AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG012436

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012436 MtrunA17_Chr4g0054981 82.394 142 24 1 54 195 241 381 8.94e-76 237
MsaG012436 MtrunA17_Chr4g0054981 100.000 55 0 0 19 73 109 163 1.09e-28 111
MsaG012436 MtrunA17_Chr5g0400241 62.698 126 46 1 70 195 258 382 3.94e-42 148
MsaG012436 MtrunA17_Chr5g0400241 60.674 89 30 1 19 107 109 192 3.20e-24 99.0
MsaG012436 MtrunA17_Chr4g0040481 57.333 75 32 0 121 195 155 229 8.81e-27 105
MsaG012436 MtrunA17_Chr2g0324891 62.121 66 25 0 121 186 158 223 6.72e-26 102
MsaG012436 MtrunA17_Chr2g0304841 35.754 179 104 3 8 184 104 273 5.07e-23 95.9
MsaG012436 MtrunA17_Chr3g0137101 36.196 163 92 3 20 182 106 256 1.12e-22 94.7
MsaG012436 MtrunA17_Chr1g0161431 34.444 180 96 4 20 194 109 271 1.39e-21 91.7
MsaG012436 MtrunA17_Chr4g0074401 36.196 163 78 5 20 177 115 256 2.80e-21 90.9
MsaG012436 MtrunA17_Chr2g0294911 34.104 173 74 4 20 182 127 269 4.15e-20 87.4
MsaG012436 MtrunA17_Chr4g0074411 38.365 159 77 4 20 177 116 254 5.43e-20 87.0
MsaG012436 MtrunA17_Chr8g0376881 33.898 177 93 3 16 189 119 274 6.62e-20 86.7
MsaG012436 MtrunA17_Chr4g0009901 32.143 168 71 2 11 178 98 222 7.53e-20 84.7
MsaG012436 MtrunA17_Chr4g0067981 61.667 60 23 0 123 182 214 273 9.40e-19 83.6
MsaG012436 MtrunA17_Chr3g0123131 35.758 165 86 5 16 178 107 253 1.27e-18 83.2
MsaG012436 MtrunA17_Chr4g0009851 28.994 169 77 2 8 176 96 221 5.20e-18 80.1
MsaG012436 MtrunA17_Chr4g0074421 32.692 156 80 3 20 173 50 182 5.52e-18 78.2
MsaG012436 MtrunA17_Chr7g0255711 60.714 56 22 0 123 178 90 145 1.81e-17 78.6
MsaG012436 MtrunA17_Chr4g0031961 60.714 56 22 0 123 178 130 185 2.33e-17 78.2
MsaG012436 MtrunA17_Chr1g0149841 30.337 178 108 3 10 187 93 254 1.06e-16 77.4
MsaG012436 MtrunA17_Chr7g0275401 32.335 167 98 4 10 176 93 244 5.64e-16 74.3
MsaG012436 MtrunA17_Chr1g0149831 30.337 178 105 4 10 187 30 188 7.91e-15 70.1
MsaG012436 MtrunA17_Chr1g0190301 42.342 111 45 3 69 176 134 228 8.69e-15 71.6
MsaG012436 MtrunA17_Chr7g0275891 27.363 201 86 3 10 182 94 262 1.52e-14 70.9
MsaG012436 MtrunA17_Chr1g0175081 40.217 92 48 3 98 188 2 87 1.56e-14 66.6
MsaG012436 MtrunA17_Chr1g0198601 38.835 103 59 2 79 180 169 268 2.05e-14 70.5
MsaG012436 MtrunA17_Chr4g0045361 42.466 73 41 1 111 182 261 333 4.98e-14 69.7
MsaG012436 MtrunA17_Chr5g0422621 43.158 95 42 3 87 180 172 255 6.25e-14 68.9
MsaG012436 MtrunA17_Chr7g0261911 52.113 71 32 2 107 176 246 315 1.21e-13 68.6
MsaG012436 MtrunA17_Chr1g0149851 29.891 184 98 4 10 178 93 260 1.35e-13 68.6
MsaG012436 MtrunA17_Chr4g0062921 49.206 63 31 1 123 184 234 296 1.77e-13 68.2
MsaG012436 MtrunA17_Chr4g0009981 51.852 54 26 0 123 176 115 168 2.62e-13 66.6
MsaG012436 MtrunA17_Chr6g0473731 46.032 63 34 0 123 185 94 156 4.55e-13 66.6
MsaG012436 MtrunA17_Chr3g0134481 53.191 47 22 0 129 175 137 183 4.88e-13 64.7
MsaG012436 MtrunA17_Chr3g0134461 54.386 57 25 1 117 173 137 192 9.95e-13 63.9
MsaG012436 MtrunA17_Chr7g0274471 55.357 56 24 1 122 176 216 271 2.08e-12 64.7
MsaG012436 MtrunA17_Chr6g0471041 30.058 173 72 6 20 191 112 236 2.18e-12 64.7
MsaG012436 MtrunA17_Chr5g0417521 44.118 68 37 1 124 190 15 82 3.23e-12 64.3
MsaG012436 MtrunA17_Chr5g0402631 49.180 61 30 1 123 182 213 273 5.13e-12 63.5
MsaG012436 MtrunA17_Chr6g0461641 47.368 57 29 1 124 179 42 98 3.17e-11 61.2
MsaG012436 MtrunA17_Chr2g0321461 47.368 57 29 1 124 179 45 101 4.21e-11 60.8
MsaG012436 MtrunA17_Chr2g0291021 52.632 57 26 1 124 179 49 105 4.57e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012436 AT4G18020.8 69.231 78 21 2 119 195 293 368 1.88e-29 113
MsaG012436 AT4G18020.8 62.500 72 25 1 19 90 116 185 4.83e-21 90.1
MsaG012436 AT4G18020.11 69.231 78 21 2 119 195 293 368 1.88e-29 113
MsaG012436 AT4G18020.11 62.500 72 25 1 19 90 116 185 4.83e-21 90.1
MsaG012436 AT4G18020.4 69.231 78 21 2 119 195 293 368 1.88e-29 113
MsaG012436 AT4G18020.4 62.500 72 25 1 19 90 116 185 4.83e-21 90.1
MsaG012436 AT4G18020.5 69.231 78 21 2 119 195 293 368 1.88e-29 113
MsaG012436 AT4G18020.5 62.500 72 25 1 19 90 116 185 4.83e-21 90.1
MsaG012436 AT4G18020.10 69.231 78 21 2 119 195 293 368 1.88e-29 113
MsaG012436 AT4G18020.10 62.500 72 25 1 19 90 116 185 4.83e-21 90.1
MsaG012436 AT4G18020.7 69.231 78 21 2 119 195 293 368 1.88e-29 113
MsaG012436 AT4G18020.7 62.500 72 25 1 19 90 116 185 4.83e-21 90.1
MsaG012436 AT4G18020.3 69.231 78 21 2 119 195 293 368 2.23e-29 114
MsaG012436 AT4G18020.3 62.500 72 25 1 19 90 116 185 5.71e-21 90.1
MsaG012436 AT4G18020.2 69.231 78 21 2 119 195 293 368 2.23e-29 114
MsaG012436 AT4G18020.2 62.500 72 25 1 19 90 116 185 5.71e-21 90.1
MsaG012436 AT4G18020.1 69.231 78 21 2 119 195 293 368 2.23e-29 114
MsaG012436 AT4G18020.1 62.500 72 25 1 19 90 116 185 5.71e-21 90.1
MsaG012436 AT4G18020.6 69.231 78 21 2 119 195 293 368 2.23e-29 114
MsaG012436 AT4G18020.6 62.500 72 25 1 19 90 116 185 5.71e-21 90.1
MsaG012436 AT4G18020.9 69.231 78 21 2 119 195 293 368 2.23e-29 114
MsaG012436 AT4G18020.9 62.500 72 25 1 19 90 116 185 5.71e-21 90.1
MsaG012436 AT5G44190.2 63.514 74 27 0 122 195 145 218 1.18e-26 104
MsaG012436 AT5G44190.1 63.514 74 27 0 122 195 145 218 1.24e-26 104
MsaG012436 AT2G20570.1 66.667 66 22 0 121 186 150 215 3.46e-26 103
MsaG012436 AT2G20570.2 55.556 90 40 0 97 186 142 231 7.89e-26 103
MsaG012436 AT5G58080.1 37.195 164 80 4 20 182 111 252 7.03e-24 98.6
MsaG012436 AT3G16857.3 40.237 169 91 4 20 182 61 225 3.90e-23 96.7
MsaG012436 AT3G16857.2 40.237 169 91 4 20 182 131 295 4.37e-23 96.3
MsaG012436 AT2G01760.3 34.831 178 100 4 8 182 29 193 4.48e-23 94.4
MsaG012436 AT3G16857.1 40.237 169 91 4 20 182 131 295 4.55e-23 96.3
MsaG012436 AT2G01760.1 34.831 178 100 4 8 182 94 258 9.05e-23 94.4
MsaG012436 AT2G01760.2 34.831 178 100 4 8 182 122 286 1.45e-22 94.0
MsaG012436 AT2G25180.1 34.783 184 82 3 8 182 99 253 1.90e-22 94.4
MsaG012436 AT2G40970.1 46.591 88 47 0 95 182 76 163 3.74e-20 85.1
MsaG012436 AT3G10760.1 45.556 90 49 0 89 178 70 159 4.45e-19 83.6
MsaG012436 AT5G59570.2 58.333 60 25 0 123 182 140 199 2.06e-18 81.3
MsaG012436 AT5G59570.1 58.333 60 25 0 123 182 140 199 2.06e-18 81.3
MsaG012436 AT4G31920.1 33.529 170 81 1 8 177 99 236 2.57e-18 82.4
MsaG012436 AT5G05090.1 60.714 56 22 0 123 178 80 135 5.28e-18 79.7
MsaG012436 AT3G46640.2 60.714 56 22 0 123 178 143 198 1.95e-17 79.0
MsaG012436 AT3G46640.1 60.714 56 22 0 123 178 143 198 1.95e-17 79.0
MsaG012436 AT3G46640.3 60.714 56 22 0 123 178 143 198 2.05e-17 79.0
MsaG012436 AT3G62670.1 33.831 201 90 10 5 193 119 288 9.29e-17 77.8
MsaG012436 AT1G25550.1 56.452 62 25 2 120 180 206 266 7.02e-16 74.7
MsaG012436 AT1G67710.3 35.088 171 80 5 16 178 27 174 7.26e-16 75.5
MsaG012436 AT1G67710.1 35.088 171 80 5 16 178 101 248 9.57e-16 75.1
MsaG012436 AT1G67710.2 35.088 171 80 5 16 178 36 183 1.12e-15 74.7
MsaG012436 AT5G07210.2 30.556 180 108 4 15 182 106 280 1.25e-14 72.0
MsaG012436 AT5G07210.1 30.556 180 108 4 15 182 114 288 1.26e-14 72.0
MsaG012436 AT1G68670.1 54.237 59 26 1 123 180 214 272 2.25e-14 70.9
MsaG012436 AT5G49240.1 31.818 154 88 4 20 173 136 272 2.53e-14 70.1
MsaG012436 AT2G03500.1 49.254 67 32 2 119 184 229 294 4.00e-14 70.1
MsaG012436 AT4G37180.1 50.667 75 32 2 107 180 197 267 9.60e-14 68.9
MsaG012436 AT4G37180.2 50.667 75 32 2 107 180 204 274 1.13e-13 68.9
MsaG012436 AT2G27070.1 32.778 180 106 7 15 183 109 284 2.52e-13 68.2
MsaG012436 AT3G25790.1 56.604 53 22 1 129 180 201 253 4.68e-13 67.0
MsaG012436 AT3G13040.3 43.000 100 53 3 93 190 209 306 5.89e-13 67.0
MsaG012436 AT3G13040.1 43.000 100 53 3 93 190 209 306 5.89e-13 67.0
MsaG012436 AT3G13040.2 43.000 100 53 3 93 190 209 306 5.89e-13 67.0
MsaG012436 AT4G28610.1 50.000 64 31 1 124 186 225 288 2.32e-12 65.1
MsaG012436 AT2G20400.2 54.688 64 28 1 124 186 231 294 2.41e-12 65.1
MsaG012436 AT2G20400.1 54.688 64 28 1 124 186 231 294 2.48e-12 65.1
MsaG012436 AT1G13300.1 37.634 93 46 3 95 186 161 242 1.01e-11 63.2
MsaG012436 AT1G25550.2 54.545 55 23 2 120 173 206 259 1.32e-11 62.4
MsaG012436 AT3G04030.2 46.429 56 30 0 124 179 45 100 1.33e-11 62.8
MsaG012436 AT5G29000.4 39.506 81 46 2 97 176 206 284 2.04e-11 62.0
MsaG012436 AT1G49560.1 50.847 59 28 1 123 180 191 249 3.07e-11 61.6
MsaG012436 AT3G04030.1 47.368 57 29 1 124 179 45 101 3.09e-11 61.6
MsaG012436 AT3G04030.3 47.368 57 29 1 124 179 45 101 3.40e-11 61.6
MsaG012436 AT2G01060.1 52.632 57 26 1 124 179 15 71 3.67e-11 61.2
MsaG012436 AT5G18240.2 49.123 57 28 1 124 179 45 101 3.79e-11 61.6
MsaG012436 AT5G18240.3 49.123 57 28 1 124 179 45 101 3.79e-11 61.6
MsaG012436 AT1G68210.1 28.342 187 105 3 25 189 111 290 4.22e-11 61.6
MsaG012436 AT5G18240.5 49.123 57 28 1 124 179 45 101 4.44e-11 61.2
MsaG012436 AT5G18240.1 49.123 57 28 1 124 179 45 101 4.62e-11 61.2
MsaG012436 AT5G18240.4 49.123 57 28 1 124 179 45 101 4.62e-11 61.2
MsaG012436 AT2G06020.1 38.000 100 50 3 92 182 49 145 5.55e-11 60.8

Find 37 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTATTCCTTCTCGAATAT+TGG 0.160903 3:+24544632 MsaT012436.1:CDS
TACCTGACACGCTAAATATA+TGG 0.350726 3:-24542545 None:intergenic
AGGACAAGCTCAGAAATATT+TGG 0.362029 3:+24544035 MsaT012436.1:CDS
TAAATATATGGCTGTGGGCT+TGG 0.382270 3:-24542533 None:intergenic
TAATGTGGCAAGCCATCTTC+AGG 0.386166 3:+24544686 MsaT012436.1:CDS
TTGTTTAGAACCTTCACATT+TGG 0.411730 3:-24544302 None:intergenic
AGCCATATATTTAGCGTGTC+AGG 0.438269 3:+24542543 MsaT012436.1:CDS
CGAAGCAGGATGATCGGAAA+TGG 0.452472 3:+24544885 MsaT012436.1:CDS
ACCTTCACATTTGGTAATTG+TGG 0.453921 3:-24544293 None:intergenic
AATGTGAGATAAAAGCTAAT+CGG 0.462021 3:+24544375 MsaT012436.1:CDS
GAGACATATCTTACCGAAGC+AGG 0.475105 3:+24544871 MsaT012436.1:CDS
GAGGCTACAGATTCCTTGAC+AGG 0.481302 3:-24544206 None:intergenic
CATTTCCGATCATCCTGCTT+CGG 0.484186 3:-24544884 None:intergenic
CTCAAACAGGCATTCAATGC+TGG 0.493866 3:+24544155 MsaT012436.1:intron
CTGAGCTTGTCCTCGGAGAG+TGG 0.496448 3:-24544025 None:intergenic
TACTTTGGTCTCAGGTAGAC+TGG 0.503714 3:+24544553 MsaT012436.1:intron
ATCTGTTTGAATCTGCAAGA+TGG 0.516940 3:-24544228 None:intergenic
AATATTGGATCTAATGAAAG+TGG 0.519493 3:+24544647 MsaT012436.1:CDS
ACACGCTAAATATATGGCTG+TGG 0.520230 3:-24542539 None:intergenic
ACAACATCTGCAAATAAAGT+AGG 0.528162 3:+24544338 MsaT012436.1:CDS
ATTAGATCCAATATTCGAGA+AGG 0.541398 3:-24544639 None:intergenic
CAGAAATATTTGGCAGCATG+TGG 0.544781 3:+24544045 MsaT012436.1:CDS
AATATTTCTGAGCTTGTCCT+CGG 0.546887 3:-24544032 None:intergenic
ACCACAATTACCAAATGTGA+AGG 0.551748 3:+24544292 MsaT012436.1:CDS
GGTAGATTATAACCTGAAGA+TGG 0.564115 3:-24544698 None:intergenic
TCTTACCGAAGCAGGATGAT+CGG 0.574745 3:+24544879 MsaT012436.1:CDS
GTGAAGGCAGTGGAGCAACT+AGG 0.575398 3:+24544600 MsaT012436.1:CDS
CACGCTAAATATATGGCTGT+GGG 0.588611 3:-24542538 None:intergenic
ATCGGAAATGGCTAAATACA+AGG 0.595293 3:+24544897 MsaT012436.1:CDS
TTGGCAGCATGTGGTTCACA+AGG 0.605863 3:+24544054 MsaT012436.1:CDS
TGAATCACTGAAACCTGTCA+AGG 0.606622 3:+24544193 MsaT012436.1:CDS
ATTGGATCTAATGAAAGTGG+AGG 0.613074 3:+24544650 MsaT012436.1:CDS
GGGCTTGACAAGGCATAATG+TGG 0.631155 3:+24544671 MsaT012436.1:CDS
TTGGATCTAATGAAAGTGGA+GGG 0.637148 3:+24544651 MsaT012436.1:CDS
TGAAAGTGGAGGGCTTGACA+AGG 0.644049 3:+24544661 MsaT012436.1:CDS
TGTTTGAATCTGCAAGATGG+AGG 0.654248 3:-24544225 None:intergenic
TCTCAGCAAACCACTCTCCG+AGG 0.676397 3:+24544015 MsaT012436.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 24542511 24544922 24542511 ID=MsaG012436
Chr3 mRNA 24542511 24544922 24542511 ID=MsaT012436.1;Parent=MsaG012436
Chr3 exon 24542511 24542564 24542511 ID=MsaT012436.1.exon1;Parent=MsaT012436.1
Chr3 CDS 24542511 24542564 24542511 ID=cds.MsaT012436.1;Parent=MsaT012436.1
Chr3 exon 24543998 24544075 24543998 ID=MsaT012436.1.exon2;Parent=MsaT012436.1
Chr3 CDS 24543998 24544075 24543998 ID=cds.MsaT012436.1;Parent=MsaT012436.1
Chr3 exon 24544164 24544409 24544164 ID=MsaT012436.1.exon3;Parent=MsaT012436.1
Chr3 CDS 24544164 24544409 24544164 ID=cds.MsaT012436.1;Parent=MsaT012436.1
Chr3 exon 24544567 24544707 24544567 ID=MsaT012436.1.exon4;Parent=MsaT012436.1
Chr3 CDS 24544567 24544707 24544567 ID=cds.MsaT012436.1;Parent=MsaT012436.1
Chr3 exon 24544854 24544922 24544854 ID=MsaT012436.1.exon5;Parent=MsaT012436.1
Chr3 CDS 24544854 24544922 24544854 ID=cds.MsaT012436.1;Parent=MsaT012436.1
Gene Sequence

>MsaT012436.1

ATGGATTCTTGGCATCAAGTCTCCAAGCCCACAGCCATATATTTAGCGTGTCAGCTTGGAGCAGTGGAGTTTCTCAGCAAACCACTCTCCGAGGACAAGCTCAGAAATATTTGGCAGCATGTGGTTCACAAGGCATTCAATGCTGGTGTAAGTGCGCTGTCTGAATCACTGAAACCTGTCAAGGAATCTGTAGCCTCCATCTTGCAGATTCAAACAGATCTAAGTGTTGCTGACACTTCTAAGTGTGAGAGTGTTGTTTCACCACAATTACCAAATGTGAAGGTTCTAAACAATAGTGAAAGTAATACAACATCTGCAAATAAAGTAGGTATTCGCAGTCATAAATGTGAGATAAAAGCTAATCGGAAGAAGATGAAAGTAGACTGGACGCCAGAGCTGCACAAAAAATTTGTGAAGGCAGTGGAGCAACTAGGCATTAATCACGCTATTCCTTCTCGAATATTGGATCTAATGAAAGTGGAGGGCTTGACAAGGCATAATGTGGCAAGCCATCTTCAGAAATATAGAATGCATAAGAGACATATCTTACCGAAGCAGGATGATCGGAAATGGCTAAATACAAGGTAG
Protein sequence

>MsaT012436.1

MDSWHQVSKPTAIYLACQLGAVEFLSKPLSEDKLRNIWQHVVHKAFNAGVSALSESLKPVKESVASILQIQTDLSVADTSKCESVVSPQLPNVKVLNNSESNTTSANKVGIRSHKCEIKANRKKMKVDWTPELHKKFVKAVEQLGINHAIPSRILDLMKVEGLTRHNVASHLQKYRMHKRHILPKQDDRKWLNTR*