AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002573

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002573.t1 MTR_2g016020 97.619 168 4 0 1 168 1 168 2.55e-120 336
MS.gene002573.t1 MTR_2g077940 35.928 167 88 4 8 161 11 171 2.81e-27 100
MS.gene002573.t1 MTR_2g077960 36.025 161 90 4 8 161 11 165 4.50e-27 100
MS.gene002573.t1 MTR_3g087540 34.091 132 79 5 28 155 25 152 6.91e-22 86.7
MS.gene002573.t1 MTR_3g073990 32.911 158 102 2 1 157 1 155 1.28e-21 86.3
MS.gene002573.t1 MTR_0390s0010 35.032 157 92 2 8 161 11 160 2.86e-19 80.1
MS.gene002573.t1 MTR_0786s0020 34.395 157 93 2 8 161 11 160 2.01e-18 77.8
MS.gene002573.t1 MTR_2g450190 33.758 157 91 3 8 161 11 157 3.47e-16 72.0
MS.gene002573.t1 MTR_0390s0040 33.758 157 91 3 8 161 11 157 3.47e-16 72.0
MS.gene002573.t1 MTR_2g077080 31.915 141 87 2 23 161 31 164 4.76e-14 66.2
MS.gene002573.t1 MTR_1678s0010 28.082 146 95 5 28 168 38 178 1.37e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002573.t1 AT1G29140 49.412 170 80 4 1 164 1 170 2.26e-50 159
MS.gene002573.t1 AT5G45880 53.571 140 63 2 27 164 34 173 8.99e-50 158
MS.gene002573.t1 AT4G18596 47.953 171 82 4 1 164 1 171 1.16e-49 158
MS.gene002573.t1 AT4G18596 47.953 171 82 4 1 164 47 217 6.37e-49 157
MS.gene002573.t1 AT4G08685 39.241 158 89 5 8 162 6 159 1.88e-31 111
MS.gene002573.t1 AT5G10130 37.349 166 94 3 1 162 1 160 6.64e-28 102
MS.gene002573.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1
MS.gene002573.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1
MS.gene002573.t1 AT1G78040 32.143 168 103 5 1 162 1 163 4.30e-21 85.1

Find 41 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAGAACCTCACCACATTT+AGG 0.300765 2.1:+69634242 None:intergenic
CGGTCAATCTGGTGATGAAT+TGG 0.316647 2.1:+69634924 None:intergenic
GTGGAATGCAAAGAAGAAAA+TGG 0.335509 2.1:-69634512 MS.gene002573:CDS
AGAGGGCTAGCAGCACGAAC+TGG 0.354642 2.1:+69634290 None:intergenic
CCTGAACGCTTCTTTGTAGA+AGG 0.366196 2.1:-69634974 MS.gene002573:CDS
AAATACAGTGTGGAGATAGA+TGG 0.398924 2.1:-69634446 MS.gene002573:CDS
GTTCGTGCTGCTAGCCCTCT+TGG 0.402448 2.1:-69634287 MS.gene002573:CDS
TAGGTAGACGCTCTTTCTTA+AGG 0.405456 2.1:+69634261 None:intergenic
TGATCCTAGCAGCTTGTTGT+AGG 0.405713 2.1:+69634342 None:intergenic
TTCAATGAACTCGGTCAATC+TGG 0.407937 2.1:+69634913 None:intergenic
TACAAAGAAGCGTTCAGGCT+TGG 0.439377 2.1:+69634979 None:intergenic
GAACTTGGAATTAATGAAGA+TGG 0.440677 2.1:-69634218 MS.gene002573:CDS
ACCTCTGAGCAATCTTTCCT+TGG 0.443518 2.1:+69634380 None:intergenic
GAAGCAACAACAGATAAATC+AGG 0.454577 2.1:-69634470 MS.gene002573:CDS
TAATGAAGATGGAACTGAAA+AGG 0.471543 2.1:-69634207 MS.gene002573:CDS
CCTTCTACAAAGAAGCGTTC+AGG 0.474728 2.1:+69634974 None:intergenic
GGAATAAGCCGCACCTAAGA+AGG 0.479861 2.1:+69635000 None:intergenic
GAGGGCTAGCAGCACGAACT+GGG 0.491624 2.1:+69634291 None:intergenic
AGATTGACCGAGTTCATTGA+AGG 0.500832 2.1:-69634911 MS.gene002573:intron
GGTGAGGTTCTCAAAGAACT+TGG 0.517638 2.1:-69634233 MS.gene002573:CDS
GGTCAATCTGGTGATGAATT+GGG 0.518245 2.1:+69634925 None:intergenic
CTTCACATGTTTCATCCTCA+TGG 0.533134 2.1:+69634420 None:intergenic
TTATTCTTTGCAAGAGTCCA+AGG 0.534437 2.1:-69634397 MS.gene002573:CDS
AAAAGCAAAGGGTGAAGACA+AGG 0.570670 2.1:+69635026 None:intergenic
TGAAGGTGCAACGGTGCGTG+TGG 0.602260 2.1:-69634531 MS.gene002573:intron
CTTTCTTAAGGAAACCAAGA+GGG 0.608256 2.1:+69634273 None:intergenic
ATCAGTGTCACAAACAACAA+TGG 0.613848 2.1:-69634323 MS.gene002573:CDS
AAGCAAAGGGTGAAGACAAG+GGG 0.617019 2.1:+69635028 None:intergenic
CTCACCTACAACAAGCTGCT+AGG 0.622703 2.1:-69634346 MS.gene002573:CDS
TGAAGATGGAACTGAAAAGG+AGG 0.627791 2.1:-69634204 MS.gene002573:CDS
GTACGTACCTTCAATGAACT+CGG 0.638216 2.1:+69634904 None:intergenic
AAAGAGCGTCTACCTAAATG+TGG 0.642536 2.1:-69634254 MS.gene002573:CDS
AGGGCTAGCAGCACGAACTG+GGG 0.655258 2.1:+69634292 None:intergenic
TATATGTAATGAAGGTGCAA+CGG 0.656510 2.1:-69634540 MS.gene002573:intron
AAAGCAAAGGGTGAAGACAA+GGG 0.660463 2.1:+69635027 None:intergenic
GCGTCTACCTAAATGTGGTG+AGG 0.675591 2.1:-69634249 MS.gene002573:CDS
TCTTTCTTAAGGAAACCAAG+AGG 0.685975 2.1:+69634272 None:intergenic
TAAATCAGGAAAATACAGTG+TGG 0.693438 2.1:-69634456 MS.gene002573:CDS
TCCAAGGAAAGATTGCTCAG+AGG 0.698789 2.1:-69634381 MS.gene002573:CDS
AGCAAAGGGTGAAGACAAGG+GGG 0.721824 2.1:+69635029 None:intergenic
GGAGATAGATGGAGACCATG+AGG 0.745188 2.1:-69634435 MS.gene002573:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATCTGAATTTTACTTTT+AGG + chr2.1:69634545-69634564 None:intergenic 15.0%
!!! GACATAAATAATAATTTTTG+TGG - chr2.1:69634679-69634698 MS.gene002573:intron 15.0%
! ACACATTTATTACTAAGAAG+CGG - chr2.1:69634605-69634624 MS.gene002573:intron 25.0%
! TAAGAAGGATAAAAAGCAAA+GGG + chr2.1:69634233-69634252 None:intergenic 25.0%
!!! TTTTACTTTTAGGTATTACG+AGG + chr2.1:69634535-69634554 None:intergenic 25.0%
CTAAGAAGGATAAAAAGCAA+AGG + chr2.1:69634234-69634253 None:intergenic 30.0%
GAACTTGGAATTAATGAAGA+TGG - chr2.1:69635027-69635046 MS.gene002573:CDS 30.0%
TAAATCAGGAAAATACAGTG+TGG - chr2.1:69634789-69634808 MS.gene002573:intron 30.0%
TAATGAAGATGGAACTGAAA+AGG - chr2.1:69635038-69635057 MS.gene002573:CDS 30.0%
TTGCACCTTCATTACATATA+TGG + chr2.1:69634705-69634724 None:intergenic 30.0%
! TATATGTAATGAAGGTGCAA+CGG - chr2.1:69634705-69634724 MS.gene002573:intron 30.0%
!!! CTTTGCTTTTTATCCTTCTT+AGG - chr2.1:69634232-69634251 MS.gene002573:CDS 30.0%
AAATACAGTGTGGAGATAGA+TGG - chr2.1:69634799-69634818 MS.gene002573:intron 35.0%
ACACGATACATATTTGACAC+CGG + chr2.1:69634421-69634440 None:intergenic 35.0%
ATATATGTGACAGTGTGTGT+TGG + chr2.1:69634450-69634469 None:intergenic 35.0%
ATCAGTGTCACAAACAACAA+TGG - chr2.1:69634922-69634941 MS.gene002573:CDS 35.0%
CTTTCTTAAGGAAACCAAGA+GGG + chr2.1:69634975-69634994 None:intergenic 35.0%
GAAGCAACAACAGATAAATC+AGG - chr2.1:69634775-69634794 MS.gene002573:intron 35.0%
GTGGAATGCAAAGAAGAAAA+TGG - chr2.1:69634733-69634752 MS.gene002573:intron 35.0%
TCTTTCTTAAGGAAACCAAG+AGG + chr2.1:69634976-69634995 None:intergenic 35.0%
TGTGGCCATATATGTAATGA+AGG - chr2.1:69634697-69634716 MS.gene002573:intron 35.0%
TTATTCTTTGCAAGAGTCCA+AGG - chr2.1:69634848-69634867 MS.gene002573:intron 35.0%
! CTTTTTATCCTTCTTAGGTG+CGG - chr2.1:69634237-69634256 MS.gene002573:CDS 35.0%
AAAAGCAAAGGGTGAAGACA+AGG + chr2.1:69634222-69634241 None:intergenic 40.0%
AAAGCAAAGGGTGAAGACAA+GGG + chr2.1:69634221-69634240 None:intergenic 40.0%
AGATTGACCGAGTTCATTGA+AGG - chr2.1:69634334-69634353 MS.gene002573:CDS 40.0%
CTTCACATGTTTCATCCTCA+TGG + chr2.1:69634828-69634847 None:intergenic 40.0%
GCAAGACATTCGATATGCTA+AGG + chr2.1:69634654-69634673 None:intergenic 40.0%
GTACGTACCTTCAATGAACT+CGG + chr2.1:69634344-69634363 None:intergenic 40.0%
TAGGTAGACGCTCTTTCTTA+AGG + chr2.1:69634987-69635006 None:intergenic 40.0%
TATACTCCTCGAATTATGCG+TGG - chr2.1:69634394-69634413 MS.gene002573:CDS 40.0%
TGAAGATGGAACTGAAAAGG+AGG - chr2.1:69635041-69635060 MS.gene002573:CDS 40.0%
TTCAATGAACTCGGTCAATC+TGG + chr2.1:69634335-69634354 None:intergenic 40.0%
TTGAGAACCTCACCACATTT+AGG + chr2.1:69635006-69635025 None:intergenic 40.0%
! GGTCAATCTGGTGATGAATT+GGG + chr2.1:69634323-69634342 None:intergenic 40.0%
!! AAAGAGCGTCTACCTAAATG+TGG - chr2.1:69634991-69635010 MS.gene002573:CDS 40.0%
AAGCAAAGGGTGAAGACAAG+GGG + chr2.1:69634220-69634239 None:intergenic 45.0%
ACCTCTGAGCAATCTTTCCT+TGG + chr2.1:69634868-69634887 None:intergenic 45.0%
CCTGAACGCTTCTTTGTAGA+AGG - chr2.1:69634271-69634290 MS.gene002573:CDS 45.0%
GGTGAGGTTCTCAAAGAACT+TGG - chr2.1:69635012-69635031 MS.gene002573:CDS 45.0%
TCCAAGGAAAGATTGCTCAG+AGG - chr2.1:69634864-69634883 MS.gene002573:intron 45.0%
! CGGTCAATCTGGTGATGAAT+TGG + chr2.1:69634324-69634343 None:intergenic 45.0%
!! CCTTCTACAAAGAAGCGTTC+AGG + chr2.1:69634274-69634293 None:intergenic 45.0%
!! TACAAAGAAGCGTTCAGGCT+TGG + chr2.1:69634269-69634288 None:intergenic 45.0%
!! TGATCCTAGCAGCTTGTTGT+AGG + chr2.1:69634906-69634925 None:intergenic 45.0%
AGCAAAGGGTGAAGACAAGG+GGG + chr2.1:69634219-69634238 None:intergenic 50.0%
CTCACCTACAACAAGCTGCT+AGG - chr2.1:69634899-69634918 MS.gene002573:intron 50.0%
GCGTCTACCTAAATGTGGTG+AGG - chr2.1:69634996-69635015 MS.gene002573:CDS 50.0%
GGAATAAGCCGCACCTAAGA+AGG + chr2.1:69634248-69634267 None:intergenic 50.0%
GGAGATAGATGGAGACCATG+AGG - chr2.1:69634810-69634829 MS.gene002573:intron 50.0%
TCCTCGAATTATGCGTGGTC+CGG - chr2.1:69634399-69634418 MS.gene002573:CDS 50.0%
ACCGGACCACGCATAATTCG+AGG + chr2.1:69634403-69634422 None:intergenic 55.0%
! AGAGGGCTAGCAGCACGAAC+TGG + chr2.1:69634958-69634977 None:intergenic 60.0%
! AGGGCTAGCAGCACGAACTG+GGG + chr2.1:69634956-69634975 None:intergenic 60.0%
! GAGGGCTAGCAGCACGAACT+GGG + chr2.1:69634957-69634976 None:intergenic 60.0%
! GTTCGTGCTGCTAGCCCTCT+TGG - chr2.1:69634958-69634977 MS.gene002573:CDS 60.0%
! TGAAGGTGCAACGGTGCGTG+TGG - chr2.1:69634714-69634733 MS.gene002573:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 69634199 69635068 69634199 ID=MS.gene002573
chr2.1 mRNA 69634199 69635068 69634199 ID=MS.gene002573.t1;Parent=MS.gene002573
chr2.1 exon 69634912 69635068 69634912 ID=MS.gene002573.t1.exon1;Parent=MS.gene002573.t1
chr2.1 CDS 69634912 69635068 69634912 ID=cds.MS.gene002573.t1;Parent=MS.gene002573.t1
chr2.1 exon 69634199 69634548 69634199 ID=MS.gene002573.t1.exon2;Parent=MS.gene002573.t1
chr2.1 CDS 69634199 69634548 69634199 ID=cds.MS.gene002573.t1;Parent=MS.gene002573.t1
Gene Sequence

>MS.gene002573

ATGGCAAAGTCTACAATCCCCCTTGTCTTCACCCTTTGCTTTTTATCCTTCTTAGGTGCGGCTTATTCCAAGCCTGAACGCTTCTTTGTAGAAGGTGTTGTTTACTGTGACACATGTCGCACCCAATTCATCACCAGATTGACCGAGTTCATTGAAGGTACGTACATATTTTTTAATGTGAATCTATGAAGCACATATACTCCTCGAATTATGCGTGGTCCGGTGTCAAATATGTATCGTGTCTGACACCAACACACACTGTCACATATATGTCATTTTCTTAAATCATTATCGATGTTCACATGTCGTGTCGTGTCTAGTGTATAGTCTGTGCCTCGTAATACCTAAAAGTAAAATTCAGATTATTGATTTTTATTTTTTTAAAGAGTCTAACGATGAAACTCACACACATTTATTACTAAGAAGCGGAGAATTAAGAGTTCTAACTCGTGCCTTAGCATATCGAATGTCTTGCAACTTGACATAAATAATAATTTTTGTGGCCATATATGTAATGAAGGTGCAACGGTGCGTGTGGAATGCAAAGAAGAAAATGGAACATTGACATTCAACAAAGAAGCAACAACAGATAAATCAGGAAAATACAGTGTGGAGATAGATGGAGACCATGAGGATGAAACATGTGAAGTTATTCTTTGCAAGAGTCCAAGGAAAGATTGCTCAGAGGTTGACTCAGAAGCTCACCTACAACAAGCTGCTAGGATCAGTGTCACAAACAACAATGGAATTGTGTCCCCAGTTCGTGCTGCTAGCCCTCTTGGTTTCCTTAAGAAAGAGCGTCTACCTAAATGTGGTGAGGTTCTCAAAGAACTTGGAATTAATGAAGATGGAACTGAAAAGGAGGACTAG
Protein sequence

>MS.gene002573.t1

MAKSTIPLVFTLCFLSFLGAAYSKPERFFVEGVVYCDTCRTQFITRLTEFIEGATVRVECKEENGTLTFNKEATTDKSGKYSVEIDGDHEDETCEVILCKSPRKDCSEVDSEAHLQQAARISVTNNNGIVSPVRAASPLGFLKKERLPKCGEVLKELGINEDGTEKED