AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043069

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043069.t1 MTR_4g031910 73.077 234 46 2 1 222 1 229 2.56e-115 328
MS.gene043069.t1 MTR_4g032290 69.262 244 40 2 1 222 1 231 5.59e-110 315
MS.gene043069.t1 MTR_4g032620 58.009 231 88 1 1 222 1 231 4.37e-94 275
MS.gene043069.t1 MTR_8g036130 57.085 247 81 4 1 222 1 247 3.43e-89 263
MS.gene043069.t1 MTR_4g032260 80.255 157 31 0 1 157 1 157 2.45e-81 240
MS.gene043069.t1 MTR_3g065100 49.793 241 96 4 1 219 1 238 1.69e-66 205
MS.gene043069.t1 MTR_3g466980 46.121 232 100 5 1 218 1 221 7.87e-65 200
MS.gene043069.t1 MTR_2g035610 72.131 122 34 0 1 122 1 122 6.33e-51 161
MS.gene043069.t1 MTR_4g032270 56.204 137 45 2 94 222 2 131 1.70e-46 150
MS.gene043069.t1 MTR_5g075380 47.742 155 80 1 1 155 1 154 6.12e-46 150
MS.gene043069.t1 MTR_3g466830 49.007 151 76 1 3 153 2 151 1.14e-45 149
MS.gene043069.t1 MTR_4g063790 45.455 154 84 0 1 154 1 154 1.70e-45 149
MS.gene043069.t1 MTR_3g467080 43.590 156 88 0 1 156 1 156 3.04e-43 143
MS.gene043069.t1 MTR_3g031100 35.268 224 133 4 1 219 1 217 6.85e-43 145
MS.gene043069.t1 MTR_5g047580 46.154 156 82 2 1 156 1 154 6.25e-41 137
MS.gene043069.t1 MTR_3g466890 46.053 152 81 1 3 154 2 152 1.22e-40 136
MS.gene043069.t1 MTR_2g016210 39.560 182 108 2 1 180 1 182 1.29e-40 139
MS.gene043069.t1 MTR_1g077390 42.308 156 88 2 1 156 1 154 2.80e-37 128
MS.gene043069.t1 MTR_1g090783 42.208 154 87 2 3 156 2 153 1.48e-35 123
MS.gene043069.t1 MTR_3g465410 44.444 126 70 0 29 154 1 126 6.64e-35 121
MS.gene043069.t1 MTR_1g077320 44.231 156 85 2 1 156 1 154 8.06e-35 121
MS.gene043069.t1 MTR_7g011950 43.590 156 86 2 1 156 1 154 2.47e-34 120
MS.gene043069.t1 MTR_4g028720 44.231 156 85 2 1 156 1 154 3.57e-34 120
MS.gene043069.t1 MTR_1g084950 44.872 156 84 2 1 156 1 154 1.78e-33 118
MS.gene043069.t1 MTR_1g090710 38.961 154 93 1 1 154 1 153 2.73e-33 117
MS.gene043069.t1 MTR_1g090697 40.667 150 87 2 1 150 1 148 9.66e-33 116
MS.gene043069.t1 MTR_1g077300 43.590 156 84 2 1 156 1 152 2.92e-32 115
MS.gene043069.t1 MTR_4g028800 77.143 70 14 1 1 70 1 68 4.16e-31 109
MS.gene043069.t1 MTR_3g031240 34.615 156 102 0 1 156 1 156 1.08e-30 112
MS.gene043069.t1 MTR_7g055800 50.427 117 30 2 1 117 1 89 4.36e-29 104
MS.gene043069.t1 MTR_3g466900 41.463 123 71 1 32 154 2 123 1.60e-28 104
MS.gene043069.t1 MTR_2g035580 38.217 157 96 1 1 157 1 156 3.68e-26 99.4
MS.gene043069.t1 MTR_3g466930 39.024 123 74 1 32 154 2 123 4.24e-26 98.6
MS.gene043069.t1 MTR_7g055790 52.252 111 35 1 1 111 59 151 5.74e-26 98.6
MS.gene043069.t1 MTR_7g106510 39.370 127 77 0 3 129 6 132 1.31e-24 101
MS.gene043069.t1 MTR_4g019670 40.157 127 76 0 3 129 6 132 2.26e-24 100
MS.gene043069.t1 MTR_7g055940 49.057 106 26 2 1 106 1 78 8.92e-24 90.9
MS.gene043069.t1 MTR_5g047560 36.538 156 81 3 1 156 1 138 3.45e-23 91.3
MS.gene043069.t1 MTR_3g093900 31.690 142 97 0 3 144 6 147 1.06e-21 93.2
MS.gene043069.t1 MTR_2g035590 58.025 81 34 0 74 154 1 81 1.55e-19 80.5
MS.gene043069.t1 MTR_1g114730 31.858 113 70 3 1 107 1 112 2.88e-13 68.2
MS.gene043069.t1 MTR_6g018920 32.743 113 69 4 1 107 1 112 4.22e-13 67.8
MS.gene043069.t1 MTR_6g005450 33.628 113 68 4 1 107 1 112 2.76e-12 65.5
MS.gene043069.t1 MTR_4g084780 38.739 111 52 2 74 168 1 111 1.20e-11 60.8
MS.gene043069.t1 MTR_6g005440 35.398 113 66 3 1 107 1 112 3.49e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043069.t1 AT5G48670 55.844 154 67 1 1 154 1 153 1.84e-46 156
MS.gene043069.t1 AT1G65330 42.246 187 94 3 3 176 2 187 8.49e-41 140
MS.gene043069.t1 AT1G65300 41.436 181 97 2 3 175 2 181 1.27e-40 140
MS.gene043069.t1 AT5G26630 44.503 191 95 2 1 181 1 190 1.18e-39 136
MS.gene043069.t1 AT5G26650 36.667 210 114 4 5 204 3 203 1.72e-35 129
MS.gene043069.t1 AT5G27960 40.476 168 89 3 5 162 3 169 5.02e-35 127
MS.gene043069.t1 AT1G31630 36.905 168 95 3 3 161 2 167 4.92e-34 124
MS.gene043069.t1 AT1G31640 39.735 151 89 2 3 153 2 150 3.04e-32 122
MS.gene043069.t1 AT3G05860 37.975 158 97 1 1 158 1 157 6.30e-31 113
MS.gene043069.t1 AT3G05860 37.975 158 97 1 1 158 1 157 1.10e-30 114
MS.gene043069.t1 AT3G05860 37.975 158 97 1 1 158 1 157 1.25e-30 114
MS.gene043069.t1 AT5G27810 55.914 93 41 0 29 121 1 93 2.33e-30 108
MS.gene043069.t1 AT2G28700 37.423 163 97 2 1 161 1 160 2.25e-29 112
MS.gene043069.t1 AT1G22590 32.099 162 106 1 1 162 1 158 2.24e-26 100
MS.gene043069.t1 AT5G26580 34.416 154 86 2 1 154 1 139 1.17e-23 97.1
MS.gene043069.t1 AT5G06500 35.669 157 99 2 1 157 1 155 5.83e-23 93.2
MS.gene043069.t1 AT2G40210 37.984 129 79 1 1 129 1 128 1.26e-17 80.9
MS.gene043069.t1 AT5G58890 37.795 127 68 5 6 123 6 130 3.16e-15 73.2
MS.gene043069.t1 AT5G55690 42.308 78 38 2 1 71 1 78 2.40e-12 65.1
MS.gene043069.t1 AT5G55690 42.308 78 38 2 1 71 1 78 2.40e-12 65.1
MS.gene043069.t1 AT5G27090 34.444 90 58 1 7 95 23 112 6.90e-11 59.7
MS.gene043069.t1 AT5G27944 39.726 73 43 1 24 95 41 113 9.89e-11 59.7

Find 57 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4.2:-73236517 MS.gene043069:CDS
CCCTTTGGTGAGATCAATTA+TGG 0.234667 4.2:-73236200 MS.gene043069:CDS
TACCAATGTCCTTCAAATTA+TGG 0.254451 4.2:+73236390 None:intergenic
ATAATTTCATCATCATTAAT+AGG 0.285530 4.2:+73236278 None:intergenic
GTGAGATCAATTATGGAGTT+TGG 0.309548 4.2:-73236193 MS.gene043069:CDS
AACAAAGGGTCTATTGAAAA+AGG 0.314581 4.2:-73236750 MS.gene043069:CDS
AGCATCTAGGAGTGAGGAAA+TGG 0.344298 4.2:-73236330 MS.gene043069:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4.2:-73236670 MS.gene043069:CDS
ATCCTTCAAGGTAGTAAATC+AGG 0.374586 4.2:+73236170 None:intergenic
TATGCAAAGTCAATTATTGA+TGG 0.385590 4.2:-73236258 MS.gene043069:CDS
GAAGGACATTGGTAGACGTT+TGG 0.410243 4.2:-73236381 MS.gene043069:CDS
CTAGATGCTGTTGGAGGTGG+TGG 0.417295 4.2:+73236344 None:intergenic
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4.2:-73236516 MS.gene043069:CDS
GGCCTGATTTACTACCTTGA+AGG 0.422090 4.2:-73236172 None:intergenic
AGTGAGGAAATGGGAATTGT+GGG 0.443118 4.2:-73236320 MS.gene043069:CDS
GTTGATTGACCATAATTTGA+AGG 0.445081 4.2:-73236399 MS.gene043069:CDS
TTGTGGGTCATGGCCATGTT+GGG 0.452922 4.2:-73236304 MS.gene043069:CDS
CACAACCATGGCTAGAAGTA+AGG 0.457305 4.2:-73236828 None:intergenic
TCTGGTGAAGGCCAAATCTC+AGG 0.467267 4.2:+73236659 None:intergenic
CTCATAAGAGCCATACACTA+TGG 0.467809 4.2:+73236688 None:intergenic
ATTGTGGGTCATGGCCATGT+TGG 0.468248 4.2:-73236305 MS.gene043069:CDS
CTCCTAGATGCTGTTGGAGG+TGG 0.476689 4.2:+73236341 None:intergenic
TCAATTATTGATGGACTCAA+TGG 0.482426 4.2:-73236249 MS.gene043069:CDS
TTGATTTGAGTTATCTTACT+TGG 0.482489 4.2:-73236421 MS.gene043069:CDS
TCCTCACTCCTAGATGCTGT+TGG 0.486555 4.2:+73236335 None:intergenic
TGCAGCATCATTGACAATGA+AGG 0.502295 4.2:+73236796 None:intergenic
TTTGTGTCAAGAAAGTCTCT+TGG 0.512375 4.2:+73236567 None:intergenic
GATGCTGTTGGAGGTGGTGG+TGG 0.513228 4.2:+73236347 None:intergenic
GAGTGAGGAAATGGGAATTG+TGG 0.516317 4.2:-73236321 MS.gene043069:CDS
GACCATAATTTGAAGGACAT+TGG 0.517963 4.2:-73236392 MS.gene043069:CDS
GGACATTGGTAGACGTTTGG+CGG 0.524285 4.2:-73236378 MS.gene043069:CDS
TCACTCCTAGATGCTGTTGG+AGG 0.527908 4.2:+73236338 None:intergenic
CACCACCTCCAACAGCATCT+AGG 0.540352 4.2:-73236343 MS.gene043069:CDS
ATGTCTCATTGTCTCAATGA+AGG 0.542205 4.2:-73236473 MS.gene043069:CDS
GCATCTAGGAGTGAGGAAAT+GGG 0.544227 4.2:-73236329 MS.gene043069:CDS
CCATAATTGATCTCACCAAA+GGG 0.558369 4.2:+73236200 None:intergenic
GAAGCCTGTGCCATAGTGTA+TGG 0.560968 4.2:-73236698 MS.gene043069:CDS
GAGATTTGGCCTTCACCAGA+GGG 0.565461 4.2:-73236656 MS.gene043069:CDS
TTTAACCTTACTTCTAGCCA+TGG 0.572129 4.2:+73236823 None:intergenic
GATTTGGCCTTCACCAGAGG+GGG 0.573799 4.2:-73236654 MS.gene043069:CDS
TCCATAATTGATCTCACCAA+AGG 0.580970 4.2:+73236199 None:intergenic
GTGCACGAGACAGTGCCCTT+TGG 0.582311 4.2:-73236215 MS.gene043069:CDS
AAGAGACTTTCTTGACACAA+AGG 0.587821 4.2:-73236565 MS.gene043069:CDS
CATTAATAGGTATCCCAACA+TGG 0.589301 4.2:+73236291 None:intergenic
GAAGGCCAAATCTCAGGTTG+AGG 0.598100 4.2:+73236665 None:intergenic
ACAGGCTTCAATGCCACAGA+GGG 0.601811 4.2:+73236712 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4.2:-73236242 MS.gene043069:CDS
TGAGATTTGGCCTTCACCAG+AGG 0.614269 4.2:-73236657 MS.gene043069:CDS
GAAATGGGAATTGTGGGTCA+TGG 0.616732 4.2:-73236314 MS.gene043069:CDS
TCCAACAGCATCTAGGAGTG+AGG 0.643310 4.2:-73236336 MS.gene043069:CDS
AGATTTGGCCTTCACCAGAG+GGG 0.650878 4.2:-73236655 MS.gene043069:CDS
TCATTGTCAATGATGCTGCA+AGG 0.652548 4.2:-73236793 MS.gene043069:CDS
AGAGCCATACACTATGGCAC+AGG 0.656790 4.2:+73236694 None:intergenic
ATTATTGATGGACTCAATGG+TGG 0.666274 4.2:-73236246 MS.gene043069:CDS
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4.2:-73236725 MS.gene043069:CDS
TGTGCACGACAATATGTCAA+CGG 0.688304 4.2:-73236444 MS.gene043069:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4.2:+73236711 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATTTCATCATCATTAAT+AGG + chr4.2:73236721-73236740 None:intergenic 15.0%
!! AACATACAAAAAAAGAACAA+AGG - chr4.2:73236231-73236250 MS.gene043069:CDS 20.0%
!! ACATACAAAAAAAGAACAAA+GGG - chr4.2:73236232-73236251 MS.gene043069:CDS 20.0%
!! AGAAACAAAGAAAAGAAAAT+AGG - chr4.2:73236479-73236498 MS.gene043069:CDS 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG - chr4.2:73236480-73236499 MS.gene043069:CDS 20.0%
! TATGCAAAGTCAATTATTGA+TGG - chr4.2:73236738-73236757 MS.gene043069:CDS 25.0%
!! TTGATTTGAGTTATCTTACT+TGG - chr4.2:73236575-73236594 MS.gene043069:CDS 25.0%
AACAAAGGGTCTATTGAAAA+AGG - chr4.2:73236246-73236265 MS.gene043069:CDS 30.0%
GTTGATTGACCATAATTTGA+AGG - chr4.2:73236597-73236616 MS.gene043069:CDS 30.0%
TACCAATGTCCTTCAAATTA+TGG + chr4.2:73236609-73236628 None:intergenic 30.0%
!! TCAATTATTGATGGACTCAA+TGG - chr4.2:73236747-73236766 MS.gene043069:CDS 30.0%
AAGAGACTTTCTTGACACAA+AGG - chr4.2:73236431-73236450 MS.gene043069:CDS 35.0%
ATGTCTCATTGTCTCAATGA+AGG - chr4.2:73236523-73236542 MS.gene043069:CDS 35.0%
CATTAATAGGTATCCCAACA+TGG + chr4.2:73236708-73236727 None:intergenic 35.0%
CCATAATTGATCTCACCAAA+GGG + chr4.2:73236799-73236818 None:intergenic 35.0%
GACCATAATTTGAAGGACAT+TGG - chr4.2:73236604-73236623 MS.gene043069:CDS 35.0%
GTGAGATCAATTATGGAGTT+TGG - chr4.2:73236803-73236822 MS.gene043069:CDS 35.0%
TCCATAATTGATCTCACCAA+AGG + chr4.2:73236800-73236819 None:intergenic 35.0%
TTTGTGTCAAGAAAGTCTCT+TGG + chr4.2:73236432-73236451 None:intergenic 35.0%
! CTTGACACAAAGGATTTTGA+AGG - chr4.2:73236441-73236460 MS.gene043069:CDS 35.0%
!! ATTATTGATGGACTCAATGG+TGG - chr4.2:73236750-73236769 MS.gene043069:CDS 35.0%
!! TGAATTTTGAGAGCACAGAT+TGG + chr4.2:73236369-73236388 None:intergenic 35.0%
AGTGAGGAAATGGGAATTGT+GGG - chr4.2:73236676-73236695 MS.gene043069:CDS 40.0%
CCCTTTGGTGAGATCAATTA+TGG - chr4.2:73236796-73236815 MS.gene043069:CDS 40.0%
CTCATAAGAGCCATACACTA+TGG + chr4.2:73236311-73236330 None:intergenic 40.0%
TCATTGTCAATGATGCTGCA+AGG - chr4.2:73236203-73236222 MS.gene043069:CDS 40.0%
TGCAGCATCATTGACAATGA+AGG + chr4.2:73236203-73236222 None:intergenic 40.0%
TGTGCACGACAATATGTCAA+CGG - chr4.2:73236552-73236571 MS.gene043069:CDS 40.0%
AGCATCTAGGAGTGAGGAAA+TGG - chr4.2:73236666-73236685 MS.gene043069:CDS 45.0%
ATGAGCCTCAACCTGAGATT+TGG - chr4.2:73236326-73236345 MS.gene043069:CDS 45.0%
GAAATGGGAATTGTGGGTCA+TGG - chr4.2:73236682-73236701 MS.gene043069:CDS 45.0%
GAAGGACATTGGTAGACGTT+TGG - chr4.2:73236615-73236634 MS.gene043069:CDS 45.0%
GAGTGAGGAAATGGGAATTG+TGG - chr4.2:73236675-73236694 MS.gene043069:CDS 45.0%
GCATCTAGGAGTGAGGAAAT+GGG - chr4.2:73236667-73236686 MS.gene043069:CDS 45.0%
ACAGGCTTCAATGCCACAGA+GGG + chr4.2:73236287-73236306 None:intergenic 50.0%
AGAGCCATACACTATGGCAC+AGG + chr4.2:73236305-73236324 None:intergenic 50.0%
ATTGTGGGTCATGGCCATGT+TGG - chr4.2:73236691-73236710 MS.gene043069:CDS 50.0%
GAAGCCTGTGCCATAGTGTA+TGG - chr4.2:73236298-73236317 MS.gene043069:CDS 50.0%
GGACATTGGTAGACGTTTGG+CGG - chr4.2:73236618-73236637 MS.gene043069:CDS 50.0%
TCACTCCTAGATGCTGTTGG+AGG + chr4.2:73236661-73236680 None:intergenic 50.0%
TCCAACAGCATCTAGGAGTG+AGG - chr4.2:73236660-73236679 MS.gene043069:CDS 50.0%
TCCTCACTCCTAGATGCTGT+TGG + chr4.2:73236664-73236683 None:intergenic 50.0%
TCTGGTGAAGGCCAAATCTC+AGG + chr4.2:73236340-73236359 None:intergenic 50.0%
TTGTGGGTCATGGCCATGTT+GGG - chr4.2:73236692-73236711 MS.gene043069:CDS 50.0%
! AGATTTGGCCTTCACCAGAG+GGG - chr4.2:73236341-73236360 MS.gene043069:CDS 50.0%
! GAAGGCCAAATCTCAGGTTG+AGG + chr4.2:73236334-73236353 None:intergenic 50.0%
! GAGATTTGGCCTTCACCAGA+GGG - chr4.2:73236340-73236359 MS.gene043069:CDS 50.0%
! TGAGATTTGGCCTTCACCAG+AGG - chr4.2:73236339-73236358 MS.gene043069:CDS 50.0%
!! TTGATGGACTCAATGGTGGC+TGG - chr4.2:73236754-73236773 MS.gene043069:CDS 50.0%
CACAGGCTTCAATGCCACAG+AGG + chr4.2:73236288-73236307 None:intergenic 55.0%
CACCACCTCCAACAGCATCT+AGG - chr4.2:73236653-73236672 MS.gene043069:CDS 55.0%
CTAGATGCTGTTGGAGGTGG+TGG + chr4.2:73236655-73236674 None:intergenic 55.0%
CTCCTAGATGCTGTTGGAGG+TGG + chr4.2:73236658-73236677 None:intergenic 55.0%
GCTGAACTTAGCACCCTCTG+TGG - chr4.2:73236271-73236290 MS.gene043069:CDS 55.0%
! GATTTGGCCTTCACCAGAGG+GGG - chr4.2:73236342-73236361 MS.gene043069:CDS 55.0%
AGCACAGATTGGACCCCCTC+TGG + chr4.2:73236358-73236377 None:intergenic 60.0%
GATTGGACCCCCTCTGGTGA+AGG + chr4.2:73236352-73236371 None:intergenic 60.0%
GTGCACGAGACAGTGCCCTT+TGG - chr4.2:73236781-73236800 MS.gene043069:CDS 60.0%
! GATGCTGTTGGAGGTGGTGG+TGG + chr4.2:73236652-73236671 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 73236175 73236843 73236175 ID=MS.gene043069
chr4.2 mRNA 73236175 73236843 73236175 ID=MS.gene043069.t1;Parent=MS.gene043069
chr4.2 exon 73236175 73236843 73236175 ID=MS.gene043069.t1.exon1;Parent=MS.gene043069.t1
chr4.2 CDS 73236175 73236843 73236175 ID=cds.MS.gene043069.t1;Parent=MS.gene043069.t1
Gene Sequence

>MS.gene043069

ATGGCTAGAAGTAAGGTTAAACTCGCCTTCATTGTCAATGATGCTGCAAGGAAAGCAACATACAAAAAAAGAACAAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCTCTTATGAGCCTCAACCTGAGATTTGGCCTTCACCAGAGGGGGTCCAATCTGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGCTGAACCAAGAGACTTTCTTGACACAAAGGATTTTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGACAATACTCATGTCTCATTGTCTCAATGAAGGTAGAGTTGTGCACGACAATATGTCAACGGTTGATTTGAGTTATCTTACTTGGTTGATTGACCATAATTTGAAGGACATTGGTAGACGTTTGGCGGCAACAGTGCCACCACCACCTCCAACAGCATCTAGGAGTGAGGAAATGGGAATTGTGGGTCATGGCCATGTTGGGATACCTATTAATGATGATGAAATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCACGAGACAGTGCCCTTTGGTGAGATCAATTATGGAGTTTGGCCTGATTTACTACCTTGA
Protein sequence

>MS.gene043069.t1

MARSKVKLAFIVNDAARKATYKKRTKGLLKKVAELSTLCGIEACAIVYGSYEPQPEIWPSPEGVQSVLSKFMTMHEFQKCKKMLNQETFLTQRILKAEEKLKKQRKENREQEMTILMSHCLNEGRVVHDNMSTVDLSYLTWLIDHNLKDIGRRLAATVPPPPPTASRSEEMGIVGHGHVGIPINDDEIMQSQLLMDSMVAGNVHETVPFGEINYGVWPDLLP