AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG009539

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009539 MtrunA17_Chr2g0291021 89.116 147 8 1 1 139 1 147 2.46e-79 243
MsaG009539 MtrunA17_Chr7g0254981 67.000 100 24 2 49 139 50 149 1.84e-37 134
MsaG009539 MtrunA17_Chr2g0310491 89.041 73 8 0 210 282 145 217 2.01e-32 120
MsaG009539 MtrunA17_Chr7g0216041 87.671 73 9 0 210 282 145 217 1.29e-31 117
MsaG009539 MtrunA17_Chr2g0322881 89.041 73 8 0 210 282 562 634 2.09e-31 123
MsaG009539 MtrunA17_Chr7g0261911 55.752 113 38 3 33 139 252 358 1.14e-30 119
MsaG009539 MtrunA17_Chr7g0231401 87.671 73 9 0 210 282 505 577 4.99e-30 119
MsaG009539 MtrunA17_Chr1g0175091 50.459 109 50 2 35 139 244 352 4.75e-29 114
MsaG009539 MtrunA17_Chr1g0190301 57.143 98 36 1 48 139 174 271 8.34e-28 110
MsaG009539 MtrunA17_Chr7g0274471 56.122 98 37 2 48 139 217 314 4.97e-27 109
MsaG009539 MtrunA17_Chr7g0258551 49.495 99 45 2 46 139 209 307 2.26e-26 106
MsaG009539 MtrunA17_Chr4g0042451 47.273 110 41 3 47 139 15 124 4.45e-25 102
MsaG009539 MtrunA17_Chr8g0356501 77.193 57 13 0 49 105 37 93 1.50e-24 101
MsaG009539 MtrunA17_Chr5g0409731 47.170 106 38 2 52 139 28 133 9.11e-24 98.2
MsaG009539 MtrunA17_Chr2g0310011 72.881 59 16 0 47 105 33 91 1.02e-23 99.0
MsaG009539 MtrunA17_Chr2g0290591 62.162 74 28 0 206 279 24 97 4.33e-23 92.8
MsaG009539 MtrunA17_Chr1g0197171 48.544 103 38 2 52 139 47 149 1.16e-22 95.1
MsaG009539 MtrunA17_Chr2g0290991 45.614 114 44 2 44 139 34 147 1.49e-22 95.1
MsaG009539 MtrunA17_Chr5g0417521 41.441 111 47 2 47 139 13 123 3.86e-22 94.7
MsaG009539 MtrunA17_Chr7g0242521 49.000 100 41 3 49 139 13 111 5.42e-22 92.0
MsaG009539 MtrunA17_Chr2g0321461 42.982 114 39 3 52 139 48 161 2.29e-20 90.1
MsaG009539 MtrunA17_Chr4g0019121 93.333 45 3 0 238 282 1 45 2.38e-20 82.8
MsaG009539 MtrunA17_Chr6g0461641 66.071 56 19 0 47 102 40 95 6.31e-20 89.0
MsaG009539 MtrunA17_Chr1g0175081 45.333 75 41 0 35 109 8 82 1.12e-19 82.0
MsaG009539 MtrunA17_Chr1g0175071 41.322 121 57 5 26 141 155 266 3.68e-19 85.9
MsaG009539 MtrunA17_Chr6g0479431 54.167 72 31 1 52 121 205 276 4.04e-16 77.8
MsaG009539 MtrunA17_Chr7g0243081 60.714 56 22 0 52 107 74 129 5.35e-16 77.0
MsaG009539 MtrunA17_Chr8g0366281 51.087 92 39 4 52 141 176 263 6.49e-16 77.0
MsaG009539 MtrunA17_Chr3g0095611 48.052 77 24 1 52 112 22 98 1.62e-15 73.9
MsaG009539 MtrunA17_Chr2g0288601 70.833 48 14 0 52 99 74 121 1.96e-15 71.6
MsaG009539 MtrunA17_Chr8g0379121 62.963 54 20 0 52 105 114 167 8.43e-15 73.9
MsaG009539 MtrunA17_Chr5g0410741 62.963 54 20 0 52 105 222 275 1.19e-14 73.6
MsaG009539 MtrunA17_Chr2g0320231 51.351 74 36 0 32 105 80 153 1.77e-14 72.8
MsaG009539 MtrunA17_Chr3g0109981 62.963 54 20 0 52 105 277 330 1.90e-14 73.2
MsaG009539 MtrunA17_Chr1g0162931 62.963 54 20 0 52 105 21 74 2.21e-14 71.6
MsaG009539 MtrunA17_Chr1g0154261 61.111 54 21 0 52 105 129 182 2.45e-14 72.0
MsaG009539 MtrunA17_Chr1g0210911 61.111 54 21 0 52 105 25 78 2.92e-14 72.0
MsaG009539 MtrunA17_Chr1g0198601 53.030 66 31 0 49 114 211 276 1.23e-13 70.5
MsaG009539 MtrunA17_Chr2g0283951 66.667 48 16 0 52 99 92 139 7.49e-13 68.2
MsaG009539 MtrunA17_Chr5g0402631 61.111 54 21 0 49 102 214 267 2.25e-12 66.6
MsaG009539 MtrunA17_Chr4g0009981 48.000 75 36 2 41 115 108 179 1.48e-11 63.5
MsaG009539 MtrunA17_Chr7g0258531 39.583 96 52 2 13 102 171 266 1.89e-11 63.9
MsaG009539 MtrunA17_Chr5g0422621 55.556 54 24 0 49 102 198 251 1.90e-11 63.9
MsaG009539 MtrunA17_Chr4g0045361 57.407 54 23 0 49 102 274 327 3.10e-11 63.5
MsaG009539 MtrunA17_Chr4g0062921 42.353 85 47 2 20 102 204 288 4.50e-11 63.2
MsaG009539 MtrunA17_Chr4g0009901 55.556 54 23 1 49 102 168 220 5.65e-11 62.0
MsaG009539 MtrunA17_Chr2g0324891 50.820 61 29 1 42 102 154 213 6.81e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009539 AT2G01060.1 82.692 104 11 1 43 139 9 112 1.00e-50 169
MsaG009539 AT4G28610.1 57.547 106 38 2 41 139 217 322 5.13e-30 117
MsaG009539 AT3G04450.4 47.059 119 52 2 30 139 181 297 6.12e-28 111
MsaG009539 AT3G04450.2 47.059 119 52 2 30 139 181 297 6.12e-28 111
MsaG009539 AT3G04450.1 47.059 119 52 2 30 139 221 337 1.09e-27 111
MsaG009539 AT5G29000.1 52.500 120 46 3 29 139 170 287 2.39e-27 109
MsaG009539 AT5G29000.3 52.500 120 46 3 29 139 170 287 2.39e-27 109
MsaG009539 AT5G29000.2 52.500 120 46 3 29 139 213 330 4.48e-27 109
MsaG009539 AT2G20400.1 58.511 94 33 2 52 139 234 327 5.46e-27 108
MsaG009539 AT2G20400.2 56.842 95 34 2 52 139 234 328 1.67e-26 107
MsaG009539 AT3G13040.3 46.457 127 48 3 24 139 225 342 3.02e-26 107
MsaG009539 AT3G13040.1 46.457 127 48 3 24 139 225 342 3.02e-26 107
MsaG009539 AT3G13040.2 46.457 127 48 3 24 139 225 342 3.02e-26 107
MsaG009539 AT3G24120.1 50.943 106 34 2 52 139 44 149 3.14e-26 105
MsaG009539 AT4G13640.1 50.943 106 34 2 52 139 40 145 3.57e-26 104
MsaG009539 AT3G24120.2 50.943 106 34 2 52 139 44 149 3.63e-26 105
MsaG009539 AT5G06800.1 50.000 110 45 3 36 139 182 287 3.67e-26 106
MsaG009539 AT4G13640.2 50.943 106 34 2 52 139 40 145 3.81e-26 104
MsaG009539 AT5G06800.2 48.276 116 43 3 36 139 182 292 1.18e-25 105
MsaG009539 AT1G79430.2 56.701 97 33 2 52 139 37 133 3.31e-25 103
MsaG009539 AT3G04450.3 62.319 69 26 0 45 113 234 302 7.55e-24 99.0
MsaG009539 AT3G12730.1 74.074 54 14 0 52 105 26 79 9.78e-24 97.1
MsaG009539 AT5G29000.4 68.750 64 20 0 48 111 230 293 6.58e-23 96.3
MsaG009539 AT2G01060.2 79.365 63 6 1 84 139 1 63 1.12e-22 94.4
MsaG009539 AT5G06800.3 60.000 65 26 0 45 109 188 252 7.57e-22 92.8
MsaG009539 AT5G45580.1 74.510 51 13 0 52 102 10 60 1.11e-21 92.0
MsaG009539 AT1G69580.1 42.373 118 41 3 47 139 32 147 1.19e-21 93.2
MsaG009539 AT5G18240.5 41.538 130 69 1 24 153 20 142 1.55e-21 94.0
MsaG009539 AT5G18240.2 41.538 130 69 1 24 153 20 142 1.56e-21 94.0
MsaG009539 AT5G18240.3 41.538 130 69 1 24 153 20 142 1.56e-21 94.0
MsaG009539 AT5G18240.1 41.538 130 69 1 24 153 20 142 1.58e-21 94.0
MsaG009539 AT5G18240.4 41.538 130 69 1 24 153 20 142 1.58e-21 94.0
MsaG009539 AT5G45580.2 74.510 51 13 0 52 102 26 76 1.59e-21 92.0
MsaG009539 AT1G69580.2 42.017 119 41 3 47 139 32 148 2.05e-21 92.8
MsaG009539 AT3G04030.1 51.685 89 35 2 23 107 19 103 6.43e-21 92.0
MsaG009539 AT3G04030.3 51.685 89 35 2 23 107 19 103 7.82e-21 91.7
MsaG009539 AT3G04030.2 50.562 89 35 3 23 107 19 102 2.13e-18 84.7
MsaG009539 AT2G42660.1 64.912 57 20 0 52 108 53 109 5.69e-17 79.0
MsaG009539 AT2G40260.1 48.315 89 46 0 17 105 50 138 1.25e-16 79.7
MsaG009539 AT4G04605.1 66.667 54 18 0 52 105 17 70 2.39e-16 76.6
MsaG009539 AT2G06020.1 51.613 62 30 0 44 105 81 142 5.00e-16 77.0
MsaG009539 AT5G16560.1 59.375 64 24 1 52 113 222 285 7.39e-15 74.7
MsaG009539 AT1G14600.1 64.815 54 19 0 52 105 26 79 1.05e-14 72.8
MsaG009539 AT1G32240.2 62.963 54 20 0 52 105 216 269 1.14e-14 73.9
MsaG009539 AT1G32240.1 62.963 54 20 0 52 105 216 269 1.24e-14 73.9
MsaG009539 AT2G38300.1 62.963 54 20 0 52 105 57 110 1.27e-14 73.6
MsaG009539 AT4G17695.1 62.963 54 20 0 52 105 167 220 1.52e-14 73.2
MsaG009539 AT5G42630.2 61.111 54 21 0 52 105 108 161 1.76e-14 71.6
MsaG009539 AT2G02060.2 64.286 56 20 0 52 107 32 87 1.92e-14 72.0
MsaG009539 AT2G02060.1 64.286 56 20 0 52 107 32 87 1.92e-14 72.0
MsaG009539 AT5G42630.1 61.111 54 21 0 52 105 108 161 3.55e-14 71.6
MsaG009539 AT4G04580.1 53.704 54 25 0 52 105 17 70 2.85e-13 67.0
MsaG009539 AT4G37180.1 59.259 54 22 0 49 102 210 263 4.34e-13 68.9
MsaG009539 AT4G37180.2 59.259 54 22 0 49 102 217 270 4.92e-13 68.9
MsaG009539 AT3G25790.1 61.224 49 19 0 54 102 201 249 1.14e-12 67.8
MsaG009539 AT1G49560.1 61.111 54 21 0 49 102 192 245 3.33e-12 66.2
MsaG009539 AT1G13300.1 44.828 87 37 2 16 102 159 234 5.31e-12 65.9
MsaG009539 AT1G25550.1 57.143 56 24 0 47 102 207 262 3.21e-11 63.5
MsaG009539 AT3G25790.2 58.696 46 19 0 54 99 201 246 6.05e-11 62.0
MsaG009539 AT4G37180.3 56.863 51 22 0 49 99 210 260 8.52e-11 61.6
MsaG009539 AT4G04555.1 54.717 53 24 0 53 105 18 70 9.90e-11 58.2

Find 63 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAAGCAATCCATTAGTTAA+TGG 0.290398 2:-60704191 MsaT009539.1:CDS
ATGGCTCTTAACATGGTAAA+TGG 0.306660 2:+60703765 None:intergenic
CATCTAAATATGACCATATA+AGG 0.310026 2:-60700867 MsaT009539.1:CDS
TAGATATTGCAGTCCTTATA+TGG 0.330057 2:+60700854 None:intergenic
CCATGTTAAGAGCCATTTGC+AGG 0.349218 2:-60703758 MsaT009539.1:intron
ATATGTTGACCATTAACTAA+TGG 0.354268 2:+60704182 None:intergenic
GATATGCTTTCCATTCTAGA+TGG 0.374580 2:-60703379 MsaT009539.1:CDS
CATAACTCTGAGGACACCTT+TGG 0.375653 2:+60703804 None:intergenic
CAAAGGTGTCCTCAGAGTTA+TGG 0.377183 2:-60703803 MsaT009539.1:CDS
AAGAAATGACACATATGGTT+TGG 0.377688 2:-60700947 MsaT009539.1:CDS
CTTATATGGTCATATTTAGA+TGG 0.381367 2:+60700868 None:intergenic
AATGGTCAACATATAGATTC+TGG 0.392543 2:-60704173 MsaT009539.1:CDS
TGAGTTGAGATTAAAGTTGT+TGG 0.397978 2:+60704109 None:intergenic
AAAGGTGTCCTCAGAGTTAT+GGG 0.402741 2:-60703802 MsaT009539.1:CDS
TTTGTTGAGAGTGGTGATCT+TGG 0.403843 2:+60702555 None:intergenic
GTTGCTGATTCGAGTTTAGT+TGG 0.426457 2:-60704212 MsaT009539.1:CDS
TTGTACTGTAGGTTAAGTTA+AGG 0.426757 2:-60701636 MsaT009539.1:intron
AGAAATGACACATATGGTTT+GGG 0.446719 2:-60700946 MsaT009539.1:CDS
AGTGGTGATCTTGGTGATGA+TGG 0.462542 2:+60702564 None:intergenic
GTTGATGCTGTGGCTCAACT+TGG 0.466308 2:-60704044 MsaT009539.1:CDS
ATAACTCTGAGGACACCTTT+GGG 0.476739 2:+60703805 None:intergenic
GGTAGAAGCGCAATGGATCC+TGG 0.480877 2:-60704152 MsaT009539.1:CDS
TGAGATGCCATCAGATGATC+TGG 0.481079 2:+60700891 None:intergenic
CTCAGAGTTATGGGTGTACA+AGG 0.485843 2:-60703793 MsaT009539.1:CDS
TGAAGCACTAAAGCTTCAAA+TGG 0.488754 2:-60703112 MsaT009539.1:CDS
TCACGATGAACCATCTAGAA+TGG 0.492563 2:+60703369 None:intergenic
AAAAGACTGACAAGAAAGAA+TGG 0.493256 2:-60703401 MsaT009539.1:intron
AAGTGCACATTACCTGCAAA+TGG 0.502884 2:+60703746 None:intergenic
AGCGCAATGGATCCTGGTAG+TGG 0.503101 2:-60704146 MsaT009539.1:CDS
CCCTTAGGTGCCACACCCAA+AGG 0.505122 2:-60703820 MsaT009539.1:intron
TCAACAAGAAATGACACATA+TGG 0.507206 2:-60700952 MsaT009539.1:CDS
GGAATTAATTCGTGCATCAC+AGG 0.512276 2:-60700782 MsaT009539.1:CDS
GATGCTGTGGCTCAACTTGG+TGG 0.512420 2:-60704041 MsaT009539.1:CDS
CTCGAATCAGCAACATTCGT+TGG 0.516899 2:+60704221 None:intergenic
AATTGCATGCTAACCTGGTA+AGG 0.524671 2:+60701553 None:intergenic
CCTGCAAATGGCTCTTAACA+TGG 0.525821 2:+60703758 None:intergenic
AGCTGAAAACATGGAACTCA+AGG 0.528038 2:-60700824 MsaT009539.1:CDS
GCCATGGCAAGCAAAAGAAA+AGG 0.530423 2:-60702529 MsaT009539.1:CDS
GTACCATCGGATGAGCAGTC+AGG 0.531157 2:+60703626 None:intergenic
AGAGCAGTCACAACAGTCAC+AGG 0.532811 2:-60700740 MsaT009539.1:CDS
ACTCAAAGCAACTCTTGCGT+TGG 0.536955 2:-60704091 MsaT009539.1:CDS
TCTGAGGACACCTTTGGGTG+TGG 0.554653 2:+60703810 None:intergenic
CACATATGGTTTGGGAGCAG+AGG 0.559522 2:-60700938 MsaT009539.1:CDS
TATACTTAGGATAGTGAACC+AGG 0.561334 2:-60702609 MsaT009539.1:intron
TAAAATGTCAGCTGAAAACA+TGG 0.565653 2:-60700833 MsaT009539.1:CDS
AGACTGTTTCCTCCACTACC+AGG 0.568775 2:+60704134 None:intergenic
AAAGGAATGTTGAGACGGCT+AGG 0.570161 2:-60701595 MsaT009539.1:CDS
GGTTGGTCGTCAAAGACTAA+AGG 0.576564 2:+60702585 None:intergenic
TGGTAAGGCAATAAAAGCAT+CGG 0.590082 2:+60701568 None:intergenic
TCAGATGATCTGGATAAAGA+AGG 0.590117 2:+60700901 None:intergenic
GTGATCTTGGTGATGATGGT+TGG 0.593758 2:+60702568 None:intergenic
TTACCTGACTGCTCATCCGA+TGG 0.595863 2:-60703629 MsaT009539.1:intron
TCTTTATCCAGATCATCTGA+TGG 0.599210 2:-60700898 MsaT009539.1:CDS
TGAACGCTTTGTTGATGCTG+TGG 0.601507 2:-60704054 MsaT009539.1:CDS
AGATTCTGGTAGAAGCGCAA+TGG 0.611720 2:-60704159 MsaT009539.1:CDS
TTGTTGCTGATATGCATCAA+AGG 0.612831 2:-60701613 MsaT009539.1:CDS
GGAGCGTTTGAAGAATAATG+AGG 0.616417 2:-60700803 MsaT009539.1:CDS
GCATCAAAGGAATGTTGAGA+CGG 0.630644 2:-60701600 MsaT009539.1:CDS
TCGTCAAAGACTAAAGGACC+TGG 0.651924 2:+60702591 None:intergenic
ATTAATTCGTGCATCACAGG+AGG 0.654566 2:-60700779 MsaT009539.1:CDS
GCAATGGATCCTGGTAGTGG+AGG 0.656586 2:-60704143 MsaT009539.1:CDS
GGGGAAAACACTCACGATCG+GGG 0.661843 2:+60704018 None:intergenic
CTTGTACACCCATAACTCTG+AGG 0.715783 2:+60703794 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 60700714 60704252 60700714 ID=MsaG009539
Chr2 mRNA 60700714 60704252 60700714 ID=MsaT009539.1;Parent=MsaG009539
Chr2 exon 60700714 60700983 60700714 ID=MsaT009539.1.exon8;Parent=MsaT009539.1
Chr2 CDS 60700714 60700983 60700714 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Chr2 exon 60701567 60701647 60701567 ID=MsaT009539.1.exon7;Parent=MsaT009539.1
Chr2 CDS 60701567 60701647 60701567 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Chr2 exon 60702521 60702622 60702521 ID=MsaT009539.1.exon6;Parent=MsaT009539.1
Chr2 CDS 60702521 60702622 60702521 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Chr2 exon 60703110 60703149 60703110 ID=MsaT009539.1.exon5;Parent=MsaT009539.1
Chr2 CDS 60703110 60703149 60703110 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Chr2 exon 60703373 60703409 60703373 ID=MsaT009539.1.exon4;Parent=MsaT009539.1
Chr2 CDS 60703373 60703409 60703373 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Chr2 exon 60703630 60703672 60703630 ID=MsaT009539.1.exon3;Parent=MsaT009539.1
Chr2 CDS 60703630 60703672 60703630 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Chr2 exon 60703759 60703835 60703759 ID=MsaT009539.1.exon2;Parent=MsaT009539.1
Chr2 CDS 60703759 60703835 60703759 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Chr2 exon 60704033 60704252 60704033 ID=MsaT009539.1.exon1;Parent=MsaT009539.1
Chr2 CDS 60704033 60704252 60704033 ID=cds.MsaT009539.1;Parent=MsaT009539.1
Gene Sequence

>MsaT009539.1

ATGTATCATCCAACGAATGTTGCTGATTCGAGTTTAGTTGGAAGCAATCCATTAGTTAATGGTCAACATATAGATTCTGGTAGAAGCGCAATGGATCCTGGTAGTGGAGGAAACAGTCTTGCCAACAACTTTAATCTCAACTCAAAGCAACTCTTGCGTTGGACACATGAGCTACATGAACGCTTTGTTGATGCTGTGGCTCAACTTGGTGGCCCCGATCGTGCCACACCCAAAGGTGTCCTCAGAGTTATGGGTGTACAAGGCTTAACCATTTACCATGTTAAGAGCCATTTGCAGAAATACCGACAAGCAAAATACTTACCTGACTGCTCATCCGATGAAAGAATGGATATGCTTTCCATTCTAGATGGTTCATCGGGGATGCAGATTACTGAAGCACTAAAGCTTCAAATGGAAGATAGTGAACCAGGTCCTTTAGTCTTTGACGACCAACCATCATCACCAAGATCACCACTCTCAACAAAAAAGCCATGGCAAGCAAAAGAAAAGGATTTGTATGTTAAGTTAAGGTTGTTGCTGATATGCATCAAAGGAATGTTGAGACGGCTAGGCATTCCGATGCTTTTATTGCCTTACCAGTTGGAGGAGTCAACAAGAAATGACACATATGGTTTGGGAGCAGAGGCAGAAAAATATAAGCCTTCTTTATCCAGATCATCTGATGGCATCTCACCATCTAAATATGACCATATAAGGACTGCAATATCTAAAATGTCAGCTGAAAACATGGAACTCAAGGAGCGTTTGAAGAATAATGAGGAATTAATTCGTGCATCACAGGAGGAGTCACGTTTAGCTCGAGAGCAGTCACAACAGTCACAGGAGATTGCTCTGAGAGCAGTTACATAA
Protein sequence

>MsaT009539.1

MYHPTNVADSSLVGSNPLVNGQHIDSGRSAMDPGSGGNSLANNFNLNSKQLLRWTHELHERFVDAVAQLGGPDRATPKGVLRVMGVQGLTIYHVKSHLQKYRQAKYLPDCSSDERMDMLSILDGSSGMQITEALKLQMEDSEPGPLVFDDQPSSPRSPLSTKKPWQAKEKDLYVKLRLLLICIKGMLRRLGIPMLLLPYQLEESTRNDTYGLGAEAEKYKPSLSRSSDGISPSKYDHIRTAISKMSAENMELKERLKNNEELIRASQEESRLAREQSQQSQEIALRAVT*