AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043830

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043830.t1 MTR_2g061450 93.680 269 17 0 1 269 164 432 0.0 516
MS.gene043830.t1 MTR_2g060620 87.387 111 12 1 139 249 61 169 1.43e-62 195
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043830.t1 AT1G74120 57.993 269 113 0 1 269 177 445 1.33e-113 334
MS.gene043830.t1 AT5G54180 30.270 185 124 4 10 191 290 472 1.24e-14 73.9
MS.gene043830.t1 AT1G62010 32.787 122 79 3 101 220 268 388 2.78e-13 69.7
MS.gene043830.t1 AT1G62120 29.167 120 84 1 102 220 291 410 4.80e-11 62.8
MS.gene043830.t1 AT5G23930 29.091 110 74 1 120 225 336 445 6.46e-11 62.8
MS.gene043830.t1 AT1G62085 25.414 181 127 4 46 220 266 444 6.55e-11 62.8
MS.gene043830.t1 AT1G62085 25.414 181 127 4 46 220 266 444 6.55e-11 62.8

Find 62 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTCATGAGCTGAGGGGTTT+GGG 0.198657 2.2:+27512894 MS.gene043830:CDS
TAGATTGTTTCCTAGGGTTT+TGG 0.199228 2.2:+27512839 MS.gene043830:CDS
CATGTTCATCACATCTTTAC+TGG 0.212061 2.2:-27513519 None:intergenic
GATTCATGAGCTGAGGGGTT+TGG 0.264040 2.2:+27512893 MS.gene043830:CDS
CAACACTATATTTCATCCTT+TGG 0.303808 2.2:-27513214 None:intergenic
GAGGTTGATTGGTTATGATT+TGG 0.308965 2.2:+27513160 MS.gene043830:CDS
AGGTCAGGGCGGAGGTTGTT+AGG 0.309694 2.2:+27512931 MS.gene043830:CDS
TTGAAAGGAAAAGGTGCAAT+TGG 0.315697 2.2:+27513317 MS.gene043830:CDS
AAATTCACACCCAAGTATTC+AGG 0.317076 2.2:-27513254 None:intergenic
GATGAACATGAAGGCTTTCA+TGG 0.369314 2.2:+27513532 MS.gene043830:CDS
GAGTTGTTAGATTGTTTCCT+AGG 0.373935 2.2:+27512832 MS.gene043830:CDS
GGTGCAATTGGGTTTGAAGT+TGG 0.399622 2.2:+27513329 MS.gene043830:CDS
ACTCTATCAATTTCATCCTT+AGG 0.408293 2.2:-27512813 None:intergenic
TGGGATTTGGTATTGAGGAT+AGG 0.409253 2.2:+27512859 MS.gene043830:CDS
GAAAGCATCCCGTTGGACTT+TGG 0.413704 2.2:+27513465 MS.gene043830:CDS
TCACATCTTTACTGGTTTGA+GGG 0.416518 2.2:-27513511 None:intergenic
AATTCGTAGGGATGCTTTGA+AGG 0.418729 2.2:+27513121 MS.gene043830:CDS
TGGAAGGAACCGAGGTTGAT+TGG 0.420423 2.2:+27513149 MS.gene043830:CDS
ATCACATCTTTACTGGTTTG+AGG 0.423102 2.2:-27513512 None:intergenic
TGAAAGGAAAAGGTGCAATT+GGG 0.424464 2.2:+27513318 MS.gene043830:CDS
ATCTCCATTCCTAAAATCCT+TGG 0.428501 2.2:-27512957 None:intergenic
TGTTGCAGAGTTTGAAATGC+AGG 0.431814 2.2:+27513006 MS.gene043830:CDS
GCATGAAGTTCCTGAATACT+TGG 0.443861 2.2:+27513244 MS.gene043830:CDS
CCCCTCAGCTCATGAATCAA+TGG 0.448660 2.2:-27512888 None:intergenic
CAGCCGAGAGGTCAGGGCGG+AGG 0.450679 2.2:+27512923 MS.gene043830:CDS
TACTCAATCACATTGTATCT+AGG 0.456654 2.2:-27513293 None:intergenic
GCGGTCACGGTTTAATTCGT+AGG 0.464329 2.2:+27513108 MS.gene043830:CDS
GTTGATTGGTTATGATTTGG+AGG 0.468999 2.2:+27513163 MS.gene043830:CDS
TTATAAAATCTAAGCCTAGT+TGG 0.470603 2.2:-27513371 None:intergenic
CTCCGCCCTGACCTCTCGGC+TGG 0.473380 2.2:-27512922 None:intergenic
ATTGAGTATTTGAAAGGAAA+AGG 0.475963 2.2:+27513308 MS.gene043830:CDS
GGTCAGGGCGGAGGTTGTTA+GGG 0.481020 2.2:+27512932 MS.gene043830:CDS
AACATCTTCCAAAGTCCAAC+GGG 0.486105 2.2:-27513473 None:intergenic
GTGGATTGTTTGTGCGGTCA+CGG 0.490001 2.2:+27513095 MS.gene043830:CDS
TGTGGAATTTGGGATTCCTA+AGG 0.495755 2.2:+27512797 MS.gene043830:CDS
AATGTGATTGAGTATTTGAA+AGG 0.505696 2.2:+27513302 MS.gene043830:CDS
TTTGAGGGAACTTCGGTGGT+TGG 0.508881 2.2:-27513496 None:intergenic
TCATGGACTCGTTGGTGTAG+TGG 0.510176 2.2:+27513549 MS.gene043830:CDS
CGGTCACGGTTTAATTCGTA+GGG 0.517633 2.2:+27513109 MS.gene043830:CDS
TTCATGAGCTGAGGGGTTTG+GGG 0.523718 2.2:+27512895 MS.gene043830:CDS
GCCATTGATTCATGAGCTGA+GGG 0.528936 2.2:+27512887 MS.gene043830:CDS
TTACTGGTTTGAGGGAACTT+CGG 0.536810 2.2:-27513503 None:intergenic
AGTTGTTAGATTGTTTCCTA+GGG 0.538107 2.2:+27512833 MS.gene043830:CDS
CGGAGGTTGTTAGGGATCCA+AGG 0.538817 2.2:+27512940 MS.gene043830:CDS
CAACCTCCGCCCTGACCTCT+CGG 0.563699 2.2:-27512926 None:intergenic
ATACCAAATCCCAAAACCCT+AGG 0.565652 2.2:-27512849 None:intergenic
GAAGGCTTTCATGGACTCGT+TGG 0.570328 2.2:+27513541 MS.gene043830:CDS
CTGGTTTGAGGGAACTTCGG+TGG 0.572836 2.2:-27513500 None:intergenic
TGCTTTGAAGGTGTTGTGGA+AGG 0.580553 2.2:+27513133 MS.gene043830:CDS
CATGAAGTTCCTGAATACTT+GGG 0.593187 2.2:+27513245 MS.gene043830:CDS
AGCCATTGATTCATGAGCTG+AGG 0.597553 2.2:+27512886 MS.gene043830:CDS
AAGACATTATCAAACCAACT+AGG 0.602970 2.2:+27513357 MS.gene043830:CDS
GTTAAAAGAAAGCATCCCGT+TGG 0.604141 2.2:+27513458 MS.gene043830:CDS
TAAAGATGTGATGAACATGA+AGG 0.609470 2.2:+27513523 MS.gene043830:CDS
GGGATGCTTTGAAGGTGTTG+TGG 0.613256 2.2:+27513129 MS.gene043830:CDS
GTTGCAGAGTTTGAAATGCA+GGG 0.619561 2.2:+27513007 MS.gene043830:CDS
GAACATCTTCCAAAGTCCAA+CGG 0.624427 2.2:-27513474 None:intergenic
CTGAGAGTGGATTGTTTGTG+CGG 0.636549 2.2:+27513089 MS.gene043830:CDS
AAATCATAACCAATCAACCT+CGG 0.663302 2.2:-27513158 None:intergenic
CCATTGATTCATGAGCTGAG+GGG 0.690477 2.2:+27512888 MS.gene043830:CDS
TTCCAGCCGAGAGGTCAGGG+CGG 0.702811 2.2:+27512920 MS.gene043830:CDS
AGGTGTTGTGGAAGGAACCG+AGG 0.744040 2.2:+27513141 MS.gene043830:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTAAAGAGAAGATTTTTG+GGG + chr2.2:27513034-27513053 MS.gene043830:CDS 20.0%
!!! CAATTAAAGAGAAGATTTTT+GGG + chr2.2:27513033-27513052 MS.gene043830:CDS 20.0%
!!! CATATATTTTTTCACATTCA+GGG - chr2.2:27513415-27513434 None:intergenic 20.0%
! AATGTGATTGAGTATTTGAA+AGG + chr2.2:27513302-27513321 MS.gene043830:CDS 25.0%
! ATTGAGTATTTGAAAGGAAA+AGG + chr2.2:27513308-27513327 MS.gene043830:CDS 25.0%
! CCTGAATGTGAAAAAATATA+TGG + chr2.2:27513413-27513432 MS.gene043830:CDS 25.0%
! TTATAAAATCTAAGCCTAGT+TGG - chr2.2:27513374-27513393 None:intergenic 25.0%
!! AGATTGAGTTTTTAATCCAA+AGG + chr2.2:27513198-27513217 MS.gene043830:CDS 25.0%
!! GCAATTAAAGAGAAGATTTT+TGG + chr2.2:27513032-27513051 MS.gene043830:CDS 25.0%
!! TTGATTTTCTTGTGGAATTT+GGG + chr2.2:27512787-27512806 MS.gene043830:CDS 25.0%
!!! ATTGATTTTCTTGTGGAATT+TGG + chr2.2:27512786-27512805 MS.gene043830:CDS 25.0%
!!! CCATATATTTTTTCACATTC+AGG - chr2.2:27513416-27513435 None:intergenic 25.0%
AAATCATAACCAATCAACCT+CGG - chr2.2:27513161-27513180 None:intergenic 30.0%
AAGACATTATCAAACCAACT+AGG + chr2.2:27513357-27513376 MS.gene043830:CDS 30.0%
ACTCTATCAATTTCATCCTT+AGG - chr2.2:27512816-27512835 None:intergenic 30.0%
AGTTGTTAGATTGTTTCCTA+GGG + chr2.2:27512833-27512852 MS.gene043830:CDS 30.0%
CAACACTATATTTCATCCTT+TGG - chr2.2:27513217-27513236 None:intergenic 30.0%
TAAAGATGTGATGAACATGA+AGG + chr2.2:27513523-27513542 MS.gene043830:CDS 30.0%
TACTCAATCACATTGTATCT+AGG - chr2.2:27513296-27513315 None:intergenic 30.0%
! ATATGGCAGATTTTCAACAA+AGG + chr2.2:27513430-27513449 MS.gene043830:CDS 30.0%
!!! ATTTTTTCACATTCAGGGTA+AGG - chr2.2:27513410-27513429 None:intergenic 30.0%
!!! TAGTGTCATTGATTTTCTTG+TGG + chr2.2:27512779-27512798 MS.gene043830:CDS 30.0%
AAATTCACACCCAAGTATTC+AGG - chr2.2:27513257-27513276 None:intergenic 35.0%
ATCTCCATTCCTAAAATCCT+TGG - chr2.2:27512960-27512979 None:intergenic 35.0%
CATGAAGTTCCTGAATACTT+GGG + chr2.2:27513245-27513264 MS.gene043830:CDS 35.0%
CATGTTCATCACATCTTTAC+TGG - chr2.2:27513522-27513541 None:intergenic 35.0%
GAGTTGTTAGATTGTTTCCT+AGG + chr2.2:27512832-27512851 MS.gene043830:CDS 35.0%
! AGATTGTTTCCTAGGGTTTT+GGG + chr2.2:27512840-27512859 MS.gene043830:CDS 35.0%
! GAGGTTGATTGGTTATGATT+TGG + chr2.2:27513160-27513179 MS.gene043830:CDS 35.0%
! GTTGATTGGTTATGATTTGG+AGG + chr2.2:27513163-27513182 MS.gene043830:CDS 35.0%
! TAGATTGTTTCCTAGGGTTT+TGG + chr2.2:27512839-27512858 MS.gene043830:CDS 35.0%
! TGAAAGGAAAAGGTGCAATT+GGG + chr2.2:27513318-27513337 MS.gene043830:CDS 35.0%
! TTGAAAGGAAAAGGTGCAAT+TGG + chr2.2:27513317-27513336 MS.gene043830:CDS 35.0%
!! AAAGAGAAGATTTTTGGGGA+GGG + chr2.2:27513038-27513057 MS.gene043830:CDS 35.0%
!! AGGATTTTAGGAATGGAGAT+TGG + chr2.2:27512960-27512979 MS.gene043830:CDS 35.0%
!! ATCACATCTTTACTGGTTTG+AGG - chr2.2:27513515-27513534 None:intergenic 35.0%
!! GATTTTAGGAATGGAGATTG+GGG + chr2.2:27512962-27512981 MS.gene043830:CDS 35.0%
!! GGATTTTAGGAATGGAGATT+GGG + chr2.2:27512961-27512980 MS.gene043830:CDS 35.0%
!! TAAAGAGAAGATTTTTGGGG+AGG + chr2.2:27513037-27513056 MS.gene043830:CDS 35.0%
!! TCACATCTTTACTGGTTTGA+GGG - chr2.2:27513514-27513533 None:intergenic 35.0%
AACATCTTCCAAAGTCCAAC+GGG - chr2.2:27513476-27513495 None:intergenic 40.0%
AATTCGTAGGGATGCTTTGA+AGG + chr2.2:27513121-27513140 MS.gene043830:CDS 40.0%
ATACCAAATCCCAAAACCCT+AGG - chr2.2:27512852-27512871 None:intergenic 40.0%
GAACATCTTCCAAAGTCCAA+CGG - chr2.2:27513477-27513496 None:intergenic 40.0%
GATGAACATGAAGGCTTTCA+TGG + chr2.2:27513532-27513551 MS.gene043830:CDS 40.0%
GCATGAAGTTCCTGAATACT+TGG + chr2.2:27513244-27513263 MS.gene043830:CDS 40.0%
! GTTAGGGATCCAAGGATTTT+AGG + chr2.2:27512948-27512967 MS.gene043830:CDS 40.0%
! GTTGCAGAGTTTGAAATGCA+GGG + chr2.2:27513007-27513026 MS.gene043830:CDS 40.0%
! TGGAGATTGGGGAATTTTCA+CGG + chr2.2:27512973-27512992 MS.gene043830:CDS 40.0%
! TGGGATTTGGTATTGAGGAT+AGG + chr2.2:27512859-27512878 MS.gene043830:CDS 40.0%
! TGTGGAATTTGGGATTCCTA+AGG + chr2.2:27512797-27512816 MS.gene043830:CDS 40.0%
! TGTTGCAGAGTTTGAAATGC+AGG + chr2.2:27513006-27513025 MS.gene043830:CDS 40.0%
!! GGATCCAAGGATTTTAGGAA+TGG + chr2.2:27512953-27512972 MS.gene043830:CDS 40.0%
!! GTTAAAAGAAAGCATCCCGT+TGG + chr2.2:27513458-27513477 MS.gene043830:CDS 40.0%
!! TTACTGGTTTGAGGGAACTT+CGG - chr2.2:27513506-27513525 None:intergenic 40.0%
!!! GGTTTTGGGATTTGGTATTG+AGG + chr2.2:27512854-27512873 MS.gene043830:CDS 40.0%
!!! TTTCCTAGGGTTTTGGGATT+TGG + chr2.2:27512846-27512865 MS.gene043830:CDS 40.0%
!!! TTTTGAAGTGAAGCTGAGAG+TGG + chr2.2:27513076-27513095 MS.gene043830:CDS 40.0%
ATTCATGAGCTGAGGGGTTT+GGG + chr2.2:27512894-27512913 MS.gene043830:CDS 45.0%
CGGTCACGGTTTAATTCGTA+GGG + chr2.2:27513109-27513128 MS.gene043830:CDS 45.0%
! GGTGCAATTGGGTTTGAAGT+TGG + chr2.2:27513329-27513348 MS.gene043830:CDS 45.0%
!! AGCCATTGATTCATGAGCTG+AGG + chr2.2:27512886-27512905 MS.gene043830:CDS 45.0%
!! CCATTGATTCATGAGCTGAG+GGG + chr2.2:27512888-27512907 MS.gene043830:CDS 45.0%
!! CTGAGAGTGGATTGTTTGTG+CGG + chr2.2:27513089-27513108 MS.gene043830:CDS 45.0%
!! GAAGATTTTTGGGGAGGGTT+TGG + chr2.2:27513043-27513062 MS.gene043830:CDS 45.0%
!! GCCATTGATTCATGAGCTGA+GGG + chr2.2:27512887-27512906 MS.gene043830:CDS 45.0%
!! TGCTTTGAAGGTGTTGTGGA+AGG + chr2.2:27513133-27513152 MS.gene043830:CDS 45.0%
!! TTTTGGGGAGGGTTTGGTTA+GGG + chr2.2:27513049-27513068 MS.gene043830:CDS 45.0%
!! TTTTTGGGGAGGGTTTGGTT+AGG + chr2.2:27513048-27513067 MS.gene043830:CDS 45.0%
CCCCTCAGCTCATGAATCAA+TGG - chr2.2:27512891-27512910 None:intergenic 50.0%
GAAGGCTTTCATGGACTCGT+TGG + chr2.2:27513541-27513560 MS.gene043830:CDS 50.0%
GATTCATGAGCTGAGGGGTT+TGG + chr2.2:27512893-27512912 MS.gene043830:CDS 50.0%
GCGGTCACGGTTTAATTCGT+AGG + chr2.2:27513108-27513127 MS.gene043830:CDS 50.0%
TTCATGAGCTGAGGGGTTTG+GGG + chr2.2:27512895-27512914 MS.gene043830:CDS 50.0%
TTTGAGGGAACTTCGGTGGT+TGG - chr2.2:27513499-27513518 None:intergenic 50.0%
! GTGGATTGTTTGTGCGGTCA+CGG + chr2.2:27513095-27513114 MS.gene043830:CDS 50.0%
! TGGAAGGAACCGAGGTTGAT+TGG + chr2.2:27513149-27513168 MS.gene043830:CDS 50.0%
!! GAAAGCATCCCGTTGGACTT+TGG + chr2.2:27513465-27513484 MS.gene043830:CDS 50.0%
!! GGGATGCTTTGAAGGTGTTG+TGG + chr2.2:27513129-27513148 MS.gene043830:CDS 50.0%
CGGAGGTTGTTAGGGATCCA+AGG + chr2.2:27512940-27512959 MS.gene043830:CDS 55.0%
! AGGTGTTGTGGAAGGAACCG+AGG + chr2.2:27513141-27513160 MS.gene043830:CDS 55.0%
! CTGGTTTGAGGGAACTTCGG+TGG - chr2.2:27513503-27513522 None:intergenic 55.0%
! GTTTTCCAGCCGAGAGGTCA+GGG + chr2.2:27512917-27512936 MS.gene043830:CDS 55.0%
!! TTTGGGGTTTTCCAGCCGAG+AGG + chr2.2:27512911-27512930 MS.gene043830:CDS 55.0%
AGGTCAGGGCGGAGGTTGTT+AGG + chr2.2:27512931-27512950 MS.gene043830:CDS 60.0%
GGTCAGGGCGGAGGTTGTTA+GGG + chr2.2:27512932-27512951 MS.gene043830:CDS 60.0%
! GGTTTTCCAGCCGAGAGGTC+AGG + chr2.2:27512916-27512935 MS.gene043830:CDS 60.0%
CAACCTCCGCCCTGACCTCT+CGG - chr2.2:27512929-27512948 None:intergenic 65.0%
TTCCAGCCGAGAGGTCAGGG+CGG + chr2.2:27512920-27512939 MS.gene043830:CDS 65.0%
CAGCCGAGAGGTCAGGGCGG+AGG + chr2.2:27512923-27512942 MS.gene043830:CDS 75.0%
CTCCGCCCTGACCTCTCGGC+TGG - chr2.2:27512925-27512944 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 27512759 27513568 27512759 ID=MS.gene043830
chr2.2 mRNA 27512759 27513568 27512759 ID=MS.gene043830.t1;Parent=MS.gene043830
chr2.2 exon 27512759 27513568 27512759 ID=MS.gene043830.t1.exon1;Parent=MS.gene043830.t1
chr2.2 CDS 27512759 27513568 27512759 ID=cds.MS.gene043830.t1;Parent=MS.gene043830.t1
Gene Sequence

>MS.gene043830

ATGGGGGAAACTCAAATTGTTAGTGTCATTGATTTTCTTGTGGAATTTGGGATTCCTAAGGATGAAATTGATAGAGTTGTTAGATTGTTTCCTAGGGTTTTGGGATTTGGTATTGAGGATAGGCTGAAGCCATTGATTCATGAGCTGAGGGGTTTGGGGTTTTCCAGCCGAGAGGTCAGGGCGGAGGTTGTTAGGGATCCAAGGATTTTAGGAATGGAGATTGGGGAATTTTCACGGTGTTTGAAGTTGTTGCAGAGTTTGAAATGCAGGGATGCAATTAAAGAGAAGATTTTTGGGGAGGGTTTGGTTAGGGCTTGTTTTGAAGTGAAGCTGAGAGTGGATTGTTTGTGCGGTCACGGTTTAATTCGTAGGGATGCTTTGAAGGTGTTGTGGAAGGAACCGAGGTTGATTGGTTATGATTTGGAGGATATTGAGAAGAAGATTGAGTTTTTAATCCAAAGGATGAAATATAGTGTTGATTGTTTGCATGAAGTTCCTGAATACTTGGGTGTGAATTTTGAAAAACAGATTGTTCCTAGATACAATGTGATTGAGTATTTGAAAGGAAAAGGTGCAATTGGGTTTGAAGTTGGATTGAAAGACATTATCAAACCAACTAGGCTTAGATTTTATAATCTTTATGTCAAGCCTTACCCTGAATGTGAAAAAATATATGGCAGATTTTCAACAAAGGTTGAAGTTAAAAGAAAGCATCCCGTTGGACTTTGGAAGATGTTCCAACCACCGAAGTTCCCTCAAACCAGTAAAGATGTGATGAACATGAAGGCTTTCATGGACTCGTTGGTGTAG
Protein sequence

>MS.gene043830.t1

MGETQIVSVIDFLVEFGIPKDEIDRVVRLFPRVLGFGIEDRLKPLIHELRGLGFSSREVRAEVVRDPRILGMEIGEFSRCLKLLQSLKCRDAIKEKIFGEGLVRACFEVKLRVDCLCGHGLIRRDALKVLWKEPRLIGYDLEDIEKKIEFLIQRMKYSVDCLHEVPEYLGVNFEKQIVPRYNVIEYLKGKGAIGFEVGLKDIIKPTRLRFYNLYVKPYPECEKIYGRFSTKVEVKRKHPVGLWKMFQPPKFPQTSKDVMNMKAFMDSLV