AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene027344

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027344.t1 MTR_7g011950 93.082 159 11 0 1 159 1 159 2.87e-101 288
MS.gene027344.t1 MTR_4g028720 92.453 159 12 0 1 159 1 159 6.77e-99 281
MS.gene027344.t1 MTR_1g077320 85.535 159 23 0 1 159 1 159 8.67e-92 263
MS.gene027344.t1 MTR_5g047580 71.795 156 44 0 1 156 1 156 3.82e-78 229
MS.gene027344.t1 MTR_1g077390 70.701 157 46 0 1 157 1 157 3.31e-77 226
MS.gene027344.t1 MTR_1g084950 76.923 156 36 0 1 156 1 156 5.19e-77 226
MS.gene027344.t1 MTR_1g077300 75.472 159 37 1 1 159 1 157 4.06e-74 219
MS.gene027344.t1 MTR_5g047560 61.538 156 44 1 1 156 1 140 1.65e-60 184
MS.gene027344.t1 MTR_1g090783 56.863 153 66 0 3 155 2 154 1.61e-58 179
MS.gene027344.t1 MTR_1g090697 54.839 155 70 0 1 155 1 155 1.74e-58 179
MS.gene027344.t1 MTR_1g090710 51.923 156 74 1 1 155 1 156 4.77e-55 171
MS.gene027344.t1 MTR_3g466980 45.752 153 82 1 1 152 1 153 3.67e-41 137
MS.gene027344.t1 MTR_4g032620 40.645 155 90 2 1 153 1 155 7.67e-41 137
MS.gene027344.t1 MTR_3g065100 47.771 157 81 1 1 156 1 157 8.24e-39 132
MS.gene027344.t1 MTR_4g063790 38.365 159 96 2 1 157 1 159 2.30e-34 118
MS.gene027344.t1 MTR_8g036130 40.252 159 91 2 1 155 1 159 2.62e-34 120
MS.gene027344.t1 MTR_5g075380 36.538 156 98 1 1 155 1 156 6.37e-34 117
MS.gene027344.t1 MTR_3g466830 41.401 157 91 1 3 158 2 158 5.98e-33 114
MS.gene027344.t1 MTR_3g466890 39.610 154 92 1 3 155 2 155 7.24e-30 107
MS.gene027344.t1 MTR_4g031910 40.667 150 87 2 1 148 1 150 1.13e-29 108
MS.gene027344.t1 MTR_3g467080 34.591 159 102 2 1 157 1 159 3.22e-29 105
MS.gene027344.t1 MTR_2g016210 38.365 159 96 2 1 157 1 159 4.57e-29 107
MS.gene027344.t1 MTR_3g031240 35.849 159 100 2 1 157 1 159 6.83e-29 105
MS.gene027344.t1 MTR_4g032260 40.000 160 94 2 1 158 1 160 2.73e-28 102
MS.gene027344.t1 MTR_4g032290 37.888 161 98 2 1 159 1 161 3.51e-26 99.4
MS.gene027344.t1 MTR_3g031100 36.076 158 97 3 1 155 1 157 7.86e-26 99.0
MS.gene027344.t1 MTR_2g035610 41.525 118 68 1 1 117 1 118 2.09e-25 94.4
MS.gene027344.t1 MTR_2g035580 34.194 155 101 1 1 154 1 155 1.25e-23 90.9
MS.gene027344.t1 MTR_3g465410 35.115 131 83 2 29 157 1 131 3.75e-21 84.0
MS.gene027344.t1 MTR_4g028800 47.945 73 36 1 1 73 1 71 4.94e-21 81.6
MS.gene027344.t1 MTR_3g466900 38.400 125 76 1 32 155 2 126 7.55e-21 82.8
MS.gene027344.t1 MTR_3g466930 36.000 125 79 1 32 155 2 126 7.59e-19 77.8
MS.gene027344.t1 MTR_4g019670 34.091 132 83 2 1 128 1 132 4.11e-17 77.8
MS.gene027344.t1 MTR_7g106510 34.259 108 70 1 3 109 6 113 6.02e-16 74.3
MS.gene027344.t1 MTR_7g055800 33.913 115 49 2 1 115 1 88 1.16e-14 65.9
MS.gene027344.t1 MTR_1g033370 45.745 94 50 1 64 156 28 121 1.27e-14 66.6
MS.gene027344.t1 MTR_1g033930 41.837 98 56 1 62 158 20 117 1.96e-14 66.2
MS.gene027344.t1 MTR_1g033790 38.938 113 62 2 53 158 5 117 2.17e-13 63.2
MS.gene027344.t1 MTR_7g055790 36.697 109 52 2 1 109 59 150 7.97e-13 62.8
MS.gene027344.t1 MTR_7g055940 34.615 104 41 3 1 104 1 77 5.49e-12 58.5
MS.gene027344.t1 MTR_6g005450 32.031 128 74 5 1 115 1 128 6.75e-12 62.4
MS.gene027344.t1 MTR_3g093900 32.292 96 63 1 3 98 6 99 3.09e-11 60.8
MS.gene027344.t1 MTR_6g018920 32.500 80 48 3 1 74 1 80 4.18e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027344.t1 AT5G48670 46.405 153 81 1 1 152 1 153 1.45e-34 123
MS.gene027344.t1 AT3G05860 39.597 149 89 1 1 148 1 149 2.67e-32 114
MS.gene027344.t1 AT3G05860 39.597 149 89 1 1 148 1 149 1.29e-31 114
MS.gene027344.t1 AT3G05860 39.597 149 89 1 1 148 1 149 2.15e-31 113
MS.gene027344.t1 AT5G26630 38.750 160 97 1 1 159 1 160 3.17e-29 107
MS.gene027344.t1 AT1G65300 36.620 142 89 1 3 143 2 143 9.71e-28 104
MS.gene027344.t1 AT1G65330 36.735 147 92 1 3 148 2 148 3.83e-27 103
MS.gene027344.t1 AT5G26650 34.641 153 99 1 4 155 2 154 4.50e-25 99.0
MS.gene027344.t1 AT5G27960 33.987 153 100 1 4 155 2 154 8.44e-24 95.1
MS.gene027344.t1 AT1G31630 29.677 155 107 2 3 156 2 155 6.47e-22 90.1
MS.gene027344.t1 AT2G28700 33.557 149 98 1 1 148 1 149 6.95e-22 90.1
MS.gene027344.t1 AT5G27810 43.750 96 53 1 29 123 1 96 4.54e-21 83.2
MS.gene027344.t1 AT1G22590 29.012 162 99 3 1 155 1 153 2.66e-20 82.4
MS.gene027344.t1 AT1G31640 32.000 150 100 2 3 151 2 150 4.15e-19 83.2
MS.gene027344.t1 AT5G26580 32.258 155 92 1 1 155 1 142 1.09e-17 78.6
MS.gene027344.t1 AT2G40210 37.815 119 69 2 1 116 1 117 4.09e-15 71.6
MS.gene027344.t1 AT5G06500 30.818 159 106 3 1 157 1 157 1.01e-14 69.3
MS.gene027344.t1 AT5G58890 35.417 96 55 2 1 89 1 96 7.39e-13 65.1

Find 28 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCTTTCTTGTTGAATCAT+TGG 0.233760 7.4:-50024126 None:intergenic
TGTTGAATCATTGGAAATAA+AGG 0.251603 7.4:-50024117 None:intergenic
AGCTGAACATTCTTATGTTT+TGG 0.259719 7.4:+50024423 MS.gene027344:CDS
TTTGCAAAAGGAAACTTTCT+TGG 0.282244 7.4:-50024343 None:intergenic
ACCTTTCCTCCTCCTCTTGT+AGG 0.282788 7.4:-50024150 None:intergenic
TGTTTGGCTTCCTTTAGATT+TGG 0.353502 7.4:-50024266 None:intergenic
ATACCTCTCAATCACCTGTT+TGG 0.354870 7.4:-50024282 None:intergenic
TTCCAATGATTCAACAAGAA+AGG 0.389550 7.4:+50024124 MS.gene027344:CDS
TCAGAAACAGTCACATCATC+TGG 0.393115 7.4:-50024467 None:intergenic
AAATCTAAAGGAAGCCAAAC+AGG 0.425294 7.4:+50024268 MS.gene027344:CDS
CTTTAGTAATCATTTGCAAA+AGG 0.447168 7.4:-50024355 None:intergenic
TGTTTCTGATTTGAAAGACT+TGG 0.473410 7.4:+50024481 MS.gene027344:CDS
TGCAAATGATTACTAAAGCT+AGG 0.481563 7.4:+50024360 MS.gene027344:CDS
TTTCACCTTCTTCCTAGTCA+TGG 0.490416 7.4:-50024090 None:intergenic
GCAAATGATTACTAAAGCTA+GGG 0.492435 7.4:+50024361 MS.gene027344:CDS
ACCTCTGTTTCAGAATCAAA+AGG 0.516061 7.4:-50024239 None:intergenic
ACCTACAAGAGGAGGAGGAA+AGG 0.522508 7.4:+50024149 MS.gene027344:CDS
AGAGGTGTGGCCAAATCTAA+AGG 0.522555 7.4:+50024256 MS.gene027344:CDS
AGAGAACTCACTATTCTTTG+TGG 0.526508 7.4:+50024188 MS.gene027344:CDS
CAAAGCCATGACTAGGAAGA+AGG 0.543154 7.4:+50024085 None:intergenic
AGGAGACCTACAAGAGGAGG+AGG 0.545154 7.4:+50024144 MS.gene027344:CDS
GAAGGAAATTGATGACAAGA+TGG 0.549956 7.4:+50024526 MS.gene027344:CDS
GAAAGGAGACCTACAAGAGG+AGG 0.592612 7.4:+50024141 MS.gene027344:CDS
TACATTGCAAAGCCATGACT+AGG 0.609749 7.4:+50024078 None:intergenic
GAGGAAAGGTATCATCAAGA+AGG 0.620547 7.4:+50024163 MS.gene027344:CDS
TTGATTCTGAAACAGAGGTG+TGG 0.630350 7.4:+50024243 MS.gene027344:CDS
AAGCCAAACAGGTGATTGAG+AGG 0.637552 7.4:+50024279 MS.gene027344:CDS
CAAGAAAGGAGACCTACAAG+AGG 0.685284 7.4:+50024138 MS.gene027344:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTAATTGAAAAAAATATGA+AGG + chr7.4:50024508-50024527 MS.gene027344:CDS 15.0%
! CTTTAGTAATCATTTGCAAA+AGG - chr7.4:50024358-50024377 None:intergenic 25.0%
! TGTTGAATCATTGGAAATAA+AGG - chr7.4:50024120-50024139 None:intergenic 25.0%
GCAAATGATTACTAAAGCTA+GGG + chr7.4:50024361-50024380 MS.gene027344:CDS 30.0%
TGCAAATGATTACTAAAGCT+AGG + chr7.4:50024360-50024379 MS.gene027344:CDS 30.0%
TTCCAATGATTCAACAAGAA+AGG + chr7.4:50024124-50024143 MS.gene027344:CDS 30.0%
TTTGCAAAAGGAAACTTTCT+TGG - chr7.4:50024346-50024365 None:intergenic 30.0%
! AGCTGAACATTCTTATGTTT+TGG + chr7.4:50024423-50024442 MS.gene027344:CDS 30.0%
! TGTTTCTGATTTGAAAGACT+TGG + chr7.4:50024481-50024500 MS.gene027344:CDS 30.0%
AAATCTAAAGGAAGCCAAAC+AGG + chr7.4:50024268-50024287 MS.gene027344:CDS 35.0%
ACCTCTGTTTCAGAATCAAA+AGG - chr7.4:50024242-50024261 None:intergenic 35.0%
AGAGAACTCACTATTCTTTG+TGG + chr7.4:50024188-50024207 MS.gene027344:CDS 35.0%
CTCCTTTCTTGTTGAATCAT+TGG - chr7.4:50024129-50024148 None:intergenic 35.0%
! GAAGGAAATTGATGACAAGA+TGG + chr7.4:50024526-50024545 MS.gene027344:CDS 35.0%
! TGTTTGGCTTCCTTTAGATT+TGG - chr7.4:50024269-50024288 None:intergenic 35.0%
!!! TCCTTTTGATTCTGAAACAG+AGG + chr7.4:50024238-50024257 MS.gene027344:CDS 35.0%
ATACCTCTCAATCACCTGTT+TGG - chr7.4:50024285-50024304 None:intergenic 40.0%
TCAGAAACAGTCACATCATC+TGG - chr7.4:50024470-50024489 None:intergenic 40.0%
!! GAGGAAAGGTATCATCAAGA+AGG + chr7.4:50024163-50024182 MS.gene027344:CDS 40.0%
!! TTGATTCTGAAACAGAGGTG+TGG + chr7.4:50024243-50024262 MS.gene027344:CDS 40.0%
AAGCCAAACAGGTGATTGAG+AGG + chr7.4:50024279-50024298 MS.gene027344:CDS 45.0%
CAAGAAAGGAGACCTACAAG+AGG + chr7.4:50024138-50024157 MS.gene027344:CDS 45.0%
! AGAGGTGTGGCCAAATCTAA+AGG + chr7.4:50024256-50024275 MS.gene027344:CDS 45.0%
ACCTACAAGAGGAGGAGGAA+AGG + chr7.4:50024149-50024168 MS.gene027344:CDS 50.0%
ACCTTTCCTCCTCCTCTTGT+AGG - chr7.4:50024153-50024172 None:intergenic 50.0%
GAAAGGAGACCTACAAGAGG+AGG + chr7.4:50024141-50024160 MS.gene027344:CDS 50.0%
AGGAGACCTACAAGAGGAGG+AGG + chr7.4:50024144-50024163 MS.gene027344:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 50024092 50024571 50024092 ID=MS.gene027344
chr7.4 mRNA 50024092 50024571 50024092 ID=MS.gene027344.t1;Parent=MS.gene027344
chr7.4 exon 50024092 50024571 50024092 ID=MS.gene027344.t1.exon1;Parent=MS.gene027344.t1
chr7.4 CDS 50024092 50024571 50024092 ID=cds.MS.gene027344.t1;Parent=MS.gene027344.t1
Gene Sequence

>MS.gene027344

ATGACTAGGAAGAAGGTGAAACTCGCCTTTATTTCCAATGATTCAACAAGAAAGGAGACCTACAAGAGGAGGAGGAAAGGTATCATCAAGAAGGTGAGAGAACTCACTATTCTTTGTGGTATTTCAGCATGTGCTATAATTTCTGATCCTTTTGATTCTGAAACAGAGGTGTGGCCAAATCTAAAGGAAGCCAAACAGGTGATTGAGAGGTATCAAAACTCATATATGAAAGATGAGAGAAAAAATGTGAACCAAGAAAGTTTCCTTTTGCAAATGATTACTAAAGCTAGGGAACAACTGAGAATGCAAAGACACGACAATCATGAGAATGAGCTGAACATTCTTATGTTTTGGTACATGCAAAACAACAAGCTTCCAGATGATGTGACTGTTTCTGATTTGAAAGACTTGGATAAGTTAATTGAAAAAAATATGAAGGAAATTGATGACAAGATGGCTTCACTTAGTTTATCAAACTGA
Protein sequence

>MS.gene027344.t1

MTRKKVKLAFISNDSTRKETYKRRRKGIIKKVRELTILCGISACAIISDPFDSETEVWPNLKEAKQVIERYQNSYMKDERKNVNQESFLLQMITKAREQLRMQRHDNHENELNILMFWYMQNNKLPDDVTVSDLKDLDKLIEKNMKEIDDKMASLSLSN