AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96218

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96218.t1 MTR_2g019810 79.412 170 35 0 1 170 196 365 4.65e-96 283
MS.gene96218.t1 MTR_2g019840 75.740 169 41 0 1 169 208 376 1.14e-87 263
MS.gene96218.t1 MTR_2g436400 49.143 175 82 3 1 168 207 381 2.62e-49 164
MS.gene96218.t1 MTR_2g437960 46.524 187 93 3 1 180 216 402 1.55e-45 155
MS.gene96218.t1 MTR_2g437960 46.524 187 93 3 1 180 216 402 1.73e-45 155
MS.gene96218.t1 MTR_2g437080 51.250 160 76 2 11 168 215 374 9.40e-45 152
MS.gene96218.t1 MTR_2g437030 51.250 160 76 2 11 168 301 460 1.85e-44 153
MS.gene96218.t1 MTR_4g119550 47.826 161 82 2 11 169 225 385 9.01e-43 147
MS.gene96218.t1 MTR_2g437090 47.500 160 82 2 11 168 3 162 3.32e-42 140
MS.gene96218.t1 MTR_2g437060 50.641 156 75 2 11 164 230 385 4.29e-42 145
MS.gene96218.t1 MTR_2g437240 43.850 187 98 3 1 180 228 414 9.44e-42 145
MS.gene96218.t1 MTR_2g436460 49.032 155 76 3 16 167 225 379 1.08e-41 144
MS.gene96218.t1 MTR_2g437020 50.617 162 73 4 11 168 216 374 1.32e-41 144
MS.gene96218.t1 MTR_2g438020 47.953 171 82 3 1 164 267 437 2.02e-41 146
MS.gene96218.t1 MTR_2g436440 46.835 158 82 2 13 168 223 380 6.71e-41 142
MS.gene96218.t1 MTR_2g437120 49.677 155 77 1 11 164 229 383 1.29e-40 142
MS.gene96218.t1 MTR_2g437170 47.953 171 82 3 1 164 220 390 1.33e-40 142
MS.gene96218.t1 MTR_2g438010 41.711 187 102 3 1 180 233 419 1.36e-40 142
MS.gene96218.t1 MTR_2g437200 47.953 171 82 3 1 164 228 398 5.47e-40 140
MS.gene96218.t1 MTR_2g437160 49.342 152 75 2 15 164 153 304 8.23e-40 138
MS.gene96218.t1 MTR_2g437150 45.143 175 89 3 1 168 220 394 1.79e-39 139
MS.gene96218.t1 MTR_2g437040 44.937 158 85 2 13 168 217 374 2.17e-39 138
MS.gene96218.t1 MTR_2g437160 49.342 152 75 2 15 164 244 395 4.66e-39 138
MS.gene96218.t1 MTR_2g437940 45.614 171 86 3 1 164 184 354 7.16e-39 137
MS.gene96218.t1 MTR_2g437100 45.665 173 87 3 1 166 225 397 6.11e-38 135
MS.gene96218.t1 MTR_2g437260 42.442 172 90 4 1 163 194 365 1.20e-37 134
MS.gene96218.t1 MTR_2g437990 42.442 172 97 2 11 180 227 398 8.24e-37 132
MS.gene96218.t1 MTR_2g437180 45.614 171 84 4 1 164 212 380 8.10e-36 129
MS.gene96218.t1 MTR_2g076320 41.860 172 98 2 11 180 228 399 1.66e-35 129
MS.gene96218.t1 MTR_4g119580 42.604 169 90 3 1 162 202 370 4.50e-35 127
MS.gene96218.t1 MTR_2g437130 39.773 176 99 3 1 169 201 376 5.85e-35 127
MS.gene96218.t1 MTR_4g120380 39.645 169 95 3 1 162 202 370 5.59e-33 121
MS.gene96218.t1 MTR_4g007490 36.196 163 102 2 5 165 209 371 2.30e-27 106
MS.gene96218.t1 MTR_3g450500 38.365 159 94 3 9 164 215 372 3.79e-27 105
MS.gene96218.t1 MTR_4g120380 37.584 149 86 3 1 142 202 350 4.39e-25 100
MS.gene96218.t1 MTR_2g019830 71.642 67 19 0 101 167 136 202 7.10e-23 91.3
MS.gene96218.t1 MTR_4g119570 34.911 169 70 4 1 162 94 229 6.40e-21 86.7
MS.gene96218.t1 MTR_8g080990 33.113 151 93 5 13 158 221 368 3.69e-14 70.1
MS.gene96218.t1 MTR_8g012210 25.843 178 119 5 1 167 178 353 2.19e-13 67.8
MS.gene96218.t1 MTR_3g085240 35.556 90 42 1 67 156 176 249 2.24e-11 61.2
MS.gene96218.t1 MTR_8g081000 26.220 164 119 2 1 162 222 385 4.13e-11 61.2
MS.gene96218.t1 MTR_8g081000 27.273 165 116 3 1 162 222 385 4.47e-11 61.2
MS.gene96218.t1 MTR_8g081000 27.273 165 116 3 1 162 222 385 4.66e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96218.t1 AT5G07900 38.462 156 93 2 9 161 244 399 1.27e-32 121
MS.gene96218.t1 AT1G21150 30.625 160 108 2 9 165 195 354 9.47e-21 88.6
MS.gene96218.t1 AT1G21150 30.625 160 108 2 9 165 231 390 1.25e-20 88.6
MS.gene96218.t1 AT1G21150 30.625 160 108 2 9 165 295 454 1.63e-20 88.6
MS.gene96218.t1 AT1G62010 26.829 205 105 6 9 174 207 405 4.31e-13 67.0
MS.gene96218.t1 AT1G61960 30.000 120 80 1 46 161 332 451 4.50e-13 67.0
MS.gene96218.t1 AT1G61990 26.804 194 100 6 9 161 216 408 4.39e-12 64.3
MS.gene96218.t1 AT1G61990 26.804 194 100 6 9 161 216 408 4.39e-12 64.3
MS.gene96218.t1 AT1G79220 31.333 150 99 2 22 167 233 382 1.87e-11 62.4
MS.gene96218.t1 AT1G62110 28.346 127 84 2 46 165 333 459 7.56e-11 60.8

Find 34 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATAAGAAGTATTGGATATT+TGG 0.165459 2.2:-65000327 None:intergenic
TTCCTTTCCCATACGGGTTT+TGG 0.211977 2.2:-65000152 None:intergenic
AATACTTCTTATGCTGAGTT+TGG 0.261332 2.2:+65000337 MS.gene96218:CDS
TCGATCCAAAGGTTTGATTA+AGG 0.285728 2.2:+65000400 MS.gene96218:CDS
AGATGTTTCAACTTTCAATA+AGG 0.340961 2.2:+65000535 MS.gene96218:CDS
AGCATCCTTAATCAAACCTT+TGG 0.342269 2.2:-65000405 None:intergenic
GTGTTGGAAGTAAAACAATT+AGG 0.360849 2.2:+65000077 MS.gene96218:CDS
GATTAATGCGTATAAGAAAT+GGG 0.369032 2.2:+65000175 MS.gene96218:CDS
AGATTAATGCGTATAAGAAA+TGG 0.381339 2.2:+65000174 MS.gene96218:CDS
AAACTCAGCATAAGAAGTAT+TGG 0.453268 2.2:-65000335 None:intergenic
TCAGAGACTTTGAAAGGTGC+AGG 0.454054 2.2:-65000434 None:intergenic
TTGAAATTTCTTCGATCCAA+AGG 0.475136 2.2:+65000389 MS.gene96218:CDS
TCTTAGCATGTAGTGCGATA+AGG 0.479997 2.2:-65000124 None:intergenic
TTAATCTTCCTTTCCCATAC+GGG 0.481781 2.2:-65000158 None:intergenic
ATTAATCTTCCTTTCCCATA+CGG 0.500717 2.2:-65000159 None:intergenic
AGATTAGTCCAAAACCCGTA+TGG 0.528933 2.2:+65000144 MS.gene96218:CDS
GATTAGTCCAAAACCCGTAT+GGG 0.549456 2.2:+65000145 MS.gene96218:CDS
GTCCAAAACCCGTATGGGAA+AGG 0.554208 2.2:+65000150 MS.gene96218:CDS
CAATCTTCGAAGCAACGCAA+AGG 0.555930 2.2:+65000569 MS.gene96218:CDS
GAAGTATCCATGGTGTATGT+TGG 0.562557 2.2:+65000232 MS.gene96218:CDS
ATGGTGTATGTTGGCATCTG+TGG 0.563796 2.2:+65000241 MS.gene96218:CDS
ACTGCCTTCTCAAATACTGC+AGG 0.569710 2.2:-65000056 None:intergenic
AGTATTTGAGAAGGCAGTGT+TGG 0.578490 2.2:+65000061 MS.gene96218:CDS
AATCTTCGAAGCAACGCAAA+GGG 0.578629 2.2:+65000570 MS.gene96218:CDS
CAGAGACTTTGAAAGGTGCA+GGG 0.587463 2.2:-65000433 None:intergenic
GATTCTAAGTTGCAGTGACA+TGG 0.589689 2.2:-65000607 None:intergenic
ATTAATGCGTATAAGAAATG+GGG 0.599170 2.2:+65000176 MS.gene96218:CDS
AATTTCAACACAAAAGCCCT+AGG 0.603574 2.2:-65000374 None:intergenic
ATGCGTATAAGAAATGGGGT+TGG 0.624037 2.2:+65000180 MS.gene96218:CDS
AGAGACTTTGAAAGGTGCAG+GGG 0.631390 2.2:-65000432 None:intergenic
GAAACCTGCAGTATTTGAGA+AGG 0.637908 2.2:+65000052 MS.gene96218:CDS
AGATCCTCAGAGACTTTGAA+AGG 0.638683 2.2:-65000440 None:intergenic
TGCACCTTTCAAAGTCTCTG+AGG 0.647402 2.2:+65000436 MS.gene96218:CDS
ACAGATGCCAACATACACCA+TGG 0.670800 2.2:-65000239 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGATGTTTCAACTTTCAATA+AGG + chr2.2:65000535-65000554 MS.gene96218:CDS 25.0%
! AGATTAATGCGTATAAGAAA+TGG + chr2.2:65000174-65000193 MS.gene96218:CDS 25.0%
! ATTAATGCGTATAAGAAATG+GGG + chr2.2:65000176-65000195 MS.gene96218:CDS 25.0%
! GATTAATGCGTATAAGAAAT+GGG + chr2.2:65000175-65000194 MS.gene96218:CDS 25.0%
!! TTTTGTTAATCACATGGATT+GGG + chr2.2:65000289-65000308 MS.gene96218:CDS 25.0%
!! TTTTTGTTAATCACATGGAT+TGG + chr2.2:65000288-65000307 MS.gene96218:CDS 25.0%
!!! ATAAGGAAAAACGTTTTTTC+AGG - chr2.2:65000110-65000129 None:intergenic 25.0%
!!! CATAAGAAGTATTGGATATT+TGG - chr2.2:65000330-65000349 None:intergenic 25.0%
AATACTTCTTATGCTGAGTT+TGG + chr2.2:65000337-65000356 MS.gene96218:CDS 30.0%
ATTAATCTTCCTTTCCCATA+CGG - chr2.2:65000162-65000181 None:intergenic 30.0%
GGAAAAAAAGGTTATTCCTA+GGG + chr2.2:65000358-65000377 MS.gene96218:CDS 30.0%
GTGTTGGAAGTAAAACAATT+AGG + chr2.2:65000077-65000096 MS.gene96218:CDS 30.0%
TATGCTGAGTTTGGAAAAAA+AGG + chr2.2:65000346-65000365 MS.gene96218:CDS 30.0%
TGGAAAAAAAGGTTATTCCT+AGG + chr2.2:65000357-65000376 MS.gene96218:CDS 30.0%
TTGAAATTTCTTCGATCCAA+AGG + chr2.2:65000389-65000408 MS.gene96218:CDS 30.0%
! AAACTCAGCATAAGAAGTAT+TGG - chr2.2:65000338-65000357 None:intergenic 30.0%
!!! GCAGTTTTTTGTTAATCACA+TGG + chr2.2:65000283-65000302 MS.gene96218:CDS 30.0%
AATTTCAACACAAAAGCCCT+AGG - chr2.2:65000377-65000396 None:intergenic 35.0%
AGCATCCTTAATCAAACCTT+TGG - chr2.2:65000408-65000427 None:intergenic 35.0%
TCGATCCAAAGGTTTGATTA+AGG + chr2.2:65000400-65000419 MS.gene96218:CDS 35.0%
TGGATACTTCAAAAATGCTG+AGG - chr2.2:65000222-65000241 None:intergenic 35.0%
TTAATCTTCCTTTCCCATAC+GGG - chr2.2:65000161-65000180 None:intergenic 35.0%
!!! CAGCATTTTTGAAGTATCCA+TGG + chr2.2:65000222-65000241 MS.gene96218:CDS 35.0%
AATCTTCGAAGCAACGCAAA+GGG + chr2.2:65000570-65000589 MS.gene96218:CDS 40.0%
AGATCCTCAGAGACTTTGAA+AGG - chr2.2:65000443-65000462 None:intergenic 40.0%
AGTATTTGAGAAGGCAGTGT+TGG + chr2.2:65000061-65000080 MS.gene96218:CDS 40.0%
ATGCGTATAAGAAATGGGGT+TGG + chr2.2:65000180-65000199 MS.gene96218:CDS 40.0%
GAAACCTGCAGTATTTGAGA+AGG + chr2.2:65000052-65000071 MS.gene96218:CDS 40.0%
TCTTAGCATGTAGTGCGATA+AGG - chr2.2:65000127-65000146 None:intergenic 40.0%
! AGATTAGTCCAAAACCCGTA+TGG + chr2.2:65000144-65000163 MS.gene96218:CDS 40.0%
! GAAGTATCCATGGTGTATGT+TGG + chr2.2:65000232-65000251 MS.gene96218:CDS 40.0%
! GATTAGTCCAAAACCCGTAT+GGG + chr2.2:65000145-65000164 MS.gene96218:CDS 40.0%
ACAGATGCCAACATACACCA+TGG - chr2.2:65000242-65000261 None:intergenic 45.0%
ACTGCCTTCTCAAATACTGC+AGG - chr2.2:65000059-65000078 None:intergenic 45.0%
ATGGTGTATGTTGGCATCTG+TGG + chr2.2:65000241-65000260 MS.gene96218:CDS 45.0%
CAATCTTCGAAGCAACGCAA+AGG + chr2.2:65000569-65000588 MS.gene96218:CDS 45.0%
TGCACCTTTCAAAGTCTCTG+AGG + chr2.2:65000436-65000455 MS.gene96218:CDS 45.0%
! AGAGACTTTGAAAGGTGCAG+GGG - chr2.2:65000435-65000454 None:intergenic 45.0%
! CAGAGACTTTGAAAGGTGCA+GGG - chr2.2:65000436-65000455 None:intergenic 45.0%
! TCAGAGACTTTGAAAGGTGC+AGG - chr2.2:65000437-65000456 None:intergenic 45.0%
! TTCCTTTCCCATACGGGTTT+TGG - chr2.2:65000155-65000174 None:intergenic 45.0%
GTCCAAAACCCGTATGGGAA+AGG + chr2.2:65000150-65000169 MS.gene96218:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 65000041 65000625 65000041 ID=MS.gene96218
chr2.2 mRNA 65000041 65000625 65000041 ID=MS.gene96218.t1;Parent=MS.gene96218
chr2.2 exon 65000041 65000625 65000041 ID=MS.gene96218.t1.exon1;Parent=MS.gene96218.t1
chr2.2 CDS 65000041 65000625 65000041 ID=cds.MS.gene96218.t1;Parent=MS.gene96218.t1
Gene Sequence

>MS.gene96218

ATGCTCTCTGAGAAACCTGCAGTATTTGAGAAGGCAGTGTTGGAAGTAAAACAATTAGGATTCAAACCTGAAAAAACGTTTTTCCTTATCGCACTACATGCTAAGATTAGTCCAAAACCCGTATGGGAAAGGAAGATTAATGCGTATAAGAAATGGGGTTGGTCTGATGAAATTATTGCCTCAGCATTTTTGAAGTATCCATGGTGTATGTTGGCATCTGTGGAAAAAATTGAAGCAGTGATGCAGTTTTTTGTTAATCACATGGATTGGGAGTCTAATGTGCTTGCCAAATATCCAATACTTCTTATGCTGAGTTTGGAAAAAAAGGTTATTCCTAGGGCTTTTGTGTTGAAATTTCTTCGATCCAAAGGTTTGATTAAGGATGCTAAATCCCCTGCACCTTTCAAAGTCTCTGAGGATCTGTTTTTGAAGAGATTTGTGACTTGTTTCGAAGAAGAAGCATCTCAGCTGTTGAAGTTGTATGAAGAGAAAAGAGATGTTTCAACTTTCAATAAGGTTTCGCAACTGCAATCTTCGAAGCAACGCAAAGGGTCTCTGCTACACGACCATGTCACTGCAACTTAG
Protein sequence

>MS.gene96218.t1

MLSEKPAVFEKAVLEVKQLGFKPEKTFFLIALHAKISPKPVWERKINAYKKWGWSDEIIASAFLKYPWCMLASVEKIEAVMQFFVNHMDWESNVLAKYPILLMLSLEKKVIPRAFVLKFLRSKGLIKDAKSPAPFKVSEDLFLKRFVTCFEEEASQLLKLYEEKRDVSTFNKVSQLQSSKQRKGSLLHDHVTAT