AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78072

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78072.t1 MTR_4g035905 94.898 196 10 0 1 196 1 196 2.92e-138 384
MS.gene78072.t1 MTR_4g035870 88.265 196 23 0 1 196 1 196 1.93e-126 354
MS.gene78072.t1 MTR_4g035880 87.245 196 25 0 1 196 1 196 2.69e-124 349
MS.gene78072.t1 MTR_3g008840 47.879 165 84 1 34 196 23 187 1.35e-47 154
MS.gene78072.t1 MTR_3g008820 46.667 165 86 1 34 196 22 186 7.61e-47 152
MS.gene78072.t1 MTR_5g012000 42.683 164 91 1 36 196 48 211 7.24e-44 145
MS.gene78072.t1 MTR_4g101760 38.857 175 104 1 25 196 28 202 1.67e-39 134
MS.gene78072.t1 MTR_4g120825 40.000 170 88 4 36 193 35 202 1.16e-36 127
MS.gene78072.t1 MTR_4g120830 39.412 170 89 4 36 193 35 202 3.07e-36 125
MS.gene78072.t1 MTR_8g104765 39.412 170 89 4 36 193 44 211 1.24e-35 124
MS.gene78072.t1 MTR_3g008760 37.107 159 97 2 36 191 66 224 1.36e-31 114
MS.gene78072.t1 MTR_2g043560 40.000 165 85 4 36 195 34 189 2.27e-31 113
MS.gene78072.t1 MTR_7g108790 35.802 162 96 2 37 195 34 190 7.17e-31 112
MS.gene78072.t1 MTR_4g035855 35.204 196 116 3 8 193 8 202 1.23e-30 111
MS.gene78072.t1 MTR_1g088540 39.516 124 73 1 72 195 22 143 7.91e-27 100
MS.gene78072.t1 MTR_4g124855 34.426 183 92 4 27 195 31 199 1.45e-24 95.9
MS.gene78072.t1 MTR_4g025610 36.364 176 91 5 36 196 32 201 9.75e-22 88.6
MS.gene78072.t1 MTR_4g025590 35.795 176 92 5 36 196 3 172 2.14e-21 87.0
MS.gene78072.t1 MTR_4g025550 34.483 203 106 7 10 196 10 201 3.07e-21 87.4
MS.gene78072.t1 MTR_4g025620 32.836 201 105 6 11 196 16 201 2.66e-20 84.7
MS.gene78072.t1 MTR_3g091380 31.868 182 107 4 19 189 59 234 5.34e-19 84.3
MS.gene78072.t1 MTR_1g008140 31.977 172 88 5 37 189 82 243 6.39e-17 78.6
MS.gene78072.t1 MTR_7g112590 29.167 168 97 5 37 195 59 213 1.83e-16 77.0
MS.gene78072.t1 MTR_7g112580 39.091 110 54 4 87 192 94 194 4.10e-15 73.2
MS.gene78072.t1 MTR_8g023310 28.205 156 107 3 37 188 68 222 1.22e-14 72.0
MS.gene78072.t1 MTR_0036s0140 26.829 164 109 3 26 189 69 221 1.19e-13 67.4
MS.gene78072.t1 MTR_8g023150 32.530 166 91 5 37 192 77 231 1.68e-13 68.6
MS.gene78072.t1 MTR_1g083510 26.875 160 107 4 37 193 56 208 4.56e-13 67.4
MS.gene78072.t1 MTR_7g108905 25.654 191 126 3 10 192 18 200 1.43e-12 65.9
MS.gene78072.t1 MTR_1g083470 27.950 161 106 4 37 193 58 212 5.29e-12 64.3
MS.gene78072.t1 MTR_1g083500 27.950 161 106 4 37 193 58 212 5.29e-12 64.3
MS.gene78072.t1 MTR_8g104580 28.750 160 91 5 40 192 27 170 1.29e-11 63.2
MS.gene78072.t1 MTR_4g005170 25.000 176 122 4 26 197 52 221 1.30e-11 63.2
MS.gene78072.t1 MTR_1g083490 26.752 157 105 4 41 193 67 217 2.76e-11 62.0
MS.gene78072.t1 MTR_8g104655 28.125 160 92 5 40 192 35 178 5.45e-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
MS.gene78072.t1 AT5G62360 59.259 162 65 1 36 197 43 203 9.94e-64 196
MS.gene78072.t1 AT5G62350 46.667 165 84 1 36 196 38 202 1.02e-43 145
MS.gene78072.t1 AT1G62770 46.023 176 89 3 28 197 25 200 2.60e-43 144
MS.gene78072.t1 AT1G14890 40.513 195 103 4 9 195 28 217 2.18e-41 139
MS.gene78072.t1 AT1G62760 45.882 170 87 2 30 196 141 308 5.06e-41 141
MS.gene78072.t1 AT2G01610 40.838 191 95 4 21 193 27 217 2.69e-40 137
MS.gene78072.t1 AT3G47380 44.848 165 87 1 36 196 38 202 4.36e-40 135
MS.gene78072.t1 AT4G25260 38.776 196 114 2 7 196 6 201 1.04e-39 134
MS.gene78072.t1 AT5G51520 38.776 196 107 5 9 192 8 202 6.95e-38 130
MS.gene78072.t1 AT4G25250 39.506 162 95 2 31 189 32 193 8.10e-38 129
MS.gene78072.t1 AT5G20740 36.316 190 111 3 8 192 9 193 2.58e-37 129
MS.gene78072.t1 AT5G20740 36.316 190 111 3 8 192 43 227 1.43e-36 127
MS.gene78072.t1 AT4G12390 43.976 166 88 1 36 196 39 204 4.50e-34 120
MS.gene78072.t1 AT1G70720 35.602 191 111 4 10 193 9 194 2.97e-32 115
MS.gene78072.t1 AT1G70720 35.602 191 111 4 10 193 21 206 3.67e-32 115
MS.gene78072.t1 AT1G23205 38.150 173 95 4 30 191 27 198 1.73e-28 106
MS.gene78072.t1 AT3G62820 32.620 187 117 5 11 193 9 190 6.23e-24 94.0
MS.gene78072.t1 AT2G47670 36.250 160 97 2 36 193 48 204 4.20e-23 92.0
MS.gene78072.t1 AT5G53370 33.766 154 97 3 37 189 111 260 3.25e-20 88.2
MS.gene78072.t1 AT5G53370 33.766 154 97 3 37 189 75 224 4.24e-20 87.8
MS.gene78072.t1 AT4G00080 32.738 168 93 6 36 189 35 196 4.38e-20 84.3
MS.gene78072.t1 AT1G53830 31.013 158 107 2 37 192 62 219 5.66e-20 87.4
MS.gene78072.t1 AT3G14310 28.994 169 118 2 26 192 48 216 4.34e-19 84.7
MS.gene78072.t1 AT3G49220 31.073 177 102 7 18 189 117 278 2.08e-15 73.9
MS.gene78072.t1 AT3G49220 31.073 177 102 7 18 189 117 278 3.68e-15 73.6
MS.gene78072.t1 AT3G49220 31.073 177 102 7 18 189 72 233 3.83e-15 73.6
MS.gene78072.t1 AT3G05610 28.750 160 104 4 37 193 58 210 5.60e-15 72.8
MS.gene78072.t1 AT5G27870 28.571 161 103 5 37 193 57 209 9.13e-15 72.4
MS.gene78072.t1 AT3G47670 31.056 161 101 5 37 192 113 268 1.18e-13 68.2
MS.gene78072.t1 AT3G14300 27.976 168 107 4 37 193 271 435 5.27e-12 64.3
MS.gene78072.t1 AT2G26450 28.994 169 99 4 37 197 109 264 2.87e-11 62.0

Find 40 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGATGCAAGAGTCACGTTT+AGG 0.288631 4.1:-64529599 None:intergenic
CCTCTCTTGGCTTCAGCCCA+TGG 0.324228 4.1:-64529662 None:intergenic
TGAATAATGTGTTTGATTGT+TGG 0.360872 4.1:-64529470 None:intergenic
TTCATAGCTGCAGCCTCTCT+TGG 0.381059 4.1:-64529675 None:intergenic
TGATGCAAGAGTCACGTTTA+GGG 0.405900 4.1:-64529598 None:intergenic
AAGCACGCGATTTGTTTGAA+TGG 0.408600 4.1:-64529562 None:intergenic
CAATGAGTGATGTACAAACT+TGG 0.417018 4.1:+64529790 MS.gene78072:CDS
TCAATTGACTAGCAATGCTT+TGG 0.428416 4.1:+64529920 MS.gene78072:CDS
GCGATTTGTTTGAATGGAAT+CGG 0.429201 4.1:-64529556 None:intergenic
AATGTGTTTGATTGTTGGTA+TGG 0.433048 4.1:-64529465 None:intergenic
GGTATGGTCTTTCAATTGCT+TGG 0.442357 4.1:-64529449 None:intergenic
TTGGGTCAGTGCCGCTTTGA+CGG 0.448660 4.1:+64529809 MS.gene78072:CDS
AAGAGAGGCTGCAGCTATGA+AGG 0.454048 4.1:+64529677 MS.gene78072:CDS
TGGAATCGGCGTGCTTCACT+AGG 0.463179 4.1:-64529542 None:intergenic
TCGGTGAAATGAGTCGCCTT+AGG 0.484339 4.1:+64529748 MS.gene78072:CDS
ACTCGAAATTTGAAGTCCTA+AGG 0.502920 4.1:-64529764 None:intergenic
ACTGTTGTCTGAACATTACC+CGG 0.509996 4.1:-64529873 None:intergenic
AGGGAGGTGTAGCATAGTCT+TGG 0.512506 4.1:-64529522 None:intergenic
ATTCGAAGAGATTAATGCCC+CGG 0.519303 4.1:+64529854 MS.gene78072:CDS
GATGAACTACGAAGGTCTAT+CGG 0.538573 4.1:+64529729 MS.gene78072:CDS
TCAACTCTCTCGAAAAGCCA+TGG 0.561307 4.1:+64529645 MS.gene78072:CDS
CTGTTGTCTGAACATTACCC+GGG 0.565359 4.1:-64529872 None:intergenic
GCATAGTCTTGGATAAGTTG+TGG 0.573599 4.1:-64529511 None:intergenic
AATGAGTGATGTACAAACTT+GGG 0.584779 4.1:+64529791 MS.gene78072:CDS
TTCGAAGAGATTAATGCCCC+GGG 0.592913 4.1:+64529855 MS.gene78072:CDS
CAACTCTCTCGAAAAGCCAT+GGG 0.604166 4.1:+64529646 MS.gene78072:CDS
AATGTTCAGACAACAGTGAG+AGG 0.607570 4.1:+64529879 MS.gene78072:CDS
TGCATCAGCGAAATCAACCT+CGG 0.612610 4.1:+64529614 MS.gene78072:CDS
AGAGTGTGTAATGAAACTAA+AGG 0.619326 4.1:-64529424 None:intergenic
ATCGGCGTGCTTCACTAGGG+AGG 0.622040 4.1:-64529538 None:intergenic
CCATGGGCTGAAGCCAAGAG+AGG 0.628752 4.1:+64529662 MS.gene78072:CDS
GGAATCGGCGTGCTTCACTA+GGG 0.632856 4.1:-64529541 None:intergenic
ATTAATCTCTTCGAATCCGT+CGG 0.641331 4.1:-64529847 None:intergenic
GATGAGAGTACTTGTACCGA+CGG 0.647497 4.1:+64529831 MS.gene78072:CDS
AGACCTTCGTAGTTCATCAA+CGG 0.656485 4.1:-64529724 None:intergenic
GAGAGTTGATATCACAGCCG+AGG 0.662740 4.1:-64529631 None:intergenic
ATGTTCAGACAACAGTGAGA+GGG 0.673943 4.1:+64529880 MS.gene78072:CDS
AGTACTCTCATCCGTCAAAG+CGG 0.677243 4.1:-64529820 None:intergenic
TGTTGTCTGAACATTACCCG+GGG 0.730077 4.1:-64529871 None:intergenic
ACTCCGTTGATGAACTACGA+AGG 0.736509 4.1:+64529721 MS.gene78072:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAATAATGTGTTTGATTGT+TGG - chr4.1:64529473-64529492 None:intergenic 25.0%
AATGAGTGATGTACAAACTT+GGG + chr4.1:64529791-64529810 MS.gene78072:CDS 30.0%
AATGTGTTTGATTGTTGGTA+TGG - chr4.1:64529468-64529487 None:intergenic 30.0%
AGAGTGTGTAATGAAACTAA+AGG - chr4.1:64529427-64529446 None:intergenic 30.0%
ATTAATCTCTTCGAATCCGT+CGG - chr4.1:64529850-64529869 None:intergenic 35.0%
CAATGAGTGATGTACAAACT+TGG + chr4.1:64529790-64529809 MS.gene78072:CDS 35.0%
TCAATTGACTAGCAATGCTT+TGG + chr4.1:64529920-64529939 MS.gene78072:CDS 35.0%
! ACTCGAAATTTGAAGTCCTA+AGG - chr4.1:64529767-64529786 None:intergenic 35.0%
! GCGATTTGTTTGAATGGAAT+CGG - chr4.1:64529559-64529578 None:intergenic 35.0%
AATGTTCAGACAACAGTGAG+AGG + chr4.1:64529879-64529898 MS.gene78072:CDS 40.0%
ACTGTTGTCTGAACATTACC+CGG - chr4.1:64529876-64529895 None:intergenic 40.0%
AGACCTTCGTAGTTCATCAA+CGG - chr4.1:64529727-64529746 None:intergenic 40.0%
ATGTTCAGACAACAGTGAGA+GGG + chr4.1:64529880-64529899 MS.gene78072:CDS 40.0%
ATTCGAAGAGATTAATGCCC+CGG + chr4.1:64529854-64529873 MS.gene78072:CDS 40.0%
GATGAACTACGAAGGTCTAT+CGG + chr4.1:64529729-64529748 MS.gene78072:CDS 40.0%
GGTATGGTCTTTCAATTGCT+TGG - chr4.1:64529452-64529471 None:intergenic 40.0%
TGATGCAAGAGTCACGTTTA+GGG - chr4.1:64529601-64529620 None:intergenic 40.0%
! AAGCACGCGATTTGTTTGAA+TGG - chr4.1:64529565-64529584 None:intergenic 40.0%
! GCATAGTCTTGGATAAGTTG+TGG - chr4.1:64529514-64529533 None:intergenic 40.0%
AGTACTCTCATCCGTCAAAG+CGG - chr4.1:64529823-64529842 None:intergenic 45.0%
CAACTCTCTCGAAAAGCCAT+GGG + chr4.1:64529646-64529665 MS.gene78072:CDS 45.0%
CTGATGCAAGAGTCACGTTT+AGG - chr4.1:64529602-64529621 None:intergenic 45.0%
CTGTTGTCTGAACATTACCC+GGG - chr4.1:64529875-64529894 None:intergenic 45.0%
TCAACTCTCTCGAAAAGCCA+TGG + chr4.1:64529645-64529664 MS.gene78072:CDS 45.0%
TGCATCAGCGAAATCAACCT+CGG + chr4.1:64529614-64529633 MS.gene78072:CDS 45.0%
TGTTGTCTGAACATTACCCG+GGG - chr4.1:64529874-64529893 None:intergenic 45.0%
TTCGAAGAGATTAATGCCCC+GGG + chr4.1:64529855-64529874 MS.gene78072:CDS 45.0%
! ACTCCGTTGATGAACTACGA+AGG + chr4.1:64529721-64529740 MS.gene78072:CDS 45.0%
! TCGCGTGCTTTTAACATGCA+CGG + chr4.1:64529575-64529594 MS.gene78072:CDS 45.0%
!! GATGAGAGTACTTGTACCGA+CGG + chr4.1:64529831-64529850 MS.gene78072:CDS 45.0%
AAGAGAGGCTGCAGCTATGA+AGG + chr4.1:64529677-64529696 MS.gene78072:CDS 50.0%
TCGGTGAAATGAGTCGCCTT+AGG + chr4.1:64529748-64529767 MS.gene78072:CDS 50.0%
TTCATAGCTGCAGCCTCTCT+TGG - chr4.1:64529678-64529697 None:intergenic 50.0%
! AGGGAGGTGTAGCATAGTCT+TGG - chr4.1:64529525-64529544 None:intergenic 50.0%
!! GAGAGTTGATATCACAGCCG+AGG - chr4.1:64529634-64529653 None:intergenic 50.0%
GGAATCGGCGTGCTTCACTA+GGG - chr4.1:64529544-64529563 None:intergenic 55.0%
TGGAATCGGCGTGCTTCACT+AGG - chr4.1:64529545-64529564 None:intergenic 55.0%
!! TTGGGTCAGTGCCGCTTTGA+CGG + chr4.1:64529809-64529828 MS.gene78072:CDS 55.0%
ATCGGCGTGCTTCACTAGGG+AGG - chr4.1:64529541-64529560 None:intergenic 60.0%
CCTCTCTTGGCTTCAGCCCA+TGG - chr4.1:64529665-64529684 None:intergenic 60.0%
! CCATGGGCTGAAGCCAAGAG+AGG + chr4.1:64529662-64529681 MS.gene78072:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 64529384 64529977 64529384 ID=MS.gene78072
chr4.1 mRNA 64529384 64529977 64529384 ID=MS.gene78072.t1;Parent=MS.gene78072
chr4.1 exon 64529384 64529977 64529384 ID=MS.gene78072.t1.exon1;Parent=MS.gene78072.t1
chr4.1 CDS 64529384 64529977 64529384 ID=cds.MS.gene78072.t1;Parent=MS.gene78072.t1
Gene Sequence

>MS.gene78072

ATGGAGGCTTTTTCTTCAAAGATCATTCTAATAATTTTTGCCTTTAGTTTCATTACACACTCTATCCAAGCAATTGAAAGACCATACCAACAATCAAACACATTATTCATTAAAAATTCTTGCAGCTCCACAACTTATCCAAGACTATGCTACACCTCCCTAGTGAAGCACGCCGATTCCATTCAAACAAATCGCGTGCTTTTAACATGCACGGCCCTAAACGTGACTCTTGCATCAGCGAAATCAACCTCGGCTGTGATATCAACTCTCTCGAAAAGCCATGGGCTGAAGCCAAGAGAGGCTGCAGCTATGAAGGATTGCGTTGAAGTGCTGAGTGACTCCGTTGATGAACTACGAAGGTCTATCGGTGAAATGAGTCGCCTTAGGACTTCAAATTTCGAGTTAACAATGAGTGATGTACAAACTTGGGTCAGTGCCGCTTTGACGGATGAGAGTACTTGTACCGACGGATTCGAAGAGATTAATGCCCCGGGTAATGTTCAGACAACAGTGAGAGGGAAAATTGTGCAAGTAGCTCAATTGACTAGCAATGCTTTGGCTTTGATAAATAAACTTGCTACATCACATAGTTAA
Protein sequence

>MS.gene78072.t1

MEAFSSKIILIIFAFSFITHSIQAIERPYQQSNTLFIKNSCSSTTYPRLCYTSLVKHADSIQTNRVLLTCTALNVTLASAKSTSAVISTLSKSHGLKPREAAAMKDCVEVLSDSVDELRRSIGEMSRLRTSNFELTMSDVQTWVSAALTDESTCTDGFEEINAPGNVQTTVRGKIVQVAQLTSNALALINKLATSHS