AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene60875

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 66 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCTTACTTCATTTAATTC+TGG 0.171204 1.4:-77192845 MS.gene60875:CDS
AATGGGCGTAATGTCAATTT+TGG 0.247122 1.4:-77192695 MS.gene60875:CDS
ACTTACATGTTTGGATTCTT+TGG 0.259911 1.4:+77192374 None:intergenic
CAAACATGCACTTACATGTT+TGG 0.290047 1.4:+77192365 None:intergenic
TCTACAAAACAAAGGATTAA+AGG 0.300147 1.4:+77192234 None:intergenic
TCTGGGGAGGCTAGTGTAAT+TGG 0.321805 1.4:-77192827 MS.gene60875:CDS
CGCCCATTTCGTGCAAGATC+AGG 0.336064 1.4:+77192710 None:intergenic
AGCTTACTTCATTTAATTCT+GGG 0.352280 1.4:-77192844 MS.gene60875:CDS
GGCCCTGATCTTGCACGAAA+TGG 0.352532 1.4:-77192713 MS.gene60875:CDS
GTTGGATTGGCAAGGGGTGT+TGG 0.364461 1.4:-77192800 MS.gene60875:CDS
GTTGCAGATACGGCACCTTC+TGG 0.372362 1.4:-77193082 None:intergenic
TACCTGTAGATGCAGTTTCC+AGG 0.381965 1.4:-77192664 MS.gene60875:CDS
AGGGGTGTTGGTGAATTTCC+AGG 0.387492 1.4:-77192788 MS.gene60875:CDS
CATCTTAGTGGTGTTGGTGG+TGG 0.387530 1.4:-77192734 MS.gene60875:CDS
TCAAGTACTTTATATGTTGA+AGG 0.393632 1.4:-77192605 MS.gene60875:CDS
TCTGCCATGGGGCATCTTAG+TGG 0.411336 1.4:-77192746 MS.gene60875:CDS
GCCCTGATCTTGCACGAAAT+GGG 0.423036 1.4:-77192712 MS.gene60875:CDS
TAGTGGTATTGTCTCAGGTC+CGG 0.435953 1.4:+77192640 None:intergenic
ACTTCTCTATATCCGACAAA+AGG 0.438290 1.4:+77192408 None:intergenic
ATGGGGCATCTTAGTGGTGT+TGG 0.442716 1.4:-77192740 MS.gene60875:CDS
CTAGGTGATCCTTCTGCCAT+GGG 0.453357 1.4:-77192758 MS.gene60875:CDS
CGAGGTAGTGGTATTGTCTC+AGG 0.454968 1.4:+77192635 None:intergenic
GCTAGTGTAATTGGTGGTGT+TGG 0.457358 1.4:-77192818 MS.gene60875:CDS
TATTGTCTCAGGTCCGGGCC+TGG 0.460416 1.4:+77192646 None:intergenic
GACCGCTTCCTTCAGAGTGC+AGG 0.461691 1.4:-77192968 MS.gene60875:CDS
GGGCATCTTAGTGGTGTTGG+TGG 0.477192 1.4:-77192737 MS.gene60875:CDS
TCTAGGTGATCCTTCTGCCA+TGG 0.481909 1.4:-77192759 MS.gene60875:CDS
TGGTGGTGTTGGATTGGCAA+GGG 0.483162 1.4:-77192807 MS.gene60875:CDS
GAATTTCCAGGCCATTCTCT+AGG 0.503129 1.4:-77192776 MS.gene60875:CDS
GGTGGTGTTGGATTGGCAAG+GGG 0.505156 1.4:-77192806 MS.gene60875:CDS
GCACCTTCTGGTGTGACCTC+AGG 0.506465 1.4:-77193070 MS.gene60875:CDS
CAAGTACTTTATATGTTGAA+GGG 0.514629 1.4:-77192604 MS.gene60875:CDS
TTGGTGGTGTTGGATTGGCA+AGG 0.517002 1.4:-77192808 MS.gene60875:CDS
AGTGGTATTGTCTCAGGTCC+GGG 0.520528 1.4:+77192641 None:intergenic
TGTAATTGGTGGTGTTGGAT+TGG 0.524220 1.4:-77192813 MS.gene60875:CDS
GGCCTGGAAACTGCATCTAC+AGG 0.525078 1.4:+77192662 None:intergenic
CTTGAAGCATCTCGAGGTAG+TGG 0.525252 1.4:+77192623 None:intergenic
CTAAACGACACTAAAACACT+CGG 0.534798 1.4:-77193001 MS.gene60875:CDS
AAGGCAGTTGCTGCACAAGC+CGG 0.544435 1.4:+77192201 None:intergenic
GCCCATTTCGTGCAAGATCA+GGG 0.546234 1.4:+77192711 None:intergenic
CAGAAGGATCACCTAGAGAA+TGG 0.547740 1.4:+77192765 None:intergenic
ACCGCTTCCTTCAGAGTGCA+GGG 0.548107 1.4:-77192967 MS.gene60875:CDS
GGGGAGGCTAGTGTAATTGG+TGG 0.550012 1.4:-77192824 MS.gene60875:CDS
GATACCTTGCAAGGCGCTCA+AGG 0.554534 1.4:+77192182 None:intergenic
TACTTCATTTAATTCTGGGG+AGG 0.558022 1.4:-77192840 MS.gene60875:CDS
GGATCACCTAGAGAATGGCC+TGG 0.562504 1.4:+77192770 None:intergenic
GTAGATGCAGTTTCCAGGCC+CGG 0.567675 1.4:-77192659 MS.gene60875:CDS
CTTCTCTATATCCGACAAAA+GGG 0.574261 1.4:+77192409 None:intergenic
ACTGCCTTGAGCGCCTTGCA+AGG 0.578510 1.4:-77192186 None:intergenic
TTGCCTGAGGTCACACCAGA+AGG 0.581169 1.4:+77193067 None:intergenic
AATTATATTGCTCAAAACAA+TGG 0.582968 1.4:-77193034 MS.gene60875:CDS
ATATTACCCCTGCACTCTGA+AGG 0.585517 1.4:+77192960 None:intergenic
CTAAGATGCCCCATGGCAGA+AGG 0.593428 1.4:+77192749 None:intergenic
TTGCAAAATCTACAAAACAA+AGG 0.594306 1.4:+77192226 None:intergenic
GCTTACTTCATTTAATTCTG+GGG 0.602966 1.4:-77192843 MS.gene60875:CDS
AAAAGAAGTGATACCTTGCA+AGG 0.614697 1.4:+77192173 None:intergenic
ACTTGTTTATTGCAGCGAGG+TGG 0.632918 1.4:-77192261 MS.gene60875:intron
TGGTGTGACCTCAGGCAATG+AGG 0.635982 1.4:-77193062 MS.gene60875:CDS
CCCCTGCACTCTGAAGGAAG+CGG 0.661189 1.4:+77192966 None:intergenic
TAAACGACACTAAAACACTC+GGG 0.665910 1.4:-77193000 MS.gene60875:CDS
AACACCACTAAGATGCCCCA+TGG 0.672556 1.4:+77192742 None:intergenic
TAGGTGATCCTTCTGCCATG+GGG 0.675793 1.4:-77192757 MS.gene60875:CDS
ATATAGAGAAGTAAGACTTG+TGG 0.681838 1.4:-77192397 MS.gene60875:CDS
AAAGTACTTGAAGCATCTCG+AGG 0.682579 1.4:+77192617 None:intergenic
ATTATGCACCTCATTGCCTG+AGG 0.687310 1.4:+77193054 None:intergenic
CCGCTTCCTTCAGAGTGCAG+GGG 0.693385 1.4:-77192966 MS.gene60875:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTAGATGTAAAATAAAA+TGG + chr1.4:77192334-77192353 None:intergenic 15.0%
!! CATTAGATGTAAAATAAAAT+GGG + chr1.4:77192333-77192352 None:intergenic 15.0%
!! AATATCTAAATATGACGTTA+AGG + chr1.4:77192828-77192847 None:intergenic 20.0%
!! AATTATATTGCTCAAAACAA+TGG - chr1.4:77192228-77192247 MS.gene60875:CDS 20.0%
! AGCTTACTTCATTTAATTCT+GGG - chr1.4:77192418-77192437 MS.gene60875:CDS 25.0%
! CAAGTACTTTATATGTTGAA+GGG - chr1.4:77192658-77192677 MS.gene60875:CDS 25.0%
! TCAAGTACTTTATATGTTGA+AGG - chr1.4:77192657-77192676 MS.gene60875:CDS 25.0%
! TCTACAAAACAAAGGATTAA+AGG + chr1.4:77193031-77193050 None:intergenic 25.0%
! TTGCAAAATCTACAAAACAA+AGG + chr1.4:77193039-77193058 None:intergenic 25.0%
!! TTTTGTAGATTTTGCAAATC+CGG - chr1.4:77193042-77193061 MS.gene60875:CDS 25.0%
ACTTACATGTTTGGATTCTT+TGG + chr1.4:77192891-77192910 None:intergenic 30.0%
ATATAGAGAAGTAAGACTTG+TGG - chr1.4:77192865-77192884 MS.gene60875:intron 30.0%
ATGTAAGTGCATGTTTGTAA+CGG - chr1.4:77192903-77192922 MS.gene60875:intron 30.0%
CAGCTTACTTCATTTAATTC+TGG - chr1.4:77192417-77192436 MS.gene60875:CDS 30.0%
CGTTAAGGAACTTGAATAAT+TGG + chr1.4:77192813-77192832 None:intergenic 30.0%
GCTTACTTCATTTAATTCTG+GGG - chr1.4:77192419-77192438 MS.gene60875:CDS 30.0%
TCGCATTATCATGCTTTAAT+CGG - chr1.4:77192760-77192779 MS.gene60875:CDS 30.0%
!!! TTTTAGTGTCGTTTAGCATT+TGG + chr1.4:77192257-77192276 None:intergenic 30.0%
AACGGAACTTTAAACCAATC+AGG + chr1.4:77192962-77192981 None:intergenic 35.0%
ACTTCTCTATATCCGACAAA+AGG + chr1.4:77192857-77192876 None:intergenic 35.0%
CAAACATGCACTTACATGTT+TGG + chr1.4:77192900-77192919 None:intergenic 35.0%
CTAAACGACACTAAAACACT+CGG - chr1.4:77192261-77192280 MS.gene60875:intron 35.0%
CTTCTCTATATCCGACAAAA+GGG + chr1.4:77192856-77192875 None:intergenic 35.0%
GATTAAAATGAATGAAGCCC+AGG + chr1.4:77192791-77192810 None:intergenic 35.0%
GTGATAAACCAAGACAAAAG+AGG + chr1.4:77192940-77192959 None:intergenic 35.0%
TAAACGACACTAAAACACTC+GGG - chr1.4:77192262-77192281 MS.gene60875:intron 35.0%
TTTACATCTAATGTTCGCAC+AGG - chr1.4:77192340-77192359 MS.gene60875:intron 35.0%
! AATGGGCGTAATGTCAATTT+TGG - chr1.4:77192567-77192586 MS.gene60875:intron 35.0%
! GATATTTTTCGCCCTTTTGT+CGG - chr1.4:77192842-77192861 MS.gene60875:CDS 35.0%
! TACTTCATTTAATTCTGGGG+AGG - chr1.4:77192422-77192441 MS.gene60875:CDS 35.0%
! TTTCAGCATAAAGAGCACAA+CGG + chr1.4:77192980-77192999 None:intergenic 35.0%
AACACTTGTTTATTGCAGCG+AGG - chr1.4:77192998-77193017 MS.gene60875:CDS 40.0%
AAGCTGCTTCACAATCAAAC+AGG + chr1.4:77192403-77192422 None:intergenic 40.0%
GTCTTGGTTTATCACCTGAT+TGG - chr1.4:77192945-77192964 MS.gene60875:intron 40.0%
TGACAGCACAAAAAGAGAAG+TGG - chr1.4:77192689-77192708 MS.gene60875:CDS 40.0%
! AAAGTACTTGAAGCATCTCG+AGG + chr1.4:77192648-77192667 None:intergenic 40.0%
! CTCTTTTTGTGCTGTCAGAT+GGG + chr1.4:77192686-77192705 None:intergenic 40.0%
! TCTCTTTTTGTGCTGTCAGA+TGG + chr1.4:77192687-77192706 None:intergenic 40.0%
! TTGCTTGTCCTCTTTTGTCT+TGG - chr1.4:77192929-77192948 MS.gene60875:intron 40.0%
!! TGTAATTGGTGGTGTTGGAT+TGG - chr1.4:77192449-77192468 MS.gene60875:intron 40.0%
ACTTGTTTATTGCAGCGAGG+TGG - chr1.4:77193001-77193020 MS.gene60875:CDS 45.0%
ATATTACCCCTGCACTCTGA+AGG + chr1.4:77192305-77192324 None:intergenic 45.0%
ATTATGCACCTCATTGCCTG+AGG + chr1.4:77192211-77192230 None:intergenic 45.0%
CAGAAGGATCACCTAGAGAA+TGG + chr1.4:77192500-77192519 None:intergenic 45.0%
GAATTTCCAGGCCATTCTCT+AGG - chr1.4:77192486-77192505 MS.gene60875:intron 45.0%
TACCTGTAGATGCAGTTTCC+AGG - chr1.4:77192598-77192617 MS.gene60875:CDS 45.0%
TAGTGGTATTGTCTCAGGTC+CGG + chr1.4:77192625-77192644 None:intergenic 45.0%
! ATGCTTTAATCGGTGTCTCC+TGG - chr1.4:77192770-77192789 MS.gene60875:CDS 45.0%
! GGGCGTAATGTCAATTTTGG+TGG - chr1.4:77192570-77192589 MS.gene60875:CDS 45.0%
! TGCTTTAATCGGTGTCTCCT+GGG - chr1.4:77192771-77192790 MS.gene60875:CDS 45.0%
!! GCTAGTGTAATTGGTGGTGT+TGG - chr1.4:77192444-77192463 MS.gene60875:intron 45.0%
!! GAAAAAAATAAAAAATAAAA+AGG + chr1.4:77192722-77192741 None:intergenic 5.0%
AACACCACTAAGATGCCCCA+TGG + chr1.4:77192523-77192542 None:intergenic 50.0%
AGTGGTATTGTCTCAGGTCC+GGG + chr1.4:77192624-77192643 None:intergenic 50.0%
CTAGGTGATCCTTCTGCCAT+GGG - chr1.4:77192504-77192523 MS.gene60875:intron 50.0%
GCCCATTTCGTGCAAGATCA+GGG + chr1.4:77192554-77192573 None:intergenic 50.0%
GCCCTGATCTTGCACGAAAT+GGG - chr1.4:77192550-77192569 MS.gene60875:intron 50.0%
TAGGTGATCCTTCTGCCATG+GGG - chr1.4:77192505-77192524 MS.gene60875:intron 50.0%
TCTAGGTGATCCTTCTGCCA+TGG - chr1.4:77192503-77192522 MS.gene60875:intron 50.0%
TCTGGGGAGGCTAGTGTAAT+TGG - chr1.4:77192435-77192454 MS.gene60875:intron 50.0%
! ATGGGGCATCTTAGTGGTGT+TGG - chr1.4:77192522-77192541 MS.gene60875:intron 50.0%
! CGAGGTAGTGGTATTGTCTC+AGG + chr1.4:77192630-77192649 None:intergenic 50.0%
! CTTGAAGCATCTCGAGGTAG+TGG + chr1.4:77192642-77192661 None:intergenic 50.0%
!! AGGGGTGTTGGTGAATTTCC+AGG - chr1.4:77192474-77192493 MS.gene60875:intron 50.0%
!! CATCTTAGTGGTGTTGGTGG+TGG - chr1.4:77192528-77192547 MS.gene60875:intron 50.0%
!! TGGTGGTGTTGGATTGGCAA+GGG - chr1.4:77192455-77192474 MS.gene60875:intron 50.0%
!! TTGGTGGTGTTGGATTGGCA+AGG - chr1.4:77192454-77192473 MS.gene60875:intron 50.0%
AAGGCAGTTGCTGCACAAGC+CGG + chr1.4:77193064-77193083 None:intergenic 55.0%
ACCGCTTCCTTCAGAGTGCA+GGG - chr1.4:77192295-77192314 MS.gene60875:intron 55.0%
CGCCCATTTCGTGCAAGATC+AGG + chr1.4:77192555-77192574 None:intergenic 55.0%
CTAAGATGCCCCATGGCAGA+AGG + chr1.4:77192516-77192535 None:intergenic 55.0%
GCACAGGTGCTAGCTATCAC+TGG - chr1.4:77192356-77192375 MS.gene60875:intron 55.0%
GGATCACCTAGAGAATGGCC+TGG + chr1.4:77192495-77192514 None:intergenic 55.0%
GGCCCTGATCTTGCACGAAA+TGG - chr1.4:77192549-77192568 MS.gene60875:intron 55.0%
GGCCTGGAAACTGCATCTAC+AGG + chr1.4:77192603-77192622 None:intergenic 55.0%
GGGGAGGCTAGTGTAATTGG+TGG - chr1.4:77192438-77192457 MS.gene60875:intron 55.0%
GTAGATGCAGTTTCCAGGCC+CGG - chr1.4:77192603-77192622 MS.gene60875:CDS 55.0%
TGGTGTGACCTCAGGCAATG+AGG - chr1.4:77192200-77192219 MS.gene60875:CDS 55.0%
TTGCCTGAGGTCACACCAGA+AGG + chr1.4:77192198-77192217 None:intergenic 55.0%
! GGGCATCTTAGTGGTGTTGG+TGG - chr1.4:77192525-77192544 MS.gene60875:intron 55.0%
! TCTGCCATGGGGCATCTTAG+TGG - chr1.4:77192516-77192535 MS.gene60875:intron 55.0%
!! GGTGGTGTTGGATTGGCAAG+GGG - chr1.4:77192456-77192475 MS.gene60875:intron 55.0%
!! GTTGGATTGGCAAGGGGTGT+TGG - chr1.4:77192462-77192481 MS.gene60875:intron 55.0%
CCGCTTCCTTCAGAGTGCAG+GGG - chr1.4:77192296-77192315 MS.gene60875:intron 60.0%
GACCGCTTCCTTCAGAGTGC+AGG - chr1.4:77192294-77192313 MS.gene60875:intron 60.0%
GCACCTTCTGGTGTGACCTC+AGG - chr1.4:77192192-77192211 MS.gene60875:CDS 60.0%
TATTGTCTCAGGTCCGGGCC+TGG + chr1.4:77192619-77192638 None:intergenic 60.0%
! CCCCTGCACTCTGAAGGAAG+CGG + chr1.4:77192299-77192318 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 77192187 77193097 77192187 ID=MS.gene60875
chr1.4 mRNA 77192187 77193097 77192187 ID=MS.gene60875.t1;Parent=MS.gene60875
chr1.4 exon 77192967 77193097 77192967 ID=MS.gene60875.t1.exon1;Parent=MS.gene60875.t1
chr1.4 CDS 77192967 77193097 77192967 ID=cds.MS.gene60875.t1;Parent=MS.gene60875.t1
chr1.4 exon 77192570 77192867 77192570 ID=MS.gene60875.t1.exon2;Parent=MS.gene60875.t1
chr1.4 CDS 77192570 77192867 77192570 ID=cds.MS.gene60875.t1;Parent=MS.gene60875.t1
chr1.4 exon 77192380 77192441 77192380 ID=MS.gene60875.t1.exon3;Parent=MS.gene60875.t1
chr1.4 CDS 77192380 77192441 77192380 ID=cds.MS.gene60875.t1;Parent=MS.gene60875.t1
chr1.4 exon 77192187 77192268 77192187 ID=MS.gene60875.t1.exon4;Parent=MS.gene60875.t1
chr1.4 CDS 77192187 77192268 77192187 ID=cds.MS.gene60875.t1;Parent=MS.gene60875.t1
Gene Sequence

>MS.gene60875

ATACGGCACCTTCTGGTGTGACCTCAGGCAATGAGGTGCATAATTATATTGCTCAAAACAATGGTCACCAAATGCTAAACGACACTAAAACACTCGGGTCTGCTTATGACCGCTTCCTTCAGAGTGCAGGGGTAATATCATAACCCATTTTATTTTACATCTAATGTTCGCACAGGTGCTAGCTATCACTGGATGTTTGCTGAAAACTATCATCCTGTTTGATTGTGAAGCAGCTTACTTCATTTAATTCTGGGGAGGCTAGTGTAATTGGTGGTGTTGGATTGGCAAGGGGTGTTGGTGAATTTCCAGGCCATTCTCTAGGTGATCCTTCTGCCATGGGGCATCTTAGTGGTGTTGGTGGTGGCCCTGATCTTGCACGAAATGGGCGTAATGTCAATTTTGGTGGTCAGCTACCTGTAGATGCAGTTTCCAGGCCCGGACCTGAGACAATACCACTACCTCGAGATGCTTCAAGTACTTTATATGTTGAAGGGCTCCCATCTGACAGCACAAAAAGAGAAGTGGCTCGTATCCTTTTTATTTTTTATTTTTTTCTTTGATACTGTTTAGAAATCGCATTATCATGCTTTAATCGGTGTCTCCTGGGCTTCATTCATTTTAATCCAATTATTCAAGTTCCTTAACGTCATATTTAGATATTTTTCGCCCTTTTGTCGGATATAGAGAAGTAAGACTTGTGGCCAAAGAATCCAAACATGTAAGTGCATGTTTGTAACGGTTGTTGCTTGTCCTCTTTTGTCTTGGTTTATCACCTGATTGGTTTAAAGTTCCGTTGTGCTCTTTATGCTGAAACACTTGTTTATTGCAGCGAGGTGGAGATCCTTTAATCCTTTGTTTTGTAGATTTTGCAAATCCGGCTTGTGCAGCAACTGCCTTGAGCGCCTTGCAAG
Protein sequence

>MS.gene60875.t1

IRHLLVUPQAMRCIIILLKTMVTKCUTTLKHSGLLMTASFRVQGSLLHLILGRLVULVVLDWQGVLVNFQAILUVILLPWGILVVLVVALILHEMGVMSILVVSYLUMQFPGPDLRQYHYLEMLQVLYMLKGSHLTAQKEKWLIFFALLSDIEKUDLWPKNPNIEVEILUSFVLUILQIRLVQQLPUAPCK