AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66978

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66978.t1 MTR_5g039760 83.193 119 20 0 1 119 1 119 4.49e-72 213
MS.gene66978.t1 MTR_7g061980 69.167 120 36 1 1 120 1 119 2.98e-58 176
MS.gene66978.t1 MTR_7g074790 69.072 97 29 1 1 97 1 96 4.32e-44 144
MS.gene66978.t1 MTR_4g069880 63.492 63 23 0 1 63 1 63 2.07e-24 89.0
MS.gene66978.t1 MTR_0402s0040 42.982 114 61 4 10 121 26 137 3.94e-21 87.4
MS.gene66978.t1 MTR_2g070590 41.905 105 58 3 10 112 17 120 1.87e-20 80.5
MS.gene66978.t1 MTR_2g099430 48.315 89 43 3 33 120 26 112 9.13e-20 78.6
MS.gene66978.t1 MTR_4g102720 40.476 84 49 1 7 90 4 86 4.55e-18 76.6
MS.gene66978.t1 MTR_5g015480 39.823 113 65 3 10 120 56 167 1.67e-17 75.9
MS.gene66978.t1 MTR_6g017200 44.186 86 46 2 10 94 58 142 2.06e-17 73.6
MS.gene66978.t1 MTR_1g019850 35.000 120 70 3 3 121 63 175 7.48e-16 70.9
MS.gene66978.t1 MTR_4g067290 36.364 110 66 3 9 117 55 161 1.30e-13 65.1
MS.gene66978.t1 MTR_4g067290 36.364 110 66 3 9 117 55 161 1.40e-13 65.1
MS.gene66978.t1 MTR_1g057920 39.535 86 50 2 10 94 34 118 1.65e-13 62.4
MS.gene66978.t1 MTR_4g067290 36.364 110 66 3 9 117 73 179 1.86e-13 64.7
MS.gene66978.t1 MTR_4g067290 36.364 110 66 3 9 117 75 181 1.95e-13 64.7
MS.gene66978.t1 MTR_4g067290 36.364 110 66 3 9 117 75 181 2.03e-13 64.7
MS.gene66978.t1 MTR_2g098880 33.929 112 64 3 9 114 60 167 2.33e-13 64.7
MS.gene66978.t1 MTR_2g098880 33.929 112 64 3 9 114 72 179 2.42e-13 64.7
MS.gene66978.t1 MTR_4g067290 36.364 110 66 3 9 117 115 221 2.99e-13 64.7
MS.gene66978.t1 MTR_7g113010 34.513 113 59 3 10 121 457 555 1.42e-11 60.5
MS.gene66978.t1 MTR_2g098920 33.654 104 66 2 9 111 79 180 3.25e-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.gene66978.t1 AT5G18960 39.423 104 48 2 9 111 42 131 1.89e-15 71.6
MS.gene66978.t1 AT5G18960 39.423 104 48 2 9 111 42 131 1.89e-15 71.6
MS.gene66978.t1 AT3G06250 38.462 104 49 2 9 111 27 116 7.79e-15 69.7
MS.gene66978.t1 AT3G06250 38.462 104 49 2 9 111 27 116 7.79e-15 69.7
MS.gene66978.t1 AT3G06250 38.462 104 49 2 9 111 27 116 7.79e-15 69.7
MS.gene66978.t1 AT4G38180 34.454 119 75 2 6 121 69 187 2.38e-14 68.6
MS.gene66978.t1 AT3G59470 35.577 104 64 2 9 111 69 170 1.04e-12 62.8
MS.gene66978.t1 AT3G59470 35.577 104 64 2 9 111 69 170 1.04e-12 62.8
MS.gene66978.t1 AT3G59470 35.577 104 64 2 9 111 81 182 1.32e-12 62.8
MS.gene66978.t1 AT4G12850 34.286 105 64 2 9 112 10 110 4.07e-12 59.3
MS.gene66978.t1 AT4G12850 34.286 105 64 2 9 112 10 110 5.51e-12 58.9
MS.gene66978.t1 AT2G43280 36.283 113 68 2 3 111 12 124 7.53e-12 60.1
MS.gene66978.t1 AT4G12850 34.286 105 64 2 9 112 10 110 1.17e-11 58.9
MS.gene66978.t1 AT3G07500 36.538 104 64 2 9 111 32 134 3.60e-11 58.2

Find 27 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAAGAGGCTAAACAATTT+TGG 0.190934 6.4:-3875983 MS.gene66978:CDS
GAATTACACTTTCACTTTGT+AGG 0.262576 6.4:-3875779 MS.gene66978:CDS
TGGAATGGGATTTGATAATA+TGG 0.291396 6.4:-3876003 MS.gene66978:CDS
TCAAATCCCATTCCAACCTT+TGG 0.351708 6.4:+3876011 None:intergenic
TATGGTTTACGTGTGGGCTT+CGG 0.418417 6.4:-3875954 MS.gene66978:CDS
ATGTAGGTTCGTTTGTTGTA+AGG 0.422514 6.4:-3875883 MS.gene66978:CDS
AAGGAAGGGGTGAAGAGTAC+AGG 0.424745 6.4:-3875864 MS.gene66978:CDS
TGGCATCTACAAATGTTGAT+TGG 0.468983 6.4:-3876037 MS.gene66978:CDS
GGTTCGTTTGTTGTAAGGAA+GGG 0.477120 6.4:-3875878 MS.gene66978:CDS
TGGAAGCCAAAGGTTGGAAT+GGG 0.484209 6.4:-3876017 MS.gene66978:CDS
CTTGCTTATGGTTTACGTGT+GGG 0.490896 6.4:-3875960 MS.gene66978:CDS
AGGTTCGTTTGTTGTAAGGA+AGG 0.507670 6.4:-3875879 MS.gene66978:CDS
CGGAGCATGTGTGTAGTCTC+TGG 0.511820 6.4:+3875699 None:intergenic
TTGGAAGCCAAAGGTTGGAA+TGG 0.512541 6.4:-3876018 MS.gene66978:CDS
GTTGATTGGAAGCCAAAGGT+TGG 0.521153 6.4:-3876023 MS.gene66978:CDS
GTTCGTTTGTTGTAAGGAAG+GGG 0.523718 6.4:-3875877 MS.gene66978:CDS
TATGTTCATCTAGAAACTCA+TGG 0.526110 6.4:+3875739 None:intergenic
ACACTTTCACTTTGTAGGAA+CGG 0.535912 6.4:-3875774 MS.gene66978:CDS
GGGATTTGATAATATGGAAG+AGG 0.538633 6.4:-3875997 MS.gene66978:CDS
ACTTTGTAGGAACGGAAAGT+TGG 0.539900 6.4:-3875766 MS.gene66978:CDS
GCTTGCTTATGGTTTACGTG+TGG 0.553841 6.4:-3875961 MS.gene66978:CDS
AAATGTTGATTGGAAGCCAA+AGG 0.556734 6.4:-3876027 MS.gene66978:CDS
GTGAAAGTGTAATTCTTGCA+AGG 0.578211 6.4:+3875787 None:intergenic
CTCCAAAACATGTTTAATGT+CGG 0.579197 6.4:+3875679 None:intergenic
AGGAAGGGGTGAAGAGTACA+GGG 0.606717 6.4:-3875863 MS.gene66978:CDS
ACGGCACTGTATCATCATGT+AGG 0.621980 6.4:-3875899 MS.gene66978:CDS
TTTACAAACAGGAAGAAAGA+CGG 0.640619 6.4:-3875918 MS.gene66978:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GAATTACACTTTCACTTTGT+AGG - chr6.4:3875951-3875970 MS.gene66978:CDS 30.0%
TATGTTCATCTAGAAACTCA+TGG + chr6.4:3875994-3876013 None:intergenic 30.0%
TTTACAAACAGGAAGAAAGA+CGG - chr6.4:3875812-3875831 MS.gene66978:CDS 30.0%
! TGGAATGGGATTTGATAATA+TGG - chr6.4:3875727-3875746 MS.gene66978:CDS 30.0%
! TTAGAGTACGTTTTACAAAC+AGG - chr6.4:3875801-3875820 MS.gene66978:CDS 30.0%
!!! AAACAATTTTGGCTTGCTTA+TGG - chr6.4:3875758-3875777 MS.gene66978:CDS 30.0%
ACACTTTCACTTTGTAGGAA+CGG - chr6.4:3875956-3875975 MS.gene66978:CDS 35.0%
GGGAACAAAAATGCATATGA+AGG - chr6.4:3875887-3875906 MS.gene66978:CDS 35.0%
TGGCATCTACAAATGTTGAT+TGG - chr6.4:3875693-3875712 MS.gene66978:CDS 35.0%
! AAATGTTGATTGGAAGCCAA+AGG - chr6.4:3875703-3875722 MS.gene66978:CDS 35.0%
! GGGATTTGATAATATGGAAG+AGG - chr6.4:3875733-3875752 MS.gene66978:CDS 35.0%
! GTGAAAGTGTAATTCTTGCA+AGG + chr6.4:3875946-3875965 None:intergenic 35.0%
! TGGAAGAGGCTAAACAATTT+TGG - chr6.4:3875747-3875766 MS.gene66978:CDS 35.0%
!! ATGTAGGTTCGTTTGTTGTA+AGG - chr6.4:3875847-3875866 MS.gene66978:CDS 35.0%
ACTTTGTAGGAACGGAAAGT+TGG - chr6.4:3875964-3875983 MS.gene66978:CDS 40.0%
CTTGCTTATGGTTTACGTGT+GGG - chr6.4:3875770-3875789 MS.gene66978:CDS 40.0%
TCAAATCCCATTCCAACCTT+TGG + chr6.4:3875722-3875741 None:intergenic 40.0%
! GTGTAGTCTCTGGATTTTGT+AGG + chr6.4:3876024-3876043 None:intergenic 40.0%
! TCTCTGGATTTTGTAGGTCA+TGG + chr6.4:3876018-3876037 None:intergenic 40.0%
!! AGGTTCGTTTGTTGTAAGGA+AGG - chr6.4:3875851-3875870 MS.gene66978:CDS 40.0%
!! GGTTCGTTTGTTGTAAGGAA+GGG - chr6.4:3875852-3875871 MS.gene66978:CDS 40.0%
!! GTTCGTTTGTTGTAAGGAAG+GGG - chr6.4:3875853-3875872 MS.gene66978:CDS 40.0%
ACGGCACTGTATCATCATGT+AGG - chr6.4:3875831-3875850 MS.gene66978:CDS 45.0%
GCTTGCTTATGGTTTACGTG+TGG - chr6.4:3875769-3875788 MS.gene66978:CDS 45.0%
GTTGATTGGAAGCCAAAGGT+TGG - chr6.4:3875707-3875726 MS.gene66978:CDS 45.0%
TATGGTTTACGTGTGGGCTT+CGG - chr6.4:3875776-3875795 MS.gene66978:CDS 45.0%
TGGAAGCCAAAGGTTGGAAT+GGG - chr6.4:3875713-3875732 MS.gene66978:CDS 45.0%
TTGGAAGCCAAAGGTTGGAA+TGG - chr6.4:3875712-3875731 MS.gene66978:CDS 45.0%
! AAGGAAGGGGTGAAGAGTAC+AGG - chr6.4:3875866-3875885 MS.gene66978:CDS 50.0%
! AGGAAGGGGTGAAGAGTACA+GGG - chr6.4:3875867-3875886 MS.gene66978:CDS 50.0%
CGGAGCATGTGTGTAGTCTC+TGG + chr6.4:3876034-3876053 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 3875692 3876060 3875692 ID=MS.gene66978
chr6.4 mRNA 3875692 3876060 3875692 ID=MS.gene66978.t1;Parent=MS.gene66978
chr6.4 exon 3875692 3876060 3875692 ID=MS.gene66978.t1.exon1;Parent=MS.gene66978.t1
chr6.4 CDS 3875692 3876060 3875692 ID=cds.MS.gene66978.t1;Parent=MS.gene66978.t1
Gene Sequence

>MS.gene66978

ATGGCATCTACAAATGTTGATTGGAAGCCAAAGGTTGGAATGGGATTTGATAATATGGAAGAGGCTAAACAATTTTGGCTTGCTTATGGTTTACGTGTGGGCTTCGGAATTAGAGTACGTTTTACAAACAGGAAGAAAGACGGCACTGTATCATCATGTAGGTTCGTTTGTTGTAAGGAAGGGGTGAAGAGTACAGGGAACAAAAATGCATATGAAGGAAAATATGAGAGAGCTGATATTAGAACAAATTGCCTTGCAAGAATTACACTTTCACTTTGTAGGAACGGAAAGTTGGTCATCCATGAGTTTCTAGATGAACATAACCATGACCTACAAAATCCAGAGACTACACACATGCTCCGACATTAA
Protein sequence

>MS.gene66978.t1

MASTNVDWKPKVGMGFDNMEEAKQFWLAYGLRVGFGIRVRFTNRKKDGTVSSCRFVCCKEGVKSTGNKNAYEGKYERADIRTNCLARITLSLCRNGKLVIHEFLDEHNHDLQNPETTHMLRH