATACAACAACCTTTCTGGAACGCCACCTAGTACAGGACAGTTTGGAGACTTTGATGAGGACAATTACAGAGGTAATCCCGGTCTGTGTGGACCACTCCTCAATCGAAAGTGTGAACATGTCGAGTCTTCAGCATCATCACAATCCAATGACAATGGAGAAAAGGAAACTGTTGTGGACATGATAACATTTTATTGGAGTTTCACAGCATCTTACATAACAATATTATTGGCCTTCATAACT
Protein sequence

>MS.gene70080.t1

UIUULYFSIITTLVEHLKIYUWETVQDYUFYPYPITQSQEKFLVQLGWFLTULSFFCLKINUKVRSLLRFPTCPVFKFUIFLKTSULDQSQISVRLNAUKSCICKRMVSLDLYHLNSLKTHNYNFUIUGRTNYQVKFRTGWTNYQSYMFFYUEGIILKELFQFSCVGUKRUTUWTYHGTCUMLQYHIASKICHLEUDNMLMMTDILLNSQRSWEYQIEILSSMLVYQLNLHLMRLRWMNMYNLKWSLEQSTMNTFTRVKFWRIULDWIYHAITUQVSSLLKLETYNKLELUIYHIITCQVPFQULFQILPKURVLTYHTIAULVKFLMNUPCUTFYQPSMYHTTTFLERHLVQDSLETLMRTITEVIPVCVDHSSIESVNMSSLQHHHNPMTMEKRKLLWTUUHFIGVSQHLTUQYYWPS