AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG020943

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG020943 MtrunA17_Chr4g0033291 82.716 324 26 5 1 312 24 329 0.0 516
MsaG020943 MtrunA17_Chr4g0033391 79.688 320 29 5 1 309 24 318 2.89e-180 500
MsaG020943 MtrunA17_Chr4g0033281 80.878 319 33 4 1 309 23 323 9.05e-173 481
MsaG020943 MtrunA17_Chr2g0307131 60.227 352 80 7 1 311 23 355 1.25e-131 378
MsaG020943 MtrunA17_Chr6g0468491 63.554 332 83 10 1 312 1 314 8.31e-130 372
MsaG020943 MtrunA17_Chr2g0307141 58.924 353 89 7 1 312 23 360 9.09e-123 356
MsaG020943 MtrunA17_Chr7g0225901 55.369 298 64 7 1 287 1 240 1.35e-97 288
MsaG020943 MtrunA17_Chr4g0054581 51.381 362 120 7 1 312 24 379 2.06e-97 292
MsaG020943 MtrunA17_Chr6g0468461 52.308 325 94 9 1 295 23 316 4.28e-90 272
MsaG020943 MtrunA17_Chr4g0054621 47.661 342 122 11 3 312 26 342 8.63e-83 253
MsaG020943 MtrunA17_Chr5g0400621 45.875 303 136 6 23 311 45 333 3.03e-65 208
MsaG020943 MtrunA17_Chr4g0002801 41.667 204 98 6 126 308 128 331 8.51e-43 150
MsaG020943 MtrunA17_Chr5g0400661 41.014 217 100 3 119 307 118 334 2.59e-42 149
MsaG020943 MtrunA17_Chr8g0336681 37.143 245 125 4 83 308 102 336 3.16e-42 149
MsaG020943 MtrunA17_Chr5g0400641 52.500 160 58 5 148 293 1 156 1.70e-41 141
MsaG020943 MtrunA17_Chr2g0280161 44.022 184 90 2 137 309 171 352 7.70e-41 145
MsaG020943 MtrunA17_Chr4g0054551 35.741 263 137 6 71 306 67 324 1.31e-40 144
MsaG020943 MtrunA17_Chr4g0049331 33.788 293 169 5 36 309 23 309 1.68e-39 140
MsaG020943 MtrunA17_Chr4g0054561 35.361 263 138 6 71 306 67 324 2.66e-39 140
MsaG020943 MtrunA17_Chr2g0333641 37.643 263 138 9 56 306 58 306 3.02e-39 140
MsaG020943 MtrunA17_Chr4g0054571 45.405 185 84 4 142 309 147 331 2.40e-38 138
MsaG020943 MtrunA17_Chr4g0002781 36.220 254 126 7 76 308 112 350 4.60e-38 138
MsaG020943 MtrunA17_Chr2g0333541 43.850 187 89 5 134 305 81 266 1.65e-37 134
MsaG020943 MtrunA17_Chr2g0333621 36.100 241 135 4 83 311 82 315 1.77e-37 135
MsaG020943 MtrunA17_Chr5g0400671 32.971 276 141 8 59 307 65 323 2.59e-36 132
MsaG020943 MtrunA17_Chr7g0249811 38.462 208 120 4 104 308 127 329 1.06e-33 126
MsaG020943 MtrunA17_Chr2g0333611 38.421 190 105 5 131 309 29 217 1.70e-33 122
MsaG020943 MtrunA17_Chr4g0002831 37.126 167 90 5 147 306 45 203 1.03e-25 101
MsaG020943 MtrunA17_Chr7g0233441 37.931 145 78 2 168 306 57 195 3.80e-24 97.4
MsaG020943 MtrunA17_Chr4g0002851 39.568 139 76 2 168 306 65 195 3.58e-23 94.7
MsaG020943 MtrunA17_Chr8g0366751 30.120 166 85 2 137 271 444 609 1.51e-15 77.0
MsaG020943 MtrunA17_Chr1g0185621 30.055 183 99 6 110 268 439 616 4.36e-15 75.9
MsaG020943 MtrunA17_Chr8g0346151 28.108 185 97 6 90 244 214 392 3.28e-14 72.8
MsaG020943 MtrunA17_Chr7g0275821 30.519 154 101 2 141 288 244 397 6.26e-14 72.0
MsaG020943 MtrunA17_Chr5g0411341 29.050 179 78 4 130 271 474 640 6.57e-14 72.4
MsaG020943 MtrunA17_Chr8g0346161 29.448 163 97 5 120 264 261 423 6.35e-13 68.9
MsaG020943 MtrunA17_Chr3g0131691 28.324 173 103 3 146 298 299 470 1.18e-12 68.2
MsaG020943 MtrunA17_Chr8g0365711 26.036 169 102 4 135 284 234 398 2.11e-12 67.4
MsaG020943 MtrunA17_Chr7g0260841 38.824 85 42 1 124 198 324 408 3.63e-12 66.6
MsaG020943 MtrunA17_Chr7g0252041 30.337 178 101 4 147 302 288 464 2.67e-11 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG020943 AT4G37850.2 38.868 265 116 11 84 309 70 327 2.74e-38 138
MsaG020943 AT4G37850.1 38.868 265 116 11 84 309 70 327 2.74e-38 138
MsaG020943 AT2G22760.1 38.298 188 102 4 134 307 108 295 2.22e-35 130
MsaG020943 AT2G22750.5 37.759 241 112 7 103 310 94 329 4.96e-34 127
MsaG020943 AT2G22750.2 37.759 241 112 7 103 310 70 305 5.47e-34 126
MsaG020943 AT2G22750.3 37.759 241 112 7 103 310 98 333 5.60e-34 127
MsaG020943 AT2G22750.1 37.759 241 111 8 103 310 70 304 8.50e-33 123
MsaG020943 AT2G22750.4 37.759 241 111 8 103 310 98 332 8.52e-33 124
MsaG020943 AT2G22770.1 37.766 188 92 2 144 306 131 318 1.97e-30 117
MsaG020943 AT2G22760.2 38.323 167 90 3 134 287 108 274 2.07e-29 114
MsaG020943 AT5G46760.1 32.161 199 96 8 130 291 396 592 1.82e-18 86.3
MsaG020943 AT4G17880.1 30.705 241 125 9 88 289 350 587 2.33e-17 82.8
MsaG020943 AT1G32640.1 32.075 159 81 3 137 271 434 589 1.41e-15 77.8
MsaG020943 AT2G46510.1 37.931 116 54 3 137 242 377 484 1.64e-14 74.3
MsaG020943 AT1G01260.1 29.114 158 87 3 135 284 420 560 2.35e-13 70.9
MsaG020943 AT1G01260.2 29.114 158 87 3 135 284 420 560 2.35e-13 70.9
MsaG020943 AT1G01260.3 29.114 158 87 3 135 284 420 560 2.35e-13 70.9
MsaG020943 AT4G09820.1 26.728 217 136 6 96 310 321 516 2.59e-13 70.9
MsaG020943 AT5G41315.3 27.322 183 95 4 136 283 437 616 1.03e-12 68.9
MsaG020943 AT5G41315.1 27.322 183 95 4 136 283 432 611 1.05e-12 68.9
MsaG020943 AT5G41315.2 27.322 183 95 4 136 283 440 619 1.07e-12 68.9
MsaG020943 AT4G16430.1 46.575 73 35 1 130 198 301 373 1.36e-12 68.6
MsaG020943 AT5G46830.1 54.839 62 24 1 141 198 335 396 3.61e-12 67.4
MsaG020943 AT3G26744.1 29.697 165 96 2 146 290 308 472 2.68e-11 64.7
MsaG020943 AT3G26744.4 29.697 165 96 2 146 290 308 472 2.68e-11 64.7
MsaG020943 AT3G26744.2 29.697 165 96 2 146 290 308 472 2.68e-11 64.7

Find 49 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTGTTCCTAACCTTAAAA+AGG 0.267726 4:-60877558 MsaT020943.1:intron
TCAAGAACAAAACAAACAAT+TGG 0.334442 4:-60877960 MsaT020943.1:CDS
CAAGTGGAAGCAAGAGTGTT+AGG 0.334987 4:-60876418 MsaT020943.1:CDS
GGGGCTTCTAGTTAAAATTA+TGG 0.343764 4:-60876356 MsaT020943.1:CDS
GATGGTGATGGAGAAATATT+TGG 0.350142 4:+60877854 None:intergenic
CTGCAAGAGCAATGAAGCTT+TGG 0.357341 4:+60877582 None:intergenic
ATCAGTGTCTCCAACCGAAT+TGG 0.364748 4:-60877747 MsaT020943.1:CDS
CAAGAACAAAACAAACAATT+GGG 0.390107 4:-60877959 MsaT020943.1:CDS
CATCTGCATCAAGAAAATTA+AGG 0.394973 4:+60878020 None:intergenic
TGCATATGCATGGTTTGGTC+GGG 0.398563 4:+60876500 None:intergenic
ATCGCTGCATATGCATGGTT+TGG 0.407010 4:+60876495 None:intergenic
ACTCTTGCTTCCACTTGAAA+TGG 0.409697 4:+60876424 None:intergenic
AATAACAGTGTCTTACCCTT+TGG 0.416567 4:-60876301 MsaT020943.1:CDS
GCCCCTTGTGCTCCTTGCAT+TGG 0.417499 4:+60876374 None:intergenic
AGAAACCTCAAAAGGGTCAT+TGG 0.430732 4:-60877705 MsaT020943.1:CDS
TAGGAAAACAAGTGTTGATT+CGG 0.449123 4:-60876399 MsaT020943.1:CDS
TGCAAGAGCAATGAAGCTTT+GGG 0.460124 4:+60877583 None:intergenic
AAAGAGGAGTTAGATGGTGA+TGG 0.464747 4:+60877842 None:intergenic
CACTCACCAGAAACCTCAAA+AGG 0.466038 4:-60877713 MsaT020943.1:CDS
TGACTTGCTGAGATCATTTG+TGG 0.473303 4:+60877928 None:intergenic
GATAACATTGAAGGTGTTGT+TGG 0.475426 4:-60876451 MsaT020943.1:CDS
CTGCATATGCATGGTTTGGT+CGG 0.481187 4:+60876499 None:intergenic
AACTGAAAAGAGGAGTTAGA+TGG 0.496291 4:+60877836 None:intergenic
GCTGAGATCATTTGTGGAAG+TGG 0.497595 4:+60877934 None:intergenic
AGCAAAAGGCCTCGTGCTCA+TGG 0.502148 4:-60877650 MsaT020943.1:CDS
GGTAGCTACCTGAGCAATGA+TGG 0.511294 4:+60876258 None:intergenic
AAGGCCTCGTGCTCATGGTA+AGG 0.535577 4:-60877645 MsaT020943.1:CDS
TCATGTGAGGATAACATTGA+AGG 0.542969 4:-60876460 MsaT020943.1:CDS
TTCTTGATGCAGATGTGGGA+GGG 0.544131 4:-60878012 MsaT020943.1:CDS
CGACATTACCATCATTGCTC+AGG 0.544333 4:-60876266 MsaT020943.1:intron
GTTGATTCGGTTCCAATGCA+AGG 0.545125 4:-60876386 MsaT020943.1:CDS
GTTCCAATGCAAGGAGCACA+AGG 0.563766 4:-60876377 MsaT020943.1:CDS
TCTTCATCGCTGCATATGCA+TGG 0.570607 4:+60876490 None:intergenic
GCATATGCATGGTTTGGTCG+GGG 0.578376 4:+60876501 None:intergenic
TTTCTTGATGCAGATGTGGG+AGG 0.583981 4:-60878013 MsaT020943.1:CDS
TGGTATTTGAAACTGAAAAG+AGG 0.585974 4:+60877826 None:intergenic
GTCGAGTGTAGAATCTCCAA+AGG 0.590011 4:+60876285 None:intergenic
TCCAATGCAAGGAGCACAAG+GGG 0.595381 4:-60876375 MsaT020943.1:CDS
AGGGTACAACTTGAGCATAA+AGG 0.600355 4:-60876078 MsaT020943.1:CDS
ACTCACCAGAAACCTCAAAA+GGG 0.604223 4:-60877712 MsaT020943.1:CDS
TGTTGGTTCACCATTTCAAG+TGG 0.611743 4:-60876434 MsaT020943.1:CDS
TCATGGTAAGGATCACATCA+TGG 0.611981 4:-60877633 MsaT020943.1:CDS
TCGAGTGTAGAATCTCCAAA+GGG 0.615421 4:+60876286 None:intergenic
CGAATACAATATATTTGCTG+AGG 0.624364 4:-60878050 MsaT020943.1:CDS
TGAAGATTCGTCATCATGTG+AGG 0.642706 4:-60876473 MsaT020943.1:CDS
TTCCAATGCAAGGAGCACAA+GGG 0.644827 4:-60876376 MsaT020943.1:CDS
AAGAACAAAACAAACAATTG+GGG 0.650416 4:-60877958 MsaT020943.1:CDS
ACTTGTGAAGAACGTACGCA+TGG 0.661373 4:-60876054 MsaT020943.1:CDS
TGATCCTTACCATGAGCACG+AGG 0.705697 4:+60877641 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr4 gene 60876028 60878077 60876028 ID=MsaG020943
Chr4 mRNA 60876028 60878077 60876028 ID=MsaT020943.1;Parent=MsaG020943
Chr4 exon 60876028 60876108 60876028 ID=MsaT020943.1.exon3;Parent=MsaT020943.1
Chr4 CDS 60876028 60876108 60876028 ID=cds.MsaT020943.1;Parent=MsaT020943.1
Chr4 exon 60876267 60876605 60876267 ID=MsaT020943.1.exon2;Parent=MsaT020943.1
Chr4 CDS 60876267 60876605 60876267 ID=cds.MsaT020943.1;Parent=MsaT020943.1
Chr4 exon 60877559 60878077 60877559 ID=MsaT020943.1.exon1;Parent=MsaT020943.1
Chr4 CDS 60877559 60878077 60877559 ID=cds.MsaT020943.1;Parent=MsaT020943.1
Gene Sequence

>MsaT020943.1

ATGGACGAATACAATATATTTGCTGAGGAATGCAACCTTAATTTTCTTGATGCAGATGTGGGAGGGTTTCTTTCAGATGACATAGCTAATGTATTTCAAGAACAAAACAAACAATTGGGGTCCACTTCCACAAATGATCTCAGCAAGTCATTCATTCACGAAACAATTGATAATAGTGACAAAATCAATGAATCACTTTCACCAAATATTTCTCCATCACCATCTAACTCCTCTTTTCAGTTTCAAATACCATCTTTTGACAACCCCCCAAATTCACCCCCTAGTAACTCAAAAGAGAATGAAACAATATCAGTGTCTCCAACCGAATTGGAAAATATGAATCACTCACCAGAAACCTCAAAAGGGTCATTGGAAAATGAAAAGTTTGAAGCCAAAACCTCAAAAAGCAAAAGGCCTCGTGCTCATGGTAAGGATCACATCATGGCTGAGAGAAATCGTAGAGAGAAACTCACCCAAAGCTTCATTGCTCTTGCAGCTCTTGTTCCTAACCTTAAAAAGATGGACAAGTTATCTGTACTAATTGACACTATCAAATACTTGAAAGAGCTTAAAAACCGTTTGGAAGTTGTGGAAAAAAAGTCCCCGACCAAACCATGCATATGCAGCGATGAAGATTCGTCATCATGTGAGGATAACATTGAAGGTGTTGTTGGTTCACCATTTCAAGTGGAAGCAAGAGTGTTAGGAAAACAAGTGTTGATTCGGTTCCAATGCAAGGAGCACAAGGGGCTTCTAGTTAAAATTATGGTCGAAATTCAAAAATTTCAACTATTTGTTGTCAATAACAGTGTCTTACCCTTTGGAGATTCTACACTCGACATTACCATCATTGCTCAGTTGGGTGAAGGGTACAACTTGAGCATAAAGGAACTTGTGAAGAACGTACGCATGGCATTATTGAAGTTTACATCATCATAA
Protein sequence

>MsaT020943.1

MDEYNIFAEECNLNFLDADVGGFLSDDIANVFQEQNKQLGSTSTNDLSKSFIHETIDNSDKINESLSPNISPSPSNSSFQFQIPSFDNPPNSPPSNSKENETISVSPTELENMNHSPETSKGSLENEKFEAKTSKSKRPRAHGKDHIMAERNRREKLTQSFIALAALVPNLKKMDKLSVLIDTIKYLKELKNRLEVVEKKSPTKPCICSDEDSSSCEDNIEGVVGSPFQVEARVLGKQVLIRFQCKEHKGLLVKIMVEIQKFQLFVVNNSVLPFGDSTLDITIIAQLGEGYNLSIKELVKNVRMALLKFTSS*