AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028485

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028485.t1 MTR_4g062370 74.074 135 35 0 1 135 118 252 3.74e-65 211
MS.gene028485.t1 MTR_1g105765 53.125 160 75 0 1 160 115 274 7.74e-58 182
MS.gene028485.t1 MTR_1g105780 53.125 160 75 0 1 160 115 274 8.18e-58 181
MS.gene028485.t1 MTR_4g032560 48.428 159 82 0 1 159 143 301 2.44e-52 168
MS.gene028485.t1 MTR_3g452180 48.428 159 82 0 1 159 30 188 4.56e-52 164
MS.gene028485.t1 MTR_4g032580 47.799 159 83 0 1 159 143 301 1.76e-51 166
MS.gene028485.t1 MTR_7g110090 47.500 160 84 0 1 160 114 273 6.19e-50 161
MS.gene028485.t1 MTR_5g094740 49.007 151 73 1 8 158 673 819 1.49e-47 164
MS.gene028485.t1 MTR_1g069260 42.941 170 85 1 1 158 119 288 1.33e-45 150
MS.gene028485.t1 MTR_1g019580 52.672 131 62 0 30 160 1 131 9.62e-42 136
MS.gene028485.t1 MTR_1g047540 45.000 140 77 0 19 158 117 256 2.91e-39 139
MS.gene028485.t1 MTR_3g070250 36.810 163 98 1 1 158 119 281 5.52e-35 123
MS.gene028485.t1 MTR_1g087870 38.415 164 96 1 1 159 62 225 8.63e-35 122
MS.gene028485.t1 MTR_3g085990 39.375 160 60 3 1 160 115 237 3.34e-33 117
MS.gene028485.t1 MTR_4g121040 39.216 153 93 0 1 153 18 170 2.31e-32 114
MS.gene028485.t1 MTR_1g084880 36.970 165 95 3 1 158 114 276 6.97e-32 115
MS.gene028485.t1 MTR_3g048970 36.970 165 95 3 1 158 114 276 7.43e-32 115
MS.gene028485.t1 MTR_8g042540 51.220 82 40 0 78 159 6 87 2.37e-26 95.9
MS.gene028485.t1 MTR_8g042540 51.220 82 40 0 78 159 18 99 4.91e-26 95.5
MS.gene028485.t1 MTR_2g100360 38.028 142 81 2 2 137 115 255 9.76e-25 96.7
MS.gene028485.t1 MTR_3g449750 36.667 120 71 1 1 115 50 169 1.23e-18 78.6
MS.gene028485.t1 MTR_5g075200 47.761 67 35 0 1 67 127 193 1.17e-17 76.3
MS.gene028485.t1 MTR_2g038740 32.812 128 81 1 1 123 114 241 6.36e-17 77.4
MS.gene028485.t1 MTR_4g057880 42.254 71 41 0 88 158 2 72 6.31e-16 68.6
MS.gene028485.t1 MTR_0521s0010 36.364 110 61 3 1 103 94 201 5.77e-15 69.7
MS.gene028485.t1 MTR_2g016390 30.851 94 65 0 51 144 602 695 1.27e-12 64.7
MS.gene028485.t1 MTR_1g054585 30.928 97 47 1 62 158 31 107 9.43e-12 58.9
MS.gene028485.t1 MTR_5g066660 36.364 88 54 1 67 154 155 240 2.24e-11 60.5
MS.gene028485.t1 MTR_6g465600 27.329 161 105 2 2 155 121 276 4.63e-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

Find 45 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACATTGAAGAGAGTAAT+AGG 0.239469 4.1:-20120727 None:intergenic
GTTCTCGGTGCTCCAGGAAT+TGG 0.283197 4.1:+20121121 MS.gene028485:CDS
ATGTTCATCAACCAACCTTA+TGG 0.330519 4.1:-20120981 None:intergenic
TGAGAGTAACGCTGGTGTTT+TGG 0.348772 4.1:+20120816 MS.gene028485:CDS
GTATCATTCGACCCAATTCC+TGG 0.348839 4.1:-20121133 None:intergenic
TTCTCGGTGCTCCAGGAATT+GGG 0.356823 4.1:+20121122 MS.gene028485:CDS
CTATCAACATAGAACTTCAT+TGG 0.381351 4.1:-20120694 None:intergenic
GCTCAAAGCCAGAGGACTTA+AGG 0.405765 4.1:+20121084 MS.gene028485:CDS
AATGATCCACACTTCTTGAT+AGG 0.409090 4.1:+20121043 MS.gene028485:CDS
CAATGAAGTTCTATGTTGAT+AGG 0.418928 4.1:+20120695 MS.gene028485:CDS
TGCACTATTCAGTTTGTGTC+GGG 0.420065 4.1:+20121019 MS.gene028485:CDS
GTGATGGAAGGTTCAACATA+AGG 0.432919 4.1:+20120623 MS.gene028485:CDS
CGCACCGTCCTTAAGTCCTC+TGG 0.445917 4.1:-20121092 None:intergenic
TGGATCACAATGGTGTTTGT+TGG 0.448027 4.1:+20120601 None:intergenic
AGGGTTGTTCTCGGTGCTCC+AGG 0.450135 4.1:+20121115 MS.gene028485:CDS
TTTAACTCATCGTGAACAAA+AGG 0.459223 4.1:-20120757 None:intergenic
GACGGTGCGAGGGTTGTTCT+CGG 0.461233 4.1:+20121106 MS.gene028485:CDS
ATACAAGCTCTACTTCCATA+AGG 0.478195 4.1:+20120966 MS.gene028485:CDS
TGATGGAAGGTTCAACATAA+GGG 0.480909 4.1:+20120624 MS.gene028485:CDS
ATAAGGGTTCAAGACAGGTT+TGG 0.481794 4.1:+20120640 MS.gene028485:CDS
TCAACATAAGGGTTCAAGAC+AGG 0.496992 4.1:+20120635 MS.gene028485:CDS
GTGTAGGTTCTTTATTACAT+TGG 0.504867 4.1:+20120923 MS.gene028485:intron
CCACACTTCTTGATAGGCGG+TGG 0.507704 4.1:+20121049 MS.gene028485:CDS
CAACATTGAAGAGAGTAATA+GGG 0.509249 4.1:-20120726 None:intergenic
ACAATGGTGTTTGTTGGTGA+TGG 0.510883 4.1:+20120607 None:intergenic
TTGCACTATTCAGTTTGTGT+CGG 0.528949 4.1:+20121018 MS.gene028485:CDS
AAGCTCTACTTCCATAAGGT+TGG 0.529629 4.1:+20120970 MS.gene028485:CDS
ATAAGGTTGGTTGATGAACA+TGG 0.536346 4.1:+20120983 MS.gene028485:CDS
ACTTCTTGATAGGCGGTGGT+TGG 0.551835 4.1:+20121053 MS.gene028485:CDS
TGGTTGATGAACATGGGAAT+CGG 0.568644 4.1:+20120990 MS.gene028485:CDS
TGGTGTTTGTTGGTGATGGA+AGG 0.570850 4.1:+20120611 MS.gene028485:CDS
TCAACATAGAACTTCATTGG+AGG 0.581003 4.1:-20120691 None:intergenic
TCATCGTGAACAAAAGGAGC+AGG 0.581833 4.1:-20120751 None:intergenic
GAGGACTTAAGGACGGTGCG+AGG 0.609306 4.1:+20121095 MS.gene028485:CDS
TTCATTGGAGGAGAAAATGT+AGG 0.613066 4.1:-20120679 None:intergenic
AACAAAATGCTCAAAGCCAG+AGG 0.613077 4.1:+20121076 MS.gene028485:CDS
AGGACTTAAGGACGGTGCGA+GGG 0.614160 4.1:+20121096 MS.gene028485:CDS
TAAGGTTGGTTGATGAACAT+GGG 0.630618 4.1:+20120984 MS.gene028485:CDS
GATTCATTTGAGAGTAACGC+TGG 0.632261 4.1:+20120808 MS.gene028485:CDS
CCACCGCCTATCAAGAAGTG+TGG 0.635779 4.1:-20121049 None:intergenic
GATCCACACTTCTTGATAGG+CGG 0.663291 4.1:+20121046 MS.gene028485:CDS
ATTGAAGAGAGTAATAGGGA+TGG 0.666125 4.1:-20120722 None:intergenic
GAGGAGAAAATGTAGGACAA+CGG 0.681485 4.1:-20120672 None:intergenic
AAAGCCAGAGGACTTAAGGA+CGG 0.688555 4.1:+20121088 MS.gene028485:CDS
TTGATGAACATGGGAATCGG+TGG 0.689380 4.1:+20120993 MS.gene028485:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAAAATGTCAACTAAA+AGG - chr4.1:20120901-20120920 None:intergenic 15.0%
!!! TCAACTAAAAGGTTATTTTA+TGG - chr4.1:20120890-20120909 None:intergenic 20.0%
!!! TGACATTTTTTATTATGTGT+AGG + chr4.1:20120907-20120926 MS.gene028485:intron 20.0%
ACAACATTGAAGAGAGTAAT+AGG - chr4.1:20120730-20120749 None:intergenic 30.0%
CAACATTGAAGAGAGTAATA+GGG - chr4.1:20120729-20120748 None:intergenic 30.0%
CAATGAAGTTCTATGTTGAT+AGG + chr4.1:20120695-20120714 MS.gene028485:CDS 30.0%
CTATCAACATAGAACTTCAT+TGG - chr4.1:20120697-20120716 None:intergenic 30.0%
GTGTAGGTTCTTTATTACAT+TGG + chr4.1:20120923-20120942 MS.gene028485:intron 30.0%
TTTAACTCATCGTGAACAAA+AGG - chr4.1:20120760-20120779 None:intergenic 30.0%
AATGATCCACACTTCTTGAT+AGG + chr4.1:20121043-20121062 MS.gene028485:CDS 35.0%
ATACAAGCTCTACTTCCATA+AGG + chr4.1:20120966-20120985 MS.gene028485:CDS 35.0%
ATGTTCATCAACCAACCTTA+TGG - chr4.1:20120984-20121003 None:intergenic 35.0%
ATTGAAGAGAGTAATAGGGA+TGG - chr4.1:20120725-20120744 None:intergenic 35.0%
TCAACATAGAACTTCATTGG+AGG - chr4.1:20120694-20120713 None:intergenic 35.0%
TGATGGAAGGTTCAACATAA+GGG + chr4.1:20120624-20120643 MS.gene028485:CDS 35.0%
TTCATTGGAGGAGAAAATGT+AGG - chr4.1:20120682-20120701 None:intergenic 35.0%
TTGCACTATTCAGTTTGTGT+CGG + chr4.1:20121018-20121037 MS.gene028485:CDS 35.0%
!! ATAAGGTTGGTTGATGAACA+TGG + chr4.1:20120983-20121002 MS.gene028485:CDS 35.0%
!! TAAGGTTGGTTGATGAACAT+GGG + chr4.1:20120984-20121003 MS.gene028485:CDS 35.0%
AACAAAATGCTCAAAGCCAG+AGG + chr4.1:20121076-20121095 MS.gene028485:CDS 40.0%
AAGCTCTACTTCCATAAGGT+TGG + chr4.1:20120970-20120989 MS.gene028485:CDS 40.0%
ATAAGGGTTCAAGACAGGTT+TGG + chr4.1:20120640-20120659 MS.gene028485:CDS 40.0%
GAGGAGAAAATGTAGGACAA+CGG - chr4.1:20120675-20120694 None:intergenic 40.0%
GATTCATTTGAGAGTAACGC+TGG + chr4.1:20120808-20120827 MS.gene028485:CDS 40.0%
TCAACATAAGGGTTCAAGAC+AGG + chr4.1:20120635-20120654 MS.gene028485:CDS 40.0%
TGCACTATTCAGTTTGTGTC+GGG + chr4.1:20121019-20121038 MS.gene028485:CDS 40.0%
! GTGATGGAAGGTTCAACATA+AGG + chr4.1:20120623-20120642 MS.gene028485:CDS 40.0%
!! TGGTTGATGAACATGGGAAT+CGG + chr4.1:20120990-20121009 MS.gene028485:CDS 40.0%
AAAGCCAGAGGACTTAAGGA+CGG + chr4.1:20121088-20121107 MS.gene028485:CDS 45.0%
GATCCACACTTCTTGATAGG+CGG + chr4.1:20121046-20121065 MS.gene028485:CDS 45.0%
GTATCATTCGACCCAATTCC+TGG - chr4.1:20121136-20121155 None:intergenic 45.0%
TCATCGTGAACAAAAGGAGC+AGG - chr4.1:20120754-20120773 None:intergenic 45.0%
TTGATGAACATGGGAATCGG+TGG + chr4.1:20120993-20121012 MS.gene028485:CDS 45.0%
! TGAGAGTAACGCTGGTGTTT+TGG + chr4.1:20120816-20120835 MS.gene028485:CDS 45.0%
!! TGGTGTTTGTTGGTGATGGA+AGG + chr4.1:20120611-20120630 MS.gene028485:CDS 45.0%
ACTTCTTGATAGGCGGTGGT+TGG + chr4.1:20121053-20121072 MS.gene028485:CDS 50.0%
GCTCAAAGCCAGAGGACTTA+AGG + chr4.1:20121084-20121103 MS.gene028485:CDS 50.0%
!! TTCTCGGTGCTCCAGGAATT+GGG + chr4.1:20121122-20121141 MS.gene028485:CDS 50.0%
AGGACTTAAGGACGGTGCGA+GGG + chr4.1:20121096-20121115 MS.gene028485:CDS 55.0%
CCACACTTCTTGATAGGCGG+TGG + chr4.1:20121049-20121068 MS.gene028485:CDS 55.0%
CCACCGCCTATCAAGAAGTG+TGG - chr4.1:20121052-20121071 None:intergenic 55.0%
!! GTTCTCGGTGCTCCAGGAAT+TGG + chr4.1:20121121-20121140 MS.gene028485:CDS 55.0%
CGCACCGTCCTTAAGTCCTC+TGG - chr4.1:20121095-20121114 None:intergenic 60.0%
GACGGTGCGAGGGTTGTTCT+CGG + chr4.1:20121106-20121125 MS.gene028485:CDS 60.0%
GAGGACTTAAGGACGGTGCG+AGG + chr4.1:20121095-20121114 MS.gene028485:CDS 60.0%
!! AGGGTTGTTCTCGGTGCTCC+AGG + chr4.1:20121115-20121134 MS.gene028485:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 20120610 20121183 20120610 ID=MS.gene028485
chr4.1 mRNA 20120610 20121183 20120610 ID=MS.gene028485.t1;Parent=MS.gene028485
chr4.1 exon 20120610 20120837 20120610 ID=MS.gene028485.t1.exon1;Parent=MS.gene028485.t1
chr4.1 CDS 20120610 20120837 20120610 ID=cds.MS.gene028485.t1;Parent=MS.gene028485.t1
chr4.1 exon 20120929 20121183 20120929 ID=MS.gene028485.t1.exon2;Parent=MS.gene028485.t1
chr4.1 CDS 20120929 20121183 20120929 ID=cds.MS.gene028485.t1;Parent=MS.gene028485.t1
Gene Sequence

>MS.gene028485

ATGGTGTTTGTTGGTGATGGAAGGTTCAACATAAGGGTTCAAGACAGGTTTGGTAAGAAGATCCGTTGTCCTACATTTTCTCCTCCAATGAAGTTCTATGTTGATAGGAATGCCATCCCTATTACTCTCTTCAATGTTGTGCCTGCTCCTTTTGTTCACGATGAGTTAAACTTTCAACACACATATGAGAAGATACTTGATTCATTTGAGAGTAACGCTGGTGTTTTGGTAAAAATTTTATTATTATTGTCTACTTTCACATTAAGTTTTCTTTTTGCCATAAAATAACCTTTTAGTTGACATTTTTTATTATGTGTAGGTTCTTTATTACATTGGATTTGCTATCATGTGTCTTGATACAAGCTCTACTTCCATAAGGTTGGTTGATGAACATGGGAATCGGTGGAATTGCACTATTCAGTTTGTGTCGGGCAATGATCCACACTTCTTGATAGGCGGTGGTTGGAACAAAATGCTCAAAGCCAGAGGACTTAAGGACGGTGCGAGGGTTGTTCTCGGTGCTCCAGGAATTGGGTCGAATGATACTGTTTACTTTAATGTGATTCGTCGCTGA
Protein sequence

>MS.gene028485.t1

MVFVGDGRFNIRVQDRFGKKIRCPTFSPPMKFYVDRNAIPITLFNVVPAPFVHDELNFQHTYEKILDSFESNAGVLVLYYIGFAIMCLDTSSTSIRLVDEHGNRWNCTIQFVSGNDPHFLIGGGWNKMLKARGLKDGARVVLGAPGIGSNDTVYFNVIRR