AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049537

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049537.t1 MTR_3g466890 96.273 161 6 0 1 161 1 161 9.42e-111 311
MS.gene049537.t1 MTR_3g466830 77.848 158 35 0 1 158 1 158 2.03e-86 250
MS.gene049537.t1 MTR_3g466900 90.152 132 13 0 30 161 1 132 1.08e-83 242
MS.gene049537.t1 MTR_3g466930 87.121 132 17 0 30 161 1 132 7.34e-81 235
MS.gene049537.t1 MTR_3g065100 48.408 157 81 0 2 158 3 159 4.82e-44 145
MS.gene049537.t1 MTR_8g036130 43.125 160 88 2 2 158 3 162 3.79e-41 138
MS.gene049537.t1 MTR_1g090697 43.871 155 86 1 2 156 3 156 9.06e-40 132
MS.gene049537.t1 MTR_3g466980 41.176 153 90 0 2 154 3 155 2.05e-39 133
MS.gene049537.t1 MTR_4g032620 40.252 159 92 2 2 158 3 160 1.12e-38 131
MS.gene049537.t1 MTR_4g031910 43.396 159 89 1 2 159 3 161 1.31e-37 129
MS.gene049537.t1 MTR_1g090783 42.038 157 90 1 1 157 1 156 3.02e-37 125
MS.gene049537.t1 MTR_3g031240 41.401 157 89 2 2 156 3 158 5.86e-37 125
MS.gene049537.t1 MTR_2g035610 47.059 119 63 0 2 120 3 121 1.16e-34 118
MS.gene049537.t1 MTR_4g032260 45.098 153 83 1 1 152 2 154 3.26e-34 118
MS.gene049537.t1 MTR_5g075380 41.772 158 92 0 4 161 5 162 4.14e-34 117
MS.gene049537.t1 MTR_4g032290 44.025 159 88 1 2 159 3 161 1.10e-33 119
MS.gene049537.t1 MTR_5g047580 41.558 154 89 1 2 155 3 155 2.66e-33 115
MS.gene049537.t1 MTR_1g090710 41.667 156 89 2 2 156 3 157 3.52e-33 115
MS.gene049537.t1 MTR_7g011950 42.857 154 87 1 2 155 3 155 2.28e-30 108
MS.gene049537.t1 MTR_4g028720 42.857 154 87 1 2 155 3 155 2.40e-30 108
MS.gene049537.t1 MTR_1g077390 40.132 152 90 1 1 152 2 152 2.76e-30 107
MS.gene049537.t1 MTR_3g031100 35.669 157 100 1 2 157 3 159 6.85e-30 109
MS.gene049537.t1 MTR_1g077320 42.857 154 87 1 2 155 3 155 4.71e-29 104
MS.gene049537.t1 MTR_1g084950 40.909 154 90 1 2 155 3 155 2.56e-28 102
MS.gene049537.t1 MTR_2g016210 37.333 150 93 1 4 152 5 154 9.40e-28 103
MS.gene049537.t1 MTR_4g063790 36.129 155 98 1 2 155 3 157 1.44e-27 101
MS.gene049537.t1 MTR_3g467080 34.839 155 100 1 2 155 3 157 5.50e-26 97.1
MS.gene049537.t1 MTR_2g035580 37.162 148 93 0 5 152 6 153 3.12e-23 90.1
MS.gene049537.t1 MTR_1g077300 39.216 153 88 3 1 152 2 150 1.04e-22 88.6
MS.gene049537.t1 MTR_4g028800 52.174 69 31 1 4 72 5 71 5.18e-21 81.6
MS.gene049537.t1 MTR_5g047560 40.909 110 48 2 2 111 3 95 1.41e-18 77.4
MS.gene049537.t1 MTR_7g106510 30.719 153 105 1 2 154 6 157 2.79e-18 80.9
MS.gene049537.t1 MTR_3g465410 33.594 128 84 1 29 155 2 129 1.01e-17 75.1
MS.gene049537.t1 MTR_4g019670 29.412 153 107 1 2 154 6 157 1.29e-17 79.3
MS.gene049537.t1 MTR_3g093900 27.742 155 112 0 2 156 6 160 3.96e-16 75.1
MS.gene049537.t1 MTR_7g055800 32.479 117 51 2 2 118 3 91 4.26e-15 67.0
MS.gene049537.t1 MTR_6g018920 31.056 161 95 7 2 155 3 154 1.59e-13 67.0
MS.gene049537.t1 MTR_7g055940 32.692 104 42 2 2 105 3 78 1.21e-12 60.5
MS.gene049537.t1 MTR_7g055790 37.037 108 50 2 2 109 61 150 3.24e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049537.t1 AT5G48670 43.709 151 85 0 2 152 3 153 8.79e-34 121
MS.gene049537.t1 AT1G65330 37.342 158 99 0 1 158 1 158 3.27e-30 111
MS.gene049537.t1 AT1G65300 36.184 152 97 0 1 152 1 152 1.01e-29 109
MS.gene049537.t1 AT5G26650 32.903 155 104 0 4 158 3 157 2.44e-25 99.8
MS.gene049537.t1 AT5G26630 35.032 157 102 0 2 158 3 159 2.66e-25 97.1
MS.gene049537.t1 AT5G27960 32.903 155 104 0 4 158 3 157 2.68e-25 99.0
MS.gene049537.t1 AT5G27810 44.565 92 51 0 29 120 2 93 4.85e-24 90.9
MS.gene049537.t1 AT3G05860 35.294 153 99 0 2 154 3 155 6.92e-24 92.8
MS.gene049537.t1 AT3G05860 35.294 153 99 0 2 154 3 155 1.70e-23 92.8
MS.gene049537.t1 AT3G05860 35.294 153 99 0 2 154 3 155 2.13e-23 92.8
MS.gene049537.t1 AT1G31630 29.193 161 113 1 1 161 1 160 7.79e-22 90.1
MS.gene049537.t1 AT1G31640 29.801 151 105 1 1 151 1 150 1.17e-19 85.1
MS.gene049537.t1 AT5G26580 32.886 149 86 2 4 152 5 139 2.87e-19 83.2
MS.gene049537.t1 AT2G28700 30.921 152 105 0 2 153 3 154 4.41e-17 77.0
MS.gene049537.t1 AT1G22590 33.962 106 69 1 2 107 3 107 1.59e-15 70.1
MS.gene049537.t1 AT2G40210 36.364 99 63 0 2 100 3 101 4.89e-12 63.2
MS.gene049537.t1 AT5G58890 33.125 160 78 9 5 151 6 149 4.37e-11 60.1

Find 32 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGAAGTCAAAAGAGAAAT+TGG 0.291455 3.2:-57692982 MS.gene049537:CDS
CAAGGTGAAACTTGCATTCA+TGG 0.351950 3.2:-57693252 MS.gene049537:CDS
AAAAGAGAAATTGGTGAAAG+TGG 0.384195 3.2:-57692973 MS.gene049537:CDS
GAACCAAGAGAGCTATTTGA+TGG 0.414546 3.2:-57693012 MS.gene049537:CDS
CTTGTCGGAGACATTCAAAC+AGG 0.421968 3.2:+57692916 None:intergenic
GGACTTCTCCATCTCCCAAT+TGG 0.425670 3.2:+57692944 None:intergenic
TCAAAAGTTATTCAGAAGTC+GGG 0.444131 3.2:-57693052 MS.gene049537:CDS
TCTCCATCAAATAGCTCTCT+TGG 0.453856 3.2:+57693009 None:intergenic
TTCAAAAGTTATTCAGAAGT+CGG 0.458207 3.2:-57693053 MS.gene049537:CDS
CTTCCCCATTGGAGGTTCAA+AGG 0.464729 3.2:-57693088 MS.gene049537:CDS
GGTCTGGCCTTCCCCATTGG+AGG 0.467393 3.2:-57693096 MS.gene049537:CDS
TTCAATCAGAGGCAGAGGTC+TGG 0.467622 3.2:-57693112 MS.gene049537:CDS
AGAGGTCTGGCCTTCCCCAT+TGG 0.477211 3.2:-57693099 MS.gene049537:CDS
TAATCCTTTGAACCTCCAAT+GGG 0.502458 3.2:+57693084 None:intergenic
TGAAAGTGGAGAAAACCAAT+TGG 0.503387 3.2:-57692959 MS.gene049537:CDS
ATTCAGAAGTCGGGCAAGGA+AGG 0.517455 3.2:-57693043 MS.gene049537:CDS
ATAATCCTTTGAACCTCCAA+TGG 0.537452 3.2:+57693083 None:intergenic
CATGAATGCAAGTTTCACCT+TGG 0.541041 3.2:+57693253 None:intergenic
GATGAACTCACTACGCTATG+TGG 0.541967 3.2:-57693167 MS.gene049537:CDS
GAAAGTGGAGAAAACCAATT+GGG 0.551602 3.2:-57692958 MS.gene049537:CDS
CGAATTTCAATCAGAGGCAG+AGG 0.555745 3.2:-57693117 MS.gene049537:CDS
GAGACATTCAAACAGGATCA+AGG 0.560270 3.2:+57692923 None:intergenic
AAGAGAGCTATTTGATGGAG+AGG 0.560879 3.2:-57693007 MS.gene049537:CDS
ATGAACTCACTACGCTATGT+GGG 0.582602 3.2:-57693166 MS.gene049537:CDS
TGAAATTAATGAGAAGCTGA+AGG 0.586463 3.2:-57692844 MS.gene049537:CDS
GGAGAAAACCAATTGGGAGA+TGG 0.587398 3.2:-57692952 MS.gene049537:CDS
TTATAGCGAATTTCAATCAG+AGG 0.601897 3.2:-57693123 MS.gene049537:CDS
AGTTATTCAGAAGTCGGGCA+AGG 0.603949 3.2:-57693047 MS.gene049537:CDS
CTTTGAACCTCCAATGGGGA+AGG 0.605253 3.2:+57693089 None:intergenic
TCATGGTCAATGATTCTGCA+AGG 0.642899 3.2:-57693235 MS.gene049537:CDS
TACATTGAGGATGAGAACCA+AGG 0.710018 3.2:-57693270 None:intergenic
AATCCTTTGAACCTCCAATG+GGG 0.726583 3.2:+57693085 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTGATAAAATTTTCTTGT+CGG + chr3.2:57693159-57693178 None:intergenic 20.0%
! TTCAAAAGTTATTCAGAAGT+CGG - chr3.2:57693004-57693023 MS.gene049537:CDS 25.0%
AAAAAAGAGTCTGAAGAAGA+TGG - chr3.2:57692865-57692884 MS.gene049537:CDS 30.0%
AAAAGAGAAATTGGTGAAAG+TGG - chr3.2:57693084-57693103 MS.gene049537:CDS 30.0%
TCAAAAGTTATTCAGAAGTC+GGG - chr3.2:57693005-57693024 MS.gene049537:CDS 30.0%
TGAAATTAATGAGAAGCTGA+AGG - chr3.2:57693213-57693232 MS.gene049537:CDS 30.0%
TGTGAAGTCAAAAGAGAAAT+TGG - chr3.2:57693075-57693094 MS.gene049537:CDS 30.0%
TTATAGCGAATTTCAATCAG+AGG - chr3.2:57692934-57692953 MS.gene049537:CDS 30.0%
ATAATCCTTTGAACCTCCAA+TGG + chr3.2:57692977-57692996 None:intergenic 35.0%
GAAAGTGGAGAAAACCAATT+GGG - chr3.2:57693099-57693118 MS.gene049537:CDS 35.0%
TAATCCTTTGAACCTCCAAT+GGG + chr3.2:57692976-57692995 None:intergenic 35.0%
TGAAAGTGGAGAAAACCAAT+TGG - chr3.2:57693098-57693117 MS.gene049537:CDS 35.0%
AAGAGAGCTATTTGATGGAG+AGG - chr3.2:57693050-57693069 MS.gene049537:CDS 40.0%
AATCCTTTGAACCTCCAATG+GGG + chr3.2:57692975-57692994 None:intergenic 40.0%
ATGAACTCACTACGCTATGT+GGG - chr3.2:57692891-57692910 MS.gene049537:CDS 40.0%
CAAGGTGAAACTTGCATTCA+TGG - chr3.2:57692805-57692824 MS.gene049537:CDS 40.0%
CATGAATGCAAGTTTCACCT+TGG + chr3.2:57692807-57692826 None:intergenic 40.0%
GAACCAAGAGAGCTATTTGA+TGG - chr3.2:57693045-57693064 MS.gene049537:CDS 40.0%
GAGACATTCAAACAGGATCA+AGG + chr3.2:57693137-57693156 None:intergenic 40.0%
TCATGGTCAATGATTCTGCA+AGG - chr3.2:57692822-57692841 MS.gene049537:CDS 40.0%
TCTCCATCAAATAGCTCTCT+TGG + chr3.2:57693051-57693070 None:intergenic 40.0%
AGTTATTCAGAAGTCGGGCA+AGG - chr3.2:57693010-57693029 MS.gene049537:CDS 45.0%
CGAATTTCAATCAGAGGCAG+AGG - chr3.2:57692940-57692959 MS.gene049537:CDS 45.0%
CTTGTCGGAGACATTCAAAC+AGG + chr3.2:57693144-57693163 None:intergenic 45.0%
GATGAACTCACTACGCTATG+TGG - chr3.2:57692890-57692909 MS.gene049537:CDS 45.0%
GGAGAAAACCAATTGGGAGA+TGG - chr3.2:57693105-57693124 MS.gene049537:CDS 45.0%
ATTCAGAAGTCGGGCAAGGA+AGG - chr3.2:57693014-57693033 MS.gene049537:CDS 50.0%
CTTCCCCATTGGAGGTTCAA+AGG - chr3.2:57692969-57692988 MS.gene049537:CDS 50.0%
CTTTGAACCTCCAATGGGGA+AGG + chr3.2:57692971-57692990 None:intergenic 50.0%
GGACTTCTCCATCTCCCAAT+TGG + chr3.2:57693116-57693135 None:intergenic 50.0%
TTCAATCAGAGGCAGAGGTC+TGG - chr3.2:57692945-57692964 MS.gene049537:CDS 50.0%
! AGAGGTCTGGCCTTCCCCAT+TGG - chr3.2:57692958-57692977 MS.gene049537:CDS 60.0%
! GGTCTGGCCTTCCCCATTGG+AGG - chr3.2:57692961-57692980 MS.gene049537:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 57692797 57693282 57692797 ID=MS.gene049537
chr3.2 mRNA 57692797 57693282 57692797 ID=MS.gene049537.t1;Parent=MS.gene049537
chr3.2 exon 57692797 57693282 57692797 ID=MS.gene049537.t1.exon1;Parent=MS.gene049537.t1
chr3.2 CDS 57692797 57693282 57692797 ID=cds.MS.gene049537.t1;Parent=MS.gene049537.t1
Gene Sequence

>MS.gene049537

ATGAGAACCAAGGTGAAACTTGCATTCATGGTCAATGATTCTGCAAGGAAAATAACTTACAACAAAAGAAAAAAGAGTCTGAAGAAGATGGTTGATGAACTCACTACGCTATGTGGGATTGATGTGTGCGCTATACTTTATAGCGAATTTCAATCAGAGGCAGAGGTCTGGCCTTCCCCATTGGAGGTTCAAAGGATTATCACAAAGTTCAAAAGTTATTCAGAAGTCGGGCAAGGAAGGAAGAAGTTGAACCAAGAGAGCTATTTGATGGAGAGGATTGTGAAGTCAAAAGAGAAATTGGTGAAAGTGGAGAAAACCAATTGGGAGATGGAGAAGTCCTTGATCCTGTTTGAATGTCTCCGACAAGAAAATTTTATCAACACTTTGAACACAAACGTTTTGAATGATCTAGCATGTGAAATTAATGAGAAGCTGAAGGAAATTACTTCAAAGATGAATCAGCTTGACACAAATGAAAGCACTTAG
Protein sequence

>MS.gene049537.t1

MRTKVKLAFMVNDSARKITYNKRKKSLKKMVDELTTLCGIDVCAILYSEFQSEAEVWPSPLEVQRIITKFKSYSEVGQGRKKLNQESYLMERIVKSKEKLVKVEKTNWEMEKSLILFECLRQENFINTLNTNVLNDLACEINEKLKEITSKMNQLDTNEST