AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24547

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24547.t1 MTR_1g016480 100.000 189 0 0 1 189 18 206 1.93e-140 390
MS.gene24547.t1 MTR_5g030500 55.429 175 72 3 9 178 31 204 2.14e-66 202
MS.gene24547.t1 MTR_3g071740 58.333 156 57 3 26 179 72 221 1.94e-59 186
MS.gene24547.t1 MTR_4g014460 52.201 159 74 2 22 179 49 206 1.63e-53 170
MS.gene24547.t1 MTR_7g070050 52.601 173 77 3 22 189 13 185 3.24e-53 168
MS.gene24547.t1 MTR_8g027805 46.512 172 90 2 9 179 4 174 7.85e-53 167
MS.gene24547.t1 MTR_5g083270 55.333 150 60 3 33 179 57 202 1.05e-52 167
MS.gene24547.t1 MTR_1g028380 49.367 158 79 1 22 179 19 175 1.09e-52 167
MS.gene24547.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.gene24547.t1 AT2G26040 69.312 189 54 3 1 187 1 187 1.33e-95 276
MS.gene24547.t1 AT1G73000 59.783 184 64 2 9 182 24 207 2.81e-78 233
MS.gene24547.t1 AT4G17870 54.070 172 76 2 10 179 5 175 2.53e-64 196
MS.gene24547.t1 AT2G40330 54.777 157 66 4 26 179 54 208 9.78e-55 173
MS.gene24547.t1 AT5G46790 49.711 173 83 2 10 178 32 204 4.71e-54 171
MS.gene24547.t1 AT5G46790 49.711 173 83 2 10 178 32 204 4.71e-54 171
MS.gene24547.t1 AT5G05440 55.414 157 64 4 22 176 45 197 1.27e-53 170
MS.gene24547.t1 AT5G53160 48.428 159 79 2 22 179 19 175 3.15e-52 166
MS.gene24547.t1 AT4G01026 47.170 159 81 2 22 179 23 179 9.36e-52 165
MS.gene24547.t1 AT1G01360 45.509 167 88 2 15 179 12 177 5.72e-51 162
MS.gene24547.t1 AT2G38310 56.329 158 63 3 24 179 41 194 6.43e-50 160
MS.gene24547.t1 AT4G27920 47.799 159 79 3 22 178 14 170 1.99e-46 151
MS.gene24547.t1 AT5G45860 52.258 155 64 3 23 176 5 150 7.53e-45 146
MS.gene24547.t1 AT5G45870 53.147 143 63 3 35 176 10 149 1.77e-41 137
MS.gene24547.t1 AT4G18620 47.651 149 70 2 35 176 9 156 6.63e-35 121
MS.gene24547.t1 AT5G53160 52.475 101 48 0 21 121 18 118 2.61e-34 119

Find 30 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTGAAAGATTAGAGATTT+TGG 0.170116 1.2:-6046797 MS.gene24547:CDS
AGAGAAGTTACCGTTGTTTC+GGG 0.231870 1.2:-6046838 MS.gene24547:CDS
TACCGTTGTTTCGGGTTTAC+CGG 0.281112 1.2:-6046830 MS.gene24547:CDS
TAAGGTTTATACTATTGTTT+TGG 0.288773 1.2:-6046671 MS.gene24547:CDS
TAGAGAAGTTACCGTTGTTT+CGG 0.323518 1.2:-6046839 MS.gene24547:CDS
TTCTCAAAGCTTCTAACATA+TGG 0.399534 1.2:+6046928 None:intergenic
GATTGAAGTGCATGTGTTTG+AGG 0.427491 1.2:+6046990 None:intergenic
AAGCTTAATCTTCAGAAACT+TGG 0.437353 1.2:-6046577 MS.gene24547:CDS
AATGAGTTTGTCAACAATGA+AGG 0.452521 1.2:-6046694 MS.gene24547:CDS
GCTTCGGTGCATAATATTCA+AGG 0.486800 1.2:-6047078 MS.gene24547:CDS
AAACTATCGTTCGGTTACTT+CGG 0.496046 1.2:-6046719 MS.gene24547:CDS
TATGGCCACACTATGCTTGA+TGG 0.499255 1.2:+6046946 None:intergenic
GTTTGTCAACAATGAAGGTA+AGG 0.501378 1.2:-6046689 MS.gene24547:CDS
TTGAGGTTGGTTCTAATATG+TGG 0.501993 1.2:+6047007 None:intergenic
AACAGTGTCAACAAACATCT+TGG 0.503428 1.2:+6046603 None:intergenic
TCGTCTTCAAAACTATCGTT+CGG 0.506349 1.2:-6046728 MS.gene24547:CDS
GAAGTGCATGTGTTTGAGGT+TGG 0.508894 1.2:+6046994 None:intergenic
ATCAAAGGTTGCAACATGAA+AGG 0.524876 1.2:-6046883 MS.gene24547:CDS
TATATATTATTGTCCATGCA+TGG 0.529703 1.2:+6046528 None:intergenic
AGTTCATGTTCTTCCATGCA+TGG 0.533444 1.2:-6046541 MS.gene24547:CDS
AAACACCCACAAAATGGCTT+CGG 0.536754 1.2:-6047094 None:intergenic
CTTTCAGTACTTGTCGAAGC+CGG 0.537971 1.2:+6046811 None:intergenic
AAATACAAACATTTCATCAA+AGG 0.541877 1.2:-6046898 MS.gene24547:CDS
GGTTGCAACATGAAAGGTGA+TGG 0.558210 1.2:-6046877 MS.gene24547:CDS
TATATTGTTGATATTCCACA+TGG 0.600252 1.2:-6046643 MS.gene24547:CDS
TCTTCTTCAGTGTTCCCATG+TGG 0.603865 1.2:+6046628 None:intergenic
ATGAAAGGTGATGGAAACGT+TGG 0.615437 1.2:-6046868 MS.gene24547:CDS
AGCCGGTAAACCCGAAACAA+CGG 0.615768 1.2:+6046828 None:intergenic
AAGCACCATCAAGCATAGTG+TGG 0.678529 1.2:-6046951 MS.gene24547:CDS
ATATTGTTGATATTCCACAT+GGG 0.707262 1.2:-6046642 MS.gene24547:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACAAACATTTCATCAA+AGG - chr1.2:6046717-6046736 MS.gene24547:CDS 20.0%
!!! ATGAAATGTTTGTATTTTTG+TGG + chr1.2:6046714-6046733 None:intergenic 20.0%
!!! ATGTGGTATTTTTTTATGAT+TGG + chr1.2:6046594-6046613 None:intergenic 20.0%
!!! TAAGGTTTATACTATTGTTT+TGG - chr1.2:6046944-6046963 MS.gene24547:CDS 20.0%
! ATATTGTTGATATTCCACAT+GGG - chr1.2:6046973-6046992 MS.gene24547:CDS 25.0%
! TATATTGTTGATATTCCACA+TGG - chr1.2:6046972-6046991 MS.gene24547:CDS 25.0%
!! TACTGAAAGATTAGAGATTT+TGG - chr1.2:6046818-6046837 MS.gene24547:CDS 25.0%
!!! GTAATAAGTTTTAGAGTTGT+TGG - chr1.2:6046855-6046874 MS.gene24547:CDS 25.0%
AAGCTTAATCTTCAGAAACT+TGG - chr1.2:6047038-6047057 MS.gene24547:CDS 30.0%
AATGAGTTTGTCAACAATGA+AGG - chr1.2:6046921-6046940 MS.gene24547:CDS 30.0%
TTCTCAAAGCTTCTAACATA+TGG + chr1.2:6046690-6046709 None:intergenic 30.0%
!!! ATAAGTTTTAGAGTTGTTGG+TGG - chr1.2:6046858-6046877 MS.gene24547:CDS 30.0%
AAACTATCGTTCGGTTACTT+CGG - chr1.2:6046896-6046915 MS.gene24547:CDS 35.0%
AACAGTGTCAACAAACATCT+TGG + chr1.2:6047015-6047034 None:intergenic 35.0%
ATCAAAGGTTGCAACATGAA+AGG - chr1.2:6046732-6046751 MS.gene24547:CDS 35.0%
GTTTGTCAACAATGAAGGTA+AGG - chr1.2:6046926-6046945 MS.gene24547:CDS 35.0%
TAGAGAAGTTACCGTTGTTT+CGG - chr1.2:6046776-6046795 MS.gene24547:CDS 35.0%
TCGTCTTCAAAACTATCGTT+CGG - chr1.2:6046887-6046906 MS.gene24547:CDS 35.0%
!! TGATGGTGCTTCTATTTTGT+AGG + chr1.2:6046655-6046674 None:intergenic 35.0%
!! TTGAGGTTGGTTCTAATATG+TGG + chr1.2:6046611-6046630 None:intergenic 35.0%
AGTTCATGTTCTTCCATGCA+TGG - chr1.2:6047074-6047093 MS.gene24547:CDS 40.0%
GATTGAAGTGCATGTGTTTG+AGG + chr1.2:6046628-6046647 None:intergenic 40.0%
! AGAGAAGTTACCGTTGTTTC+GGG - chr1.2:6046777-6046796 MS.gene24547:CDS 40.0%
! GCTTCGGTGCATAATATTCA+AGG - chr1.2:6046537-6046556 MS.gene24547:CDS 40.0%
!! ATGAAAGGTGATGGAAACGT+TGG - chr1.2:6046747-6046766 MS.gene24547:CDS 40.0%
AAGCACCATCAAGCATAGTG+TGG - chr1.2:6046664-6046683 MS.gene24547:CDS 45.0%
CTTTCAGTACTTGTCGAAGC+CGG + chr1.2:6046807-6046826 None:intergenic 45.0%
GGTTGCAACATGAAAGGTGA+TGG - chr1.2:6046738-6046757 MS.gene24547:CDS 45.0%
TATGGCCACACTATGCTTGA+TGG + chr1.2:6046672-6046691 None:intergenic 45.0%
TCTTCTTCAGTGTTCCCATG+TGG + chr1.2:6046990-6047009 None:intergenic 45.0%
! GAAGTGCATGTGTTTGAGGT+TGG + chr1.2:6046624-6046643 None:intergenic 45.0%
!! TACCGTTGTTTCGGGTTTAC+CGG - chr1.2:6046785-6046804 MS.gene24547:CDS 45.0%
AGCCGGTAAACCCGAAACAA+CGG + chr1.2:6046790-6046809 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 6046534 6047103 6046534 ID=MS.gene24547
chr1.2 mRNA 6046534 6047103 6046534 ID=MS.gene24547.t1;Parent=MS.gene24547
chr1.2 exon 6046534 6047103 6046534 ID=MS.gene24547.t1.exon1;Parent=MS.gene24547.t1
chr1.2 CDS 6046534 6047103 6046534 ID=cds.MS.gene24547.t1;Parent=MS.gene24547.t1
Gene Sequence

>MS.gene24547

ATGGCTTCGGTGCATAATATTCAAGGTCTAACAGAAGAAGAATACAAAGAACTCGAACCAATCATAAAAAAATACCACATATTAGAACCAACCTCAAACACATGCACTTCAATCATAACCTACAAAATAGAAGCACCATCAAGCATAGTGTGGCCATATGTTAGAAGCTTTGAGAATCCACAAAAATACAAACATTTCATCAAAGGTTGCAACATGAAAGGTGATGGAAACGTTGGTAGCATTAGAGAAGTTACCGTTGTTTCGGGTTTACCGGCTTCGACAAGTACTGAAAGATTAGAGATTTTGGATGATGAAAAACATGTAATAAGTTTTAGAGTTGTTGGTGGTGAACATCGTCTTCAAAACTATCGTTCGGTTACTTCGGTTAATGAGTTTGTCAACAATGAAGGTAAGGTTTATACTATTGTTTTGGAATCTTATATTGTTGATATTCCACATGGGAACACTGAAGAAGATACCAAGATGTTTGTTGACACTGTTGTCAAGCTTAATCTTCAGAAACTTGGAGTTGTTGCTATGAGTTCATGTTCTTCCATGCATGGACAATAA
Protein sequence

>MS.gene24547.t1

MASVHNIQGLTEEEYKELEPIIKKYHILEPTSNTCTSIITYKIEAPSSIVWPYVRSFENPQKYKHFIKGCNMKGDGNVGSIREVTVVSGLPASTSTERLEILDDEKHVISFRVVGGEHRLQNYRSVTSVNEFVNNEGKVYTIVLESYIVDIPHGNTEEDTKMFVDTVVKLNLQKLGVVAMSSCSSMHGQ