AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene045669

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045669.t1 MTR_4g035905 94.388 196 11 0 1 196 1 196 8.03e-137 380
MS.gene045669.t1 MTR_4g035870 88.265 196 23 0 1 196 1 196 1.93e-126 354
MS.gene045669.t1 MTR_4g035880 87.245 196 25 0 1 196 1 196 3.20e-124 348
MS.gene045669.t1 MTR_3g008840 48.485 165 83 1 34 196 23 187 9.83e-48 154
MS.gene045669.t1 MTR_3g008820 47.273 165 85 1 34 196 22 186 6.19e-47 152
MS.gene045669.t1 MTR_5g012000 42.683 164 91 1 36 196 48 211 2.36e-43 144
MS.gene045669.t1 MTR_4g101760 38.857 175 104 1 25 196 28 202 3.64e-39 133
MS.gene045669.t1 MTR_4g120825 40.000 170 88 4 36 193 35 202 9.85e-36 124
MS.gene045669.t1 MTR_4g120830 39.412 170 89 4 36 193 35 202 2.71e-35 123
MS.gene045669.t1 MTR_8g104765 39.412 170 89 4 36 193 44 211 9.35e-35 122
MS.gene045669.t1 MTR_3g008760 37.107 159 97 2 36 191 66 224 1.88e-31 114
MS.gene045669.t1 MTR_4g035855 35.204 196 116 3 8 193 8 202 3.43e-31 112
MS.gene045669.t1 MTR_2g043560 40.000 165 85 4 36 195 34 189 4.41e-31 112
MS.gene045669.t1 MTR_7g108790 35.185 162 97 2 37 195 34 190 2.08e-30 110
MS.gene045669.t1 MTR_1g088540 39.516 124 73 1 72 195 22 143 7.41e-27 100
MS.gene045669.t1 MTR_4g124855 32.075 212 113 5 1 195 2 199 1.28e-24 96.3
MS.gene045669.t1 MTR_4g025610 36.628 172 96 4 36 196 32 201 3.92e-21 87.0
MS.gene045669.t1 MTR_4g025590 36.628 172 96 4 36 196 3 172 7.62e-21 85.5
MS.gene045669.t1 MTR_4g025550 35.176 199 110 6 10 196 10 201 8.01e-21 86.3
MS.gene045669.t1 MTR_4g025620 33.500 200 111 5 8 196 13 201 7.43e-20 83.6
MS.gene045669.t1 MTR_3g091380 31.868 182 107 4 19 189 59 234 1.87e-18 82.8
MS.gene045669.t1 MTR_1g008140 31.395 172 89 5 37 189 82 243 4.20e-16 76.3
MS.gene045669.t1 MTR_7g112590 28.571 168 98 5 37 195 59 213 8.79e-16 75.1
MS.gene045669.t1 MTR_8g023310 28.846 156 106 3 37 188 68 222 1.74e-15 74.3
MS.gene045669.t1 MTR_7g112580 38.182 110 55 4 87 192 94 194 1.02e-14 72.0
MS.gene045669.t1 MTR_0036s0140 25.543 184 124 4 8 189 49 221 2.44e-13 66.6
MS.gene045669.t1 MTR_8g023150 31.928 166 92 5 37 192 77 231 4.82e-13 67.4
MS.gene045669.t1 MTR_1g083510 26.250 160 108 4 37 193 56 208 3.66e-12 64.7
MS.gene045669.t1 MTR_7g108905 25.654 191 126 3 10 192 18 200 5.22e-12 64.3
MS.gene045669.t1 MTR_8g104580 28.750 160 91 5 40 192 27 170 1.11e-11 63.2
MS.gene045669.t1 MTR_2g044810 31.098 164 101 6 37 197 41 195 3.44e-11 61.6
MS.gene045669.t1 MTR_2g044810 31.098 164 101 6 37 197 41 195 3.76e-11 61.6
MS.gene045669.t1 MTR_1g083470 27.329 161 107 4 37 193 58 212 4.43e-11 61.6
MS.gene045669.t1 MTR_1g083500 27.329 161 107 4 37 193 58 212 4.43e-11 61.6
MS.gene045669.t1 MTR_8g104655 28.125 160 92 5 40 192 35 178 5.35e-11 61.2
MS.gene045669.t1 MTR_4g005170 24.432 176 123 4 26 197 52 221 8.07e-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
MS.gene045669.t1 AT5G62360 58.642 162 66 1 36 197 43 203 1.33e-63 196
MS.gene045669.t1 AT1G62770 46.591 176 88 3 28 197 25 200 2.13e-44 147
MS.gene045669.t1 AT5G62350 47.273 165 83 1 36 196 38 202 9.99e-44 145
MS.gene045669.t1 AT1G62760 45.882 170 87 2 30 196 141 308 1.12e-41 143
MS.gene045669.t1 AT1G14890 41.026 195 102 4 9 195 28 217 2.27e-41 139
MS.gene045669.t1 AT4G25260 39.896 193 110 2 10 196 9 201 4.82e-41 138
MS.gene045669.t1 AT3G47380 44.848 165 87 1 36 196 38 202 3.26e-39 133
MS.gene045669.t1 AT2G01610 39.791 191 97 4 21 193 27 217 1.41e-38 132
MS.gene045669.t1 AT5G51520 38.265 196 108 5 9 192 8 202 4.35e-37 128
MS.gene045669.t1 AT4G25250 38.272 162 97 2 31 189 32 193 1.11e-36 127
MS.gene045669.t1 AT5G20740 36.316 190 111 3 8 192 9 193 4.31e-36 125
MS.gene045669.t1 AT5G20740 40.373 161 90 2 37 192 68 227 1.75e-35 125
MS.gene045669.t1 AT4G12390 44.578 166 87 1 36 196 39 204 8.85e-35 122
MS.gene045669.t1 AT1G70720 36.126 191 110 4 10 193 9 194 4.86e-32 115
MS.gene045669.t1 AT1G70720 36.126 191 110 4 10 193 21 206 5.39e-32 115
MS.gene045669.t1 AT1G23205 39.306 173 93 4 30 191 27 198 7.37e-29 107
MS.gene045669.t1 AT3G62820 32.086 187 118 5 11 193 9 190 5.37e-24 94.0
MS.gene045669.t1 AT2G47670 35.625 160 98 2 36 193 48 204 1.42e-22 90.9
MS.gene045669.t1 AT5G53370 34.416 154 96 3 37 189 111 260 2.25e-20 88.6
MS.gene045669.t1 AT5G53370 34.416 154 96 3 37 189 75 224 2.60e-20 88.2
MS.gene045669.t1 AT4G00080 32.738 168 93 6 36 189 35 196 9.53e-20 83.2
MS.gene045669.t1 AT1G53830 30.380 158 108 2 37 192 62 219 2.21e-19 85.5
MS.gene045669.t1 AT3G14310 29.412 170 116 4 26 192 48 216 1.15e-18 83.6
MS.gene045669.t1 AT3G49220 31.638 177 101 7 18 189 117 278 5.87e-16 75.5
MS.gene045669.t1 AT3G49220 31.638 177 101 7 18 189 72 233 1.03e-15 75.1
MS.gene045669.t1 AT3G49220 31.638 177 101 7 18 189 117 278 1.07e-15 75.1
MS.gene045669.t1 AT3G05610 28.125 160 105 4 37 193 58 210 7.94e-14 69.7
MS.gene045669.t1 AT5G27870 27.950 161 104 5 37 193 57 209 1.33e-13 68.9
MS.gene045669.t1 AT3G47670 30.435 161 102 5 37 192 113 268 4.29e-13 66.6
MS.gene045669.t1 AT3G14300 28.571 168 106 4 37 193 271 435 1.74e-12 65.9
MS.gene045669.t1 AT3G05620 24.631 203 126 7 9 192 7 201 8.59e-11 60.8

Find 39 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 4.3:-64323494 None:intergenic
CCTCTCTTGGCTTCAGCCCA+TGG 0.324228 4.3:-64323557 None:intergenic
TGAATAATGTGTTTGATTGT+TGG 0.360872 4.3:-64323365 None:intergenic
TTCATAGCTGCAGCCTCTCT+TGG 0.381059 4.3:-64323570 None:intergenic
TGATGCAAGAGTCACGTTTA+GGG 0.405900 4.3:-64323493 None:intergenic
AAGCACGCGATTTGTTTGAA+TGG 0.408600 4.3:-64323457 None:intergenic
CAATGAGTGATGTACAAACT+TGG 0.417018 4.3:+64323685 MS.gene045669:CDS
TCAATTGACTAGCAATGCTT+TGG 0.428416 4.3:+64323815 MS.gene045669:CDS
AATGTGTTTGATTGTTGGTA+TGG 0.433048 4.3:-64323360 None:intergenic
ACTATTGTCTGAACGTTACC+CGG 0.435716 4.3:-64323768 None:intergenic
GCGATTTGTTTGAATGGAAT+CGG 0.438794 4.3:-64323451 None:intergenic
GGTATGGTCTTTCAATTGCT+TGG 0.442357 4.3:-64323344 None:intergenic
TTGGGTCAGTGCCGCTTTGA+CGG 0.448660 4.3:+64323704 MS.gene045669:CDS
AAGAGAGGCTGCAGCTATGA+AGG 0.454048 4.3:+64323572 MS.gene045669:CDS
TGGAATCGGCATGCTTCACT+AGG 0.461647 4.3:-64323437 None:intergenic
TCGGTGAAATGAGTCGCCTT+AGG 0.484339 4.3:+64323643 MS.gene045669:CDS
ACTCGAAATTTGAAGTCCTA+AGG 0.502920 4.3:-64323659 None:intergenic
CTATTGTCTGAACGTTACCC+GGG 0.505053 4.3:-64323767 None:intergenic
AGGGAGGTGTAGCATAGTCT+TGG 0.512506 4.3:-64323417 None:intergenic
ATTCGATGAGATTAATGCCC+CGG 0.519303 4.3:+64323749 MS.gene045669:CDS
GATGAACTACGAAGGTCTAT+CGG 0.538573 4.3:+64323624 MS.gene045669:CDS
TCAACTCTCTCGAAAAGCCA+TGG 0.561307 4.3:+64323540 MS.gene045669:CDS
TTCGATGAGATTAATGCCCC+GGG 0.571739 4.3:+64323750 MS.gene045669:CDS
AATGAGTGATGTACAAACTT+GGG 0.584779 4.3:+64323686 MS.gene045669:CDS
CAACTCTCTCGAAAAGCCAT+GGG 0.604166 4.3:+64323541 MS.gene045669:CDS
TGCATCAGCGAAATCAACCT+CGG 0.612610 4.3:+64323509 MS.gene045669:CDS
AGAGTGTGTAATGAAACTAA+AGG 0.619326 4.3:-64323319 None:intergenic
ATCGGCATGCTTCACTAGGG+AGG 0.623272 4.3:-64323433 None:intergenic
CCATGGGCTGAAGCCAAGAG+AGG 0.628752 4.3:+64323557 MS.gene045669:CDS
GGAATCGGCATGCTTCACTA+GGG 0.640072 4.3:-64323436 None:intergenic
AACGTTCAGACAATAGTGAG+AGG 0.646752 4.3:+64323774 MS.gene045669:CDS
GATGAGAGTACTTGTACCGA+CGG 0.647497 4.3:+64323726 MS.gene045669:CDS
AGACCTTCGTAGTTCATCAA+CGG 0.656485 4.3:-64323619 None:intergenic
GAGAGTTGATATCACAGCCG+AGG 0.662740 4.3:-64323526 None:intergenic
ATTAATCTCATCGAATCCGT+CGG 0.670402 4.3:-64323742 None:intergenic
ACGTTCAGACAATAGTGAGA+GGG 0.675715 4.3:+64323775 MS.gene045669:CDS
AGTACTCTCATCCGTCAAAG+CGG 0.677243 4.3:-64323715 None:intergenic
TATTGTCTGAACGTTACCCG+GGG 0.732517 4.3:-64323766 None:intergenic
ACTCCGTTGATGAACTACGA+AGG 0.736509 4.3:+64323616 MS.gene045669:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAGGCAAAAATTATTAGA+AGG - chr4.3:64323305-64323324 None:intergenic 20.0%
! TGAATAATGTGTTTGATTGT+TGG - chr4.3:64323368-64323387 None:intergenic 25.0%
AATGAGTGATGTACAAACTT+GGG + chr4.3:64323686-64323705 MS.gene045669:CDS 30.0%
AATGTGTTTGATTGTTGGTA+TGG - chr4.3:64323363-64323382 None:intergenic 30.0%
AGAGTGTGTAATGAAACTAA+AGG - chr4.3:64323322-64323341 None:intergenic 30.0%
ATTAATCTCATCGAATCCGT+CGG - chr4.3:64323745-64323764 None:intergenic 35.0%
CAATGAGTGATGTACAAACT+TGG + chr4.3:64323685-64323704 MS.gene045669:CDS 35.0%
TCAATTGACTAGCAATGCTT+TGG + chr4.3:64323815-64323834 MS.gene045669:CDS 35.0%
! ACTCGAAATTTGAAGTCCTA+AGG - chr4.3:64323662-64323681 None:intergenic 35.0%
! GCGATTTGTTTGAATGGAAT+CGG - chr4.3:64323454-64323473 None:intergenic 35.0%
AACGTTCAGACAATAGTGAG+AGG + chr4.3:64323774-64323793 MS.gene045669:CDS 40.0%
ACGTTCAGACAATAGTGAGA+GGG + chr4.3:64323775-64323794 MS.gene045669:CDS 40.0%
ACTATTGTCTGAACGTTACC+CGG - chr4.3:64323771-64323790 None:intergenic 40.0%
AGACCTTCGTAGTTCATCAA+CGG - chr4.3:64323622-64323641 None:intergenic 40.0%
ATTCGATGAGATTAATGCCC+CGG + chr4.3:64323749-64323768 MS.gene045669:CDS 40.0%
GATGAACTACGAAGGTCTAT+CGG + chr4.3:64323624-64323643 MS.gene045669:CDS 40.0%
GGTATGGTCTTTCAATTGCT+TGG - chr4.3:64323347-64323366 None:intergenic 40.0%
TGATGCAAGAGTCACGTTTA+GGG - chr4.3:64323496-64323515 None:intergenic 40.0%
! AAGCACGCGATTTGTTTGAA+TGG - chr4.3:64323460-64323479 None:intergenic 40.0%
AGTACTCTCATCCGTCAAAG+CGG - chr4.3:64323718-64323737 None:intergenic 45.0%
CAACTCTCTCGAAAAGCCAT+GGG + chr4.3:64323541-64323560 MS.gene045669:CDS 45.0%
CTATTGTCTGAACGTTACCC+GGG - chr4.3:64323770-64323789 None:intergenic 45.0%
CTGATGCAAGAGTCACGTTT+AGG - chr4.3:64323497-64323516 None:intergenic 45.0%
TATTGTCTGAACGTTACCCG+GGG - chr4.3:64323769-64323788 None:intergenic 45.0%
TCAACTCTCTCGAAAAGCCA+TGG + chr4.3:64323540-64323559 MS.gene045669:CDS 45.0%
TGCATCAGCGAAATCAACCT+CGG + chr4.3:64323509-64323528 MS.gene045669:CDS 45.0%
TTCGATGAGATTAATGCCCC+GGG + chr4.3:64323750-64323769 MS.gene045669:CDS 45.0%
! ACTCCGTTGATGAACTACGA+AGG + chr4.3:64323616-64323635 MS.gene045669:CDS 45.0%
! TCGCGTGCTTTTAACATGCA+CGG + chr4.3:64323470-64323489 MS.gene045669:CDS 45.0%
!! GATGAGAGTACTTGTACCGA+CGG + chr4.3:64323726-64323745 MS.gene045669:CDS 45.0%
AAGAGAGGCTGCAGCTATGA+AGG + chr4.3:64323572-64323591 MS.gene045669:CDS 50.0%
GGAATCGGCATGCTTCACTA+GGG - chr4.3:64323439-64323458 None:intergenic 50.0%
TCGGTGAAATGAGTCGCCTT+AGG + chr4.3:64323643-64323662 MS.gene045669:CDS 50.0%
TGGAATCGGCATGCTTCACT+AGG - chr4.3:64323440-64323459 None:intergenic 50.0%
TTCATAGCTGCAGCCTCTCT+TGG - chr4.3:64323573-64323592 None:intergenic 50.0%
! AGGGAGGTGTAGCATAGTCT+TGG - chr4.3:64323420-64323439 None:intergenic 50.0%
!! GAGAGTTGATATCACAGCCG+AGG - chr4.3:64323529-64323548 None:intergenic 50.0%
ATCGGCATGCTTCACTAGGG+AGG - chr4.3:64323436-64323455 None:intergenic 55.0%
!! TTGGGTCAGTGCCGCTTTGA+CGG + chr4.3:64323704-64323723 MS.gene045669:CDS 55.0%
CCTCTCTTGGCTTCAGCCCA+TGG - chr4.3:64323560-64323579 None:intergenic 60.0%
! CCATGGGCTGAAGCCAAGAG+AGG + chr4.3:64323557-64323576 MS.gene045669:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 64323279 64323872 64323279 ID=MS.gene045669
chr4.3 mRNA 64323279 64323872 64323279 ID=MS.gene045669.t1;Parent=MS.gene045669
chr4.3 exon 64323279 64323872 64323279 ID=MS.gene045669.t1.exon1;Parent=MS.gene045669.t1
chr4.3 CDS 64323279 64323872 64323279 ID=cds.MS.gene045669.t1;Parent=MS.gene045669.t1
Gene Sequence

>MS.gene045669

ATGGAGGCTTTTTCTTCAAAGATCCTTCTAATAATTTTTGCCTTTAGTTTCATTACACACTCTATCCAAGCAATTGAAAGACCATACCAACAATCAAACACATTATTCATTAAAAATTCTTGCAGCACTACAACTTATCCAAGACTATGCTACACCTCCCTAGTGAAGCATGCCGATTCCATTCAAACAAATCGCGTGCTTTTAACATGCACGGCCCTAAACGTGACTCTTGCATCAGCGAAATCAACCTCGGCTGTGATATCAACTCTCTCGAAAAGCCATGGGCTGAAGCCAAGAGAGGCTGCAGCTATGAAGGATTGCGTTGAAGTGCTGAGTGACTCCGTTGATGAACTACGAAGGTCTATCGGTGAAATGAGTCGCCTTAGGACTTCAAATTTCGAGTTAACAATGAGTGATGTACAAACTTGGGTCAGTGCCGCTTTGACGGATGAGAGTACTTGTACCGACGGATTCGATGAGATTAATGCCCCGGGTAACGTTCAGACAATAGTGAGAGGGAAAATTGTGCAAGTAGCTCAATTGACTAGCAATGCTTTGGCTTTGATAAATAAACTTGCTACATCACATAGTTAA
Protein sequence

>MS.gene045669.t1

MEAFSSKILLIIFAFSFITHSIQAIERPYQQSNTLFIKNSCSTTTYPRLCYTSLVKHADSIQTNRVLLTCTALNVTLASAKSTSAVISTLSKSHGLKPREAAAMKDCVEVLSDSVDELRRSIGEMSRLRTSNFELTMSDVQTWVSAALTDESTCTDGFDEINAPGNVQTIVRGKIVQVAQLTSNALALINKLATSHS