AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene018226

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene018226.t1 MTR_6g016375 99.500 200 1 0 1 200 1 200 5.81e-147 406
MS.gene018226.t1 MTR_7g017880 64.286 196 58 6 1 189 1 191 7.30e-66 201
MS.gene018226.t1 MTR_7g029400 59.627 161 56 5 9 167 8 161 1.87e-54 172
MS.gene018226.t1 MTR_8g015250 59.375 160 48 5 9 167 8 151 4.60e-54 171
MS.gene018226.t1 MTR_4g070860 52.326 86 38 2 73 158 16 98 2.37e-18 78.6
MS.gene018226.t1 MTR_1g022495 40.196 102 61 0 64 165 4 105 1.89e-17 76.3
MS.gene018226.t1 MTR_3g117120 50.000 80 40 0 79 158 19 98 4.64e-17 75.1
MS.gene018226.t1 MTR_4g097440 36.620 142 66 3 43 162 8 147 1.40e-16 74.3
MS.gene018226.t1 MTR_5g015090 41.509 106 57 1 65 165 31 136 7.10e-13 63.9
MS.gene018226.t1 MTR_1g087040 39.362 94 52 2 65 158 7 95 6.47e-12 61.2
MS.gene018226.t1 MTR_8g086020 34.375 96 63 0 63 158 8 103 9.52e-12 60.8
MS.gene018226.t1 MTR_5g028850 48.438 64 33 0 90 153 310 373 7.08e-11 60.8
MS.gene018226.t1 MTR_5g028850 41.111 90 49 2 67 153 283 371 8.95e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene018226.t1 AT3G30530 74.545 110 25 2 65 171 53 162 4.96e-50 160
MS.gene018226.t1 AT5G38800 61.207 116 38 2 71 186 53 161 1.19e-41 138
MS.gene018226.t1 AT5G15830 60.909 110 43 0 57 166 41 150 5.82e-39 132
MS.gene018226.t1 AT1G13600 56.693 127 45 3 71 195 68 186 1.41e-36 126
MS.gene018226.t1 AT2G04038 64.583 96 34 0 70 165 54 149 4.07e-36 124
MS.gene018226.t1 AT1G68880 46.316 95 49 1 74 168 33 125 1.53e-21 86.3
MS.gene018226.t1 AT1G75390 47.423 97 50 1 62 158 14 109 8.62e-19 80.1
MS.gene018226.t1 AT5G60830 45.192 104 52 2 89 189 70 171 1.75e-17 77.4
MS.gene018226.t1 AT1G75390 46.237 93 49 1 62 154 14 105 3.55e-16 72.0
MS.gene018226.t1 AT2G18160 48.611 72 37 0 87 158 28 99 1.87e-15 71.2
MS.gene018226.t1 AT3G62420 44.304 79 44 0 80 158 15 93 4.69e-15 69.7
MS.gene018226.t1 AT4G34590 45.946 74 40 0 85 158 22 95 3.34e-13 65.1
MS.gene018226.t1 AT2G22850 36.522 115 61 3 70 172 106 220 3.50e-11 60.8
MS.gene018226.t1 AT2G22850 36.522 115 61 3 70 172 106 220 3.50e-11 60.8

Find 30 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTTTGGTCACAAGTTCTT+TGG 0.273917 6.3:+11683095 MS.gene018226:CDS
TTAGGTAATTACCATATAAT+TGG 0.292562 6.3:-11682883 None:intergenic
GGACTAAAAGAAGGGATTAA+AGG 0.295805 6.3:-11683259 None:intergenic
TCAAGTTCAATGGATCTTCT+TGG 0.335013 6.3:+11683328 MS.gene018226:CDS
AAATTCTCAAACCAATTATA+TGG 0.356492 6.3:+11682872 MS.gene018226:CDS
ATTGTTGATGAGGGGTGTTT+AGG 0.356793 6.3:-11682901 None:intergenic
TCCTCTCATTGATGAGACTA+AGG 0.387624 6.3:-11683000 None:intergenic
AGAAACACCTTGATGAGCTT+TGG 0.415939 6.3:+11683080 MS.gene018226:CDS
TCAGCTTAAAGAAGAAGCTT+TGG 0.440839 6.3:+11683198 MS.gene018226:CDS
TGTTACTTCTCTTGTTTGCA+TGG 0.445242 6.3:-11682750 None:intergenic
CTGCTTATGCATGATGATTG+TGG 0.470545 6.3:-11682944 None:intergenic
CAATTCCATCTCAAGTTCAA+TGG 0.471344 6.3:+11683318 MS.gene018226:CDS
GGTCACAAGTTCTTTGGCTG+AGG 0.486097 6.3:+11683101 MS.gene018226:CDS
AGATAAGGTGATGTGTTTGA+TGG 0.498736 6.3:-11682794 None:intergenic
TCATCCAAAGGACTAAAAGA+AGG 0.506277 6.3:-11683268 None:intergenic
GTGACCGACGTGCTGATTCG+CGG 0.510591 6.3:-11683045 None:intergenic
CAAACAAGAGAAGTAACAAC+AGG 0.515554 6.3:+11682755 MS.gene018226:CDS
TGTGGACTATAGTTGAAGTC+AGG 0.518116 6.3:-11682926 None:intergenic
AAGATCCATTGAACTTGAGA+TGG 0.525838 6.3:-11683323 None:intergenic
AAGTCAGGAAATTGTTGATG+AGG 0.551877 6.3:-11682911 None:intergenic
CTTGTGACCAAAGCTCATCA+AGG 0.582135 6.3:-11683087 None:intergenic
AGTCAGGAAATTGTTGATGA+GGG 0.582558 6.3:-11682910 None:intergenic
CATCCAAAGGACTAAAAGAA+GGG 0.584492 6.3:-11683267 None:intergenic
CTAAGATATGTATCATCCAA+AGG 0.603956 6.3:-11683280 None:intergenic
CAGCACGTCGGTCACGCATG+AGG 0.614637 6.3:+11683053 MS.gene018226:CDS
TCAATGAGAGGAAACACAGA+AGG 0.630812 6.3:+11683011 MS.gene018226:CDS
ACCTTAGTCTCATCAATGAG+AGG 0.631783 6.3:+11682999 MS.gene018226:CDS
GATCATGATTCTCAGAAACA+TGG 0.641220 6.3:-11683156 None:intergenic
GTCAGGAAATTGTTGATGAG+GGG 0.693054 6.3:-11682909 None:intergenic
CAAACCGCGAATCAGCACGT+CGG 0.801689 6.3:+11683041 MS.gene018226:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTCTCAAACCAATTATA+TGG + chr6.3:11682872-11682891 MS.gene018226:CDS 20.0%
!! TTAGGTAATTACCATATAAT+TGG - chr6.3:11682886-11682905 None:intergenic 20.0%
!!! ATAATTGGTTTGAGAATTTT+TGG - chr6.3:11682871-11682890 None:intergenic 20.0%
!!! TTGTTATAGTTTTGTAGATA+AGG - chr6.3:11682812-11682831 None:intergenic 20.0%
CTAAGATATGTATCATCCAA+AGG - chr6.3:11683283-11683302 None:intergenic 30.0%
!!! GAATTTTTGGAGTTGATATG+AGG - chr6.3:11682858-11682877 None:intergenic 30.0%
AAGATCCATTGAACTTGAGA+TGG - chr6.3:11683326-11683345 None:intergenic 35.0%
AAGTCAGGAAATTGTTGATG+AGG - chr6.3:11682914-11682933 None:intergenic 35.0%
AGATAAGGTGATGTGTTTGA+TGG - chr6.3:11682797-11682816 None:intergenic 35.0%
CAAACAAGAGAAGTAACAAC+AGG + chr6.3:11682755-11682774 MS.gene018226:CDS 35.0%
CAATTCCATCTCAAGTTCAA+TGG + chr6.3:11683318-11683337 MS.gene018226:CDS 35.0%
CATCCAAAGGACTAAAAGAA+GGG - chr6.3:11683270-11683289 None:intergenic 35.0%
GATCATGATTCTCAGAAACA+TGG - chr6.3:11683159-11683178 None:intergenic 35.0%
GGACTAAAAGAAGGGATTAA+AGG - chr6.3:11683262-11683281 None:intergenic 35.0%
TCAAGTTCAATGGATCTTCT+TGG + chr6.3:11683328-11683347 MS.gene018226:CDS 35.0%
TCAGCTTAAAGAAGAAGCTT+TGG + chr6.3:11683198-11683217 MS.gene018226:CDS 35.0%
TCATCCAAAGGACTAAAAGA+AGG - chr6.3:11683271-11683290 None:intergenic 35.0%
! AATCCCTTCTTTTAGTCCTT+TGG + chr6.3:11683264-11683283 MS.gene018226:CDS 35.0%
! AGTCAGGAAATTGTTGATGA+GGG - chr6.3:11682913-11682932 None:intergenic 35.0%
ACCTTAGTCTCATCAATGAG+AGG + chr6.3:11682999-11683018 MS.gene018226:CDS 40.0%
AGAAACACCTTGATGAGCTT+TGG + chr6.3:11683080-11683099 MS.gene018226:CDS 40.0%
CTGCTTATGCATGATGATTG+TGG - chr6.3:11682947-11682966 None:intergenic 40.0%
TCAATGAGAGGAAACACAGA+AGG + chr6.3:11683011-11683030 MS.gene018226:CDS 40.0%
TCCTCTCATTGATGAGACTA+AGG - chr6.3:11683003-11683022 None:intergenic 40.0%
! AGCTTTGGTCACAAGTTCTT+TGG + chr6.3:11683095-11683114 MS.gene018226:CDS 40.0%
! GTCAGGAAATTGTTGATGAG+GGG - chr6.3:11682912-11682931 None:intergenic 40.0%
! TGTGGACTATAGTTGAAGTC+AGG - chr6.3:11682929-11682948 None:intergenic 40.0%
!! ATTGTTGATGAGGGGTGTTT+AGG - chr6.3:11682904-11682923 None:intergenic 40.0%
CTTGTGACCAAAGCTCATCA+AGG - chr6.3:11683090-11683109 None:intergenic 45.0%
GGTCACAAGTTCTTTGGCTG+AGG + chr6.3:11683101-11683120 MS.gene018226:CDS 50.0%
CAAACCGCGAATCAGCACGT+CGG + chr6.3:11683041-11683060 MS.gene018226:CDS 55.0%
!! GTGACCGACGTGCTGATTCG+CGG - chr6.3:11683048-11683067 None:intergenic 60.0%
CAGCACGTCGGTCACGCATG+AGG + chr6.3:11683053-11683072 MS.gene018226:CDS 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 11682752 11683354 11682752 ID=MS.gene018226
chr6.3 mRNA 11682752 11683354 11682752 ID=MS.gene018226.t1;Parent=MS.gene018226
chr6.3 exon 11682752 11683354 11682752 ID=MS.gene018226.t1.exon1;Parent=MS.gene018226.t1
chr6.3 CDS 11682752 11683354 11682752 ID=cds.MS.gene018226.t1;Parent=MS.gene018226.t1
Gene Sequence

>MS.gene018226

ATGCAAACAAGAGAAGTAACAACAGGACTCAATTACATGCTACCATCAAACACATCACCTTATCTACAAAACTATAACAACATGATTCAAAATAACAACATTTCCTCATATCAACTCCAAAAATTCTCAAACCAATTATATGGTAATTACCTAAACACCCCTCATCAACAATTTCCTGACTTCAACTATAGTCCACAATCATCATGCATAAGCAGCAACTCAACTTCTGATGAAGCAGATGAACAAAACCTTAGTCTCATCAATGAGAGGAAACACAGAAGGATGATATCAAACCGCGAATCAGCACGTCGGTCACGCATGAGGAAGCAGAAACACCTTGATGAGCTTTGGTCACAAGTTCTTTGGCTGAGGAATGAAAATCATCAACTTATAGAGAAACTTAACCATGTTTCTGAGAATCATGATCAAGTTGTTCAAGAGAATGCTCAGCTTAAAGAAGAAGCTTTGGAACTTCGACAAATGATAAAAGATATGCAGATTCATAGTCCTTTAATCCCTTCTTTTAGTCCTTTGGATGATACATATCTTAGAGATGATTCTTCAAACAATTCCATCTCAAGTTCAATGGATCTTCTTGGCTGA
Protein sequence

>MS.gene018226.t1

MQTREVTTGLNYMLPSNTSPYLQNYNNMIQNNNISSYQLQKFSNQLYGNYLNTPHQQFPDFNYSPQSSCISSNSTSDEADEQNLSLINERKHRRMISNRESARRSRMRKQKHLDELWSQVLWLRNENHQLIEKLNHVSENHDQVVQENAQLKEEALELRQMIKDMQIHSPLIPSFSPLDDTYLRDDSSNNSISSSMDLLG