AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067639

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067639.t1 MTR_4g031910 71.795 234 49 2 1 222 1 229 1.13e-111 319
MS.gene067639.t1 MTR_4g032290 70.082 244 38 2 1 222 1 231 1.81e-110 316
MS.gene067639.t1 MTR_4g032620 58.442 231 87 1 1 222 1 231 3.18e-94 275
MS.gene067639.t1 MTR_8g036130 57.895 247 79 4 1 222 1 247 2.21e-89 263
MS.gene067639.t1 MTR_4g032260 80.255 157 31 0 1 157 1 157 1.33e-81 241
MS.gene067639.t1 MTR_3g065100 46.888 241 103 4 1 219 1 238 1.45e-61 192
MS.gene067639.t1 MTR_3g466980 44.749 219 105 4 1 214 1 208 8.65e-58 182
MS.gene067639.t1 MTR_2g035610 69.672 122 37 0 1 122 1 122 2.08e-48 155
MS.gene067639.t1 MTR_4g032270 79.167 96 12 1 135 222 36 131 4.16e-48 154
MS.gene067639.t1 MTR_3g466830 46.358 151 80 1 3 153 2 151 1.03e-43 144
MS.gene067639.t1 MTR_5g075380 44.516 155 85 1 1 155 1 154 1.03e-42 142
MS.gene067639.t1 MTR_4g063790 40.909 154 91 0 1 154 1 154 6.60e-41 137
MS.gene067639.t1 MTR_2g016210 38.983 177 107 1 1 176 1 177 3.80e-39 135
MS.gene067639.t1 MTR_5g047580 43.590 156 86 2 1 156 1 154 4.36e-39 132
MS.gene067639.t1 MTR_3g031100 37.647 170 106 0 1 170 1 170 6.19e-39 135
MS.gene067639.t1 MTR_3g467080 38.462 156 96 0 1 156 1 156 8.23e-38 129
MS.gene067639.t1 MTR_3g466890 42.763 152 86 1 3 154 2 152 3.28e-37 127
MS.gene067639.t1 MTR_1g077390 40.127 157 90 3 1 156 1 154 6.06e-35 122
MS.gene067639.t1 MTR_7g011950 43.590 156 86 2 1 156 1 154 2.73e-34 120
MS.gene067639.t1 MTR_1g077320 42.949 156 87 2 1 156 1 154 2.35e-33 118
MS.gene067639.t1 MTR_4g028720 42.949 156 87 2 1 156 1 154 2.98e-33 117
MS.gene067639.t1 MTR_1g090783 38.961 154 92 2 3 156 2 153 1.57e-32 115
MS.gene067639.t1 MTR_1g077300 42.949 156 85 2 1 156 1 152 2.76e-32 115
MS.gene067639.t1 MTR_1g084950 42.308 156 88 2 1 156 1 154 4.05e-32 114
MS.gene067639.t1 MTR_1g090697 39.333 150 89 2 1 150 1 148 2.75e-31 112
MS.gene067639.t1 MTR_4g028800 75.714 70 15 1 1 70 1 68 5.22e-31 109
MS.gene067639.t1 MTR_3g465410 39.683 126 76 0 29 154 1 126 6.43e-31 111
MS.gene067639.t1 MTR_1g090710 36.364 154 97 1 1 154 1 153 9.32e-31 111
MS.gene067639.t1 MTR_3g031240 31.410 156 107 0 1 156 1 156 8.48e-28 104
MS.gene067639.t1 MTR_3g466900 39.024 123 74 1 32 154 2 123 2.50e-27 101
MS.gene067639.t1 MTR_7g055800 48.276 116 32 2 1 116 1 88 2.40e-26 97.8
MS.gene067639.t1 MTR_3g466930 37.398 123 76 1 32 154 2 123 6.86e-25 95.5
MS.gene067639.t1 MTR_4g019670 39.370 127 77 0 3 129 6 132 4.17e-24 99.8
MS.gene067639.t1 MTR_7g106510 39.370 127 77 0 3 129 6 132 4.60e-24 99.8
MS.gene067639.t1 MTR_3g093900 29.126 206 127 4 3 196 6 204 9.71e-24 99.0
MS.gene067639.t1 MTR_2g035580 34.395 157 102 1 1 157 1 156 1.46e-23 92.8
MS.gene067639.t1 MTR_7g055790 50.450 111 37 1 1 111 59 151 3.60e-23 91.7
MS.gene067639.t1 MTR_7g055940 47.170 106 28 2 1 106 1 78 4.25e-22 86.7
MS.gene067639.t1 MTR_5g047560 33.974 156 85 3 1 156 1 138 5.05e-21 85.5
MS.gene067639.t1 MTR_2g035590 55.556 81 36 0 74 154 1 81 6.09e-18 76.3
MS.gene067639.t1 MTR_6g005450 35.398 113 66 4 1 107 1 112 6.66e-13 67.0
MS.gene067639.t1 MTR_6g018920 35.398 113 66 4 1 107 1 112 9.29e-13 66.6
MS.gene067639.t1 MTR_1g114730 32.743 113 69 3 1 107 1 112 1.29e-12 66.2
MS.gene067639.t1 MTR_6g005440 36.283 113 65 4 1 107 1 112 4.88e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067639.t1 AT5G48670 53.247 154 71 1 1 154 1 153 4.50e-44 150
MS.gene067639.t1 AT1G65300 43.421 152 85 1 3 154 2 152 8.61e-39 135
MS.gene067639.t1 AT1G65330 41.667 168 88 2 3 161 2 168 1.88e-38 134
MS.gene067639.t1 AT5G26630 40.976 205 110 2 1 195 1 204 9.44e-38 131
MS.gene067639.t1 AT5G26650 40.476 168 89 2 5 162 3 169 1.11e-35 129
MS.gene067639.t1 AT5G27960 40.476 168 89 3 5 162 3 169 2.47e-35 127
MS.gene067639.t1 AT1G31630 35.119 168 98 3 3 161 2 167 3.00e-33 122
MS.gene067639.t1 AT1G31640 39.073 151 90 2 3 153 2 150 6.52e-32 121
MS.gene067639.t1 AT3G05860 37.975 158 97 1 1 158 1 157 2.31e-31 114
MS.gene067639.t1 AT3G05860 37.975 158 97 1 1 158 1 157 6.44e-31 114
MS.gene067639.t1 AT3G05860 37.975 158 97 1 1 158 1 157 8.09e-31 114
MS.gene067639.t1 AT5G27810 53.763 93 43 0 29 121 1 93 1.92e-29 106
MS.gene067639.t1 AT2G28700 34.463 177 111 2 1 175 1 174 5.34e-28 108
MS.gene067639.t1 AT1G22590 32.099 162 106 1 1 162 1 158 9.79e-26 98.6
MS.gene067639.t1 AT5G26580 35.714 154 84 2 1 154 1 139 4.14e-25 100
MS.gene067639.t1 AT5G06500 33.758 157 102 2 1 157 1 155 1.41e-20 87.0
MS.gene067639.t1 AT2G40210 37.209 129 80 1 1 129 1 128 1.32e-17 80.9
MS.gene067639.t1 AT5G58890 37.795 127 68 5 6 123 6 130 1.91e-15 73.9
MS.gene067639.t1 AT5G55690 38.679 106 57 3 1 99 1 105 3.77e-14 70.1
MS.gene067639.t1 AT5G55690 38.679 106 57 3 1 99 1 105 3.77e-14 70.1
MS.gene067639.t1 AT2G15660 28.492 179 98 6 11 179 18 176 3.92e-12 64.3
MS.gene067639.t1 AT5G27944 36.082 97 57 3 24 116 41 136 2.50e-11 61.6
MS.gene067639.t1 AT5G27090 32.456 114 72 3 7 116 23 135 6.69e-11 59.7

Find 58 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGAGACTTTCTTGACAAAA+AGG 0.228423 4.1:-69132346 MS.gene067639:CDS
CCCTTTGGTGAGATCAATTC+TGG 0.238779 4.1:-69131981 MS.gene067639:CDS
ATTATGGGTCATGGCCATTT+TGG 0.243830 4.1:-69132086 MS.gene067639:CDS
GAGCGAAGAAATGGCAATTA+TGG 0.251384 4.1:-69132102 MS.gene067639:CDS
TACCAATGTCCTTCAAATTA+TGG 0.254451 4.1:+69132171 None:intergenic
TGAAACAAAGAAAAGATAAT+AGG 0.275750 4.1:-69132298 MS.gene067639:CDS
ATCCTTCAAGGTAGTAAATC+AGG 0.301540 4.1:+69131951 None:intergenic
TATTAATAGGTATTCCAAAA+TGG 0.302744 4.1:+69132072 None:intergenic
CACAACCATGGCTAGAAATA+AGG 0.308050 4.1:-69132609 None:intergenic
ATAATGTCATCATTATTAAT+AGG 0.321721 4.1:+69132059 None:intergenic
AACGAAGGGTCTATTGAAAA+AGG 0.335070 4.1:-69132531 MS.gene067639:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4.1:-69132451 MS.gene067639:CDS
ATCTCAGGTTGAGGCTCATA+AGG 0.373927 4.1:+69132455 None:intergenic
GCCCTGATTTACTACCTTGA+AGG 0.388674 4.1:-69131953 None:intergenic
TATGCAAAGTCAATTATTGA+TGG 0.408286 4.1:-69132039 MS.gene067639:CDS
GAAGGACATTGGTAGACGTT+TGG 0.410243 4.1:-69132162 MS.gene067639:CDS
GAAACAAAGAAAAGATAATA+GGG 0.419680 4.1:-69132297 MS.gene067639:CDS
AGCGAAGAAATGGCAATTAT+GGG 0.425600 4.1:-69132101 MS.gene067639:CDS
AGCATCTAGGAGCGAAGAAA+TGG 0.428793 4.1:-69132111 MS.gene067639:CDS
GATGCTGCTGGAGGTGGTGG+TGG 0.431714 4.1:+69132128 None:intergenic
CTAGATGCTGCTGGAGGTGG+TGG 0.435830 4.1:+69132125 None:intergenic
GTTGATTGACCATAATTTGA+AGG 0.445081 4.1:-69132180 MS.gene067639:CDS
TCTGGTGAAGGCCAAATCTC+AGG 0.467267 4.1:+69132440 None:intergenic
CTCATAAGGGCCATACACTA+TGG 0.468858 4.1:+69132469 None:intergenic
CTCCTAGATGCTGCTGGAGG+TGG 0.480058 4.1:+69132122 None:intergenic
TCAATTATTGATGGACTCAA+TGG 0.482426 4.1:-69132030 MS.gene067639:CDS
TTGATTTGAGTTATCTTACT+TGG 0.482489 4.1:-69132202 MS.gene067639:CDS
TCTTCGCTCCTAGATGCTGC+TGG 0.487238 4.1:+69132116 None:intergenic
TTTAACCTTATTTCTAGCCA+TGG 0.493379 4.1:+69132604 None:intergenic
GACCATAATTTGAAGGACAT+TGG 0.517963 4.1:-69132173 MS.gene067639:CDS
GGACATTGGTAGACGTTTGG+CGG 0.524285 4.1:-69132159 MS.gene067639:CDS
CACCACCTCCAGCAGCATCT+AGG 0.525167 4.1:-69132124 MS.gene067639:CDS
TCTCAGGTTGAGGCTCATAA+GGG 0.533923 4.1:+69132456 None:intergenic
ACTTGCCTTCATTGTCAATG+AGG 0.536135 4.1:-69132582 MS.gene067639:CDS
GAAATGGCAATTATGGGTCA+TGG 0.549964 4.1:-69132095 MS.gene067639:CDS
GTGTCTCATTGTCTCAATGA+AGG 0.550221 4.1:-69132254 MS.gene067639:CDS
TCATTGTCAATGAGGCTACA+AGG 0.551605 4.1:-69132574 MS.gene067639:CDS
TGTAGCCTCATTGACAATGA+AGG 0.553670 4.1:+69132577 None:intergenic
CCAGAATTGATCTCACCAAA+GGG 0.554343 4.1:+69131981 None:intergenic
GTGCAAGAGACAGTGCCCTT+TGG 0.557727 4.1:-69131996 MS.gene067639:CDS
GAAGCCTGTGCCATAGTGTA+TGG 0.559714 4.1:-69132479 MS.gene067639:CDS
GAGATTTGGCCTTCACCAGA+GGG 0.565461 4.1:-69132437 MS.gene067639:CDS
GATTTGGCCTTCACCAGAGG+GGG 0.573799 4.1:-69132435 MS.gene067639:CDS
TCCTTCAAGGTAGTAAATCA+GGG 0.588454 4.1:+69131952 None:intergenic
TCCAGAATTGATCTCACCAA+AGG 0.590517 4.1:+69131980 None:intergenic
GAAGGCCAAATCTCAGGTTG+AGG 0.598100 4.1:+69132446 None:intergenic
ACAGGCTTCAATGCCACAGA+GGG 0.601811 4.1:+69132493 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4.1:-69132023 MS.gene067639:CDS
TGAGATTTGGCCTTCACCAG+AGG 0.614269 4.1:-69132438 MS.gene067639:CDS
ATCATACAAGAAAAGAACGA+AGG 0.618898 4.1:-69132546 MS.gene067639:CDS
TCATACAAGAAAAGAACGAA+GGG 0.620354 4.1:-69132545 MS.gene067639:CDS
AGGGCCATACACTATGGCAC+AGG 0.641363 4.1:+69132475 None:intergenic
AGATTTGGCCTTCACCAGAG+GGG 0.650878 4.1:-69132436 MS.gene067639:CDS
ATTATTGATGGACTCAATGG+TGG 0.666274 4.1:-69132027 MS.gene067639:CDS
TCGCTCCTAGATGCTGCTGG+AGG 0.676090 4.1:+69132119 None:intergenic
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4.1:-69132506 MS.gene067639:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4.1:+69132492 None:intergenic
TGTGCATGACAATATGTCAA+CGG 0.712181 4.1:-69132225 MS.gene067639:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATGTCATCATTATTAAT+AGG + chr4.1:69132502-69132521 None:intergenic 15.0%
!! GAAACAAAGAAAAGATAATA+GGG - chr4.1:69132261-69132280 MS.gene067639:CDS 20.0%
!! TATTAATAGGTATTCCAAAA+TGG + chr4.1:69132489-69132508 None:intergenic 20.0%
!! TGAAACAAAGAAAAGATAAT+AGG - chr4.1:69132260-69132279 MS.gene067639:CDS 20.0%
! TATGCAAAGTCAATTATTGA+TGG - chr4.1:69132519-69132538 MS.gene067639:CDS 25.0%
!! TTGATTTGAGTTATCTTACT+TGG - chr4.1:69132356-69132375 MS.gene067639:CDS 25.0%
AAGAGACTTTCTTGACAAAA+AGG - chr4.1:69132212-69132231 MS.gene067639:CDS 30.0%
AGAGACTTTCTTGACAAAAA+GGG - chr4.1:69132213-69132232 MS.gene067639:CDS 30.0%
ATCATACAAGAAAAGAACGA+AGG - chr4.1:69132012-69132031 MS.gene067639:CDS 30.0%
GTTGATTGACCATAATTTGA+AGG - chr4.1:69132378-69132397 MS.gene067639:CDS 30.0%
TACCAATGTCCTTCAAATTA+TGG + chr4.1:69132390-69132409 None:intergenic 30.0%
TCATACAAGAAAAGAACGAA+GGG - chr4.1:69132013-69132032 MS.gene067639:CDS 30.0%
! TTTTTGTCAAGAAAGTCTCT+TGG + chr4.1:69132213-69132232 None:intergenic 30.0%
!! TCAATTATTGATGGACTCAA+TGG - chr4.1:69132528-69132547 MS.gene067639:CDS 30.0%
!! TGAATTTTGAGAGCACATAT+TGG + chr4.1:69132150-69132169 None:intergenic 30.0%
AACGAAGGGTCTATTGAAAA+AGG - chr4.1:69132027-69132046 MS.gene067639:CDS 35.0%
AGCGAAGAAATGGCAATTAT+GGG - chr4.1:69132457-69132476 MS.gene067639:CDS 35.0%
GACCATAATTTGAAGGACAT+TGG - chr4.1:69132385-69132404 MS.gene067639:CDS 35.0%
TGTGCATGACAATATGTCAA+CGG - chr4.1:69132333-69132352 MS.gene067639:CDS 35.0%
!! ATTATTGATGGACTCAATGG+TGG - chr4.1:69132531-69132550 MS.gene067639:CDS 35.0%
ACTTGCCTTCATTGTCAATG+AGG - chr4.1:69131976-69131995 MS.gene067639:CDS 40.0%
CCAGAATTGATCTCACCAAA+GGG + chr4.1:69132580-69132599 None:intergenic 40.0%
GAAATGGCAATTATGGGTCA+TGG - chr4.1:69132463-69132482 MS.gene067639:CDS 40.0%
GAGCGAAGAAATGGCAATTA+TGG - chr4.1:69132456-69132475 MS.gene067639:CDS 40.0%
GTGTCTCATTGTCTCAATGA+AGG - chr4.1:69132304-69132323 MS.gene067639:CDS 40.0%
TCATTGTCAATGAGGCTACA+AGG - chr4.1:69131984-69132003 MS.gene067639:CDS 40.0%
TCCAGAATTGATCTCACCAA+AGG + chr4.1:69132581-69132600 None:intergenic 40.0%
TGTAGCCTCATTGACAATGA+AGG + chr4.1:69131984-69132003 None:intergenic 40.0%
! ATTATGGGTCATGGCCATTT+TGG - chr4.1:69132472-69132491 MS.gene067639:CDS 40.0%
! CTTGACAAAAAGGGTTCTGA+AGG - chr4.1:69132222-69132241 MS.gene067639:CDS 40.0%
AGCATCTAGGAGCGAAGAAA+TGG - chr4.1:69132447-69132466 MS.gene067639:CDS 45.0%
ATGAGCCTCAACCTGAGATT+TGG - chr4.1:69132107-69132126 MS.gene067639:CDS 45.0%
CCCTTTGGTGAGATCAATTC+TGG - chr4.1:69132577-69132596 MS.gene067639:CDS 45.0%
CTCATAAGGGCCATACACTA+TGG + chr4.1:69132092-69132111 None:intergenic 45.0%
GAAGGACATTGGTAGACGTT+TGG - chr4.1:69132396-69132415 MS.gene067639:CDS 45.0%
!! ATCTCAGGTTGAGGCTCATA+AGG + chr4.1:69132106-69132125 None:intergenic 45.0%
!! TCTCAGGTTGAGGCTCATAA+GGG + chr4.1:69132105-69132124 None:intergenic 45.0%
ACAGGCTTCAATGCCACAGA+GGG + chr4.1:69132068-69132087 None:intergenic 50.0%
GAAGCCTGTGCCATAGTGTA+TGG - chr4.1:69132079-69132098 MS.gene067639:CDS 50.0%
GGACATTGGTAGACGTTTGG+CGG - chr4.1:69132399-69132418 MS.gene067639:CDS 50.0%
TCTGGTGAAGGCCAAATCTC+AGG + chr4.1:69132121-69132140 None:intergenic 50.0%
! AGATTTGGCCTTCACCAGAG+GGG - chr4.1:69132122-69132141 MS.gene067639:CDS 50.0%
! GAAGGCCAAATCTCAGGTTG+AGG + chr4.1:69132115-69132134 None:intergenic 50.0%
! GAGATTTGGCCTTCACCAGA+GGG - chr4.1:69132121-69132140 MS.gene067639:CDS 50.0%
! TGAGATTTGGCCTTCACCAG+AGG - chr4.1:69132120-69132139 MS.gene067639:CDS 50.0%
!! TTGATGGACTCAATGGTGGC+TGG - chr4.1:69132535-69132554 MS.gene067639:CDS 50.0%
AGCACATATTGGACCCCCTC+TGG + chr4.1:69132139-69132158 None:intergenic 55.0%
AGGGCCATACACTATGGCAC+AGG + chr4.1:69132086-69132105 None:intergenic 55.0%
CACAGGCTTCAATGCCACAG+AGG + chr4.1:69132069-69132088 None:intergenic 55.0%
GCTGAACTTAGCACCCTCTG+TGG - chr4.1:69132052-69132071 MS.gene067639:CDS 55.0%
GTGCAAGAGACAGTGCCCTT+TGG - chr4.1:69132562-69132581 MS.gene067639:CDS 55.0%
TATTGGACCCCCTCTGGTGA+AGG + chr4.1:69132133-69132152 None:intergenic 55.0%
TCTTCGCTCCTAGATGCTGC+TGG + chr4.1:69132445-69132464 None:intergenic 55.0%
! GATTTGGCCTTCACCAGAGG+GGG - chr4.1:69132123-69132142 MS.gene067639:CDS 55.0%
CACCACCTCCAGCAGCATCT+AGG - chr4.1:69132434-69132453 MS.gene067639:CDS 60.0%
CTAGATGCTGCTGGAGGTGG+TGG + chr4.1:69132436-69132455 None:intergenic 60.0%
CTCCTAGATGCTGCTGGAGG+TGG + chr4.1:69132439-69132458 None:intergenic 60.0%
TCGCTCCTAGATGCTGCTGG+AGG + chr4.1:69132442-69132461 None:intergenic 60.0%
! GATGCTGCTGGAGGTGGTGG+TGG + chr4.1:69132433-69132452 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 69131956 69132624 69131956 ID=MS.gene067639
chr4.1 mRNA 69131956 69132624 69131956 ID=MS.gene067639.t1;Parent=MS.gene067639
chr4.1 exon 69131956 69132624 69131956 ID=MS.gene067639.t1.exon1;Parent=MS.gene067639.t1
chr4.1 CDS 69131956 69132624 69131956 ID=cds.MS.gene067639.t1;Parent=MS.gene067639.t1
Gene Sequence

>MS.gene067639

ATGGCTAGAAATAAGGTTAAACTTGCCTTCATTGTCAATGAGGCTACAAGGAAAGCATCATACAAGAAAAGAACGAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCCCTTATGAGCCTCAACCTGAGATTTGGCCTTCACCAGAGGGGGTCCAATATGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGATGAACCAAGAGACTTTCTTGACAAAAAGGGTTCTGAAGGCTGAAGAGAAATTGATGAAACAAAGAAAAGATAATAGGGAGCAAGAGATGAAAATACTCGTGTCTCATTGTCTCAATGAAGGTAGAGTTGTGCATGACAATATGTCAACGGTTGATTTGAGTTATCTTACTTGGTTGATTGACCATAATTTGAAGGACATTGGTAGACGTTTGGCGGCAACAGTGCCACCACCACCTCCAGCAGCATCTAGGAGCGAAGAAATGGCAATTATGGGTCATGGCCATTTTGGAATACCTATTAATAATGATGACATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCAAGAGACAGTGCCCTTTGGTGAGATCAATTCTGGAGTTTGCCCTGATTTACTACCTTGA
Protein sequence

>MS.gene067639.t1

MARNKVKLAFIVNEATRKASYKKRTKGLLKKVAELSTLCGIEACAIVYGPYEPQPEIWPSPEGVQYVLSKFMTMHEFQKCKKMMNQETFLTKRVLKAEEKLMKQRKDNREQEMKILVSHCLNEGRVVHDNMSTVDLSYLTWLIDHNLKDIGRRLAATVPPPPPAASRSEEMAIMGHGHFGIPINNDDIMQSQLLMDSMVAGNVQETVPFGEINSGVCPDLLP