AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001323


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001323 MtrunA17_Chr1g0161901 93.023 258 11 2 1 258 1 251 1.31e-178 491
MsaG001323 MtrunA17_Chr8g0376021 51.751 257 84 8 2 258 1 217 7.40e-75 227
MsaG001323 MtrunA17_Chr3g0110091 40.157 254 134 6 5 258 3 238 1.71e-56 181
MsaG001323 MtrunA17_Chr5g0434121 43.985 266 104 11 6 258 4 237 3.47e-56 180
MsaG001323 MtrunA17_Chr2g0333741 66.234 77 21 2 98 169 81 157 3.47e-26 102
MsaG001323 MtrunA17_Chr1g0149811 38.356 146 71 2 43 169 35 180 1.66e-23 95.9
MsaG001323 MtrunA17_Chr4g0001081 58.108 74 19 3 98 169 67 130 6.91e-19 82.8
MsaG001323 MtrunA17_Chr1g0207691 38.889 126 59 4 98 219 64 175 1.17e-18 81.3
MsaG001323 MtrunA17_Chr3g0137111 43.103 116 45 5 69 169 49 158 3.31e-18 80.9
MsaG001323 MtrunA17_Chr4g0072571 36.719 128 63 4 98 223 45 156 1.57e-16 75.1
MsaG001323 MtrunA17_Chr4g0053691 36.364 143 66 7 90 229 57 177 1.21e-14 70.1
MsaG001323 MtrunA17_Chr7g0254221 52.830 53 23 2 82 134 19 69 1.12e-11 61.6
MsaG001323 MtrunA17_Chr7g0251581 69.697 33 10 0 98 130 39 71 2.21e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001323 AT1G66140.1 41.758 182 81 6 98 258 83 260 3.43e-37 132
MsaG001323 AT1G24625.1 39.648 227 94 10 39 258 19 209 2.55e-32 118
MsaG001323 AT1G80730.1 57.955 88 21 3 98 169 66 153 1.09e-23 95.9
MsaG001323 AT5G10970.1 56.579 76 29 2 97 169 101 175 1.77e-21 90.9
MsaG001323 AT5G25160.1 55.263 76 30 2 98 169 59 134 7.29e-21 88.6
MsaG001323 AT5G57520.1 51.515 66 32 0 98 163 50 115 1.60e-15 72.0
MsaG001323 AT5G14010.1 47.945 73 27 1 94 155 32 104 2.40e-15 72.0
MsaG001323 AT5G01860.1 55.814 43 19 0 95 137 62 104 4.04e-11 61.6
MsaG001323 AT3G58070.1 55.769 52 20 1 82 133 76 124 7.81e-11 61.2

Find 45 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGCTTCCAAGTTCAAATT+TGG 0.203450 1:-18554670 None:intergenic
ATGAAGATGTCGGCGTATTT+TGG 0.224650 1:+18555271 MsaT001323.1:CDS
GACATCAGAATGCTCATAAA+AGG 0.253478 1:+18555007 MsaT001323.1:CDS
TTAGCTTCTTTACCTCTTCA+TGG 0.299313 1:+18555090 MsaT001323.1:CDS
AGAAGTTGTAGCACTGTCTT+TGG 0.324664 1:-18554761 None:intergenic
ATGATGATGGCATGTGGTTT+TGG 0.332220 1:-18555161 None:intergenic
TTTATCTGCCTGAAACTTCC+AGG 0.347691 1:-18555294 None:intergenic
CATATCCTGATCTTACTTTG+AGG 0.427108 1:+18555406 MsaT001323.1:CDS
TCCGAGCGATGAAGATTTGA+AGG 0.428555 1:+18554849 MsaT001323.1:CDS
TCCTTCAAATCTTCATCGCT+CGG 0.432671 1:-18554850 None:intergenic
AAATTTGAGAAAGATTGTTT+CGG 0.446566 1:+18555225 MsaT001323.1:CDS
AACTTCTTCTTGTCTTACTA+AGG 0.451364 1:+18554777 MsaT001323.1:CDS
GAATACTCCAAATTTGAACT+TGG 0.473476 1:+18554663 MsaT001323.1:CDS
TCGGATTGAAGTTGAGAGTC+AGG 0.475494 1:-18554831 None:intergenic
TTCTTTAGCTCACAAGCGTT+AGG 0.479990 1:+18554982 MsaT001323.1:CDS
CAAAGCGCGCTATGCGAGTA+GGG 0.487145 1:+18555043 MsaT001323.1:CDS
ACTAAGGCAGACATTAATCC+AGG 0.488717 1:+18554793 MsaT001323.1:CDS
AGCTAAGCTTGTATACCCTT+CGG 0.491197 1:-18555073 None:intergenic
TCTTTCTCAAATTTCGCTGT+AGG 0.497994 1:-18555216 None:intergenic
GTAGTAGATGTTTGTTGAGG+AGG 0.505399 1:-18555384 None:intergenic
TAAAGCCTCAAAGTAAGATC+AGG 0.515851 1:-18555411 None:intergenic
TCTCTTGTAATTATTGTAGG+AGG 0.522769 1:+18554956 MsaT001323.1:CDS
TGATTCTTGTAAGTATATGT+TGG 0.525252 1:-18554725 None:intergenic
GAGAAAACTCTATGAATCGC+TGG 0.540223 1:-18554937 None:intergenic
GCAAAGCGCGCTATGCGAGT+AGG 0.540707 1:+18555042 MsaT001323.1:CDS
AGGTCAAGGGAAATAGAACC+TGG 0.542650 1:-18554811 None:intergenic
ACATCAGAATGCTCATAAAA+GGG 0.543025 1:+18555008 MsaT001323.1:CDS
AGTATATGTTGGAACCTACT+TGG 0.544787 1:-18554714 None:intergenic
ATCAGCATCGACGATGATGA+TGG 0.545503 1:-18555174 None:intergenic
CATCATCGTCGATGCTGATG+AGG 0.552605 1:+18555178 MsaT001323.1:CDS
AACTCTATGAATCGCTGGTG+CGG 0.556385 1:-18554932 None:intergenic
TATGTAGTAGATGTTTGTTG+AGG 0.576983 1:-18555387 None:intergenic
TTTAGCTCACAAGCGTTAGG+TGG 0.582305 1:+18554985 MsaT001323.1:CDS
TGAAGTTGAGAGTCAGGTCA+AGG 0.584371 1:-18554825 None:intergenic
TTAGAAGTAAGCAGCCAAGT+AGG 0.598009 1:+18554700 MsaT001323.1:CDS
ATCATCGTCGATGCTGATGA+GGG 0.599898 1:+18555179 MsaT001323.1:CDS
CGAGTAGGGATGTTTACCGA+AGG 0.601367 1:+18555057 MsaT001323.1:CDS
GACACTAACAGTGAAGTACT+AGG 0.613028 1:+18554880 MsaT001323.1:CDS
AAAGAAGAAGAACCATGAAG+AGG 0.622542 1:-18555102 None:intergenic
GAAGTTGAGAGTCAGGTCAA+GGG 0.634039 1:-18554824 None:intergenic
TTTATGCATAATGAAGATGT+CGG 0.651635 1:+18555261 MsaT001323.1:CDS
GAGTAGGGATGTTTACCGAA+GGG 0.666419 1:+18555058 MsaT001323.1:CDS
TCTTCATTATGCATAAACAT+CGG 0.674163 1:-18555255 None:intergenic
TCATAAAAGGGAGAGAACGA+TGG 0.677286 1:+18555020 MsaT001323.1:CDS
TCGACGATGATGATGGCATG+TGG 0.731879 1:-18555167 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 18554658 18555434 18554658 ID=MsaG001323
Chr1 mRNA 18554658 18555434 18554658 ID=MsaT001323.1;Parent=MsaG001323
Chr1 exon 18554658 18555434 18554658 ID=MsaT001323.1.exon1;Parent=MsaT001323.1
Chr1 CDS 18554658 18555434 18554658 ID=cds.MsaT001323.1;Parent=MsaT001323.1
Gene Sequence

>MsaT001323.1

ATGATGAATACTCCAAATTTGAACTTGGAAGCTGAAAATAGTTTAGAAGTAAGCAGCCAAGTAGGTTCCAACATATACTTACAAGAATCATCTCATGATCTTACCAAAGACAGTGCTACAACTTCTTCTTGTCTTACTAAGGCAGACATTAATCCAGGTTCTATTTCCCTTGACCTGACTCTCAACTTCAATCCGAGCGATGAAGATTTGAAGGAAACAAGCGACACTAACAGTGAAGTACTAGGAGCTAATCAAGCTCATCATAATACTGTTTCCGCACCAGCGATTCATAGAGTTTTCTCTTGTAATTATTGTAGGAGGAAATTCTTTAGCTCACAAGCGTTAGGTGGACATCAGAATGCTCATAAAAGGGAGAGAACGATGGCAAAGCGCGCTATGCGAGTAGGGATGTTTACCGAAGGGTATACAAGCTTAGCTTCTTTACCTCTTCATGGTTCTTCTTCTTTTCATTCTCTTGGTATTCAAGCTCATGCTGCAATGCACCAAAACCACATGCCATCATCATCGTCGATGCTGATGAGGGCTCATGATATGAGACCTACAGCGAAATTTGAGAAAGATTGTTTCGGAGCAGCACCGATGTTTATGCATAATGAAGATGTCGGCGTATTTTGGCCTGGAAGTTTCAGGCAGATAAATCAAAGTGTTCATAATTCAAATTTGAATCATAACTCAAATTTGAATACTAGTTTTGTAGCAACTGAACCTCCTCAACAAACATCTACTACATATCCTGATCTTACTTTGAGGCTTTAA

Protein sequence

>MsaT001323.1

MMNTPNLNLEAENSLEVSSQVGSNIYLQESSHDLTKDSATTSSCLTKADINPGSISLDLTLNFNPSDEDLKETSDTNSEVLGANQAHHNTVSAPAIHRVFSCNYCRRKFFSSQALGGHQNAHKRERTMAKRAMRVGMFTEGYTSLASLPLHGSSSFHSLGIQAHAAMHQNHMPSSSSMLMRAHDMRPTAKFEKDCFGAAPMFMHNEDVGVFWPGSFRQINQSVHNSNLNHNSNLNTSFVATEPPQQTSTTYPDLTLRL*