AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG016001

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016001 MtrunA17_Chr3g0123691 98.675 302 3 1 1 301 1 302 0.0 611
MsaG016001 MtrunA17_Chr8g0381741 59.021 327 92 11 1 301 1 311 6.23e-117 339
MsaG016001 MtrunA17_Chr3g0119291 41.638 293 132 7 1 292 1 255 4.30e-50 166
MsaG016001 MtrunA17_Chr5g0415941 57.258 124 49 1 45 164 69 192 2.22e-39 140
MsaG016001 MtrunA17_Chr8g0362751 57.377 122 48 1 47 168 81 198 3.00e-39 139
MsaG016001 MtrunA17_Chr8g0362151 51.656 151 60 4 25 165 33 180 6.48e-39 138
MsaG016001 MtrunA17_Chr5g0416391 57.500 120 48 1 46 165 64 180 2.63e-37 134
MsaG016001 MtrunA17_Chr4g0060031 59.459 111 45 0 50 160 86 196 5.39e-37 134
MsaG016001 MtrunA17_Chr6g0450991 62.264 106 40 0 58 163 66 171 1.41e-36 132
MsaG016001 MtrunA17_Chr6g0453021 61.856 97 37 0 58 154 95 191 1.94e-35 129
MsaG016001 MtrunA17_Chr7g0217111 59.794 97 39 0 58 154 79 175 2.96e-30 115
MsaG016001 MtrunA17_Chr7g0265521 40.571 175 90 4 35 209 41 201 5.32e-29 110
MsaG016001 MtrunA17_Chr8g0346251 36.702 188 106 5 66 241 48 234 4.99e-26 103
MsaG016001 MtrunA17_Chr3g0127511 50.549 91 45 0 61 151 40 130 5.66e-25 100
MsaG016001 MtrunA17_Chr1g0179581 50.000 92 39 1 58 149 27 111 1.43e-24 95.5
MsaG016001 MtrunA17_Chr5g0403691 48.182 110 57 0 51 160 45 154 7.98e-23 94.0
MsaG016001 MtrunA17_Chr5g0403701 57.317 82 35 0 51 132 45 126 8.25e-23 93.6
MsaG016001 MtrunA17_Chr4g0055851 41.406 128 67 2 51 178 112 231 1.32e-18 84.0
MsaG016001 MtrunA17_Chr1g0151971 42.500 120 62 1 59 178 130 242 1.27e-17 81.3
MsaG016001 MtrunA17_Chr2g0308611 36.879 141 78 3 56 195 197 327 3.65e-17 80.5
MsaG016001 MtrunA17_Chr4g0054421 41.085 129 65 3 51 178 119 237 8.23e-17 78.6
MsaG016001 MtrunA17_Chr5g0399491 40.625 128 68 2 51 178 128 247 1.66e-16 78.2
MsaG016001 MtrunA17_Chr1g0175651 37.063 143 81 2 42 184 137 270 2.43e-16 77.8
MsaG016001 MtrunA17_Chr5g0400781 42.718 103 52 1 51 153 115 210 6.11e-16 76.3
MsaG016001 MtrunA17_Chr8g0335131 41.322 121 61 3 59 178 146 257 1.35e-15 75.9
MsaG016001 MtrunA17_Chr4g0044091 41.346 104 53 2 54 156 60 156 1.94e-15 73.6
MsaG016001 MtrunA17_Chr7g0258831 36.478 159 80 4 32 178 121 270 7.33e-15 73.6
MsaG016001 MtrunA17_Chr4g0071411 45.055 91 43 1 62 152 91 174 8.17e-15 72.0
MsaG016001 MtrunA17_Chr3g0135331 50.000 72 36 0 59 130 145 216 1.03e-12 67.4
MsaG016001 MtrunA17_Chr2g0299031 37.288 118 64 3 42 156 63 173 1.46e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016001 AT4G40060.1 47.284 313 134 15 1 301 1 294 1.44e-70 220
MsaG016001 AT2G22430.1 45.181 332 129 14 1 301 2 311 5.82e-63 201
MsaG016001 AT5G65310.1 42.296 331 141 12 1 301 1 311 5.63e-62 199
MsaG016001 AT5G65310.2 44.097 288 117 9 38 301 26 293 1.65e-60 194
MsaG016001 AT3G01470.1 63.810 105 37 1 58 161 67 171 4.47e-38 136
MsaG016001 AT1G69780.1 55.000 120 51 1 46 165 72 188 1.83e-36 132
MsaG016001 AT5G15150.1 48.428 159 78 2 42 197 95 252 6.22e-36 131
MsaG016001 AT3G01220.1 53.982 113 50 1 44 154 70 182 1.49e-32 122
MsaG016001 AT2G46680.1 40.123 162 91 2 50 205 23 184 3.61e-30 115
MsaG016001 AT1G26960.1 44.138 145 74 2 57 201 69 206 2.59e-29 112
MsaG016001 AT2G46680.2 40.000 160 92 2 50 205 23 182 3.63e-29 112
MsaG016001 AT3G61890.1 48.936 94 48 0 62 155 33 126 4.94e-26 103
MsaG016001 AT1G27045.1 49.565 115 58 0 45 159 54 168 9.68e-26 102
MsaG016001 AT1G27045.5 49.565 115 58 0 45 159 11 125 1.70e-25 100
MsaG016001 AT1G27045.3 49.565 115 58 0 45 159 11 125 1.70e-25 100
MsaG016001 AT1G27045.2 49.565 115 58 0 45 159 3 117 2.00e-25 100
MsaG016001 AT5G03790.1 43.200 125 55 3 59 180 77 188 5.88e-25 100
MsaG016001 AT1G27045.4 49.533 107 54 0 45 151 54 160 7.45e-24 98.2
MsaG016001 AT5G03790.2 50.000 90 38 1 59 148 77 159 1.05e-22 93.6
MsaG016001 AT4G36740.2 46.789 109 51 1 52 160 49 150 2.05e-21 90.5
MsaG016001 AT4G36740.1 46.789 109 51 1 52 160 48 149 2.21e-21 90.5
MsaG016001 AT2G18550.1 44.275 131 58 3 46 173 50 168 2.68e-21 90.5
MsaG016001 AT5G66700.1 60.811 74 29 0 59 132 71 144 3.43e-21 90.1
MsaG016001 AT2G36610.1 39.535 129 61 3 38 158 52 171 1.06e-20 87.8
MsaG016001 AT5G53980.1 53.521 71 33 0 59 129 11 81 4.65e-17 77.4
MsaG016001 AT2G01430.1 38.129 139 73 5 42 179 122 248 2.14e-16 78.2
MsaG016001 AT4G16780.1 39.062 128 70 2 51 178 121 240 2.92e-16 77.8
MsaG016001 AT4G37790.1 42.718 103 52 1 51 153 118 213 6.12e-16 76.6
MsaG016001 AT2G22800.1 44.660 103 50 1 51 153 105 200 1.34e-15 75.9
MsaG016001 AT5G06710.1 35.758 165 81 5 57 221 188 327 3.80e-15 75.1
MsaG016001 AT4G17460.1 43.000 100 50 1 54 153 130 222 1.81e-14 72.8
MsaG016001 AT5G47370.1 42.718 103 52 1 51 153 122 217 2.28e-14 72.4
MsaG016001 AT2G44910.1 39.167 120 65 2 59 178 163 274 9.26e-14 70.9
MsaG016001 AT3G60390.1 38.525 122 67 2 57 178 160 273 5.66e-13 68.6
MsaG016001 AT2G01430.2 45.714 70 38 0 42 111 122 191 8.78e-11 60.8

Find 60 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATCTTGCTCTCCTGTTT+TGG 0.182991 3:-93109606 None:intergenic
TCTTCACATGATAAGATTTC+TGG 0.185572 3:-93110615 None:intergenic
GTCATAATCCAATTGATCTT+TGG 0.265734 3:-93110416 None:intergenic
CCATACACATGTTTGTTCCT+TGG 0.325978 3:-93109370 None:intergenic
CAATTCATGGAGGAAGATTC+AGG 0.342389 3:-93110583 None:intergenic
GGAATTGATGTTTCTGAAGA+TGG 0.346885 3:-93110382 None:intergenic
AAGCAGTTGGAAAGAGATTA+TGG 0.359328 3:+93109634 MsaT016001.1:CDS
TTCAGAATCCAAAGATCAAT+TGG 0.360161 3:+93110408 MsaT016001.1:CDS
TAGCTGTTTGGTTCCAAAAC+AGG 0.367018 3:+93109593 MsaT016001.1:CDS
GAGAAGCTTGCCATTGAACT+TGG 0.376848 3:+93109553 MsaT016001.1:CDS
ATTAATGATTAACCTGTTGA+TGG 0.378350 3:-93109196 None:intergenic
TCCAGCGCAATTTCTTCATC+CGG 0.382294 3:+93110526 MsaT016001.1:CDS
TGATCTTTGGATTCTGAACT+AGG 0.386464 3:-93110403 None:intergenic
AGTGGATCAAGTTAAGGCTT+TGG 0.405768 3:+93109486 MsaT016001.1:CDS
AGCCTAGACAAGTAGCTGTT+TGG 0.421533 3:+93109581 MsaT016001.1:CDS
CTGGTACTGGAAACAATTCA+TGG 0.434538 3:-93110596 None:intergenic
ATTAAGAGTGGATCAAGTTA+AGG 0.434553 3:+93109480 MsaT016001.1:CDS
CCAGCGCAATTTCTTCATCC+GGG 0.438421 3:+93110527 MsaT016001.1:CDS
GAAGGGTGTGTTGAAGAAAC+TGG 0.440606 3:+93109433 MsaT016001.1:CDS
ATCACAATCTCTCCATCAAC+AGG 0.446409 3:+93109184 MsaT016001.1:CDS
CATGATAAGATTTCTGGTAC+TGG 0.447688 3:-93110609 None:intergenic
AGACTTGAAAGACGGTTCTT+CGG 0.453631 3:+93110495 MsaT016001.1:CDS
GAACCGTCTTTCAAGTCTAC+TGG 0.456218 3:-93110490 None:intergenic
TTGGATGGATTTGAAGAAGA+AGG 0.464593 3:+93109415 MsaT016001.1:CDS
TTTCAATCAATGATGTTGGA+TGG 0.484310 3:+93109400 MsaT016001.1:CDS
TGAAGAAGAATCTGAGGTGT+TGG 0.489416 3:-93109152 None:intergenic
CCAAGGAACAAACATGTGTA+TGG 0.493903 3:+93109370 MsaT016001.1:CDS
GGTCAGGACAGTACCATTGT+AGG 0.494776 3:-93110705 None:intergenic
AACAACAATGATGTTGGTAT+TGG 0.500792 3:+93110448 MsaT016001.1:CDS
GAACAAACATGTGTATGGTA+TGG 0.501372 3:+93109375 MsaT016001.1:CDS
AGGAGTTGAAGAAGAATCTG+AGG 0.515030 3:-93109158 None:intergenic
ATAATCTCTTTCCAACTGCT+TGG 0.516725 3:-93109632 None:intergenic
GGAGTTTCAATCAATGATGT+TGG 0.518927 3:+93109396 MsaT016001.1:CDS
GAAGAAGAATCTGAGGTGTT+GGG 0.524763 3:-93109151 None:intergenic
GAATTGATGTTTCTGAAGAT+GGG 0.525493 3:-93110381 None:intergenic
GAAATCTTATCATGTGAAGA+TGG 0.526190 3:+93110618 MsaT016001.1:CDS
AGGCTGCAACCCAAGTTCAA+TGG 0.529892 3:-93109563 None:intergenic
CCCGGATGAAGAAATTGCGC+TGG 0.538230 3:-93110527 None:intergenic
AAGGAATTGAAATCAAAGCT+TGG 0.543819 3:+93110277 MsaT016001.1:CDS
AAGATTCAGGAGACAACAAA+AGG 0.555354 3:-93110570 None:intergenic
AGAAGCTTGCCATTGAACTT+GGG 0.559661 3:+93109554 MsaT016001.1:CDS
ATAATCAACAACAATGATGT+TGG 0.562748 3:+93110442 MsaT016001.1:CDS
CAGCGCAATTTCTTCATCCG+GGG 0.572338 3:+93110528 MsaT016001.1:CDS
GGACAGTACCATTGTAGGGT+TGG 0.574109 3:-93110700 None:intergenic
TCCAAAACAGGAGAGCAAGA+TGG 0.577020 3:+93109605 MsaT016001.1:CDS
GTCAGGACAGTACCATTGTA+GGG 0.584883 3:-93110704 None:intergenic
GAAGAAACGTAGATTAAGAG+TGG 0.588824 3:+93109468 MsaT016001.1:CDS
AACCAAACAGCTACTTGTCT+AGG 0.590010 3:-93109583 None:intergenic
CAATTTCTTAAGTGCCGATG+AGG 0.590118 3:+93110648 MsaT016001.1:CDS
TGGATGGATTTGAAGAAGAA+GGG 0.596251 3:+93109416 MsaT016001.1:CDS
AAGATGGAAGACCAAGCAGT+TGG 0.606063 3:+93109621 MsaT016001.1:CDS
TTTCCAGTAGACTTGAAAGA+CGG 0.606889 3:+93110487 MsaT016001.1:CDS
ATTTAGAGGAACATAGTCCA+AGG 0.623460 3:+93109353 MsaT016001.1:intron
TTCATCACAAGATTCAAGCA+TGG 0.624852 3:-93110347 None:intergenic
AATGGTACTGTCCTGACCAG+TGG 0.629087 3:+93110710 MsaT016001.1:CDS
CTGCTGACTCTGAAGAACCC+CGG 0.637223 3:-93110545 None:intergenic
AGCAAGCACCAACCCTACAA+TGG 0.659727 3:+93110692 MsaT016001.1:CDS
ATCTTATCATGTGAAGATGG+AGG 0.661383 3:+93110621 MsaT016001.1:CDS
GATGGAGAGATTGTGATGAG+AGG 0.700166 3:-93109178 None:intergenic
GTACTGGAAACAATTCATGG+AGG 0.765506 3:-93110593 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 93109142 93110738 93109142 ID=MsaG016001
Chr3 mRNA 93109142 93110738 93109142 ID=MsaT016001.1;Parent=MsaG016001
Chr3 exon 93109142 93109205 93109142 ID=MsaT016001.1.exon1;Parent=MsaT016001.1
Chr3 CDS 93109142 93109205 93109142 ID=cds.MsaT016001.1;Parent=MsaT016001.1
Chr3 exon 93109359 93109735 93109359 ID=MsaT016001.1.exon2;Parent=MsaT016001.1
Chr3 CDS 93109359 93109735 93109359 ID=cds.MsaT016001.1;Parent=MsaT016001.1
Chr3 exon 93110274 93110738 93110274 ID=MsaT016001.1.exon3;Parent=MsaT016001.1
Chr3 CDS 93110274 93110738 93110274 ID=cds.MsaT016001.1;Parent=MsaT016001.1
Gene Sequence

>MsaT016001.1

ATGAAGAGACCCAACACCTCAGATTCTTCTTCAACTCCTCTCATCACAATCTCTCCATCAACAGAGGAACATAGTCCAAGGAACAAACATGTGTATGGTATGGAGTTTCAATCAATGATGTTGGATGGATTTGAAGAAGAAGGGTGTGTTGAAGAAACTGGTCATCATTCTGAGAAGAAACGTAGATTAAGAGTGGATCAAGTTAAGGCTTTGGAGAAAAACTTTGAGGTAGAAAACAAGCTTGAACCTGAAAGAAAAGAGAAGCTTGCCATTGAACTTGGGTTGCAGCCTAGACAAGTAGCTGTTTGGTTCCAAAACAGGAGAGCAAGATGGAAGACCAAGCAGTTGGAAAGAGATTATGGTGTTCTTAAAGCTAATTATGATGCTCTTAAGCTCAAGTTTGATGCAATTGCTCAAGACAACAAAGCTTTTCACAAGGAGATTAAGGAATTGAAATCAAAGCTTGGAGAAGAAGAAAAAAGCACAATCAATGTTTTGGTGAAGGAGGAGTTAACCATGCTTGAATCTTGTGATGAAGACAAGCATAACCCATCTTCAGAAACATCAATTCCTAGTTCAGAATCCAAAGATCAATTGGATTATGACTGCATAATCAACAACAATGATGTTGGTATTGGTGAAACTTCTTCACTCTTTCCAGTAGACTTGAAAGACGGTTCTTCGGACAGCGACTCCAGCGCAATTTCTTCATCCGGGGTTCTTCAGAGTCAGCAGCACCTTTTGTTGTCTCCTGAATCTTCCTCCATGAATTGTTTCCAGTACCAGAAATCTTATCATGTGAAGATGGAGGAGCACAATTTCTTAAGTGCCGATGAGGCGTGCAACTTTTTCTCGGACGAGCAAGCACCAACCCTACAATGGTACTGTCCTGACCAGTGGAGTTAA
Protein sequence

>MsaT016001.1

MKRPNTSDSSSTPLITISPSTEEHSPRNKHVYGMEFQSMMLDGFEEEGCVEETGHHSEKKRRLRVDQVKALEKNFEVENKLEPERKEKLAIELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALKLKFDAIAQDNKAFHKEIKELKSKLGEEEKSTINVLVKEELTMLESCDEDKHNPSSETSIPSSESKDQLDYDCIINNNDVGIGETSSLFPVDLKDGSSDSDSSAISSSGVLQSQQHLLLSPESSSMNCFQYQKSYHVKMEEHNFLSADEACNFFSDEQAPTLQWYCPDQWS*