AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040648

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040648.t1 MTR_1g050472 99.394 330 2 0 1 330 1 330 0.0 678
MS.gene040648.t1 MTR_0268s0080 96.970 330 10 0 1 330 1 330 0.0 667
MS.gene040648.t1 MTR_7g029110 96.061 330 13 0 1 330 1 330 0.0 641
MS.gene040648.t1 MTR_8g469010 92.727 330 19 1 1 330 1 325 0.0 634
MS.gene040648.t1 MTR_4g117370 76.308 325 76 1 6 330 18 341 0.0 532
MS.gene040648.t1 MTR_6g005270 67.442 43 14 0 265 307 25 67 1.63e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040648.t1 AT3G27060 83.735 332 52 2 1 330 1 332 0.0 558
MS.gene040648.t1 AT3G23580 76.308 325 76 1 6 330 18 341 0.0 518

Find 63 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAGAATCGGTCTGGGTTT+GGG 0.237047 1.2:-33462839 None:intergenic
GATTTCTTTCATGAATCTTC+CGG 0.282404 1.2:-33463054 None:intergenic
TGCGCATTGGTTGGGATGAA+TGG 0.293239 1.2:+33463542 MS.gene040648:CDS
GATGGAATTGATTTCGCTTC+AGG 0.300115 1.2:+33463661 MS.gene040648:CDS
CGCTTCCTTGCGCATTGGTT+GGG 0.302060 1.2:+33463534 MS.gene040648:CDS
GTTTGTTGCTGATAGGTTAT+TGG 0.303774 1.2:+33463589 MS.gene040648:CDS
GGGGCAAGAAGGGGTTCTTC+TGG 0.330658 1.2:-33462819 None:intergenic
ATGCAGAATCGGTCTGGGTT+TGG 0.338926 1.2:-33462840 None:intergenic
GCGCATTGGTTGGGATGAAT+GGG 0.350139 1.2:+33463543 MS.gene040648:CDS
AAGCTGATTGGGCGATGAAA+TGG 0.358474 1.2:+33463234 MS.gene040648:CDS
AATCGCTTATATAAGTTTCC+AGG 0.367855 1.2:-33463154 None:intergenic
ACAATTTCTTTCACGCGCTC+TGG 0.374811 1.2:-33463470 None:intergenic
TTTGTTGCTGATAGGTTATT+GGG 0.379609 1.2:+33463590 MS.gene040648:CDS
ATGTTCAGAATCCGTTTGAT+TGG 0.390491 1.2:+33463639 MS.gene040648:CDS
ACCGTAGAAGGCACGTGCTT+CGG 0.402800 1.2:-33463084 None:intergenic
GTCTGGGTTTGGGGCAAGAA+GGG 0.415976 1.2:-33462829 None:intergenic
GGGAACATGCAGAATCGGTC+TGG 0.418807 1.2:-33462846 None:intergenic
GCGCTTCCTTGCGCATTGGT+TGG 0.429604 1.2:+33463533 MS.gene040648:CDS
GTTGCATTTGCTTGTGTTGA+AGG 0.436600 1.2:+33463290 MS.gene040648:CDS
TCTGTTATGAATAGCTTGAA+TGG 0.443380 1.2:+33463731 MS.gene040648:CDS
TCAGAATCCGTTTGATTGGA+TGG 0.443597 1.2:+33463643 MS.gene040648:CDS
TCTGGGTTTGGGGCAAGAAG+GGG 0.444554 1.2:-33462828 None:intergenic
AGGCACGTGCTTCGGAGACT+TGG 0.444676 1.2:-33463076 None:intergenic
GCCGTCGGAGGCGGCGAAGA+AGG 0.452615 1.2:-33463012 None:intergenic
TGCAATCTGGAAACCGTAGA+AGG 0.456220 1.2:-33463096 None:intergenic
ATCGTCCTCGAAAATCTTGC+CGG 0.459150 1.2:+33463035 MS.gene040648:CDS
TGCGGTCCAGAATGAGGCTT+CGG 0.467026 1.2:-33462907 None:intergenic
GAAAATCGCACAGAAACTTC+CGG 0.473049 1.2:-33463324 None:intergenic
GAGGACGATGCCGTCGGAGG+CGG 0.474359 1.2:-33463021 None:intergenic
ATCAATTCCATCCAATCAAA+CGG 0.480364 1.2:-33463650 None:intergenic
CGACGCGCTTCCTTGCGCAT+TGG 0.483293 1.2:+33463529 MS.gene040648:CDS
GAGCTTATTTCACGTGATGA+AGG 0.484978 1.2:+33463392 MS.gene040648:CDS
TCCGAAGCACGTGCCTTCTA+CGG 0.485174 1.2:+33463083 MS.gene040648:CDS
GATAGGTTATTGGGTGAGCT+TGG 0.486660 1.2:+33463599 MS.gene040648:CDS
GGAACATGCAGAATCGGTCT+GGG 0.489835 1.2:-33462845 None:intergenic
CGCATTGGTTGGGATGAATG+GGG 0.491773 1.2:+33463544 MS.gene040648:CDS
ATATTGAGTTTGTTGCTGAT+AGG 0.493329 1.2:+33463582 MS.gene040648:CDS
TGAGATGTATTCTCTTCTCC+TGG 0.494276 1.2:+33463136 MS.gene040648:CDS
ATGGAATTGATTTCGCTTCA+GGG 0.495575 1.2:+33463662 MS.gene040648:CDS
GTGATGCTGTTGAAATTGAA+AGG 0.499878 1.2:+33463495 MS.gene040648:CDS
AGGGGTTCTTCTGGAAAAGC+AGG 0.505225 1.2:-33462810 None:intergenic
GGGTGAGCTTGGTTGTGAAA+AGG 0.505349 1.2:+33463610 MS.gene040648:CDS
GCCTTCTTCGCCGCCTCCGA+CGG 0.505987 1.2:+33463011 MS.gene040648:CDS
GGTCTGGGTTTGGGGCAAGA+AGG 0.509820 1.2:-33462830 None:intergenic
TTCTTCTGCGGTCCAGAATG+AGG 0.510696 1.2:-33462913 None:intergenic
GGATTGGGAACATGCAGAAT+CGG 0.521690 1.2:-33462851 None:intergenic
GCAGAATCGGTCTGGGTTTG+GGG 0.524980 1.2:-33462838 None:intergenic
TGAAATAAGCTCGTTTGAGA+AGG 0.538441 1.2:-33463381 None:intergenic
CGAGGACATGTGAGATGAAG+TGG 0.543318 1.2:-33462989 None:intergenic
TGATGCTGTTGAAATTGAAA+GGG 0.545948 1.2:+33463496 MS.gene040648:CDS
ATGAATAGCTTGAATGGTAA+TGG 0.546534 1.2:+33463737 MS.gene040648:CDS
TTTCCTCCGATCTCAAGCAC+TGG 0.566756 1.2:+33462943 MS.gene040648:CDS
TTCGAGGACGATGCCGTCGG+AGG 0.583990 1.2:-33463024 None:intergenic
TCGTTTGAGAAGGTTAATCC+CGG 0.587906 1.2:-33463371 None:intergenic
CGGAGGCGGCGAAGAAGGCG+AGG 0.590500 1.2:-33463007 None:intergenic
TGGAATTGATTTCGCTTCAG+GGG 0.591747 1.2:+33463663 MS.gene040648:CDS
GCATTGGTTGGGATGAATGG+GGG 0.596821 1.2:+33463545 MS.gene040648:CDS
TTCATCCCAACCAATGCGCA+AGG 0.604485 1.2:-33463539 None:intergenic
TTGCCAGTGCTTGAGATCGG+AGG 0.610798 1.2:-33462946 None:intergenic
CACTGGCAAAACCTCACTGA+CGG 0.643079 1.2:+33462960 MS.gene040648:CDS
AGTGGCGTTCGCCGTCAGTG+AGG 0.654051 1.2:-33462971 None:intergenic
GGAAAGATCGACTTCTTCTG+CGG 0.673797 1.2:-33462925 None:intergenic
GAAGAGAATACATCTCAGAG+TGG 0.694344 1.2:-33463130 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACACGCTTCTCAAAAAAAT+TGG - chr1.2:33463693-33463712 None:intergenic 30.0%
AATCCAATACCCAAAAATCT+GGG + chr1.2:33462869-33462888 MS.gene040648:CDS 30.0%
AATCGCTTATATAAGTTTCC+AGG - chr1.2:33463157-33463176 None:intergenic 30.0%
ATCAATTCCATCCAATCAAA+CGG - chr1.2:33463653-33463672 None:intergenic 30.0%
ATGAATAGCTTGAATGGTAA+TGG + chr1.2:33463737-33463756 MS.gene040648:CDS 30.0%
GATTTCTTTCATGAATCTTC+CGG - chr1.2:33463057-33463076 None:intergenic 30.0%
TCTGTTATGAATAGCTTGAA+TGG + chr1.2:33463731-33463750 MS.gene040648:CDS 30.0%
TGATGCTGTTGAAATTGAAA+GGG + chr1.2:33463496-33463515 MS.gene040648:CDS 30.0%
TTTGTTGCTGATAGGTTATT+GGG + chr1.2:33463590-33463609 MS.gene040648:CDS 30.0%
! TGTACATTTCCCAGATTTTT+GGG - chr1.2:33462881-33462900 None:intergenic 30.0%
! TTGTACATTTCCCAGATTTT+TGG - chr1.2:33462882-33462901 None:intergenic 30.0%
!! ATATTGAGTTTGTTGCTGAT+AGG + chr1.2:33463582-33463601 MS.gene040648:CDS 30.0%
!!! AATTTTTTTGAGAAGCGTGT+TGG + chr1.2:33463692-33463711 MS.gene040648:CDS 30.0%
!!! AGATTTTTGGGTATTGGATT+GGG - chr1.2:33462869-33462888 None:intergenic 30.0%
!!! ATTTTCTGGTTGAAAAAACG+TGG + chr1.2:33463341-33463360 MS.gene040648:CDS 30.0%
!!! ATTTTTTTGAGAAGCGTGTT+GGG + chr1.2:33463693-33463712 MS.gene040648:CDS 30.0%
AAAAAACGTGGTTTAATGCC+GGG + chr1.2:33463353-33463372 MS.gene040648:CDS 35.0%
ATGTTCAGAATCCGTTTGAT+TGG + chr1.2:33463639-33463658 MS.gene040648:CDS 35.0%
CAATCCAATACCCAAAAATC+TGG + chr1.2:33462868-33462887 MS.gene040648:CDS 35.0%
GAAAAAACGTGGTTTAATGC+CGG + chr1.2:33463352-33463371 MS.gene040648:CDS 35.0%
GTGATGCTGTTGAAATTGAA+AGG + chr1.2:33463495-33463514 MS.gene040648:CDS 35.0%
TATCGCGAAAAAAGCTGATT+GGG + chr1.2:33463223-33463242 MS.gene040648:CDS 35.0%
TGAAATAAGCTCGTTTGAGA+AGG - chr1.2:33463384-33463403 None:intergenic 35.0%
! ATGGAATTGATTTCGCTTCA+GGG + chr1.2:33463662-33463681 MS.gene040648:CDS 35.0%
! GGATGTTTTCAATTGCAATC+TGG - chr1.2:33463112-33463131 None:intergenic 35.0%
! GTTGAAGGAATCTTTTTCTC+CGG + chr1.2:33463305-33463324 MS.gene040648:CDS 35.0%
! GTTTGTTGCTGATAGGTTAT+TGG + chr1.2:33463589-33463608 MS.gene040648:CDS 35.0%
!!! CAGATTTTTGGGTATTGGAT+TGG - chr1.2:33462870-33462889 None:intergenic 35.0%
!!! TGCTGATTTTTGCTTCAAGT+TGG + chr1.2:33463763-33463782 MS.gene040648:CDS 35.0%
!!! TTTCCCAGATTTTTGGGTAT+TGG - chr1.2:33462875-33462894 None:intergenic 35.0%
!!! TTTTTTTGAGAAGCGTGTTG+GGG + chr1.2:33463694-33463713 MS.gene040648:CDS 35.0%
GAAAATCGCACAGAAACTTC+CGG - chr1.2:33463327-33463346 None:intergenic 40.0%
GAAGAGAATACATCTCAGAG+TGG - chr1.2:33463133-33463152 None:intergenic 40.0%
GAGCTTATTTCACGTGATGA+AGG + chr1.2:33463392-33463411 MS.gene040648:CDS 40.0%
GTATCGCGAAAAAAGCTGAT+TGG + chr1.2:33463222-33463241 MS.gene040648:CDS 40.0%
GTTGCATTTGCTTGTGTTGA+AGG + chr1.2:33463290-33463309 MS.gene040648:CDS 40.0%
TCAGAATCCGTTTGATTGGA+TGG + chr1.2:33463643-33463662 MS.gene040648:CDS 40.0%
TCGTTTGAGAAGGTTAATCC+CGG - chr1.2:33463374-33463393 None:intergenic 40.0%
TGAGATGTATTCTCTTCTCC+TGG + chr1.2:33463136-33463155 MS.gene040648:CDS 40.0%
! GAAGTTTCTGTGCGATTTTC+TGG + chr1.2:33463327-33463346 MS.gene040648:CDS 40.0%
! GATGGAATTGATTTCGCTTC+AGG + chr1.2:33463661-33463680 MS.gene040648:CDS 40.0%
! TGGAATTGATTTCGCTTCAG+GGG + chr1.2:33463663-33463682 MS.gene040648:CDS 40.0%
!!! TCAGCTTTTTTCGCGATACA+TGG - chr1.2:33463221-33463240 None:intergenic 40.0%
AAAAAGCCGAAGCCTCATTC+TGG + chr1.2:33462901-33462920 MS.gene040648:CDS 45.0%
AAGCTGATTGGGCGATGAAA+TGG + chr1.2:33463234-33463253 MS.gene040648:CDS 45.0%
ACAATTTCTTTCACGCGCTC+TGG - chr1.2:33463473-33463492 None:intergenic 45.0%
ATCGTCCTCGAAAATCTTGC+CGG + chr1.2:33463035-33463054 MS.gene040648:CDS 45.0%
GATAGGTTATTGGGTGAGCT+TGG + chr1.2:33463599-33463618 MS.gene040648:CDS 45.0%
GGATTGGGAACATGCAGAAT+CGG - chr1.2:33462854-33462873 None:intergenic 45.0%
TGCAATCTGGAAACCGTAGA+AGG - chr1.2:33463099-33463118 None:intergenic 45.0%
! ATCTTCCGGCAAGATTTTCG+AGG - chr1.2:33463043-33463062 None:intergenic 45.0%
! GGAAAGATCGACTTCTTCTG+CGG - chr1.2:33462928-33462947 None:intergenic 45.0%
! GTTTTGCCAGTGCTTGAGAT+CGG - chr1.2:33462952-33462971 None:intergenic 45.0%
ATGCAGAATCGGTCTGGGTT+TGG - chr1.2:33462843-33462862 None:intergenic 50.0%
CACTGGCAAAACCTCACTGA+CGG + chr1.2:33462960-33462979 MS.gene040648:CDS 50.0%
CGAGGACATGTGAGATGAAG+TGG - chr1.2:33462992-33463011 None:intergenic 50.0%
GGAACATGCAGAATCGGTCT+GGG - chr1.2:33462848-33462867 None:intergenic 50.0%
GGGTGAGCTTGGTTGTGAAA+AGG + chr1.2:33463610-33463629 MS.gene040648:CDS 50.0%
TGCAGAATCGGTCTGGGTTT+GGG - chr1.2:33462842-33462861 None:intergenic 50.0%
TTCATCCCAACCAATGCGCA+AGG - chr1.2:33463542-33463561 None:intergenic 50.0%
TTCTTCTGCGGTCCAGAATG+AGG - chr1.2:33462916-33462935 None:intergenic 50.0%
TTTCCTCCGATCTCAAGCAC+TGG + chr1.2:33462943-33462962 MS.gene040648:CDS 50.0%
! AGGGGTTCTTCTGGAAAAGC+AGG - chr1.2:33462813-33462832 None:intergenic 50.0%
!! ATTTTCGAGGACGATGCCGT+CGG - chr1.2:33463030-33463049 None:intergenic 50.0%
!! CGCATTGGTTGGGATGAATG+GGG + chr1.2:33463544-33463563 MS.gene040648:CDS 50.0%
!! GCATTGGTTGGGATGAATGG+GGG + chr1.2:33463545-33463564 MS.gene040648:CDS 50.0%
!! GCGCATTGGTTGGGATGAAT+GGG + chr1.2:33463543-33463562 MS.gene040648:CDS 50.0%
!! TGCGCATTGGTTGGGATGAA+TGG + chr1.2:33463542-33463561 MS.gene040648:CDS 50.0%
GCAGAATCGGTCTGGGTTTG+GGG - chr1.2:33462841-33462860 None:intergenic 55.0%
GGGAACATGCAGAATCGGTC+TGG - chr1.2:33462849-33462868 None:intergenic 55.0%
TCCGAAGCACGTGCCTTCTA+CGG + chr1.2:33463083-33463102 MS.gene040648:CDS 55.0%
TGCGGTCCAGAATGAGGCTT+CGG - chr1.2:33462910-33462929 None:intergenic 55.0%
TTGCCAGTGCTTGAGATCGG+AGG - chr1.2:33462949-33462968 None:intergenic 55.0%
! ACCGTAGAAGGCACGTGCTT+CGG - chr1.2:33463087-33463106 None:intergenic 55.0%
! GTCTGGGTTTGGGGCAAGAA+GGG - chr1.2:33462832-33462851 None:intergenic 55.0%
! TCTGGGTTTGGGGCAAGAAG+GGG - chr1.2:33462831-33462850 None:intergenic 55.0%
!! CGCTTCCTTGCGCATTGGTT+GGG + chr1.2:33463534-33463553 MS.gene040648:CDS 55.0%
AGGCACGTGCTTCGGAGACT+TGG - chr1.2:33463079-33463098 None:intergenic 60.0%
GGGGCAAGAAGGGGTTCTTC+TGG - chr1.2:33462822-33462841 None:intergenic 60.0%
! GCGCTTCCTTGCGCATTGGT+TGG + chr1.2:33463533-33463552 MS.gene040648:CDS 60.0%
! GGTCTGGGTTTGGGGCAAGA+AGG - chr1.2:33462833-33462852 None:intergenic 60.0%
AGTGGCGTTCGCCGTCAGTG+AGG - chr1.2:33462974-33462993 None:intergenic 65.0%
CGACGCGCTTCCTTGCGCAT+TGG + chr1.2:33463529-33463548 MS.gene040648:CDS 65.0%
TTCGAGGACGATGCCGTCGG+AGG - chr1.2:33463027-33463046 None:intergenic 65.0%
GAGGACGATGCCGTCGGAGG+CGG - chr1.2:33463024-33463043 None:intergenic 70.0%
GCCTTCTTCGCCGCCTCCGA+CGG + chr1.2:33463011-33463030 MS.gene040648:CDS 70.0%
CGGAGGCGGCGAAGAAGGCG+AGG - chr1.2:33463010-33463029 None:intergenic 75.0%
GCCGTCGGAGGCGGCGAAGA+AGG - chr1.2:33463015-33463034 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 33462807 33463799 33462807 ID=MS.gene040648
chr1.2 mRNA 33462807 33463799 33462807 ID=MS.gene040648.t1;Parent=MS.gene040648
chr1.2 exon 33462807 33463799 33462807 ID=MS.gene040648.t1.exon1;Parent=MS.gene040648.t1
chr1.2 CDS 33462807 33463799 33462807 ID=cds.MS.gene040648.t1;Parent=MS.gene040648.t1
Gene Sequence

>MS.gene040648

ATGCCTGCTTTTCCAGAAGAACCCCTTCTTGCCCCAAACCCAGACCGATTCTGCATGTTCCCAATCCAATACCCAAAAATCTGGGAAATGTACAAAAAAGCCGAAGCCTCATTCTGGACCGCAGAAGAAGTCGATCTTTCCTCCGATCTCAAGCACTGGCAAAACCTCACTGACGGCGAACGCCACTTCATCTCACATGTCCTCGCCTTCTTCGCCGCCTCCGACGGCATCGTCCTCGAAAATCTTGCCGGAAGATTCATGAAAGAAATCCAAGTCTCCGAAGCACGTGCCTTCTACGGTTTCCAGATTGCAATTGAAAACATCCACTCTGAGATGTATTCTCTTCTCCTGGAAACTTATATAAGCGATTCTGCTGAAAAGAATCGCTTATTTCACGCAATTGAAACAATTCCATGTATCGCGAAAAAAGCTGATTGGGCGATGAAATGGATCGATTCAAGCGATTCTTTTGCAGAAAGAATCGTTGCATTTGCTTGTGTTGAAGGAATCTTTTTCTCCGGAAGTTTCTGTGCGATTTTCTGGTTGAAAAAACGTGGTTTAATGCCGGGATTAACCTTCTCAAACGAGCTTATTTCACGTGATGAAGGATTACACTGTGATTTCGCTTGTTTGTTATACTCACTTCTACGCAAGAAGCTAAGTCCAGAGCGCGTGAAAGAAATTGTTTGTGATGCTGTTGAAATTGAAAGGGAGTTTGTGTGCGACGCGCTTCCTTGCGCATTGGTTGGGATGAATGGGGGTTTGATGAGTACGTATATTGAGTTTGTTGCTGATAGGTTATTGGGTGAGCTTGGTTGTGAAAAGGTTTACAATGTTCAGAATCCGTTTGATTGGATGGAATTGATTTCGCTTCAGGGGAAAACCAATTTTTTTGAGAAGCGTGTTGGGGAGTATCAGAAAGCTTCTGTTATGAATAGCTTGAATGGTAATGGTGCTGCTGATTTTTGCTTCAAGTTGGATGAAGATTTTTAG
Protein sequence

>MS.gene040648.t1

MPAFPEEPLLAPNPDRFCMFPIQYPKIWEMYKKAEASFWTAEEVDLSSDLKHWQNLTDGERHFISHVLAFFAASDGIVLENLAGRFMKEIQVSEARAFYGFQIAIENIHSEMYSLLLETYISDSAEKNRLFHAIETIPCIAKKADWAMKWIDSSDSFAERIVAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRKKLSPERVKEIVCDAVEIEREFVCDALPCALVGMNGGLMSTYIEFVADRLLGELGCEKVYNVQNPFDWMELISLQGKTNFFEKRVGEYQKASVMNSLNGNGAADFCFKLDEDF