AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1341850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1341850 MtrunA17_Chr8g0380641 97.297 148 4 0 1 148 1 148 5.68e-107 301
Msa1341850 MtrunA17_Chr2g0277481 63.816 152 44 3 4 148 3 150 1.48e-63 191
Msa1341850 MtrunA17_Chr1g0210661 55.782 147 62 3 1 146 9 153 4.89e-50 157
Msa1341850 MtrunA17_Chr2g0321501 61.789 123 45 2 25 146 33 154 8.25e-50 156
Msa1341850 MtrunA17_Chr1g0210631 56.164 146 57 5 4 146 76 217 9.96e-50 158
Msa1341850 MtrunA17_Chr4g0026331 57.037 135 51 3 19 146 20 154 4.55e-48 152
Msa1341850 MtrunA17_Chr5g0394481 36.634 101 63 1 48 148 46 145 1.30e-17 74.7
Msa1341850 MtrunA17_Chr4g0054691 36.585 82 52 0 65 146 77 158 2.57e-16 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1341850 AT1G60950.1 64.000 150 49 3 1 147 1 148 1.08e-65 197
Msa1341850 AT1G10960.1 61.333 150 53 3 1 147 1 148 5.76e-59 180
Msa1341850 AT2G27510.1 50.658 152 65 4 5 146 3 154 2.07e-44 143
Msa1341850 AT5G10000.1 43.182 132 71 3 19 147 18 148 1.28e-32 113
Msa1341850 AT4G14890.1 35.333 150 80 4 3 148 10 146 7.77e-17 72.8
Msa1341850 AT1G32550.1 40.244 82 49 0 65 146 72 153 1.30e-16 73.2
Msa1341850 AT1G32550.2 34.783 92 44 2 71 146 75 166 5.37e-12 60.8

Find 56 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACGTGGGTCAGACTTTATT+TGG 0.300570 tig0004894:+44948 Msa1341850:CDS
CCACGTTAGGGAATGCTGTT+AGG 0.301806 tig0004894:-44932 None:intergenic
GTAAGTTCTTTAGTTCCATC+TGG 0.311839 tig0004894:-45035 None:intergenic
GCTGTTAGGGTTGTGTTCAT+TGG 0.358114 tig0004894:-44918 None:intergenic
ACCACCACAGCAGCCCTATC+AGG 0.384793 tig0004894:+44861 Msa1341850:CDS
TGCTCACCATGGTTCCTGAT+AGG 0.397541 tig0004894:-44875 None:intergenic
TGTGCTGGAAAAGTTGTAGA+AGG 0.411785 tig0004894:+45146 Msa1341850:CDS
AATAAAGTCTGACCCACGTT+AGG 0.420347 tig0004894:-44945 None:intergenic
TCGAGAATGTACTCATTATC+CGG 0.426007 tig0004894:-45062 None:intergenic
GATGAGCTTGATCTTGTAAC+TGG 0.426566 tig0004894:-45009 None:intergenic
CTTCCTTACTCATGCAGGGC+TGG 0.437541 tig0004894:+45110 Msa1341850:CDS
GGTGCTTGCTCTTCATGTGC+TGG 0.439901 tig0004894:+45131 Msa1341850:CDS
TCGATCTTCCTTACTCATGC+AGG 0.452165 tig0004894:+45105 Msa1341850:CDS
TAAGTTCTTTAGTTCCATCT+GGG 0.455484 tig0004894:-45034 None:intergenic
GCTCACCATGGTTCCTGATA+GGG 0.466904 tig0004894:-44874 None:intergenic
TCCTGATAGGGCTGCTGTGG+TGG 0.470793 tig0004894:-44862 None:intergenic
CATTGGCTGCCTCCTGATGA+AGG 0.472321 tig0004894:-44901 None:intergenic
ACTTTATTTGGTGTGAAGGC+CGG 0.475879 tig0004894:+44960 Msa1341850:CDS
TGATAGGGCTGCTGTGGTGG+TGG 0.476979 tig0004894:-44859 None:intergenic
TGGTGAGCACCTCCTTCATC+AGG 0.483290 tig0004894:+44889 Msa1341850:CDS
CACGTTAGGGAATGCTGTTA+GGG 0.501804 tig0004894:-44931 None:intergenic
GCACCAGCCCTGCATGAGTA+AGG 0.502602 tig0004894:-45113 None:intergenic
GATGATGATCAATTAAGTGC+TGG 0.507761 tig0004894:+45200 Msa1341850:CDS
TCAGACTTTATTTGGTGTGA+AGG 0.514081 tig0004894:+44956 Msa1341850:CDS
ATAAAGTCTGACCCACGTTA+GGG 0.523812 tig0004894:-44944 None:intergenic
AAAAGTTGTAGAAGGGGAAG+TGG 0.534366 tig0004894:+45154 Msa1341850:CDS
ATCAAGCTCATCACCCCAGA+TGG 0.540257 tig0004894:+45020 Msa1341850:CDS
CTTGATCTTGTAACTGGCCA+TGG 0.544201 tig0004894:-45003 None:intergenic
ATGATGATCAATTAAGTGCT+GGG 0.551795 tig0004894:+45201 Msa1341850:CDS
AAGATCGATGCCTTGTTCCT+CGG 0.553403 tig0004894:-45090 None:intergenic
CTCGACGTAGCCGAGGAACA+AGG 0.555180 tig0004894:+45080 Msa1341850:CDS
CACTTAATTGATCATCATCA+AGG 0.556300 tig0004894:-45196 None:intergenic
AACTAAAGAACTTACCTGCC+CGG 0.559896 tig0004894:+45043 Msa1341850:CDS
TTTGGTGTGAAGGCCGGACG+TGG 0.560810 tig0004894:+44966 Msa1341850:CDS
AATGTACTCATTATCCGGGC+AGG 0.566913 tig0004894:-45057 None:intergenic
CGATCTTCCTTACTCATGCA+GGG 0.578511 tig0004894:+45106 Msa1341850:CDS
GTGCTGGAAAAGTTGTAGAA+GGG 0.579438 tig0004894:+45147 Msa1341850:CDS
GGTTCCTGATAGGGCTGCTG+TGG 0.579627 tig0004894:-44865 None:intergenic
AGTGATACGACTTCCACGTC+CGG 0.584494 tig0004894:-44979 None:intergenic
CGAGAATGTACTCATTATCC+GGG 0.584894 tig0004894:-45061 None:intergenic
CCTTGTGTGTCTCAATAACA+AGG 0.591064 tig0004894:-45259 None:intergenic
CCTAACAGCATTCCCTAACG+TGG 0.597665 tig0004894:+44932 Msa1341850:CDS
TGCTGGAAAAGTTGTAGAAG+GGG 0.598351 tig0004894:+45148 Msa1341850:CDS
TGGAAGTCGTATCACTGCCA+TGG 0.614707 tig0004894:+44986 Msa1341850:CDS
GTACATTCTCGACGTAGCCG+AGG 0.630338 tig0004894:+45073 Msa1341850:CDS
AAGTTCTTTAGTTCCATCTG+GGG 0.632400 tig0004894:-45033 None:intergenic
AGCAGCCCTATCAGGAACCA+TGG 0.637647 tig0004894:+44869 Msa1341850:CDS
TGGCTGCCTCCTGATGAAGG+AGG 0.644050 tig0004894:-44898 None:intergenic
GTGTGTCTCAATAACAAGGT+CGG 0.646026 tig0004894:-45255 None:intergenic
CCTTGTTATTGAGACACACA+AGG 0.649100 tig0004894:+45259 Msa1341850:CDS
GATGAAGGAGGTGCTCACCA+TGG 0.650251 tig0004894:-44886 None:intergenic
TCAATAACAAGGTCGGAACG+AGG 0.657316 tig0004894:-45248 None:intergenic
CAATAACAAGGTCGGAACGA+GGG 0.670427 tig0004894:-45247 None:intergenic
TGAGCACCTCCTTCATCAGG+AGG 0.676610 tig0004894:+44892 Msa1341850:CDS
CTAACAGCATTCCCTAACGT+GGG 0.718396 tig0004894:+44933 Msa1341850:CDS
TGTTATTGAGACACACAAGG+AGG 0.740119 tig0004894:+45262 Msa1341850:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAAGTTCTTTAGTTCCATCT+GGG - tig0004894:45037-45056 None:intergenic 30.0%
CACTTAATTGATCATCATCA+AGG - tig0004894:45199-45218 None:intergenic 30.0%
ATGATGATCAATTAAGTGCT+GGG + tig0004894:45201-45220 Msa1341850:CDS 30.0%
!! TCAGACTTTATTTGGTGTGA+AGG + tig0004894:44956-44975 Msa1341850:CDS 35.0%
! AAGTTCTTTAGTTCCATCTG+GGG - tig0004894:45036-45055 None:intergenic 35.0%
! GTAAGTTCTTTAGTTCCATC+TGG - tig0004894:45038-45057 None:intergenic 35.0%
TCGAGAATGTACTCATTATC+CGG - tig0004894:45065-45084 None:intergenic 35.0%
GATGATGATCAATTAAGTGC+TGG + tig0004894:45200-45219 Msa1341850:CDS 35.0%
ATAAAGTCTGACCCACGTTA+GGG - tig0004894:44947-44966 None:intergenic 40.0%
AATAAAGTCTGACCCACGTT+AGG - tig0004894:44948-44967 None:intergenic 40.0%
AACGTGGGTCAGACTTTATT+TGG + tig0004894:44948-44967 Msa1341850:CDS 40.0%
!! ACTTTATTTGGTGTGAAGGC+CGG + tig0004894:44960-44979 Msa1341850:CDS 40.0%
GATGAGCTTGATCTTGTAAC+TGG - tig0004894:45012-45031 None:intergenic 40.0%
AACTAAAGAACTTACCTGCC+CGG + tig0004894:45043-45062 Msa1341850:CDS 40.0%
CGAGAATGTACTCATTATCC+GGG - tig0004894:45064-45083 None:intergenic 40.0%
TGTGCTGGAAAAGTTGTAGA+AGG + tig0004894:45146-45165 Msa1341850:CDS 40.0%
GTGCTGGAAAAGTTGTAGAA+GGG + tig0004894:45147-45166 Msa1341850:CDS 40.0%
TGCTGGAAAAGTTGTAGAAG+GGG + tig0004894:45148-45167 Msa1341850:CDS 40.0%
AAAAGTTGTAGAAGGGGAAG+TGG + tig0004894:45154-45173 Msa1341850:CDS 40.0%
GTGTGTCTCAATAACAAGGT+CGG - tig0004894:45258-45277 None:intergenic 40.0%
CCTTGTGTGTCTCAATAACA+AGG - tig0004894:45262-45281 None:intergenic 40.0%
!! CCTTGTTATTGAGACACACA+AGG + tig0004894:45259-45278 Msa1341850:CDS 40.0%
TGTTATTGAGACACACAAGG+AGG + tig0004894:45262-45281 Msa1341850:CDS 40.0%
GCTGTTAGGGTTGTGTTCAT+TGG - tig0004894:44921-44940 None:intergenic 45.0%
CACGTTAGGGAATGCTGTTA+GGG - tig0004894:44934-44953 None:intergenic 45.0%
CTAACAGCATTCCCTAACGT+GGG + tig0004894:44933-44952 Msa1341850:CDS 45.0%
CTTGATCTTGTAACTGGCCA+TGG - tig0004894:45006-45025 None:intergenic 45.0%
AATGTACTCATTATCCGGGC+AGG - tig0004894:45060-45079 None:intergenic 45.0%
! AAGATCGATGCCTTGTTCCT+CGG - tig0004894:45093-45112 None:intergenic 45.0%
TCGATCTTCCTTACTCATGC+AGG + tig0004894:45105-45124 Msa1341850:CDS 45.0%
CGATCTTCCTTACTCATGCA+GGG + tig0004894:45106-45125 Msa1341850:CDS 45.0%
CAATAACAAGGTCGGAACGA+GGG - tig0004894:45250-45269 None:intergenic 45.0%
TCAATAACAAGGTCGGAACG+AGG - tig0004894:45251-45270 None:intergenic 45.0%
GCTCACCATGGTTCCTGATA+GGG - tig0004894:44877-44896 None:intergenic 50.0%
TGCTCACCATGGTTCCTGAT+AGG - tig0004894:44878-44897 None:intergenic 50.0%
CCACGTTAGGGAATGCTGTT+AGG - tig0004894:44935-44954 None:intergenic 50.0%
CCTAACAGCATTCCCTAACG+TGG + tig0004894:44932-44951 Msa1341850:CDS 50.0%
AGTGATACGACTTCCACGTC+CGG - tig0004894:44982-45001 None:intergenic 50.0%
TGGAAGTCGTATCACTGCCA+TGG + tig0004894:44986-45005 Msa1341850:CDS 50.0%
ATCAAGCTCATCACCCCAGA+TGG + tig0004894:45020-45039 Msa1341850:CDS 50.0%
AGCAGCCCTATCAGGAACCA+TGG + tig0004894:44869-44888 Msa1341850:CDS 55.0%
!! GATGAAGGAGGTGCTCACCA+TGG - tig0004894:44889-44908 None:intergenic 55.0%
TGGTGAGCACCTCCTTCATC+AGG + tig0004894:44889-44908 Msa1341850:CDS 55.0%
TGAGCACCTCCTTCATCAGG+AGG + tig0004894:44892-44911 Msa1341850:CDS 55.0%
! CATTGGCTGCCTCCTGATGA+AGG - tig0004894:44904-44923 None:intergenic 55.0%
GTACATTCTCGACGTAGCCG+AGG + tig0004894:45073-45092 Msa1341850:CDS 55.0%
CTTCCTTACTCATGCAGGGC+TGG + tig0004894:45110-45129 Msa1341850:CDS 55.0%
GGTGCTTGCTCTTCATGTGC+TGG + tig0004894:45131-45150 Msa1341850:CDS 55.0%
TGATAGGGCTGCTGTGGTGG+TGG - tig0004894:44862-44881 None:intergenic 60.0%
ACCACCACAGCAGCCCTATC+AGG + tig0004894:44861-44880 Msa1341850:CDS 60.0%
TCCTGATAGGGCTGCTGTGG+TGG - tig0004894:44865-44884 None:intergenic 60.0%
GGTTCCTGATAGGGCTGCTG+TGG - tig0004894:44868-44887 None:intergenic 60.0%
TGGCTGCCTCCTGATGAAGG+AGG - tig0004894:44901-44920 None:intergenic 60.0%
! TTTGGTGTGAAGGCCGGACG+TGG + tig0004894:44966-44985 Msa1341850:CDS 60.0%
CTCGACGTAGCCGAGGAACA+AGG + tig0004894:45080-45099 Msa1341850:CDS 60.0%
GCACCAGCCCTGCATGAGTA+AGG - tig0004894:45116-45135 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0004894 gene 44855 45301 44855 ID=Msa1341850;Name=Msa1341850
tig0004894 mRNA 44855 45301 44855 ID=Msa1341850-mRNA-1;Parent=Msa1341850;Name=Msa1341850-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|148
tig0004894 exon 44855 45301 44855 ID=Msa1341850-mRNA-1:exon:3337;Parent=Msa1341850-mRNA-1
tig0004894 CDS 44855 45301 44855 ID=Msa1341850-mRNA-1:cds;Parent=Msa1341850-mRNA-1
Gene Sequence

>Msa1341850

ATGGCCACCACCACAGCAGCCCTATCAGGAACCATGGTGAGCACCTCCTTCATCAGGAGGCAGCCAATGAACACAACCCTAACAGCATTCCCTAACGTGGGTCAGACTTTATTTGGTGTGAAGGCCGGACGTGGAAGTCGTATCACTGCCATGGCCAGTTACAAGATCAAGCTCATCACCCCAGATGGAACTAAAGAACTTACCTGCCCGGATAATGAGTACATTCTCGACGTAGCCGAGGAACAAGGCATCGATCTTCCTTACTCATGCAGGGCTGGTGCTTGCTCTTCATGTGCTGGAAAAGTTGTAGAAGGGGAAGTGGATAATTCAGATAATAGCTTCCTTGATGATGATCAATTAAGTGCTGGGTTTGTTCTCACATGTGTTGCTTACCCTCGTTCCGACCTTGTTATTGAGACACACAAGGAGGAAGATCTTGTTTCTTAA

Protein sequence

>Msa1341850

MATTTAALSGTMVSTSFIRRQPMNTTLTAFPNVGQTLFGVKAGRGSRITAMASYKIKLITPDGTKELTCPDNEYILDVAEEQGIDLPYSCRAGACSSCAGKVVEGEVDNSDNSFLDDDQLSAGFVLTCVAYPRSDLVIETHKEEDLVS*