AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88154

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88154.t1 MTR_4g031910 73.362 229 54 1 1 222 1 229 1.59e-113 324
MS.gene88154.t1 MTR_4g032290 70.902 244 36 2 1 222 1 231 1.21e-111 319
MS.gene88154.t1 MTR_4g032620 58.874 231 86 1 1 222 1 231 7.89e-96 279
MS.gene88154.t1 MTR_8g036130 58.704 247 77 4 1 222 1 247 1.71e-91 269
MS.gene88154.t1 MTR_4g032260 82.051 156 28 0 1 156 1 156 3.71e-83 244
MS.gene88154.t1 MTR_3g065100 47.521 242 100 4 1 219 1 238 1.25e-62 195
MS.gene88154.t1 MTR_3g466980 46.119 219 102 4 1 214 1 208 5.26e-61 190
MS.gene88154.t1 MTR_2g035610 72.131 122 34 0 1 122 1 122 5.80e-51 161
MS.gene88154.t1 MTR_4g032270 77.083 96 14 1 135 222 36 131 4.48e-46 149
MS.gene88154.t1 MTR_3g466830 47.682 151 78 1 3 153 2 151 1.94e-45 149
MS.gene88154.t1 MTR_5g075380 44.586 157 86 1 1 157 1 156 5.08e-45 147
MS.gene88154.t1 MTR_4g063790 40.881 159 94 0 1 159 1 159 1.23e-42 142
MS.gene88154.t1 MTR_5g047580 44.586 157 85 2 1 157 1 155 5.03e-41 137
MS.gene88154.t1 MTR_3g031100 41.139 158 93 0 1 158 1 158 7.89e-41 139
MS.gene88154.t1 MTR_3g467080 40.127 157 94 0 1 157 1 157 2.39e-40 135
MS.gene88154.t1 MTR_2g016210 39.548 177 106 1 1 176 1 177 2.08e-39 136
MS.gene88154.t1 MTR_3g466890 42.763 152 86 1 3 154 2 152 1.57e-38 131
MS.gene88154.t1 MTR_7g011950 45.283 159 85 2 1 159 1 157 1.45e-37 129
MS.gene88154.t1 MTR_1g077390 40.881 159 92 2 1 159 1 157 1.07e-36 126
MS.gene88154.t1 MTR_4g028720 44.654 159 86 2 1 159 1 157 2.01e-36 125
MS.gene88154.t1 MTR_1g077320 44.654 159 86 2 1 159 1 157 8.09e-36 124
MS.gene88154.t1 MTR_1g090783 40.645 155 90 2 3 157 2 154 3.83e-35 122
MS.gene88154.t1 MTR_1g077300 43.396 159 86 2 1 159 1 155 8.61e-34 119
MS.gene88154.t1 MTR_1g084950 43.312 157 87 2 1 157 1 155 1.50e-33 118
MS.gene88154.t1 MTR_1g090697 38.854 157 94 2 1 157 1 155 1.76e-33 118
MS.gene88154.t1 MTR_3g465410 40.458 131 78 0 29 159 1 131 2.53e-33 117
MS.gene88154.t1 MTR_1g090710 36.943 157 98 1 1 157 1 156 2.21e-32 115
MS.gene88154.t1 MTR_4g028800 75.714 70 15 1 1 70 1 68 1.61e-31 110
MS.gene88154.t1 MTR_3g031240 33.962 159 101 2 1 157 1 157 1.70e-29 108
MS.gene88154.t1 MTR_7g055800 50.427 117 30 2 1 117 1 89 7.48e-29 104
MS.gene88154.t1 MTR_3g466900 38.889 126 76 1 32 157 2 126 1.36e-28 105
MS.gene88154.t1 MTR_4g019670 37.580 157 82 2 3 159 6 146 2.30e-26 106
MS.gene88154.t1 MTR_3g466930 36.508 126 79 1 32 157 2 126 1.44e-25 97.1
MS.gene88154.t1 MTR_7g106510 36.306 157 84 2 3 159 6 146 4.55e-25 102
MS.gene88154.t1 MTR_2g035580 35.897 156 99 1 1 156 1 155 5.20e-25 96.7
MS.gene88154.t1 MTR_7g055790 51.351 111 36 1 1 111 59 151 1.43e-24 95.1
MS.gene88154.t1 MTR_7g055940 49.057 106 26 2 1 106 1 78 1.48e-23 90.1
MS.gene88154.t1 MTR_3g093900 29.500 200 134 3 3 196 6 204 3.24e-23 97.4
MS.gene88154.t1 MTR_5g047560 35.032 157 84 3 1 157 1 139 4.05e-23 90.9
MS.gene88154.t1 MTR_2g035590 55.952 84 37 0 74 157 1 84 8.14e-19 78.6
MS.gene88154.t1 MTR_6g018920 35.398 113 66 4 1 107 1 112 2.79e-13 68.2
MS.gene88154.t1 MTR_6g005450 35.398 113 66 4 1 107 1 112 2.88e-13 68.2
MS.gene88154.t1 MTR_1g114730 32.743 113 69 3 1 107 1 112 4.36e-13 67.8
MS.gene88154.t1 MTR_4g084780 38.739 111 52 2 74 168 1 111 2.29e-12 62.8
MS.gene88154.t1 MTR_6g005440 36.283 113 65 4 1 107 1 112 1.91e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88154.t1 AT5G48670 55.195 154 68 1 1 154 1 153 3.80e-46 155
MS.gene88154.t1 AT1G65300 40.331 181 99 2 3 175 2 181 1.83e-40 140
MS.gene88154.t1 AT1G65330 42.262 168 88 2 3 162 2 168 2.03e-38 134
MS.gene88154.t1 AT5G26630 42.408 191 99 3 1 181 1 190 1.37e-37 130
MS.gene88154.t1 AT5G26650 43.137 153 86 1 5 157 3 154 2.08e-36 131
MS.gene88154.t1 AT5G27960 42.484 153 87 1 5 157 3 154 9.24e-36 129
MS.gene88154.t1 AT1G31630 36.310 168 97 3 3 162 2 167 3.20e-34 125
MS.gene88154.t1 AT1G31640 39.073 151 90 2 3 153 2 150 1.05e-32 123
MS.gene88154.t1 AT3G05860 40.000 150 89 1 1 150 1 149 1.92e-32 117
MS.gene88154.t1 AT5G27810 56.989 93 40 0 29 121 1 93 7.87e-32 112
MS.gene88154.t1 AT3G05860 40.000 150 89 1 1 150 1 149 9.92e-32 116
MS.gene88154.t1 AT3G05860 40.000 150 89 1 1 150 1 149 1.11e-31 116
MS.gene88154.t1 AT2G28700 31.858 226 119 5 1 221 1 196 4.48e-28 108
MS.gene88154.t1 AT1G22590 32.099 162 106 1 1 162 1 158 3.87e-26 99.8
MS.gene88154.t1 AT5G26580 36.364 154 83 2 1 154 1 139 4.36e-25 100
MS.gene88154.t1 AT5G06500 34.615 156 100 2 1 156 1 154 4.51e-21 88.2
MS.gene88154.t1 AT2G40210 34.783 161 103 2 1 161 1 159 1.06e-18 84.0
MS.gene88154.t1 AT5G58890 37.795 127 68 5 6 123 6 130 6.30e-16 75.1
MS.gene88154.t1 AT5G55690 44.872 78 36 2 1 71 1 78 2.48e-14 70.5
MS.gene88154.t1 AT5G55690 44.872 78 36 2 1 71 1 78 2.48e-14 70.5
MS.gene88154.t1 AT2G15660 27.429 175 99 5 11 176 18 173 5.69e-14 69.3
MS.gene88154.t1 AT5G27944 32.727 110 62 3 24 131 41 140 7.28e-11 60.1

Find 59 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCTTTGGTGAGATCAATTC+TGG 0.238779 4.3:-68855231 MS.gene88154:CDS
GAGCGAAGAAATGGCAATTA+TGG 0.251384 4.3:-68855352 MS.gene88154:CDS
TACCAATGTCCTTCAAATTA+TGG 0.254451 4.3:+68855421 None:intergenic
TGAAACAAAGAAAAGATAAT+AGG 0.275750 4.3:-68855548 MS.gene88154:CDS
ATTCTTCAAGGTAGTAAATC+AGG 0.300880 4.3:+68855201 None:intergenic
ATAATGTCATCATTATTAAT+AGG 0.321721 4.3:+68855309 None:intergenic
TATTAATAGGTATTCCAATA+TGG 0.324054 4.3:+68855322 None:intergenic
AACGAAGGGTCTATTGAAAA+AGG 0.335070 4.3:-68855781 MS.gene88154:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4.3:-68855701 MS.gene88154:CDS
ATCTCAGGTTGAGGCTCATA+AGG 0.373927 4.3:+68855705 None:intergenic
TATGCAAAGTCAATTATTGA+TGG 0.408286 4.3:-68855289 MS.gene88154:CDS
GAAGGACATTGGTAGACGTT+TGG 0.410243 4.3:-68855412 MS.gene88154:CDS
GAAACAAAGAAAAGATAATA+GGG 0.419680 4.3:-68855547 MS.gene88154:CDS
ATTATGGGTCATGGCCATAT+TGG 0.424355 4.3:-68855336 MS.gene88154:CDS
AGCGAAGAAATGGCAATTAT+GGG 0.425600 4.3:-68855351 MS.gene88154:CDS
AGCATCTAGGAGCGAAGAAA+TGG 0.428793 4.3:-68855361 MS.gene88154:CDS
GTTGATTGACCATAATTTGA+AGG 0.445081 4.3:-68855430 MS.gene88154:CDS
CTAGATGCTGCTGGAGGTGG+TGG 0.445358 4.3:+68855375 None:intergenic
CACAACCATGGCTAGAAGTA+AGG 0.457305 4.3:-68855859 None:intergenic
TCTGGTGAAGGCCAAATCTC+AGG 0.467267 4.3:+68855690 None:intergenic
CTCATAAGGGCCATACACTA+TGG 0.468858 4.3:+68855719 None:intergenic
CTTGACACAAAGGGTTCTGA+AGG 0.478789 4.3:-68855586 MS.gene88154:CDS
CTCCTAGATGCTGCTGGAGG+TGG 0.480058 4.3:+68855372 None:intergenic
TCAATTATTGATGGACTCAA+TGG 0.482426 4.3:-68855280 MS.gene88154:CDS
TTGATTTGAGTTATCTTACT+TGG 0.482489 4.3:-68855452 MS.gene88154:CDS
TCTTCGCTCCTAGATGCTGC+TGG 0.487238 4.3:+68855366 None:intergenic
AGAGACTTTCTTGACACAAA+GGG 0.517022 4.3:-68855595 MS.gene88154:CDS
GACCATAATTTGAAGGACAT+TGG 0.517963 4.3:-68855423 MS.gene88154:CDS
CACCACCTCCAGCAGCATCT+AGG 0.522994 4.3:-68855374 MS.gene88154:CDS
GGACATTGGTAGACGTTTGG+CGG 0.524285 4.3:-68855409 MS.gene88154:CDS
TTTGTGTCAAGAAAGTCTCT+TGG 0.525855 4.3:+68855598 None:intergenic
TTTAACCTTACTTCTAGCCA+TGG 0.533701 4.3:+68855854 None:intergenic
TCTCAGGTTGAGGCTCATAA+GGG 0.533923 4.3:+68855706 None:intergenic
ACTTGCCTTCATTGTCAATG+AGG 0.536135 4.3:-68855832 MS.gene88154:CDS
ATGTCTCATTGTCTCAATGA+AGG 0.542205 4.3:-68855504 MS.gene88154:CDS
GAAATGGCAATTATGGGTCA+TGG 0.549964 4.3:-68855345 MS.gene88154:CDS
TCATTGTCAATGAGGCTACA+AGG 0.551605 4.3:-68855824 MS.gene88154:CDS
TGTAGCCTCATTGACAATGA+AGG 0.553670 4.3:+68855827 None:intergenic
CCAGAATTGATCTCACCAAA+GGG 0.554343 4.3:+68855231 None:intergenic
GTGCAAGAGACAGTGCCCTT+TGG 0.557727 4.3:-68855246 MS.gene88154:CDS
GAAGCCTGTGCCATAGTGTA+TGG 0.559714 4.3:-68855729 MS.gene88154:CDS
GAGATTTGGCCTTCACCAGA+GGG 0.565461 4.3:-68855687 MS.gene88154:CDS
GATTTGGCCTTCACCAGAGG+GGG 0.573799 4.3:-68855685 MS.gene88154:CDS
TTCTTCAAGGTAGTAAATCA+GGG 0.588454 4.3:+68855202 None:intergenic
TCCAGAATTGATCTCACCAA+AGG 0.590517 4.3:+68855230 None:intergenic
GAAGGCCAAATCTCAGGTTG+AGG 0.598100 4.3:+68855696 None:intergenic
ACAGGCTTCAATGCCACAGA+GGG 0.601811 4.3:+68855743 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4.3:-68855273 MS.gene88154:CDS
AAGAGACTTTCTTGACACAA+AGG 0.607804 4.3:-68855596 MS.gene88154:CDS
TGAGATTTGGCCTTCACCAG+AGG 0.614269 4.3:-68855688 MS.gene88154:CDS
ATCATACAAGAAAAGAACGA+AGG 0.618898 4.3:-68855796 MS.gene88154:CDS
TCATACAAGAAAAGAACGAA+GGG 0.620354 4.3:-68855795 MS.gene88154:CDS
AGGGCCATACACTATGGCAC+AGG 0.641363 4.3:+68855725 None:intergenic
TGTTGACGACAATATGTCAA+CGG 0.648930 4.3:-68855475 MS.gene88154:CDS
AGATTTGGCCTTCACCAGAG+GGG 0.650878 4.3:-68855686 MS.gene88154:CDS
ATTATTGATGGACTCAATGG+TGG 0.666274 4.3:-68855277 MS.gene88154:CDS
TCGCTCCTAGATGCTGCTGG+AGG 0.676090 4.3:+68855369 None:intergenic
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4.3:-68855756 MS.gene88154:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4.3:+68855742 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATGTCATCATTATTAAT+AGG + chr4.3:68855752-68855771 None:intergenic 15.0%
!! GAAACAAAGAAAAGATAATA+GGG - chr4.3:68855511-68855530 MS.gene88154:CDS 20.0%
!! TATTAATAGGTATTCCAATA+TGG + chr4.3:68855739-68855758 None:intergenic 20.0%
!! TGAAACAAAGAAAAGATAAT+AGG - chr4.3:68855510-68855529 MS.gene88154:CDS 20.0%
! TATGCAAAGTCAATTATTGA+TGG - chr4.3:68855769-68855788 MS.gene88154:CDS 25.0%
!! TTGATTTGAGTTATCTTACT+TGG - chr4.3:68855606-68855625 MS.gene88154:CDS 25.0%
ATCATACAAGAAAAGAACGA+AGG - chr4.3:68855262-68855281 MS.gene88154:CDS 30.0%
GTTGATTGACCATAATTTGA+AGG - chr4.3:68855628-68855647 MS.gene88154:CDS 30.0%
TACCAATGTCCTTCAAATTA+TGG + chr4.3:68855640-68855659 None:intergenic 30.0%
TCATACAAGAAAAGAACGAA+GGG - chr4.3:68855263-68855282 MS.gene88154:CDS 30.0%
!! TCAATTATTGATGGACTCAA+TGG - chr4.3:68855778-68855797 MS.gene88154:CDS 30.0%
AACGAAGGGTCTATTGAAAA+AGG - chr4.3:68855277-68855296 MS.gene88154:CDS 35.0%
AAGAGACTTTCTTGACACAA+AGG - chr4.3:68855462-68855481 MS.gene88154:CDS 35.0%
AGAGACTTTCTTGACACAAA+GGG - chr4.3:68855463-68855482 MS.gene88154:CDS 35.0%
AGCGAAGAAATGGCAATTAT+GGG - chr4.3:68855707-68855726 MS.gene88154:CDS 35.0%
ATGTCTCATTGTCTCAATGA+AGG - chr4.3:68855554-68855573 MS.gene88154:CDS 35.0%
GACCATAATTTGAAGGACAT+TGG - chr4.3:68855635-68855654 MS.gene88154:CDS 35.0%
TGTTGACGACAATATGTCAA+CGG - chr4.3:68855583-68855602 MS.gene88154:CDS 35.0%
TTTGTGTCAAGAAAGTCTCT+TGG + chr4.3:68855463-68855482 None:intergenic 35.0%
!! ATTATTGATGGACTCAATGG+TGG - chr4.3:68855781-68855800 MS.gene88154:CDS 35.0%
!! TGAATTTTGAGAGCACAGAT+TGG + chr4.3:68855400-68855419 None:intergenic 35.0%
ACTTGCCTTCATTGTCAATG+AGG - chr4.3:68855226-68855245 MS.gene88154:CDS 40.0%
ATTATGGGTCATGGCCATAT+TGG - chr4.3:68855722-68855741 MS.gene88154:CDS 40.0%
CCAGAATTGATCTCACCAAA+GGG + chr4.3:68855830-68855849 None:intergenic 40.0%
GAAATGGCAATTATGGGTCA+TGG - chr4.3:68855713-68855732 MS.gene88154:CDS 40.0%
GAGCGAAGAAATGGCAATTA+TGG - chr4.3:68855706-68855725 MS.gene88154:CDS 40.0%
TCATTGTCAATGAGGCTACA+AGG - chr4.3:68855234-68855253 MS.gene88154:CDS 40.0%
TCCAGAATTGATCTCACCAA+AGG + chr4.3:68855831-68855850 None:intergenic 40.0%
TGTAGCCTCATTGACAATGA+AGG + chr4.3:68855234-68855253 None:intergenic 40.0%
AGCATCTAGGAGCGAAGAAA+TGG - chr4.3:68855697-68855716 MS.gene88154:CDS 45.0%
ATGAGCCTCAACCTGAGATT+TGG - chr4.3:68855357-68855376 MS.gene88154:CDS 45.0%
CCCTTTGGTGAGATCAATTC+TGG - chr4.3:68855827-68855846 MS.gene88154:CDS 45.0%
CTCATAAGGGCCATACACTA+TGG + chr4.3:68855342-68855361 None:intergenic 45.0%
GAAGGACATTGGTAGACGTT+TGG - chr4.3:68855646-68855665 MS.gene88154:CDS 45.0%
! CTTGACACAAAGGGTTCTGA+AGG - chr4.3:68855472-68855491 MS.gene88154:CDS 45.0%
!! ATCTCAGGTTGAGGCTCATA+AGG + chr4.3:68855356-68855375 None:intergenic 45.0%
!! TCTCAGGTTGAGGCTCATAA+GGG + chr4.3:68855355-68855374 None:intergenic 45.0%
ACAGGCTTCAATGCCACAGA+GGG + chr4.3:68855318-68855337 None:intergenic 50.0%
GAAGCCTGTGCCATAGTGTA+TGG - chr4.3:68855329-68855348 MS.gene88154:CDS 50.0%
GGACATTGGTAGACGTTTGG+CGG - chr4.3:68855649-68855668 MS.gene88154:CDS 50.0%
TCTGGTGAAGGCCAAATCTC+AGG + chr4.3:68855371-68855390 None:intergenic 50.0%
! AGATTTGGCCTTCACCAGAG+GGG - chr4.3:68855372-68855391 MS.gene88154:CDS 50.0%
! GAAGGCCAAATCTCAGGTTG+AGG + chr4.3:68855365-68855384 None:intergenic 50.0%
! GAGATTTGGCCTTCACCAGA+GGG - chr4.3:68855371-68855390 MS.gene88154:CDS 50.0%
! TGAGATTTGGCCTTCACCAG+AGG - chr4.3:68855370-68855389 MS.gene88154:CDS 50.0%
!! TTGATGGACTCAATGGTGGC+TGG - chr4.3:68855785-68855804 MS.gene88154:CDS 50.0%
AGGGCCATACACTATGGCAC+AGG + chr4.3:68855336-68855355 None:intergenic 55.0%
CACAGGCTTCAATGCCACAG+AGG + chr4.3:68855319-68855338 None:intergenic 55.0%
GCTGAACTTAGCACCCTCTG+TGG - chr4.3:68855302-68855321 MS.gene88154:CDS 55.0%
GTGCAAGAGACAGTGCCCTT+TGG - chr4.3:68855812-68855831 MS.gene88154:CDS 55.0%
TCTTCGCTCCTAGATGCTGC+TGG + chr4.3:68855695-68855714 None:intergenic 55.0%
! GATTTGGCCTTCACCAGAGG+GGG - chr4.3:68855373-68855392 MS.gene88154:CDS 55.0%
AGCACAGATTGGACCCCCTC+TGG + chr4.3:68855389-68855408 None:intergenic 60.0%
CACCACCTCCAGCAGCATCT+AGG - chr4.3:68855684-68855703 MS.gene88154:CDS 60.0%
CTAGATGCTGCTGGAGGTGG+TGG + chr4.3:68855686-68855705 None:intergenic 60.0%
CTCCTAGATGCTGCTGGAGG+TGG + chr4.3:68855689-68855708 None:intergenic 60.0%
GATTGGACCCCCTCTGGTGA+AGG + chr4.3:68855383-68855402 None:intergenic 60.0%
TCGCTCCTAGATGCTGCTGG+AGG + chr4.3:68855692-68855711 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 68855206 68855874 68855206 ID=MS.gene88154
chr4.3 mRNA 68855206 68855874 68855206 ID=MS.gene88154.t1;Parent=MS.gene88154
chr4.3 exon 68855206 68855874 68855206 ID=MS.gene88154.t1.exon1;Parent=MS.gene88154.t1
chr4.3 CDS 68855206 68855874 68855206 ID=cds.MS.gene88154.t1;Parent=MS.gene88154.t1
Gene Sequence

>MS.gene88154

ATGGCTAGAAGTAAGGTTAAACTTGCCTTCATTGTCAATGAGGCTACAAGGAAAGCATCATACAAGAAAAGAACGAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCCCTTATGAGCCTCAACCTGAGATTTGGCCTTCACCAGAGGGGGTCCAATCTGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACACAAAGGGTTCTGAAGGCTGAAGAGAAATTGATGAAACAAAGAAAAGATAATAGGGAGCAAGAGATGACAATACTCATGTCTCATTGTCTCAATGAAGGTAGAGTTGTTGACGACAATATGTCAACGGTTGATTTGAGTTATCTTACTTGGTTGATTGACCATAATTTGAAGGACATTGGTAGACGTTTGGCGGCAATAGTGCTACCACCACCTCCAGCAGCATCTAGGAGCGAAGAAATGGCAATTATGGGTCATGGCCATATTGGAATACCTATTAATAATGATGACATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCAAGAGACAGTGCCCTTTGGTGAGATCAATTCTGGAGTTTGCCCTGATTTACTACCTTGA
Protein sequence

>MS.gene88154.t1

MARSKVKLAFIVNEATRKASYKKRTKGLLKKVAELSTLCGIEACAIVYGPYEPQPEIWPSPEGVQSVLSKFMTMHEFQKCKKMMNQETFLTQRVLKAEEKLMKQRKDNREQEMTILMSHCLNEGRVVDDNMSTVDLSYLTWLIDHNLKDIGRRLAAIVLPPPPAASRSEEMAIMGHGHIGIPINNDDIMQSQLLMDSMVAGNVQETVPFGEINSGVCPDLLP