AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049462

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049462.t1 MTR_5g082910 89.041 73 8 0 16 88 5 77 2.37e-41 138
MS.gene049462.t1 MTR_5g016510 65.574 61 21 0 27 87 2 62 1.72e-23 92.8
MS.gene049462.t1 MTR_3g101290 52.564 78 33 1 27 104 34 107 1.02e-22 89.0
MS.gene049462.t1 MTR_4g094982 63.934 61 22 0 27 87 2 62 1.36e-22 89.4
MS.gene049462.t1 MTR_6g015455 62.295 61 23 0 27 87 2 62 3.90e-20 85.1
MS.gene049462.t1 MTR_4g019370 61.017 59 23 0 28 86 36 94 5.30e-19 80.9
MS.gene049462.t1 MTR_6g027340 39.130 69 42 0 18 86 4 72 1.88e-13 64.3
MS.gene049462.t1 MTR_5g010650 46.774 62 33 0 25 86 105 166 4.62e-13 64.7
MS.gene049462.t1 MTR_3g089045 49.123 57 29 0 30 86 16 72 9.04e-13 63.5
MS.gene049462.t1 MTR_6g027360 39.130 69 42 0 18 86 66 134 9.65e-13 63.5
MS.gene049462.t1 MTR_6g027370 48.276 58 30 0 29 86 98 155 1.33e-12 63.2
MS.gene049462.t1 MTR_3g110028 48.214 56 29 0 25 80 80 135 2.80e-12 62.4
MS.gene049462.t1 MTR_6g074860 47.368 57 30 0 30 86 4 60 6.44e-12 60.5
MS.gene049462.t1 MTR_5g488170 49.180 61 30 1 27 86 11 71 1.90e-11 59.3
MS.gene049462.t1 MTR_5g088080 49.180 61 30 1 27 86 11 71 2.05e-11 59.3
MS.gene049462.t1 MTR_5g088150 49.180 61 30 1 27 86 11 71 2.05e-11 59.3
MS.gene049462.t1 MTR_5g488210 49.180 61 30 1 27 86 11 71 2.05e-11 59.3
MS.gene049462.t1 MTR_5g088640 49.180 61 30 1 27 86 11 71 2.06e-11 59.7
MS.gene049462.t1 MTR_1g026870 44.643 56 31 0 25 80 80 135 2.61e-11 59.7
MS.gene049462.t1 MTR_5g041570 40.000 75 41 1 16 86 116 190 2.62e-11 59.7
MS.gene049462.t1 MTR_5g062790 49.180 61 30 1 27 86 8 68 3.04e-11 59.3
MS.gene049462.t1 MTR_3g077650 47.170 53 28 0 29 81 180 232 5.13e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049462.t1 AT3G50060 53.165 79 33 1 26 104 2 76 2.95e-23 92.0
MS.gene049462.t1 AT5G67300 63.333 60 22 0 27 86 3 62 1.73e-21 87.0
MS.gene049462.t1 AT2G23290 52.564 78 33 1 27 104 10 83 6.24e-21 85.9
MS.gene049462.t1 AT4G37260 57.143 63 27 0 24 86 7 69 4.16e-20 83.6
MS.gene049462.t1 AT2G39880 52.703 74 31 1 13 86 37 106 5.77e-20 84.0
MS.gene049462.t1 AT3G55730 59.322 59 24 0 28 86 54 112 5.00e-19 81.3
MS.gene049462.t1 AT3G09230 57.353 68 29 0 19 86 44 111 1.46e-18 80.1
MS.gene049462.t1 AT1G73410 49.123 57 29 0 30 86 6 62 6.28e-13 62.8
MS.gene049462.t1 AT1G73410 49.123 57 29 0 30 86 6 62 6.68e-13 63.2
MS.gene049462.t1 AT1G17950 47.368 57 30 0 30 86 5 61 5.73e-12 60.8
MS.gene049462.t1 AT4G33450 45.614 57 31 0 30 86 19 75 6.40e-12 60.8
MS.gene049462.t1 AT5G11050 45.283 53 29 0 29 81 104 156 1.24e-11 60.5
MS.gene049462.t1 AT4G32730 48.214 56 29 0 25 80 82 137 1.45e-11 60.5
MS.gene049462.t1 AT4G32730 48.214 56 29 0 25 80 82 137 1.45e-11 60.5
MS.gene049462.t1 AT4G32730 48.214 56 29 0 25 80 82 137 1.45e-11 60.5
MS.gene049462.t1 AT4G32730 48.214 56 29 0 25 80 82 137 1.45e-11 60.5
MS.gene049462.t1 AT4G32730 48.214 56 29 0 25 80 82 137 1.62e-11 60.5
MS.gene049462.t1 AT3G09370 44.643 56 31 0 25 80 138 193 1.66e-11 60.5
MS.gene049462.t1 AT3G09370 44.643 56 31 0 25 80 125 180 1.71e-11 60.1
MS.gene049462.t1 AT3G09370 44.643 56 31 0 25 80 130 185 1.73e-11 60.1
MS.gene049462.t1 AT5G11510 44.643 56 31 0 25 80 76 131 2.01e-11 60.1
MS.gene049462.t1 AT5G11510 44.643 56 31 0 25 80 76 131 2.01e-11 60.1
MS.gene049462.t1 AT5G11510 44.643 56 31 0 25 80 76 131 2.01e-11 60.1
MS.gene049462.t1 AT5G17800 47.368 57 30 0 30 86 93 149 2.17e-11 59.7
MS.gene049462.t1 AT5G02320 45.614 57 31 0 25 81 122 178 2.19e-11 60.1
MS.gene049462.t1 AT5G02320 45.614 57 31 0 25 81 122 178 2.19e-11 60.1
MS.gene049462.t1 AT5G02320 43.548 62 35 0 25 86 62 123 2.32e-11 59.7
MS.gene049462.t1 AT5G11510 44.643 56 31 0 25 80 76 131 2.35e-11 60.1
MS.gene049462.t1 AT5G11510 44.643 56 31 0 25 80 76 131 2.51e-11 59.7
MS.gene049462.t1 AT5G58850 41.509 53 31 0 29 81 104 156 3.87e-11 59.3

Find 28 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTAAAATTTCCATATGTTT+TGG 0.296719 3.2:+56631272 MS.gene049462:intron
GCCACCACCGCCGGTGTAAA+AGG 0.337215 3.2:-56630805 None:intergenic
AACGGAATCCCCGATCGTTC+TGG 0.385664 3.2:+56630727 MS.gene049462:CDS
AGGAAAACGGTGCAAGAAAC+TGG 0.414736 3.2:+56630692 MS.gene049462:CDS
TCAAAAGGAACCAAAACATA+TGG 0.425019 3.2:-56631282 None:intergenic
ACCACCGTTTGAATTCGAAT+TGG 0.426843 3.2:-56630593 None:intergenic
AGATGAAACATTGGTGAAAC+TGG 0.432466 3.2:+56630666 MS.gene049462:CDS
ACGGAATCCCCGATCGTTCT+GGG 0.435316 3.2:+56630728 MS.gene049462:CDS
TCGAATTCAAACGGTGGTGG+TGG 0.444499 3.2:+56630598 MS.gene049462:CDS
GTGATGAAGTGAAGAGTTCA+TGG 0.455401 3.2:+56630632 MS.gene049462:CDS
CAAAACTTCCCAGAACGATC+GGG 0.482750 3.2:-56630736 None:intergenic
ATGGCCAAGGGACGATCAAA+AGG 0.494112 3.2:-56631297 None:intergenic
CGAATTCAAACGGTGGTGGT+GGG 0.506583 3.2:+56630599 MS.gene049462:CDS
GCAAAACTTCCCAGAACGAT+CGG 0.556052 3.2:-56630737 None:intergenic
AGTACCAATTCGAATTCAAA+CGG 0.564007 3.2:+56630589 MS.gene049462:CDS
GAATTCAAACGGTGGTGGTG+GGG 0.567365 3.2:+56630600 MS.gene049462:CDS
AAAGGAAGGTGTTGAACGGT+TGG 0.567448 3.2:-56630787 None:intergenic
GGTGGTGGTGGGGATGAAAA+CGG 0.571134 3.2:+56630610 MS.gene049462:CDS
CCACCGCCGGTGTAAAAGGA+AGG 0.581661 3.2:-56630801 None:intergenic
GATTGTTGTGCCACCACCGC+CGG 0.590963 3.2:-56630814 None:intergenic
AACTGGTCTGTGATAAGCAA+CGG 0.591578 3.2:+56630709 MS.gene049462:CDS
GTGAAACTGGTGAAGGAAAA+CGG 0.592557 3.2:+56630679 MS.gene049462:CDS
GCTGATTACACCACCGCAGA+CGG 0.606009 3.2:-56630759 None:intergenic
AATTCGAATTCAAACGGTGG+TGG 0.622740 3.2:+56630595 MS.gene049462:CDS
TGTAAAAGGAAGGTGTTGAA+CGG 0.650810 3.2:-56630791 None:intergenic
AACATTGGTGAAACTGGTGA+AGG 0.661429 3.2:+56630672 MS.gene049462:CDS
AAAACTTCCCAGAACGATCG+GGG 0.663763 3.2:-56630735 None:intergenic
ACCAATTCGAATTCAAACGG+TGG 0.728179 3.2:+56630592 MS.gene049462:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTTTGTTAAAATGT+AGG + chr3.2:56631251-56631270 MS.gene049462:intron 15.0%
!! ATATATGTGTAAAGTGTAAT+TGG + chr3.2:56631188-56631207 MS.gene049462:intron 20.0%
! TAAAAACGAAGATGAAACAT+TGG + chr3.2:56630657-56630676 MS.gene049462:CDS 25.0%
!! GGTAAAATTTCCATATGTTT+TGG + chr3.2:56631272-56631291 MS.gene049462:intron 25.0%
!!! ATTCTTCGATTTTTTGGAAT+GGG + chr3.2:56630869-56630888 MS.gene049462:intron 25.0%
ACGAGATTCAATCCTAAAAA+TGG - chr3.2:56631319-56631338 None:intergenic 30.0%
AGTACCAATTCGAATTCAAA+CGG + chr3.2:56630589-56630608 MS.gene049462:CDS 30.0%
CAAAAATCAGCAATGTTGTA+AGG - chr3.2:56631026-56631045 None:intergenic 30.0%
TCAAAAGGAACCAAAACATA+TGG - chr3.2:56631285-56631304 None:intergenic 30.0%
TCCAAAAAATCGAAGAATCT+TGG - chr3.2:56630867-56630886 None:intergenic 30.0%
!! TGATAGCTTTGTTAAAGTCT+TGG + chr3.2:56631134-56631153 MS.gene049462:intron 30.0%
!!! ACCAAGATTCTTCGATTTTT+TGG + chr3.2:56630863-56630882 MS.gene049462:intron 30.0%
!!! GATTCTTCGATTTTTTGGAA+TGG + chr3.2:56630868-56630887 MS.gene049462:intron 30.0%
AAGCTTTACCAAGCAATTTG+AGG - chr3.2:56631089-56631108 None:intergenic 35.0%
AGAAGAAGAAGAAGAGAAGA+AGG + chr3.2:56630976-56630995 MS.gene049462:intron 35.0%
AGATGAAACATTGGTGAAAC+TGG + chr3.2:56630666-56630685 MS.gene049462:CDS 35.0%
GTCTGATTCAGAGTGAAATT+CGG + chr3.2:56630893-56630912 MS.gene049462:intron 35.0%
TCAATCCTAAAAATGGCCAA+GGG - chr3.2:56631312-56631331 None:intergenic 35.0%
TCTGATTCAGAGTGAAATTC+GGG + chr3.2:56630894-56630913 MS.gene049462:intron 35.0%
TTCAATCCTAAAAATGGCCA+AGG - chr3.2:56631313-56631332 None:intergenic 35.0%
TTCTTCTTCTTTCCTTCTTC+TGG - chr3.2:56630966-56630985 None:intergenic 35.0%
TTTACGTGTTAGAATCGCTT+AGG + chr3.2:56631162-56631181 MS.gene049462:intron 35.0%
!! TGTAAAAGGAAGGTGTTGAA+CGG - chr3.2:56630794-56630813 None:intergenic 35.0%
AACATTGGTGAAACTGGTGA+AGG + chr3.2:56630672-56630691 MS.gene049462:CDS 40.0%
AATTCGAATTCAAACGGTGG+TGG + chr3.2:56630595-56630614 MS.gene049462:CDS 40.0%
ACCAATTCGAATTCAAACGG+TGG + chr3.2:56630592-56630611 MS.gene049462:CDS 40.0%
ACCACCGTTTGAATTCGAAT+TGG - chr3.2:56630596-56630615 None:intergenic 40.0%
ATCAGCAATGTTGTAAGGCA+AGG - chr3.2:56631021-56631040 None:intergenic 40.0%
GGAAGAAGAAGAAGAAGTGA+CGG + chr3.2:56630915-56630934 MS.gene049462:intron 40.0%
GTGAAACTGGTGAAGGAAAA+CGG + chr3.2:56630679-56630698 MS.gene049462:CDS 40.0%
GTGATGAAGTGAAGAGTTCA+TGG + chr3.2:56630632-56630651 MS.gene049462:CDS 40.0%
! AACTGGTCTGTGATAAGCAA+CGG + chr3.2:56630709-56630728 MS.gene049462:CDS 40.0%
! ACCAAGCAATTTGAGGCAAA+CGG - chr3.2:56631082-56631101 None:intergenic 40.0%
! TCAACACCTTCCTTTTACAC+CGG + chr3.2:56630795-56630814 MS.gene049462:CDS 40.0%
!! TCTTTCCTTCTTCTGGTTTG+CGG - chr3.2:56630959-56630978 None:intergenic 40.0%
AAAACTTCCCAGAACGATCG+GGG - chr3.2:56630738-56630757 None:intergenic 45.0%
AAACCTACTTGGCAAGAAGG+AGG - chr3.2:56631059-56631078 None:intergenic 45.0%
AACCTACTTGGCAAGAAGGA+GGG - chr3.2:56631058-56631077 None:intergenic 45.0%
AGAAGAAGAAGAAGTGACGG+TGG + chr3.2:56630918-56630937 MS.gene049462:intron 45.0%
AGGAAAACGGTGCAAGAAAC+TGG + chr3.2:56630692-56630711 MS.gene049462:CDS 45.0%
CAAAACTTCCCAGAACGATC+GGG - chr3.2:56630739-56630758 None:intergenic 45.0%
GCAAAACTTCCCAGAACGAT+CGG - chr3.2:56630740-56630759 None:intergenic 45.0%
TCCGTTTGCCTCAAATTGCT+TGG + chr3.2:56631078-56631097 MS.gene049462:intron 45.0%
!! AAAGGAAGGTGTTGAACGGT+TGG - chr3.2:56630790-56630809 None:intergenic 45.0%
!!! ATCGTCCCTTGGCCATTTTT+AGG + chr3.2:56631304-56631323 MS.gene049462:CDS 45.0%
AATGTTGTAAGGCAAGGCCC+AGG - chr3.2:56631015-56631034 None:intergenic 50.0%
AGAAGAAGAAGTGACGGTGG+AGG + chr3.2:56630921-56630940 MS.gene049462:intron 50.0%
ATGGCCAAGGGACGATCAAA+AGG - chr3.2:56631300-56631319 None:intergenic 50.0%
CGGAAACCTACTTGGCAAGA+AGG - chr3.2:56631062-56631081 None:intergenic 50.0%
GAAGAAGAAGTGACGGTGGA+GGG + chr3.2:56630922-56630941 MS.gene049462:intron 50.0%
GAGGCAAACGGAAACCTACT+TGG - chr3.2:56631070-56631089 None:intergenic 50.0%
! ACACCTTCCTTTTACACCGG+CGG + chr3.2:56630798-56630817 MS.gene049462:CDS 50.0%
! CGAATTCAAACGGTGGTGGT+GGG + chr3.2:56630599-56630618 MS.gene049462:CDS 50.0%
! GAATTCAAACGGTGGTGGTG+GGG + chr3.2:56630600-56630619 MS.gene049462:CDS 50.0%
! GGTTCCTTTTGATCGTCCCT+TGG + chr3.2:56631293-56631312 MS.gene049462:CDS 50.0%
! TCGAATTCAAACGGTGGTGG+TGG + chr3.2:56630598-56630617 MS.gene049462:CDS 50.0%
!! AGAGAAGAAGGAGTGCTACG+TGG + chr3.2:56630988-56631007 MS.gene049462:intron 50.0%
!! GAGAAGAAGGAGTGCTACGT+GGG + chr3.2:56630989-56631008 MS.gene049462:intron 50.0%
AACGGAATCCCCGATCGTTC+TGG + chr3.2:56630727-56630746 MS.gene049462:CDS 55.0%
AAGTGACGGTGGAGGGAGAA+AGG + chr3.2:56630929-56630948 MS.gene049462:intron 55.0%
ACGGAATCCCCGATCGTTCT+GGG + chr3.2:56630728-56630747 MS.gene049462:CDS 55.0%
CACCCTCCTTCTTGCCAAGT+AGG + chr3.2:56631053-56631072 MS.gene049462:intron 55.0%
GACTGCCGCAAACCAGAAGA+AGG + chr3.2:56630951-56630970 MS.gene049462:intron 55.0%
GCTGATTACACCACCGCAGA+CGG - chr3.2:56630762-56630781 None:intergenic 55.0%
! CTGGGAAGTTTTGCCGTCTG+CGG + chr3.2:56630746-56630765 MS.gene049462:CDS 55.0%
!! GGTGGTGGTGGGGATGAAAA+CGG + chr3.2:56630610-56630629 MS.gene049462:CDS 55.0%
CCACCGCCGGTGTAAAAGGA+AGG - chr3.2:56630804-56630823 None:intergenic 60.0%
GATTGTTGTGCCACCACCGC+CGG - chr3.2:56630817-56630836 None:intergenic 60.0%
! CCTTCCTTTTACACCGGCGG+TGG + chr3.2:56630801-56630820 MS.gene049462:CDS 60.0%
! CTTGGCAAGAAGGAGGGTGC+AGG - chr3.2:56631052-56631071 None:intergenic 60.0%
! GGAAGTTTTGCCGTCTGCGG+TGG + chr3.2:56630749-56630768 MS.gene049462:CDS 60.0%
! TCCTTTTACACCGGCGGTGG+TGG + chr3.2:56630804-56630823 MS.gene049462:CDS 60.0%
!! AAGGAGTGCTACGTGGGCCT+GGG + chr3.2:56630995-56631014 MS.gene049462:intron 60.0%
GCCACCACCGCCGGTGTAAA+AGG - chr3.2:56630808-56630827 None:intergenic 65.0%
!! GAAGGAGTGCTACGTGGGCC+TGG + chr3.2:56630994-56631013 MS.gene049462:intron 65.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 56630556 56631344 56630556 ID=MS.gene049462
chr3.2 mRNA 56630556 56631344 56630556 ID=MS.gene049462.t1;Parent=MS.gene049462
chr3.2 exon 56630556 56630858 56630556 ID=MS.gene049462.t1.exon1;Parent=MS.gene049462.t1
chr3.2 CDS 56630556 56630858 56630556 ID=cds.MS.gene049462.t1;Parent=MS.gene049462.t1
chr3.2 exon 56631273 56631344 56631273 ID=MS.gene049462.t1.exon2;Parent=MS.gene049462.t1
chr3.2 CDS 56631273 56631344 56631273 ID=cds.MS.gene049462.t1;Parent=MS.gene049462.t1
Gene Sequence

>MS.gene049462

ATGGTAGAAGAAAAGAGGATCAGTGCAAATTCGAGTACCAATTCGAATTCAAACGGTGGTGGTGGGGATGAAAACGGTGATGAAGTGAAGAGTTCATGGAGTAAAAACGAAGATGAAACATTGGTGAAACTGGTGAAGGAAAACGGTGCAAGAAACTGGTCTGTGATAAGCAACGGAATCCCCGATCGTTCTGGGAAGTTTTGCCGTCTGCGGTGGTGTAATCAGCTGAGTCCAACCGTTCAACACCTTCCTTTTACACCGGCGGTGGTGGCACAACAATCATCGACGAGAATTACTGAATCTGTGCACCAAGATTCTTCGATTTTTTGGAATGGGAGTCTGATTCAGAGTGAAATTCGGGAAGAAGAAGAAGAAGTGACGGTGGAGGGAGAAAGGACTGCCGCAAACCAGAAGAAGGAAAGAAGAAGAAGAAGAGAAGAAGGAGTGCTACGTGGGCCTGGGCCTTGCCTTACAACATTGCTGATTTTTGCTACCTGCACCCTCCTTCTTGCCAAGTAGGTTTCCGTTTGCCTCAAATTGCTTGGTAAAGCTTCTAAAATTCTTCTAATTGTTTTTCTTGATAGCTTTGTTAAAGTCTTGGTGTGTTTTACGTGTTAGAATCGCTTAGGAAAATATATGTGTAAAGTGTAATTGGTATTGTTACTTTTTTTTTTTTTTTTTAATTCTTGATAAATGTTTTTTTTTGTTAAAATGTAGGTAAAATTTCCATATGTTTTGGTTCCTTTTGATCGTCCCTTGGCCATTTTTAGGATTGAATCTCGTTCTTGA
Protein sequence

>MS.gene049462.t1

MVEEKRISANSSTNSNSNGGGGDENGDEVKSSWSKNEDETLVKLVKENGARNWSVISNGIPDRSGKFCRLRWCNQLSPTVQHLPFTPAVVAQQSSTRITESVKFPYVLVPFDRPLAIFRIESRS