AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG006543

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG006543 MtrunA17_Chr2g0282511 88.629 299 16 4 1 299 29 309 2.46e-143 405
MsaG006543 MtrunA17_Chr4g0047001 45.479 365 113 19 1 299 40 384 2.88e-57 189
MsaG006543 MtrunA17_Chr4g0031411 68.605 86 26 1 14 98 72 157 1.90e-32 122
MsaG006543 MtrunA17_Chr4g0010151 52.101 119 44 2 1 118 66 172 5.58e-32 122
MsaG006543 MtrunA17_Chr8g0374251 71.429 70 20 0 12 81 63 132 8.12e-32 120
MsaG006543 MtrunA17_Chr2g0328021 76.190 63 15 0 17 79 62 124 1.41e-31 119
MsaG006543 MtrunA17_Chr8g0374111 67.647 68 22 0 13 80 25 92 6.08e-31 115
MsaG006543 MtrunA17_Chr7g0223311 65.753 73 25 0 7 79 67 139 8.60e-31 119
MsaG006543 MtrunA17_Chr4g0030051 84.211 57 9 0 13 69 37 93 1.58e-30 116
MsaG006543 MtrunA17_Chr1g0177251 47.407 135 65 2 7 141 2 130 1.63e-30 116
MsaG006543 MtrunA17_Chr1g0188851 70.312 64 19 0 10 73 36 99 1.74e-30 116
MsaG006543 MtrunA17_Chr7g0237921 60.417 96 34 2 13 105 72 166 5.42e-30 116
MsaG006543 MtrunA17_Chr8g0367161 61.176 85 27 1 12 96 27 105 9.38e-30 115
MsaG006543 MtrunA17_Chr8g0341671 72.727 66 16 1 13 78 16 79 1.16e-29 112
MsaG006543 MtrunA17_Chr3g0127201 79.310 58 12 0 12 69 22 79 1.40e-29 114
MsaG006543 MtrunA17_Chr2g0326001 72.059 68 18 1 3 69 25 92 2.14e-29 113
MsaG006543 MtrunA17_Chr2g0282051 69.118 68 20 1 6 73 35 101 7.35e-29 111
MsaG006543 MtrunA17_Chr8g0346551 53.333 105 34 3 3 107 11 100 7.66e-29 111
MsaG006543 MtrunA17_Chr5g0411951 79.630 54 11 0 14 67 40 93 1.56e-28 112
MsaG006543 MtrunA17_Chr4g0061761 81.132 53 10 0 15 67 38 90 8.18e-28 109
MsaG006543 MtrunA17_Chr3g0126201 73.016 63 17 0 16 78 50 112 8.34e-28 110
MsaG006543 MtrunA17_Chr2g0308011 86.000 50 7 0 16 65 36 85 8.82e-28 107
MsaG006543 MtrunA17_Chr2g0282441 77.586 58 13 0 11 68 19 76 1.17e-27 109
MsaG006543 MtrunA17_Chr3g0117601 82.692 52 9 0 16 67 60 111 1.94e-27 108
MsaG006543 MtrunA17_Chr4g0047761 75.000 60 14 1 15 74 70 128 4.30e-27 107
MsaG006543 MtrunA17_Chr3g0092111 62.687 67 25 0 6 72 125 191 2.58e-26 107
MsaG006543 MtrunA17_Chr4g0042481 53.947 76 35 0 6 81 111 186 5.56e-25 103
MsaG006543 MtrunA17_Chr8g0355261 50.588 85 38 1 6 90 107 187 1.10e-24 102
MsaG006543 MtrunA17_Chr5g0417551 45.690 116 62 1 1 115 111 226 2.09e-24 101
MsaG006543 MtrunA17_Chr7g0217581 63.934 61 22 0 11 71 226 286 2.53e-24 102
MsaG006543 MtrunA17_Chr6g0453321 64.407 59 21 0 11 69 130 188 4.54e-24 101
MsaG006543 MtrunA17_Chr2g0283811 61.017 59 23 0 10 68 40 98 5.07e-24 95.5
MsaG006543 MtrunA17_Chr7g0254161 55.882 68 30 0 2 69 86 153 5.75e-24 100
MsaG006543 MtrunA17_Chr5g0417561 48.000 100 52 0 1 100 103 202 7.77e-24 99.8
MsaG006543 MtrunA17_Chr5g0417571 59.375 64 26 0 6 69 127 190 9.44e-24 98.6
MsaG006543 MtrunA17_Chr6g0460721 57.812 64 27 0 6 69 78 141 1.34e-23 98.6
MsaG006543 MtrunA17_Chr6g0460731 56.250 64 28 0 6 69 85 148 1.02e-22 96.7
MsaG006543 MtrunA17_Chr5g0417601 58.209 67 28 0 6 72 129 195 2.27e-22 95.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG006543 AT1G28310.1 42.208 308 130 13 17 299 27 311 7.84e-45 154
MsaG006543 AT1G28310.2 42.208 308 130 13 17 299 51 335 1.30e-44 155
MsaG006543 AT1G51700.1 44.242 165 78 6 3 164 21 174 1.53e-32 119
MsaG006543 AT3G45610.1 39.521 167 79 3 14 180 37 181 2.32e-32 120
MsaG006543 AT3G55370.1 70.588 68 20 0 14 81 73 140 4.88e-32 121
MsaG006543 AT3G55370.2 70.588 68 20 0 14 81 73 140 5.78e-32 122
MsaG006543 AT3G55370.3 70.588 68 20 0 14 81 118 185 8.40e-32 121
MsaG006543 AT3G50410.1 65.333 75 26 0 1 75 14 88 1.10e-31 119
MsaG006543 AT1G07640.1 78.689 61 13 0 17 77 21 81 5.60e-31 117
MsaG006543 AT2G28810.2 81.034 58 11 0 11 68 71 128 6.33e-31 118
MsaG006543 AT1G07640.2 78.689 61 13 0 17 77 77 137 6.84e-31 118
MsaG006543 AT2G28810.1 81.034 58 11 0 11 68 88 145 8.39e-31 118
MsaG006543 AT1G07640.3 78.689 61 13 0 17 77 85 145 9.42e-31 118
MsaG006543 AT5G65590.1 73.846 65 17 0 12 76 36 100 1.41e-30 117
MsaG006543 AT2G37590.1 65.753 73 25 0 1 73 73 145 1.79e-30 117
MsaG006543 AT5G60200.1 64.865 74 26 0 11 84 49 122 2.92e-30 115
MsaG006543 AT5G02460.1 87.037 54 7 0 16 69 94 147 1.34e-29 116
MsaG006543 AT3G21270.1 78.947 57 12 0 17 73 29 85 2.67e-29 111
MsaG006543 AT2G28510.1 39.459 185 81 6 15 191 46 207 5.20e-29 112
MsaG006543 AT5G60850.1 54.545 99 26 2 13 111 47 126 1.50e-28 111
MsaG006543 AT4G38000.1 78.947 57 12 0 14 70 38 94 1.69e-28 110
MsaG006543 AT5G66940.1 66.667 63 21 0 13 75 28 90 4.44e-28 108
MsaG006543 AT4G24060.1 66.154 65 22 0 5 69 41 105 6.29e-28 110
MsaG006543 AT1G21340.1 68.571 70 17 1 10 74 31 100 9.35e-28 108
MsaG006543 AT3G61850.2 66.667 63 21 0 7 69 52 114 1.56e-27 108
MsaG006543 AT3G61850.3 66.667 63 21 0 7 69 52 114 1.56e-27 108
MsaG006543 AT3G61850.5 65.217 69 21 1 7 75 52 117 2.16e-27 108
MsaG006543 AT3G61850.1 66.667 63 21 0 7 69 64 126 2.49e-27 108
MsaG006543 AT3G61850.4 65.217 69 21 1 7 75 64 129 2.92e-27 108
MsaG006543 AT3G52440.1 74.194 62 14 1 19 78 27 88 1.90e-26 104
MsaG006543 AT3G52440.2 74.194 62 14 1 19 78 46 107 2.60e-26 104
MsaG006543 AT4G00940.1 75.000 56 14 0 14 69 65 120 8.00e-26 104
MsaG006543 AT4G00940.3 75.000 56 14 0 14 69 65 120 8.00e-26 104
MsaG006543 AT4G00940.2 75.000 56 14 0 14 69 65 120 8.00e-26 104
MsaG006543 AT5G62940.1 82.000 50 9 0 18 67 74 123 9.25e-26 105
MsaG006543 AT1G64620.1 75.926 54 13 0 12 65 44 97 1.17e-25 104
MsaG006543 AT5G39660.3 63.636 66 24 0 6 71 127 192 1.22e-25 106
MsaG006543 AT5G39660.1 63.636 66 24 0 6 71 127 192 1.22e-25 106
MsaG006543 AT5G39660.2 63.636 66 24 0 6 71 127 192 1.22e-25 106
MsaG006543 AT2G46590.1 78.431 51 11 0 14 64 65 115 1.37e-25 104
MsaG006543 AT3G47500.1 71.930 57 16 0 15 71 108 164 1.39e-25 105
MsaG006543 AT2G46590.2 78.431 51 11 0 14 64 77 127 1.64e-25 104
MsaG006543 AT5G62430.1 67.241 58 19 0 15 72 52 109 4.90e-25 102
MsaG006543 AT1G47655.1 72.549 51 14 0 15 65 27 77 4.36e-24 97.4
MsaG006543 AT1G26790.1 57.353 68 27 1 2 69 98 163 9.20e-24 100
MsaG006543 AT4G21050.1 76.000 50 12 0 19 68 26 75 9.42e-24 96.7
MsaG006543 AT1G29160.1 56.923 65 28 0 10 74 55 119 1.47e-23 95.1
MsaG006543 AT2G34140.1 61.017 59 23 0 10 68 51 109 1.74e-23 94.7
MsaG006543 AT1G69570.1 56.716 67 29 0 11 77 126 192 6.38e-23 97.8
MsaG006543 AT4G21040.1 75.510 49 12 0 19 67 27 75 1.03e-21 91.7
MsaG006543 AT4G21080.1 71.429 49 14 0 19 67 27 75 1.18e-20 89.4
MsaG006543 AT4G21030.1 60.870 46 18 0 19 64 23 68 5.45e-13 67.0

Find 53 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGCTTGGAATTTAACAATT+TGG 0.140338 2:-6739321 MsaT006543.1:CDS
GCAAAGCTTGCAAACGTTAT+TGG 0.143992 2:-6739895 MsaT006543.1:CDS
AGGACTAATATTATGATTTA+AGG 0.162696 2:+6739688 None:intergenic
CACCAGCTTCTTCACTTTAC+TGG 0.188996 2:-6739229 MsaT006543.1:CDS
GGCTTGGAATTTAACAATTT+GGG 0.228469 2:-6739320 MsaT006543.1:CDS
AACGATCAAGCTTCTAATAT+TGG 0.247824 2:-6739173 MsaT006543.1:CDS
TGTATAACCATTATGATCAT+TGG 0.338919 2:+6739505 None:intergenic
GGACAAGAGGTGGTACTCTT+AGG 0.348242 2:-6739874 MsaT006543.1:CDS
TCTAGAATCTCAACAAGTTC+AGG 0.387293 2:-6739596 MsaT006543.1:CDS
CATCATCAGCTATTGGTGTT+TGG 0.393178 2:-6739196 MsaT006543.1:CDS
GTGGTGTTTGGTTTGGAAGT+AGG 0.405131 2:+6739725 None:intergenic
GATCATAATGGTTATACAAA+TGG 0.418978 2:-6739500 MsaT006543.1:CDS
ATTATGATCATTGGCTTCGC+TGG 0.424556 2:+6739514 None:intergenic
CTTAGGAATGTTCCTGTTGG+TGG 0.434008 2:-6739857 MsaT006543.1:CDS
GAATTTGAAGAAGTGGTGTT+TGG 0.444730 2:+6739713 None:intergenic
ACAGCATCATCATCAGCTAT+TGG 0.454258 2:-6739203 MsaT006543.1:CDS
TGAAGAAGTGGTGTTTGGTT+TGG 0.459504 2:+6739718 None:intergenic
TTGGGGAATGGAAGTGAGAA+AGG 0.465690 2:-6739302 MsaT006543.1:CDS
AGAAGAATTAGTAGTATCAA+TGG 0.471958 2:+6739769 None:intergenic
CTTCTGTAACCACCACCAAC+AGG 0.474357 2:+6739845 None:intergenic
GAATTTAACAATTTGGGGAA+TGG 0.481892 2:-6739314 MsaT006543.1:CDS
TAAGGTTGAATTTGAAGAAG+TGG 0.481982 2:+6739706 None:intergenic
CAACATAAATTCATGAATGA+TGG 0.486443 2:-6739359 MsaT006543.1:CDS
CAAGCTTTGCAGAAATGTCT+TGG 0.496012 2:+6739908 None:intergenic
CAGCCTCAGATGAATACCAT+TGG 0.500808 2:-6739563 MsaT006543.1:CDS
AAAGGAATGAAGAAAGATGA+AGG 0.500974 2:-6739284 MsaT006543.1:CDS
GAAGAAAGATGAAGGAGAGA+TGG 0.502257 2:-6739276 MsaT006543.1:CDS
GGCATAACTGATGCATTACT+TGG 0.503446 2:+6739407 None:intergenic
GAGATATTGAACCTTGAGAA+TGG 0.505952 2:+6739617 None:intergenic
TTGGAAGTAGGAGTTGAAGA+AGG 0.509651 2:+6739737 None:intergenic
AGGAATGTTCCTGTTGGTGG+TGG 0.516563 2:-6739854 MsaT006543.1:CDS
AGCGAAGCCAATGATCATAA+TGG 0.521310 2:-6739512 MsaT006543.1:CDS
ATGTGAATCTTCCATTCTCA+AGG 0.533312 2:-6739628 MsaT006543.1:CDS
CTTGATAAACCATAAAACAT+AGG 0.540160 2:+6739668 None:intergenic
GGCTTCGCTGGACGTAAACC+CGG 0.542853 2:+6739526 None:intergenic
GCTTGGAATTTAACAATTTG+GGG 0.544684 2:-6739319 MsaT006543.1:CDS
ATTAGTAGTATCAATGGTGG+AGG 0.545112 2:+6739775 None:intergenic
AGAATTAGTAGTATCAATGG+TGG 0.550623 2:+6739772 None:intergenic
CAGATGAATACCATTGGAGT+AGG 0.575150 2:-6739557 MsaT006543.1:CDS
GTAGGAGTTGAAGAAGGAGA+AGG 0.577148 2:+6739743 None:intergenic
TGCAAACGTTATTGGACAAG+AGG 0.578125 2:-6739887 MsaT006543.1:CDS
ACTCTTAGGAATGTTCCTGT+TGG 0.582456 2:-6739860 MsaT006543.1:CDS
TTCCAGTAAAGTGAAGAAGC+TGG 0.599918 2:+6739227 None:intergenic
TGAAGGAGAGATGGAACATG+TGG 0.611078 2:-6739267 MsaT006543.1:CDS
ACTCCAATGGTATTCATCTG+AGG 0.617945 2:+6739560 None:intergenic
AGAGCAGAACTCAACAGAGA+AGG 0.622062 2:+6739386 None:intergenic
GGATGAAAAGCCTACTCCAA+TGG 0.628438 2:+6739547 None:intergenic
AAACGTTATTGGACAAGAGG+TGG 0.639210 2:-6739884 MsaT006543.1:CDS
CAGTAAAGTGAAGAAGCTGG+TGG 0.648703 2:+6739230 None:intergenic
GAAGGAGAGATGGAACATGT+GGG 0.678274 2:-6739266 MsaT006543.1:CDS
TTAGTAGTATCAATGGTGGA+GGG 0.679047 2:+6739776 None:intergenic
GGAGAGATGGAACATGTGGG+TGG 0.710445 2:-6739263 MsaT006543.1:CDS
GTGTTTGATGAGTCACAACG+TGG 0.749573 2:+6739968 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 6739148 6740047 6739148 ID=MsaG006543
Chr2 mRNA 6739148 6740047 6739148 ID=MsaT006543.1;Parent=MsaG006543
Chr2 exon 6739148 6740047 6739148 ID=MsaT006543.1.exon1;Parent=MsaT006543.1
Chr2 CDS 6739148 6740047 6739148 ID=cds.MsaT006543.1;Parent=MsaT006543.1
Gene Sequence

>MsaT006543.1

ATGGAAAAACAAGGTCAAGAACTTCAGCAGCAGCAGCAACAACAAGCTCTCAAGTGTCCACGTTGTGACTCATCAAACACAAAGTTTTGTTACTACAACAACTACAGTTTGTCACAACCAAGACATTTCTGCAAAGCTTGCAAACGTTATTGGACAAGAGGTGGTACTCTTAGGAATGTTCCTGTTGGTGGTGGTTACAGAAGAAACAACTCAAACAAACGTAGTAACAATACTACTCTCATCAAAAGACCCTCCACCATTGATACTACTAATTCTTCTTCTCCTTCTCCTTCTTCAACTCCTACTTCCAAACCAAACACCACTTCTTCAAATTCAACCTTAAATCATAATATTAGTCCTATGTTTTATGGTTTATCAAGTAGTAATAACTCTTGTGATGTGAATCTTCCATTCTCAAGGTTCAATATCTCTAGAATCTCAACAAGTTCAGGTTATGATTTTCAGCCTCAGATGAATACCATTGGAGTAGGCTTTTCATCCGGGTTTACGTCCAGCGAAGCCAATGATCATAATGGTTATACAAATGGATTTACTTCAAATAATAATAATAACACTCTTGTCTCAAGATATGATTCAATCTTTAGCTCTTCTTCTGCACCAAGTAATGCATCAGTTATGCCTTCTCTGTTGAGTTCTGCTCTGCTGCAACATAAATTCATGAATGATGGTAGCAACACTTTTCAGGGCTTGGAATTTAACAATTTGGGGAATGGAAGTGAGAAAGGAATGAAGAAAGATGAAGGAGAGATGGAACATGTGGGTGGTTTGTATGATCCACCAGCTTCTTCACTTTACTGGAATACAGCATCATCATCAGCTATTGGTGTTTGGAACGATCAAGCTTCTAATATTGGTTCATCAGTTACTTCTTTGATCTAG
Protein sequence

>MsaT006543.1

MEKQGQELQQQQQQQALKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGYRRNNSNKRSNNTTLIKRPSTIDTTNSSSPSPSSTPTSKPNTTSSNSTLNHNISPMFYGLSSSNNSCDVNLPFSRFNISRISTSSGYDFQPQMNTIGVGFSSGFTSSEANDHNGYTNGFTSNNNNNTLVSRYDSIFSSSSAPSNASVMPSLLSSALLQHKFMNDGSNTFQGLEFNNLGNGSEKGMKKDEGEMEHVGGLYDPPASSLYWNTASSSAIGVWNDQASNIGSSVTSLI*