AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051624

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051624.t1 MTR_1g016480 100.000 189 0 0 1 189 18 206 1.93e-140 390
MS.gene051624.t1 MTR_5g030500 55.429 175 72 3 9 178 31 204 2.14e-66 202
MS.gene051624.t1 MTR_3g071740 58.333 156 57 3 26 179 72 221 1.94e-59 186
MS.gene051624.t1 MTR_4g014460 52.201 159 74 2 22 179 49 206 1.63e-53 170
MS.gene051624.t1 MTR_7g070050 52.601 173 77 3 22 189 13 185 3.24e-53 168
MS.gene051624.t1 MTR_8g027805 46.512 172 90 2 9 179 4 174 7.85e-53 167
MS.gene051624.t1 MTR_5g083270 55.333 150 60 3 33 179 57 202 1.05e-52 167
MS.gene051624.t1 MTR_1g028380 49.367 158 79 1 22 179 19 175 1.09e-52 167
MS.gene051624.t1 MTR_3g090980 46.471 170 82 3 11 179 16 177 1.37e-52 167
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051624.t1 AT2G26040 69.312 189 54 3 1 187 1 187 1.33e-95 276
MS.gene051624.t1 AT1G73000 59.783 184 64 2 9 182 24 207 2.81e-78 233
MS.gene051624.t1 AT4G17870 54.070 172 76 2 10 179 5 175 2.53e-64 196
MS.gene051624.t1 AT2G40330 54.777 157 66 4 26 179 54 208 9.78e-55 173
MS.gene051624.t1 AT5G46790 49.711 173 83 2 10 178 32 204 4.71e-54 171
MS.gene051624.t1 AT5G46790 49.711 173 83 2 10 178 32 204 4.71e-54 171
MS.gene051624.t1 AT5G05440 55.414 157 64 4 22 176 45 197 1.27e-53 170
MS.gene051624.t1 AT5G53160 48.428 159 79 2 22 179 19 175 3.15e-52 166
MS.gene051624.t1 AT4G01026 47.170 159 81 2 22 179 23 179 9.36e-52 165
MS.gene051624.t1 AT1G01360 45.509 167 88 2 15 179 12 177 5.72e-51 162
MS.gene051624.t1 AT2G38310 56.329 158 63 3 24 179 41 194 6.43e-50 160
MS.gene051624.t1 AT4G27920 47.799 159 79 3 22 178 14 170 1.99e-46 151
MS.gene051624.t1 AT5G45860 52.258 155 64 3 23 176 5 150 7.53e-45 146
MS.gene051624.t1 AT5G45870 53.147 143 63 3 35 176 10 149 1.77e-41 137
MS.gene051624.t1 AT4G18620 47.651 149 70 2 35 176 9 156 6.63e-35 121
MS.gene051624.t1 AT5G53160 52.475 101 48 0 21 121 18 118 2.61e-34 119

Find 30 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCGAAAGATTAGAGATTT+TGG 0.159379 1.3:-5764003 MS.gene051624:CDS
AGAGAAGTTACCGTTGTTTC+GGG 0.231870 1.3:-5764044 MS.gene051624:CDS
TACCGTTGTTTCGGGTTTAC+CGG 0.281112 1.3:-5764036 MS.gene051624:CDS
TAAGGTTTATACTATTGTTT+TGG 0.288773 1.3:-5763877 MS.gene051624:CDS
TAGAGAAGTTACCGTTGTTT+CGG 0.323518 1.3:-5764045 MS.gene051624:CDS
ATCCAAAATCTCTAATCTTT+CGG 0.343309 1.3:+5764001 None:intergenic
TTCTCAAAGCTTCTAACATA+TGG 0.399534 1.3:+5764134 None:intergenic
GATTGAAGTGCATGTGTTTG+AGG 0.427491 1.3:+5764196 None:intergenic
AAGCTTAATCTTCAGAAACT+TGG 0.437353 1.3:-5763783 MS.gene051624:CDS
AATGAGTTTGTCAACAATGA+AGG 0.452521 1.3:-5763900 MS.gene051624:CDS
GCTTCGGTGCATAATATTCA+AGG 0.486800 1.3:-5764284 MS.gene051624:CDS
CTTTCGGTACTTGTCGAAGC+CGG 0.492858 1.3:+5764017 None:intergenic
AAACTATCGTTCGGTTACTT+CGG 0.496046 1.3:-5763925 MS.gene051624:CDS
TATGGCCACACTATGCTTGA+TGG 0.499255 1.3:+5764152 None:intergenic
GTTTGTCAACAATGAAGGTA+AGG 0.501378 1.3:-5763895 MS.gene051624:CDS
TTGAGGTTGGTTCTAATATG+TGG 0.501993 1.3:+5764213 None:intergenic
AACAGTGTCAACAAACATCT+TGG 0.503428 1.3:+5763809 None:intergenic
TCGTCTTCAAAACTATCGTT+CGG 0.506349 1.3:-5763934 MS.gene051624:CDS
GAAGTGCATGTGTTTGAGGT+TGG 0.508894 1.3:+5764200 None:intergenic
ATCAAAGGTTGCAACATGAA+AGG 0.524876 1.3:-5764089 MS.gene051624:CDS
AGTTCATGTTCTTCCATGCA+TGG 0.533444 1.3:-5763747 MS.gene051624:CDS
AAACACACACAAAATGGCTT+CGG 0.534458 1.3:-5764300 None:intergenic
AAATACAAACATTTCATCAA+AGG 0.541877 1.3:-5764104 MS.gene051624:CDS
GGTTGCAACATGAAAGGTGA+TGG 0.558210 1.3:-5764083 MS.gene051624:CDS
TATATTGTTGATATTCCACA+TGG 0.600252 1.3:-5763849 MS.gene051624:CDS
TCTTCTTCAGTGTTCCCATG+TGG 0.603865 1.3:+5763834 None:intergenic
ATGAAAGGTGATGGAAACGT+TGG 0.615437 1.3:-5764074 MS.gene051624:CDS
AGCCGGTAAACCCGAAACAA+CGG 0.615768 1.3:+5764034 None:intergenic
AAGCACCATCAAGCATAGTG+TGG 0.678529 1.3:-5764157 MS.gene051624:CDS
ATATTGTTGATATTCCACAT+GGG 0.707262 1.3:-5763848 MS.gene051624:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACAAACATTTCATCAA+AGG - chr1.3:5763923-5763942 MS.gene051624:CDS 20.0%
!!! ATGAAATGTTTGTATTTTTG+TGG + chr1.3:5763920-5763939 None:intergenic 20.0%
!!! ATGTGGTATTTTTTTATGAT+TGG + chr1.3:5763800-5763819 None:intergenic 20.0%
!!! TAAGGTTTATACTATTGTTT+TGG - chr1.3:5764150-5764169 MS.gene051624:CDS 20.0%
! ATATTGTTGATATTCCACAT+GGG - chr1.3:5764179-5764198 MS.gene051624:CDS 25.0%
! ATCCAAAATCTCTAATCTTT+CGG + chr1.3:5764029-5764048 None:intergenic 25.0%
! TATATTGTTGATATTCCACA+TGG - chr1.3:5764178-5764197 MS.gene051624:CDS 25.0%
!!! GTAATAAGTTTTAGAGTTGT+TGG - chr1.3:5764061-5764080 MS.gene051624:CDS 25.0%
AAGCTTAATCTTCAGAAACT+TGG - chr1.3:5764244-5764263 MS.gene051624:CDS 30.0%
AATGAGTTTGTCAACAATGA+AGG - chr1.3:5764127-5764146 MS.gene051624:CDS 30.0%
TTCTCAAAGCTTCTAACATA+TGG + chr1.3:5763896-5763915 None:intergenic 30.0%
! TACCGAAAGATTAGAGATTT+TGG - chr1.3:5764024-5764043 MS.gene051624:CDS 30.0%
!!! ATAAGTTTTAGAGTTGTTGG+TGG - chr1.3:5764064-5764083 MS.gene051624:CDS 30.0%
AAACTATCGTTCGGTTACTT+CGG - chr1.3:5764102-5764121 MS.gene051624:CDS 35.0%
AACAGTGTCAACAAACATCT+TGG + chr1.3:5764221-5764240 None:intergenic 35.0%
ATCAAAGGTTGCAACATGAA+AGG - chr1.3:5763938-5763957 MS.gene051624:CDS 35.0%
GTTTGTCAACAATGAAGGTA+AGG - chr1.3:5764132-5764151 MS.gene051624:CDS 35.0%
TAGAGAAGTTACCGTTGTTT+CGG - chr1.3:5763982-5764001 MS.gene051624:CDS 35.0%
TCGTCTTCAAAACTATCGTT+CGG - chr1.3:5764093-5764112 MS.gene051624:CDS 35.0%
!! TGATGGTGCTTCTATTTTGT+AGG + chr1.3:5763861-5763880 None:intergenic 35.0%
!! TTGAGGTTGGTTCTAATATG+TGG + chr1.3:5763817-5763836 None:intergenic 35.0%
AGTTCATGTTCTTCCATGCA+TGG - chr1.3:5764280-5764299 MS.gene051624:CDS 40.0%
GATTGAAGTGCATGTGTTTG+AGG + chr1.3:5763834-5763853 None:intergenic 40.0%
! AGAGAAGTTACCGTTGTTTC+GGG - chr1.3:5763983-5764002 MS.gene051624:CDS 40.0%
! GCTTCGGTGCATAATATTCA+AGG - chr1.3:5763743-5763762 MS.gene051624:CDS 40.0%
!! ATGAAAGGTGATGGAAACGT+TGG - chr1.3:5763953-5763972 MS.gene051624:CDS 40.0%
AAGCACCATCAAGCATAGTG+TGG - chr1.3:5763870-5763889 MS.gene051624:CDS 45.0%
GGTTGCAACATGAAAGGTGA+TGG - chr1.3:5763944-5763963 MS.gene051624:CDS 45.0%
TATGGCCACACTATGCTTGA+TGG + chr1.3:5763878-5763897 None:intergenic 45.0%
TCTTCTTCAGTGTTCCCATG+TGG + chr1.3:5764196-5764215 None:intergenic 45.0%
! GAAGTGCATGTGTTTGAGGT+TGG + chr1.3:5763830-5763849 None:intergenic 45.0%
!! TACCGTTGTTTCGGGTTTAC+CGG - chr1.3:5763991-5764010 MS.gene051624:CDS 45.0%
AGCCGGTAAACCCGAAACAA+CGG + chr1.3:5763996-5764015 None:intergenic 50.0%
CTTTCGGTACTTGTCGAAGC+CGG + chr1.3:5764013-5764032 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 5763740 5764309 5763740 ID=MS.gene051624
chr1.3 mRNA 5763740 5764309 5763740 ID=MS.gene051624.t1;Parent=MS.gene051624
chr1.3 exon 5763740 5764309 5763740 ID=MS.gene051624.t1.exon1;Parent=MS.gene051624.t1
chr1.3 CDS 5763740 5764309 5763740 ID=cds.MS.gene051624.t1;Parent=MS.gene051624.t1
Gene Sequence

>MS.gene051624

ATGGCTTCGGTGCATAATATTCAAGGTCTAACAGAAGAAGAATACAAAGAACTCGAACCAATCATAAAAAAATACCACATATTAGAACCAACCTCAAACACATGCACTTCAATCATAACCTACAAAATAGAAGCACCATCAAGCATAGTGTGGCCATATGTTAGAAGCTTTGAGAATCCACAAAAATACAAACATTTCATCAAAGGTTGCAACATGAAAGGTGATGGAAACGTTGGTAGCATTAGAGAAGTTACCGTTGTTTCGGGTTTACCGGCTTCGACAAGTACCGAAAGATTAGAGATTTTGGATGATGAAAAACATGTAATAAGTTTTAGAGTTGTTGGTGGTGAACATCGTCTTCAAAACTATCGTTCGGTTACTTCGGTTAATGAGTTTGTCAACAATGAAGGTAAGGTTTATACTATTGTTTTGGAATCTTATATTGTTGATATTCCACATGGGAACACTGAAGAAGATACCAAGATGTTTGTTGACACTGTTGTCAAGCTTAATCTTCAGAAACTTGGAGTTGTTGCTATGAGTTCATGTTCTTCCATGCATGGACAATAA
Protein sequence

>MS.gene051624.t1

MASVHNIQGLTEEEYKELEPIIKKYHILEPTSNTCTSIITYKIEAPSSIVWPYVRSFENPQKYKHFIKGCNMKGDGNVGSIREVTVVSGLPASTSTERLEILDDEKHVISFRVVGGEHRLQNYRSVTSVNEFVNNEGKVYTIVLESYIVDIPHGNTEEDTKMFVDTVVKLNLQKLGVVAMSSCSSMHGQ