AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040028

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040028.t1 MTR_3g071420 97.297 185 5 0 1 185 1 185 2.07e-136 379
MS.gene040028.t1 MTR_5g083010 73.077 182 44 1 4 185 1 177 1.67e-89 259
MS.gene040028.t1 MTR_7g033800 64.151 106 38 0 11 116 8 113 7.06e-46 149
MS.gene040028.t1 MTR_6g005070 65.094 106 37 0 11 116 6 111 2.20e-45 147
MS.gene040028.t1 MTR_5g083230 64.078 103 37 0 12 114 4 106 6.39e-44 144
MS.gene040028.t1 MTR_3g031660 52.000 125 59 1 12 136 5 128 2.94e-43 142
MS.gene040028.t1 MTR_3g071590 62.500 104 39 0 11 114 5 108 3.60e-43 141
MS.gene040028.t1 MTR_4g105170 45.087 173 72 4 12 184 9 158 3.72e-43 142
MS.gene040028.t1 MTR_4g083680 46.667 150 77 1 11 160 12 158 6.08e-43 141
MS.gene040028.t1 MTR_3g077240 61.905 105 40 0 12 116 8 112 8.03e-43 142
MS.gene040028.t1 MTR_6g005080 62.264 106 40 0 11 116 7 112 8.22e-43 140
MS.gene040028.t1 MTR_3g073690 61.905 105 40 0 11 115 6 110 1.04e-41 139
MS.gene040028.t1 MTR_5g083960 47.826 138 70 1 11 148 36 171 2.77e-41 138
MS.gene040028.t1 MTR_2g068760 58.491 106 44 0 6 111 5 110 2.18e-40 134
MS.gene040028.t1 MTR_5g017950 56.303 119 52 0 11 129 5 123 3.05e-40 139
MS.gene040028.t1 MTR_3g452660 60.000 105 42 0 11 115 4 108 3.77e-40 138
MS.gene040028.t1 MTR_8g040900 55.725 131 51 2 11 134 4 134 3.15e-39 134
MS.gene040028.t1 MTR_3g094690 55.046 109 49 0 15 123 48 156 2.02e-37 129
MS.gene040028.t1 MTR_5g075020 55.263 114 51 0 15 128 44 157 2.36e-36 126
MS.gene040028.t1 MTR_5g075020 55.263 114 51 0 15 128 48 161 4.02e-36 126
MS.gene040028.t1 MTR_2g093310 54.902 102 46 0 13 114 32 133 6.13e-36 124
MS.gene040028.t1 MTR_3g094690 54.128 109 49 1 15 123 48 155 6.84e-35 122
MS.gene040028.t1 MTR_7g096530 48.276 116 59 1 1 115 1 116 3.14e-34 120
MS.gene040028.t1 MTR_1g070220 50.435 115 55 2 1 113 1 115 3.52e-34 120
MS.gene040028.t1 MTR_1g095850 44.000 150 73 3 15 158 73 217 4.24e-34 120
MS.gene040028.t1 MTR_4g060950 56.701 97 41 1 13 108 23 119 5.66e-34 119
MS.gene040028.t1 MTR_8g036085 39.752 161 93 3 15 174 24 181 6.51e-34 120
MS.gene040028.t1 MTR_8g036105 49.558 113 56 1 4 115 8 120 9.85e-34 119
MS.gene040028.t1 MTR_7g074990 51.485 101 48 1 15 114 21 121 2.13e-33 119
MS.gene040028.t1 MTR_6g027710 39.716 141 83 2 15 153 41 181 1.47e-32 116
MS.gene040028.t1 MTR_7g096610 49.541 109 53 2 11 117 5 113 5.06e-32 115
MS.gene040028.t1 MTR_7g028905 44.660 103 57 0 13 115 4 106 4.00e-31 109
MS.gene040028.t1 MTR_1g070205 48.544 103 52 1 15 116 13 115 1.00e-30 112
MS.gene040028.t1 MTR_5g080470 45.283 106 57 1 12 116 5 110 1.73e-30 110
MS.gene040028.t1 MTR_7g075230 39.073 151 85 3 15 162 13 159 5.18e-30 109
MS.gene040028.t1 MTR_5g093010 43.564 101 57 0 15 115 6 106 2.92e-29 105
MS.gene040028.t1 MTR_8g079660 48.039 102 53 0 15 116 9 110 1.46e-27 104
MS.gene040028.t1 MTR_6g027700 40.517 116 68 1 15 129 8 123 1.23e-26 100
MS.gene040028.t1 MTR_8g079620 44.118 102 57 0 15 116 9 110 6.29e-24 94.7
MS.gene040028.t1 MTR_4g107450 39.815 108 65 0 11 118 7 114 9.70e-24 95.5
MS.gene040028.t1 MTR_6g011230 34.266 143 86 2 11 152 8 143 4.43e-22 89.0
MS.gene040028.t1 MTR_6g011200 37.273 110 68 1 10 118 5 114 9.17e-22 89.4
MS.gene040028.t1 MTR_8g079580 42.718 103 58 1 15 116 9 111 2.24e-21 87.8
MS.gene040028.t1 MTR_2g100020 33.028 109 73 0 11 119 16 124 1.42e-20 86.7
MS.gene040028.t1 MTR_6g011250 36.364 110 69 1 10 118 5 114 2.76e-20 84.0
MS.gene040028.t1 MTR_8g017090 33.333 108 72 0 11 118 9 116 1.28e-19 84.3
MS.gene040028.t1 MTR_5g085390 29.814 161 97 4 10 165 5 154 6.30e-19 81.3
MS.gene040028.t1 MTR_4g099230 32.231 121 73 3 15 130 3 119 1.53e-18 78.6
MS.gene040028.t1 MTR_4g088035 31.818 88 60 0 13 100 5 92 8.56e-14 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040028.t1 AT3G11090 78.378 111 24 0 4 114 1 111 4.40e-62 190
MS.gene040028.t1 AT3G27650 64.151 106 38 0 11 116 36 141 2.06e-44 145
MS.gene040028.t1 AT5G66870 62.857 105 39 0 11 115 4 108 6.61e-43 145
MS.gene040028.t1 AT5G63090 52.239 134 60 1 12 145 9 138 1.10e-42 141
MS.gene040028.t1 AT5G63090 52.239 134 60 1 12 145 9 138 1.10e-42 141
MS.gene040028.t1 AT5G63090 52.239 134 60 1 12 145 9 138 1.10e-42 141
MS.gene040028.t1 AT5G63090 52.239 134 60 1 12 145 9 138 1.10e-42 141
MS.gene040028.t1 AT2G23660 60.577 104 41 0 11 114 2 105 1.49e-41 142
MS.gene040028.t1 AT2G23660 60.577 104 41 0 11 114 2 105 1.49e-41 142
MS.gene040028.t1 AT2G23660 60.577 104 41 0 11 114 2 105 1.49e-41 142
MS.gene040028.t1 AT2G30130 59.615 104 42 0 11 114 5 108 4.79e-41 137
MS.gene040028.t1 AT2G30340 55.263 114 50 1 15 128 54 166 1.68e-38 133
MS.gene040028.t1 AT2G30340 55.263 114 50 1 15 128 53 165 1.99e-38 133
MS.gene040028.t1 AT1G16530 47.887 142 66 3 10 144 10 150 2.16e-38 129
MS.gene040028.t1 AT1G65620 55.652 115 51 0 11 125 6 120 7.36e-38 129
MS.gene040028.t1 AT1G65620 55.652 115 51 0 11 125 6 120 7.36e-38 129
MS.gene040028.t1 AT1G65620 55.652 115 51 0 11 125 6 120 7.36e-38 129
MS.gene040028.t1 AT1G65620 55.652 115 51 0 11 125 6 120 7.36e-38 129
MS.gene040028.t1 AT1G65620 55.652 115 51 0 11 125 6 120 7.36e-38 129
MS.gene040028.t1 AT2G40470 53.333 120 56 0 15 134 21 140 2.67e-37 128
MS.gene040028.t1 AT2G40470 53.333 120 56 0 15 134 46 165 5.27e-37 128
MS.gene040028.t1 AT1G07900 58.586 99 41 0 13 111 32 130 8.12e-37 126
MS.gene040028.t1 AT1G31320 60.000 90 36 0 11 100 10 99 8.79e-37 125
MS.gene040028.t1 AT2G28500 58.333 96 40 0 13 108 54 149 1.75e-35 124
MS.gene040028.t1 AT4G00210 52.336 107 50 1 15 120 12 118 1.40e-34 121
MS.gene040028.t1 AT3G03760 48.649 111 56 1 13 122 50 160 3.36e-34 122
MS.gene040028.t1 AT2G42430 47.500 120 62 1 5 123 6 125 3.77e-33 119
MS.gene040028.t1 AT3G26660 48.515 101 52 0 15 115 6 106 7.78e-33 114
MS.gene040028.t1 AT3G26620 48.515 101 52 0 15 115 6 106 9.26e-33 114
MS.gene040028.t1 AT4G00220 53.000 100 46 1 17 115 20 119 2.13e-32 116
MS.gene040028.t1 AT2G45420 50.000 100 49 1 17 115 40 139 4.35e-32 116
MS.gene040028.t1 AT3G58190 39.597 149 78 4 15 162 12 149 5.85e-32 115
MS.gene040028.t1 AT2G42440 39.130 138 75 2 11 147 4 133 1.11e-30 112
MS.gene040028.t1 AT2G45410 51.000 100 48 1 17 115 19 118 4.71e-30 109
MS.gene040028.t1 AT5G06080 45.631 103 55 1 13 114 6 108 4.71e-30 108
MS.gene040028.t1 AT2G31310 43.396 106 59 1 12 116 5 110 3.25e-29 107
MS.gene040028.t1 AT3G50510 46.226 106 57 0 10 115 8 113 1.01e-27 103
MS.gene040028.t1 AT3G50510 46.226 106 57 0 10 115 8 113 1.01e-27 103
MS.gene040028.t1 AT5G35900 35.971 139 87 1 11 149 2 138 7.10e-27 101
MS.gene040028.t1 AT3G13850 33.793 145 88 2 14 158 36 172 2.18e-23 94.0
MS.gene040028.t1 AT1G72980 33.846 130 86 0 11 140 10 139 8.22e-22 88.6
MS.gene040028.t1 AT3G47870 34.862 109 71 0 11 119 33 141 1.92e-19 84.3
MS.gene040028.t1 AT4G22700 39.252 107 61 3 11 115 2 106 1.88e-18 79.3
MS.gene040028.t1 AT1G06280 44.872 78 43 0 14 91 24 101 5.32e-18 78.2
MS.gene040028.t1 AT5G15060 39.474 76 42 2 13 85 16 90 2.51e-12 62.0
MS.gene040028.t1 AT2G19820 36.905 84 52 1 15 97 13 96 4.11e-12 60.8

Find 28 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTAAAGTTCACAAAGTATT+TGG 0.136847 3.2:-64735992 MS.gene040028:CDS
AGGCTTAAAGACCCAGTTTA+TGG 0.242004 3.2:-64735881 MS.gene040028:CDS
CCATATGATCAAAATGTATA+AGG 0.308499 3.2:+64735578 None:intergenic
GAACCAATGCATCCATAAAC+TGG 0.317210 3.2:+64735869 None:intergenic
GATGGAACTTCAACATGATT+TGG 0.337444 3.2:-64735822 MS.gene040028:CDS
AAGTGAAATGAAAGGCATAA+AGG 0.382977 3.2:-64736128 None:intergenic
ATTTCTTGCACTCGTTAGAA+TGG 0.427400 3.2:+64736017 None:intergenic
GACCCAGTTTATGGATGCAT+TGG 0.436697 3.2:-64735872 MS.gene040028:CDS
AGTGAAATGAAAGGCATAAA+GGG 0.450119 3.2:-64736127 None:intergenic
GAAGTGGAAAACTCAGGAAA+TGG 0.459553 3.2:+64735686 None:intergenic
TAAGGTGCAAATAAGCAATC+TGG 0.484939 3.2:+64736043 None:intergenic
CTTCCTTTGCAACATAGCTA+TGG 0.497960 3.2:+64735847 None:intergenic
ACATGATTTGGCCATTGCTA+AGG 0.501000 3.2:-64735810 MS.gene040028:CDS
CACTCGTTAGAATGGAAGTA+AGG 0.514845 3.2:+64736025 None:intergenic
ATCATTGAGATCGTTAGAAG+TGG 0.559617 3.2:+64735670 None:intergenic
TATGTTGCAAAGGAAGATGA+TGG 0.575914 3.2:-64735840 MS.gene040028:CDS
GTTCCATAGCTATGTTGCAA+AGG 0.579187 3.2:-64735850 MS.gene040028:CDS
AGCAAGACGTTCCTTAGCAA+TGG 0.581078 3.2:+64735799 None:intergenic
TGCAAACTATCAATTACAGA+AGG 0.600990 3.2:+64735728 None:intergenic
TCGTTAGAAGTGGAAAACTC+AGG 0.603635 3.2:+64735680 None:intergenic
AATTACAGAAGGAGTTGTTG+TGG 0.604155 3.2:+64735739 None:intergenic
TTGCTTATGAAGCAGAAGCA+AGG 0.610245 3.2:-64735901 MS.gene040028:CDS
TTTGGGTCGAAATGAAACAA+TGG 0.611284 3.2:-64735618 MS.gene040028:CDS
AACCAATGCATCCATAAACT+GGG 0.613188 3.2:+64735870 None:intergenic
GTGGAAAACTCAGGAAATGG+AGG 0.620928 3.2:+64735689 None:intergenic
GTGCACACAAGTGAAATGAA+AGG 0.632849 3.2:-64736136 None:intergenic
GCACAAGATGAGCTTGAACG+TGG 0.651989 3.2:+64736097 None:intergenic
TACAGAAGGAGTTGTTGTGG+TGG 0.695339 3.2:+64735742 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGCAAACTATCAATTACAGA+AGG + chr3.2:64735982-64736001 None:intergenic 30.0%
! CTCAATGATATCTTTTGTCA+TGG - chr3.2:64736051-64736070 MS.gene040028:CDS 30.0%
! GCTAAAGTTCACAAAGTATT+TGG - chr3.2:64735715-64735734 MS.gene040028:CDS 30.0%
AACCAATGCATCCATAAACT+GGG + chr3.2:64735840-64735859 None:intergenic 35.0%
AATTACAGAAGGAGTTGTTG+TGG + chr3.2:64735971-64735990 None:intergenic 35.0%
ATCATTGAGATCGTTAGAAG+TGG + chr3.2:64736040-64736059 None:intergenic 35.0%
ATTTCTTGCACTCGTTAGAA+TGG + chr3.2:64735693-64735712 None:intergenic 35.0%
GATGGAACTTCAACATGATT+TGG - chr3.2:64735885-64735904 MS.gene040028:CDS 35.0%
TAAGGTGCAAATAAGCAATC+TGG + chr3.2:64735667-64735686 None:intergenic 35.0%
TATGTTGCAAAGGAAGATGA+TGG - chr3.2:64735867-64735886 MS.gene040028:CDS 35.0%
TTTGGGTCGAAATGAAACAA+TGG - chr3.2:64736089-64736108 MS.gene040028:CDS 35.0%
!!! GTGTCTTCTCTTTGTTTTTC+TGG + chr3.2:64735775-64735794 None:intergenic 35.0%
AGGCTTAAAGACCCAGTTTA+TGG - chr3.2:64735826-64735845 MS.gene040028:CDS 40.0%
CACTCGTTAGAATGGAAGTA+AGG + chr3.2:64735685-64735704 None:intergenic 40.0%
CTTCCTTTGCAACATAGCTA+TGG + chr3.2:64735863-64735882 None:intergenic 40.0%
GAACCAATGCATCCATAAAC+TGG + chr3.2:64735841-64735860 None:intergenic 40.0%
GAAGTGGAAAACTCAGGAAA+TGG + chr3.2:64736024-64736043 None:intergenic 40.0%
GTTCCATAGCTATGTTGCAA+AGG - chr3.2:64735857-64735876 MS.gene040028:CDS 40.0%
TCGTTAGAAGTGGAAAACTC+AGG + chr3.2:64736030-64736049 None:intergenic 40.0%
TTGCTTATGAAGCAGAAGCA+AGG - chr3.2:64735806-64735825 MS.gene040028:CDS 40.0%
! ACATGATTTGGCCATTGCTA+AGG - chr3.2:64735897-64735916 MS.gene040028:CDS 40.0%
! GGCTCTTCTTCGCAATTTTT+GGG - chr3.2:64736072-64736091 MS.gene040028:CDS 40.0%
! TGGCTCTTCTTCGCAATTTT+TGG - chr3.2:64736071-64736090 MS.gene040028:CDS 40.0%
AGCAAGACGTTCCTTAGCAA+TGG + chr3.2:64735911-64735930 None:intergenic 45.0%
GACCCAGTTTATGGATGCAT+TGG - chr3.2:64735835-64735854 MS.gene040028:CDS 45.0%
GTGGAAAACTCAGGAAATGG+AGG + chr3.2:64736021-64736040 None:intergenic 45.0%
TACAGAAGGAGTTGTTGTGG+TGG + chr3.2:64735968-64735987 None:intergenic 45.0%
GCACAAGATGAGCTTGAACG+TGG + chr3.2:64735613-64735632 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 64735586 64736143 64735586 ID=MS.gene040028
chr3.2 mRNA 64735586 64736143 64735586 ID=MS.gene040028.t1;Parent=MS.gene040028
chr3.2 exon 64735586 64736143 64735586 ID=MS.gene040028.t1.exon1;Parent=MS.gene040028.t1
chr3.2 CDS 64735586 64736143 64735586 ID=cds.MS.gene040028.t1;Parent=MS.gene040028.t1
Gene Sequence

>MS.gene040028

ATGAAAGGCATAAAGGGTTATGAGCCACGTTCAAGCTCATCTTGTGCAGCTTGCAAATTATTGAAAAGAAGATGCACACCAGATTGCTTATTTGCACCTTACTTCCATTCTAACGAGTGCAAGAAATTTGCTAAAGTTCACAAAGTATTTGGAGCAAGCAATGTTAGCAAGATACTCATTGAAGTACCAGAAAAACAAAGAGAAGACACAGTGAATTCTCTTGCTTATGAAGCAGAAGCAAGGCTTAAAGACCCAGTTTATGGATGCATTGGTTCCATAGCTATGTTGCAAAGGAAGATGATGGAACTTCAACATGATTTGGCCATTGCTAAGGAACGTCTTGCTCGCTGTCGTGCTGTTGCTGCAGCTGCTACAATCACCACCACAACAACTCCTTCTGTAATTGATAGTTTGCATTCTGATGTTACTTTGCCTCCATTTCCTGAGTTTTCCACTTCTAACGATCTCAATGATATCTTTTGTCATGGCTCTTCTTCGCAATTTTTGGGTCGAAATGAAACAATGGATGATTTCAATCAAATTCCTTATACATTTTGA
Protein sequence

>MS.gene040028.t1

MKGIKGYEPRSSSSCAACKLLKRRCTPDCLFAPYFHSNECKKFAKVHKVFGASNVSKILIEVPEKQREDTVNSLAYEAEARLKDPVYGCIGSIAMLQRKMMELQHDLAIAKERLARCRAVAAAATITTTTTPSVIDSLHSDVTLPPFPEFSTSNDLNDIFCHGSSSQFLGRNETMDDFNQIPYTF