AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG032496

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG032496 MtrunA17_Chr8g0370121 66.265 249 55 7 1 228 1 241 7.43e-99 287
MsaG032496 MtrunA17_Chr8g0370131 55.556 234 89 9 1 229 1 224 2.41e-63 196
MsaG032496 MtrunA17_Chr6g0467271 76.522 115 26 1 1 114 1 115 6.37e-39 130
MsaG032496 MtrunA17_Chr5g0409841 40.260 77 43 1 103 179 89 162 6.96e-13 65.9
MsaG032496 MtrunA17_Chr4g0062741 37.037 81 42 2 103 178 135 211 1.80e-12 65.5
MsaG032496 MtrunA17_Chr5g0436501 38.272 81 45 2 103 183 122 197 2.88e-12 64.7
MsaG032496 MtrunA17_Chr3g0104071 48.000 50 26 0 103 152 144 193 4.37e-12 64.3
MsaG032496 MtrunA17_Chr5g0429521 48.000 50 26 0 103 152 129 178 4.94e-12 64.3
MsaG032496 MtrunA17_Chr1g0162081 38.571 70 38 1 103 172 119 183 6.95e-12 63.5
MsaG032496 MtrunA17_Chr7g0241761 43.103 58 33 0 95 152 129 186 9.45e-12 63.5
MsaG032496 MtrunA17_Chr8g0389241 36.486 74 42 1 99 172 98 166 1.28e-11 62.8
MsaG032496 MtrunA17_Chr2g0331031 37.143 70 40 1 103 172 106 171 1.44e-11 63.2
MsaG032496 MtrunA17_Chr1g0210471 37.975 79 42 2 88 166 111 182 2.91e-11 61.2
MsaG032496 MtrunA17_Chr5g0440731 33.824 68 45 0 101 168 100 167 6.27e-11 60.8
MsaG032496 MtrunA17_Chr5g0415191 46.000 50 27 0 103 152 99 148 7.42e-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
MsaG032496 AT5G05790.2 42.424 66 37 1 88 153 114 178 1.56e-12 65.9
MsaG032496 AT5G05790.1 42.424 66 37 1 88 153 114 178 1.56e-12 65.9
MsaG032496 AT5G58900.1 50.000 50 25 0 103 152 138 187 1.64e-12 65.9
MsaG032496 AT2G38090.1 37.500 80 46 1 92 171 127 202 4.21e-12 64.7
MsaG032496 AT1G49010.1 45.283 53 29 0 103 155 131 183 4.55e-12 64.7
MsaG032496 AT5G01200.1 46.575 73 33 3 97 167 136 204 5.67e-12 63.9
MsaG032496 AT3G11280.2 45.098 51 28 0 103 153 124 174 8.50e-12 63.5
MsaG032496 AT3G11280.1 45.098 51 28 0 103 153 124 174 8.50e-12 63.5
MsaG032496 AT5G08520.1 45.283 53 29 0 103 155 115 167 1.47e-11 63.2
MsaG032496 AT3G16350.1 40.625 64 38 0 89 152 120 183 2.59e-11 62.8

Find 75 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAGAAACATGGTCAAAATT+AGG 0.177575 6:-54116651 None:intergenic
CCATAAAATGTTGGAACTTC+TGG 0.186491 6:-54117776 None:intergenic
ACACATATGTGCATGGTTTA+AGG 0.242121 6:+54117690 MsaT032496.1:CDS
ACCACCATGTGTGGTAGGTT+GGG 0.275905 6:-54116787 None:intergenic
TGGACATGGTGGTGAAGATT+AGG 0.319556 6:-54116678 None:intergenic
TAGAAACATGGTCAAAATTA+GGG 0.358281 6:-54116650 None:intergenic
AGTTGATGTGGAACTTCGTT+TGG 0.364719 6:+54117877 MsaT032496.1:CDS
CTGTCTTAGCTTATTTGTGA+TGG 0.386082 6:+54117553 MsaT032496.1:intron
TGTCTTAGCTTATTTGTGAT+GGG 0.388102 6:+54117554 MsaT032496.1:intron
CGGACACCAAACTACTTTGT+TGG 0.394254 6:+54116707 MsaT032496.1:CDS
GTGATGGGGATGATTAAGTA+TGG 0.397169 6:+54117569 MsaT032496.1:CDS
CATGGTGCCTTGGAGTCAAT+TGG 0.422876 6:+54116881 MsaT032496.1:CDS
TGTGGTAGGTTGGGGCCAAT+TGG 0.422957 6:-54116778 None:intergenic
GCTATGCTACTAGCTTCTTC+AGG 0.423580 6:+54117657 MsaT032496.1:CDS
GTCGGAGAACCCTAGCAATT+AGG 0.429758 6:-54116812 None:intergenic
ACCATGCGCCTAGATGCATT+TGG 0.430946 6:-54116864 None:intergenic
GTAAGATCAGTGATCTCAAT+AGG 0.430973 6:-54116573 None:intergenic
TTAAGTATGGAAAAGGGAAA+TGG 0.433708 6:+54117582 MsaT032496.1:CDS
TACCACCATGTGTGGTAGGT+TGG 0.433974 6:-54116788 None:intergenic
TGGGTGTGTCCTTGAGCTGT+TGG 0.438020 6:-54116735 None:intergenic
GGGATGATTAAGTATGGAAA+AGG 0.439099 6:+54117575 MsaT032496.1:CDS
AGGGTTCTCCGACCGTTACC+TGG 0.445297 6:+54116822 MsaT032496.1:CDS
CCATGCGCCTAGATGCATTT+GGG 0.445348 6:-54116863 None:intergenic
ATGTGCATGGTTTAAGGAAA+AGG 0.449777 6:+54117696 MsaT032496.1:CDS
ATGACTCTTCCTGTTTGTGA+TGG 0.453409 6:+54117851 MsaT032496.1:CDS
GTTGATGTGGAACTTCGTTT+GGG 0.455063 6:+54117878 MsaT032496.1:CDS
CCACCATGTGTGGTAGGTTG+GGG 0.457806 6:-54116786 None:intergenic
TAGTTTGGTGTCCGTGGAGT+TGG 0.473185 6:-54116698 None:intergenic
GTGGTGCCAACAAAGTAGTT+TGG 0.480218 6:-54116713 None:intergenic
TCAACTTCTCCATCACAAAC+AGG 0.481736 6:-54117860 None:intergenic
TGGTCAAAATTAGGGATCAT+TGG 0.484624 6:-54116642 None:intergenic
CATCTAGGCGCATGGTGCCT+TGG 0.485387 6:+54116871 MsaT032496.1:CDS
AAACCATGCACATATGTGTC+TGG 0.497935 6:-54117686 None:intergenic
CAGTGATTCGAAAGGACTCA+TGG 0.501395 6:-54116755 None:intergenic
CCTTTCGAATCACTGCCAAT+TGG 0.501751 6:+54116763 MsaT032496.1:CDS
ATGGTTTAAGGAAAAGGAAA+AGG 0.505645 6:+54117702 MsaT032496.1:CDS
CGCCTAGATGCATTTGGGAA+TGG 0.509101 6:-54116858 None:intergenic
GCATAGCTTTGAACTTGTTG+TGG 0.515534 6:-54117641 None:intergenic
TGCCATTCCCAAATGCATCT+AGG 0.516055 6:+54116856 MsaT032496.1:CDS
GTCTTAGCTTATTTGTGATG+GGG 0.518234 6:+54117555 MsaT032496.1:intron
ATGGTGGTAGCCTAATTGCT+AGG 0.520937 6:+54116802 MsaT032496.1:CDS
GATGAAGATATGTGTGGTGA+TGG 0.524416 6:-54116612 None:intergenic
AATGGCATGGTGTCTGATCC+AGG 0.529965 6:-54116840 None:intergenic
GGTGTCCGTGGAGTTGGACA+TGG 0.533444 6:-54116692 None:intergenic
AGTGCTTGCATCATAGTTGT+TGG 0.542629 6:-54117825 None:intergenic
GCTTCTCCTCCATAAAATGT+TGG 0.545997 6:-54117785 None:intergenic
TTGGCACCACCAACAGCTCA+AGG 0.554738 6:+54116726 MsaT032496.1:CDS
GGATGATTAAGTATGGAAAA+GGG 0.561038 6:+54117576 MsaT032496.1:CDS
GTGTGTCCTTGAGCTGTTGG+TGG 0.563165 6:-54116732 None:intergenic
AAGATATGTGTGGTGATGGA+GGG 0.566805 6:-54116608 None:intergenic
ACAAAGTAGTTTGGTGTCCG+TGG 0.571688 6:-54116704 None:intergenic
CCCAAATGCATCTAGGCGCA+TGG 0.572869 6:+54116863 MsaT032496.1:CDS
GAAGATATGTGTGGTGATGG+AGG 0.578211 6:-54116609 None:intergenic
TGTTAACAATGATCTTGCAA+AGG 0.578401 6:+54117736 MsaT032496.1:CDS
AGGCTACCACCATGTGTGGT+AGG 0.580621 6:-54116792 None:intergenic
GTGGTGATGGAGGGGAGTCA+AGG 0.585853 6:-54116599 None:intergenic
TGGTGGTAGCCTAATTGCTA+GGG 0.591304 6:+54116803 MsaT032496.1:CDS
TCATGATCCAATTGACTCCA+AGG 0.595729 6:-54116888 None:intergenic
ATCACAAACAGGAAGAGTCA+TGG 0.601796 6:-54117849 None:intergenic
TGGCCCCAACCTACCACACA+TGG 0.605392 6:+54116783 MsaT032496.1:CDS
CATGCACATATGTGTCTGGT+AGG 0.610902 6:-54117682 None:intergenic
AGATATGTGTGGTGATGGAG+GGG 0.610906 6:-54116607 None:intergenic
CACCACCATGTCCAACTCCA+CGG 0.614682 6:+54116687 MsaT032496.1:CDS
ATGGTGTCTGATCCAGGTAA+CGG 0.615417 6:-54116834 None:intergenic
AGTGATTCGAAAGGACTCAT+GGG 0.623065 6:-54116754 None:intergenic
AATTAGGCTACCACCATGTG+TGG 0.648314 6:-54116796 None:intergenic
CTACCAGACACATATGTGCA+TGG 0.648995 6:+54117683 MsaT032496.1:CDS
CCAATTGGCAGTGATTCGAA+AGG 0.649536 6:-54116763 None:intergenic
TTGTGATGGAGAAGTTGATG+TGG 0.654638 6:+54117865 MsaT032496.1:CDS
GTCCGTGGAGTTGGACATGG+TGG 0.658224 6:-54116689 None:intergenic
TGTCTGATCCAGGTAACGGT+CGG 0.658940 6:-54116830 None:intergenic
AGATGCATTTGGGAATGGCA+TGG 0.666400 6:-54116853 None:intergenic
GATTAGGATTGATAGAAACA+TGG 0.682877 6:-54116662 None:intergenic
CCCCAACCTACCACACATGG+TGG 0.700133 6:+54116786 MsaT032496.1:CDS
GCATTAGATGAAGATATGTG+TGG 0.745900 6:-54116618 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 54116570 54117910 54116570 ID=MsaG032496
Chr6 mRNA 54116570 54117910 54116570 ID=MsaT032496.1;Parent=MsaG032496
Chr6 exon 54116570 54116910 54116570 ID=MsaT032496.1.exon1;Parent=MsaT032496.1
Chr6 CDS 54116570 54116910 54116570 ID=cds.MsaT032496.1;Parent=MsaT032496.1
Chr6 exon 54117562 54117910 54117562 ID=MsaT032496.1.exon2;Parent=MsaT032496.1
Chr6 CDS 54117562 54117910 54117562 ID=cds.MsaT032496.1;Parent=MsaT032496.1
Gene Sequence

>MsaT032496.1

ATGCCTATTGAGATCACTGATCTTACACTCCTTGACTCCCCTCCATCACCACACATATCTTCATCTAATGCACCAATGATCCCTAATTTTGACCATGTTTCTATCAATCCTAATCTTCACCACCATGTCCAACTCCACGGACACCAAACTACTTTGTTGGCACCACCAACAGCTCAAGGACACACCCATGAGTCCTTTCGAATCACTGCCAATTGGCCCCAACCTACCACACATGGTGGTAGCCTAATTGCTAGGGTTCTCCGACCGTTACCTGGATCAGACACCATGCCATTCCCAAATGCATCTAGGCGCATGGTGCCTTGGAGTCAATTGGATCATGACTTATTTGTGATGGGGATGATTAAGTATGGAAAAGGGAAATGGAGTGAAATTGCTAAGAACTTTGTATGCAACAAGACTCCACAACAAGTTCAAAGCTATGCTACTAGCTTCTTCAGGTACCTACCAGACACATATGTGCATGGTTTAAGGAAAAGGAAAAGGAACAACATGATTGTTAACAATGATCTTGCAAAGGAAACTCTCACTCTTTTTCCAGAAGTTCCAACATTTTATGGAGGAGAAGCTAGCAGTAGCAAGAACACCAACAACTATGATGCAAGCACTTCCATGACTCTTCCTGTTTGTGATGGAGAAGTTGATGTGGAACTTCGTTTGGGTTTAAATTAG
Protein sequence

>MsaT032496.1

MPIEITDLTLLDSPPSPHISSSNAPMIPNFDHVSINPNLHHHVQLHGHQTTLLAPPTAQGHTHESFRITANWPQPTTHGGSLIARVLRPLPGSDTMPFPNASRRMVPWSQLDHDLFVMGMIKYGKGKWSEIAKNFVCNKTPQQVQSYATSFFRYLPDTYVHGLRKRKRNNMIVNNDLAKETLTLFPEVPTFYGGEASSSKNTNNYDASTSMTLPVCDGEVDVELRLGLN*