AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene046833

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046833.t1 MTR_3g089045 87.500 64 8 0 1 64 1 64 6.19e-35 119
MS.gene046833.t1 MTR_7g086960 70.370 54 16 0 11 64 84 137 8.55e-24 91.3
MS.gene046833.t1 MTR_6g074860 74.510 51 13 0 14 64 2 52 1.02e-23 89.4
MS.gene046833.t1 MTR_4g082040 74.074 54 14 0 11 64 100 153 5.61e-23 89.7
MS.gene046833.t1 MTR_5g041570 72.222 54 15 0 11 64 129 182 9.64e-23 89.0
MS.gene046833.t1 MTR_6g027370 55.224 67 27 1 1 64 81 147 1.09e-20 82.8
MS.gene046833.t1 MTR_6g027340 66.667 48 16 0 17 64 17 64 3.86e-20 79.3
MS.gene046833.t1 MTR_6g027360 66.667 48 16 0 17 64 79 126 6.23e-20 80.5
MS.gene046833.t1 MTR_6g015455 54.167 48 22 0 17 64 6 53 2.48e-14 65.5
MS.gene046833.t1 MTR_4g019370 60.417 48 19 0 17 64 39 86 2.57e-14 65.5
MS.gene046833.t1 MTR_5g016510 56.250 48 21 0 17 64 6 53 2.81e-14 65.1
MS.gene046833.t1 MTR_5g070020 58.333 48 20 0 17 64 123 170 1.04e-13 63.5
MS.gene046833.t1 MTR_4g094982 56.250 48 21 0 17 64 6 53 1.14e-13 63.2
MS.gene046833.t1 MTR_5g082910 54.167 48 22 0 17 64 20 67 2.27e-13 62.4
MS.gene046833.t1 MTR_3g463400 55.769 52 23 0 13 64 130 181 2.31e-13 62.8
MS.gene046833.t1 MTR_3g101290 56.250 48 21 0 17 64 38 85 1.30e-12 59.7
MS.gene046833.t1 MTR_4g105660 48.333 60 31 0 5 64 169 228 2.98e-12 59.7
MS.gene046833.t1 MTR_5g049190 56.250 48 21 0 17 64 20 67 3.28e-12 58.9
MS.gene046833.t1 MTR_7g035350 52.174 46 22 0 19 64 228 273 1.16e-11 58.2
MS.gene046833.t1 MTR_3g110028 50.000 48 24 0 17 64 86 133 5.04e-11 56.2
MS.gene046833.t1 MTR_3g077650 52.083 48 23 0 17 64 182 229 7.67e-11 55.5
MS.gene046833.t1 MTR_7g451170 52.083 48 23 0 17 64 192 239 7.79e-11 55.5
MS.gene046833.t1 MTR_5g010650 52.174 46 22 0 19 64 113 158 9.08e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046833.t1 AT1G73410 78.431 51 11 0 14 64 4 54 2.30e-24 90.9
MS.gene046833.t1 AT1G73410 78.431 51 11 0 14 64 4 54 7.65e-24 89.0
MS.gene046833.t1 AT1G17950 76.471 51 12 0 14 64 3 53 8.22e-24 89.7
MS.gene046833.t1 AT1G69560 76.923 52 12 0 13 64 104 155 1.11e-22 88.2
MS.gene046833.t1 AT1G69560 76.923 52 12 0 13 64 120 171 1.41e-22 88.2
MS.gene046833.t1 AT1G26780 81.250 48 9 0 17 64 99 146 2.29e-22 86.7
MS.gene046833.t1 AT4G33450 71.154 52 15 0 13 64 16 67 4.68e-22 85.1
MS.gene046833.t1 AT1G26780 81.250 48 9 0 17 64 99 146 6.45e-22 86.3
MS.gene046833.t1 AT5G17800 67.273 55 18 0 10 64 87 141 1.14e-21 85.1
MS.gene046833.t1 AT3G29020 64.815 54 19 0 11 64 60 113 1.76e-21 83.2
MS.gene046833.t1 AT3G29020 64.815 54 19 0 11 64 62 115 5.60e-21 83.2
MS.gene046833.t1 AT5G67300 56.250 48 21 0 17 64 7 54 9.94e-14 63.5
MS.gene046833.t1 AT5G39700 51.786 56 27 0 9 64 49 104 2.81e-13 61.2
MS.gene046833.t1 AT3G50060 54.167 48 22 0 17 64 7 54 4.98e-13 61.6
MS.gene046833.t1 AT5G40360 54.167 48 22 0 17 64 159 206 5.84e-13 61.6
MS.gene046833.t1 AT3G27785 54.167 48 22 0 17 64 190 237 9.38e-13 61.2
MS.gene046833.t1 AT5G58850 54.167 48 22 0 17 64 106 153 2.77e-12 59.7
MS.gene046833.t1 AT2G39880 54.717 53 24 0 12 64 46 98 3.09e-12 59.7
MS.gene046833.t1 AT2G23290 52.083 48 23 0 17 64 14 61 5.18e-12 58.9
MS.gene046833.t1 AT3G09230 54.167 48 22 0 17 64 56 103 5.33e-12 58.9
MS.gene046833.t1 AT5G11050 54.167 48 22 0 17 64 106 153 6.30e-12 58.9
MS.gene046833.t1 AT4G37260 52.083 48 23 0 17 64 14 61 6.45e-12 58.5
MS.gene046833.t1 AT3G09370 54.167 48 22 0 17 64 144 191 9.68e-12 58.2
MS.gene046833.t1 AT3G09370 54.167 48 22 0 17 64 136 183 1.01e-11 58.2
MS.gene046833.t1 AT3G09370 54.167 48 22 0 17 64 131 178 1.02e-11 58.2
MS.gene046833.t1 AT5G11510 52.083 48 23 0 17 64 82 129 1.67e-11 57.8
MS.gene046833.t1 AT5G11510 52.083 48 23 0 17 64 82 129 1.70e-11 57.8
MS.gene046833.t1 AT5G11510 52.083 48 23 0 17 64 82 129 1.70e-11 57.8
MS.gene046833.t1 AT5G11510 52.083 48 23 0 17 64 82 129 1.70e-11 57.8
MS.gene046833.t1 AT5G11510 52.083 48 23 0 17 64 82 129 1.71e-11 57.4
MS.gene046833.t1 AT3G55730 54.167 48 22 0 17 64 57 104 3.65e-11 56.6
MS.gene046833.t1 AT4G18770 54.167 48 22 0 17 64 218 265 4.50e-11 56.2
MS.gene046833.t1 AT5G02320 50.000 48 24 0 17 64 128 175 9.47e-11 55.5
MS.gene046833.t1 AT5G02320 50.000 48 24 0 17 64 128 175 9.47e-11 55.5

Find 11 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAATATGGTGCTCAAAAT+TGG 0.232647 3.1:-27348161 MS.gene046833:CDS
CCTCAACTTGTTGAACAATA+TGG 0.300197 3.1:-27348174 MS.gene046833:CDS
TAGGGAAACGTTGTAGGTTG+AGG 0.463106 3.1:-27347882 MS.gene046833:CDS
AACTTGTAGGGAAACGTTGT+AGG 0.477303 3.1:-27347888 MS.gene046833:intron
AGAGTTGTCCATGTGGTCAC+TGG 0.512701 3.1:-27348221 MS.gene046833:CDS
GTGACCACATGGACAACTCT+TGG 0.543251 3.1:+27348224 None:intergenic
CCATATTGTTCAACAAGTTG+AGG 0.564383 3.1:+27348174 None:intergenic
GGAAACGTTGTAGGTTGAGG+TGG 0.592608 3.1:-27347879 MS.gene046833:CDS
GCGGGTCGCCAGTGACCACA+TGG 0.607822 3.1:+27348213 None:intergenic
ACTTCCATAATCCATATGGA+GGG 0.628080 3.1:-27348270 None:intergenic
GATACCAAGAGTTGTCCATG+TGG 0.733953 3.1:-27348228 MS.gene046833:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGAATTTGAAAATTAAATA+AGG + chr3.1:27348066-27348085 None:intergenic 10.0%
!! AATTTGAAAATTAAATAAGG+AGG + chr3.1:27348063-27348082 None:intergenic 15.0%
!! AATATTACATAATACATACC+TGG + chr3.1:27348008-27348027 None:intergenic 20.0%
!!! ATTTTTTCCTTTTAACTTGT+AGG - chr3.1:27348212-27348231 MS.gene046833:CDS 20.0%
!!! TTTTTTCCTTTTAACTTGTA+GGG - chr3.1:27348213-27348232 MS.gene046833:CDS 20.0%
AACAATATGGTGCTCAAAAT+TGG - chr3.1:27347952-27347971 MS.gene046833:intron 30.0%
TCAATTGCTGAAAAACTTCA+AGG - chr3.1:27347978-27347997 MS.gene046833:intron 30.0%
ACGTTTCCCTACAAGTTAAA+AGG + chr3.1:27348222-27348241 None:intergenic 35.0%
CCATATTGTTCAACAAGTTG+AGG + chr3.1:27347942-27347961 None:intergenic 35.0%
! AGGAAGTTTTTCATCTTCAG+CGG + chr3.1:27347922-27347941 None:intergenic 35.0%
!! CCTCAACTTGTTGAACAATA+TGG - chr3.1:27347939-27347958 MS.gene046833:intron 35.0%
AACTTGTAGGGAAACGTTGT+AGG - chr3.1:27348225-27348244 MS.gene046833:CDS 40.0%
GAAAAACTTCAAGGAAGACC+AGG - chr3.1:27347987-27348006 MS.gene046833:intron 40.0%
! GGAAGTTTTTCATCTTCAGC+GGG + chr3.1:27347921-27347940 None:intergenic 40.0%
GATACCAAGAGTTGTCCATG+TGG - chr3.1:27347885-27347904 MS.gene046833:intron 45.0%
TAGGGAAACGTTGTAGGTTG+AGG - chr3.1:27348231-27348250 MS.gene046833:CDS 45.0%
!! TATTATGTAATATTAATTAA+AGG - chr3.1:27348014-27348033 MS.gene046833:intron 5.0%
AGAGTTGTCCATGTGGTCAC+TGG - chr3.1:27347892-27347911 MS.gene046833:intron 50.0%
GTGACCACATGGACAACTCT+TGG + chr3.1:27347892-27347911 None:intergenic 50.0%
! GGAAACGTTGTAGGTTGAGG+TGG - chr3.1:27348234-27348253 MS.gene046833:CDS 50.0%
GCGGGTCGCCAGTGACCACA+TGG + chr3.1:27347903-27347922 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 27347858 27348277 27347858 ID=MS.gene046833
chr3.1 mRNA 27347858 27348277 27347858 ID=MS.gene046833.t1;Parent=MS.gene046833
chr3.1 exon 27348127 27348277 27348127 ID=MS.gene046833.t1.exon1;Parent=MS.gene046833.t1
chr3.1 CDS 27348127 27348277 27348127 ID=cds.MS.gene046833.t1;Parent=MS.gene046833.t1
chr3.1 exon 27347858 27347901 27347858 ID=MS.gene046833.t1.exon2;Parent=MS.gene046833.t1
chr3.1 CDS 27347858 27347901 27347858 ID=cds.MS.gene046833.t1;Parent=MS.gene046833.t1
Gene Sequence

>MS.gene046833

ATGGAGGGTTTTTCTTTTGCAGCTGAAGATACCAAGAGTTGTCCATGTGGTCACTGGCGACCCGCTGAAGATGAAAAACTTCCTCAACTTGTTGAACAATATGGTGCTCAAAATTGGAATTCAATTGCTGAAAAACTTCAAGGAAGACCAGGTATGTATTATGTAATATTAATTAAAGGTTTATTATTAATTGACTGATTGACCTCCTTATTTAATTTTCAAATTCATAGTAAAATTCATATAGTTGATTATTATGATCTCTTAAATTCATCTTGTACTCAACTAATATAGTTTTTCATCAATTAATTTTCTCATATACTTCTGTGTATAAAAGAAAAAATTAATCAATATATAATTTTTTCCTTTTAACTTGTAGGGAAACGTTGTAGGTTGAGGTGGTTCAATCAGCTAGATCCATGA
Protein sequence

>MS.gene046833.t1

MEGFSFAAEDTKSCPCGHWRPAEDEKLPQLVEQYGAQNWNSIAEKLQGRPGKRCRLRWFNQLDP