AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene032616

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032616.t1 MTR_6g005070 99.310 145 1 0 1 145 1 145 1.74e-106 300
MS.gene032616.t1 MTR_6g005080 92.143 140 11 0 1 140 2 141 2.12e-94 269
MS.gene032616.t1 MTR_7g033800 68.675 166 32 4 2 149 4 167 9.43e-72 213
MS.gene032616.t1 MTR_3g077240 64.151 159 30 2 1 132 1 159 1.10e-65 198
MS.gene032616.t1 MTR_4g105170 83.810 105 17 0 7 111 9 113 4.25e-64 194
MS.gene032616.t1 MTR_4g083680 56.522 138 56 3 8 141 14 151 1.40e-49 157
MS.gene032616.t1 MTR_5g083230 57.377 122 52 0 7 128 4 125 1.13e-48 154
MS.gene032616.t1 MTR_5g017950 67.290 107 35 0 3 109 2 108 1.53e-48 159
MS.gene032616.t1 MTR_3g073690 66.972 109 36 0 1 109 1 109 4.55e-48 154
MS.gene032616.t1 MTR_2g068760 60.714 112 43 1 8 118 12 123 4.98e-48 152
MS.gene032616.t1 MTR_8g040900 69.643 112 32 1 1 112 1 110 7.78e-48 154
MS.gene032616.t1 MTR_3g071590 51.613 155 65 4 6 151 5 158 1.36e-46 149
MS.gene032616.t1 MTR_3g452660 65.455 110 38 0 4 113 2 111 1.65e-46 153
MS.gene032616.t1 MTR_3g031660 56.637 113 49 0 7 119 5 117 9.06e-46 147
MS.gene032616.t1 MTR_5g083010 64.151 106 38 0 6 111 8 113 2.28e-44 144
MS.gene032616.t1 MTR_3g071420 68.041 97 31 0 6 102 11 107 7.37e-44 143
MS.gene032616.t1 MTR_2g093310 53.279 122 57 0 1 122 25 146 8.55e-44 143
MS.gene032616.t1 MTR_5g083960 60.577 104 41 0 6 109 36 139 1.22e-42 140
MS.gene032616.t1 MTR_3g094690 59.615 104 42 0 8 111 46 149 3.54e-42 140
MS.gene032616.t1 MTR_4g060950 47.015 134 70 1 8 140 23 156 4.79e-40 133
MS.gene032616.t1 MTR_3g094690 58.654 104 42 1 8 111 46 148 1.18e-39 134
MS.gene032616.t1 MTR_1g095850 51.327 113 55 0 10 122 73 185 1.53e-38 130
MS.gene032616.t1 MTR_5g075020 56.637 113 49 0 8 120 42 154 2.84e-38 130
MS.gene032616.t1 MTR_5g075020 56.637 113 49 0 8 120 46 158 3.83e-38 130
MS.gene032616.t1 MTR_7g096530 56.881 109 46 1 2 109 7 115 1.52e-37 127
MS.gene032616.t1 MTR_1g070220 49.296 142 64 4 6 139 12 153 1.52e-36 125
MS.gene032616.t1 MTR_8g036085 55.882 102 44 1 9 109 23 124 2.37e-34 120
MS.gene032616.t1 MTR_7g074990 58.947 95 38 1 9 102 20 114 3.83e-34 119
MS.gene032616.t1 MTR_8g036105 54.717 106 47 1 9 113 18 123 5.20e-34 119
MS.gene032616.t1 MTR_6g027710 48.276 116 57 2 8 120 39 154 1.70e-33 117
MS.gene032616.t1 MTR_7g028905 48.039 102 53 0 8 109 4 105 4.78e-32 110
MS.gene032616.t1 MTR_5g080470 52.577 97 45 1 8 103 6 102 5.22e-32 113
MS.gene032616.t1 MTR_8g079660 49.074 108 54 1 9 115 8 115 9.86e-32 114
MS.gene032616.t1 MTR_7g075230 53.704 108 47 2 9 113 12 119 1.95e-31 111
MS.gene032616.t1 MTR_7g096610 54.082 98 44 1 6 102 5 102 2.92e-31 112
MS.gene032616.t1 MTR_5g093010 48.113 106 48 1 10 115 6 104 9.15e-31 108
MS.gene032616.t1 MTR_1g070205 51.579 95 45 1 9 102 12 106 2.56e-30 109
MS.gene032616.t1 MTR_6g011200 45.918 98 52 1 7 103 7 104 9.36e-28 103
MS.gene032616.t1 MTR_4g107450 47.000 100 53 0 10 109 11 110 2.61e-27 103
MS.gene032616.t1 MTR_8g079620 43.689 103 58 0 9 111 8 110 4.79e-27 101
MS.gene032616.t1 MTR_6g027700 46.535 101 53 1 9 108 7 107 1.12e-26 99.8
MS.gene032616.t1 MTR_8g079580 47.115 104 54 1 9 111 8 111 3.03e-26 99.4
MS.gene032616.t1 MTR_6g011230 41.000 100 59 0 6 105 8 107 2.16e-25 96.3
MS.gene032616.t1 MTR_6g011250 42.857 105 59 1 6 109 6 110 1.76e-24 93.6
MS.gene032616.t1 MTR_2g100020 43.750 96 54 0 10 105 20 115 8.44e-24 94.0
MS.gene032616.t1 MTR_8g017090 40.385 104 62 0 6 109 9 112 1.55e-23 93.6
MS.gene032616.t1 MTR_4g099230 40.000 95 56 1 10 103 3 97 5.58e-21 83.6
MS.gene032616.t1 MTR_5g085390 41.837 98 56 1 7 103 7 104 2.03e-20 84.0
MS.gene032616.t1 MTR_4g088035 31.111 90 62 0 8 97 5 94 3.27e-15 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032616.t1 AT3G27650 76.423 123 25 1 3 121 33 155 2.37e-67 201
MS.gene032616.t1 AT5G63090 75.591 127 29 1 1 125 1 127 9.43e-65 196
MS.gene032616.t1 AT5G63090 75.591 127 29 1 1 125 1 127 9.43e-65 196
MS.gene032616.t1 AT5G63090 75.591 127 29 1 1 125 1 127 9.43e-65 196
MS.gene032616.t1 AT5G63090 75.591 127 29 1 1 125 1 127 9.43e-65 196
MS.gene032616.t1 AT2G30130 60.169 118 47 0 7 124 6 123 1.71e-49 157
MS.gene032616.t1 AT1G65620 66.379 116 39 0 1 116 1 116 2.06e-48 155
MS.gene032616.t1 AT1G65620 66.379 116 39 0 1 116 1 116 2.06e-48 155
MS.gene032616.t1 AT1G65620 66.379 116 39 0 1 116 1 116 2.06e-48 155
MS.gene032616.t1 AT1G65620 66.379 116 39 0 1 116 1 116 2.06e-48 155
MS.gene032616.t1 AT1G65620 66.379 116 39 0 1 116 1 116 2.06e-48 155
MS.gene032616.t1 AT5G66870 66.055 109 35 1 1 109 1 107 5.00e-48 157
MS.gene032616.t1 AT2G23660 64.762 105 37 0 6 110 2 106 7.40e-48 157
MS.gene032616.t1 AT2G23660 64.762 105 37 0 6 110 2 106 7.40e-48 157
MS.gene032616.t1 AT2G23660 64.762 105 37 0 6 110 2 106 7.40e-48 157
MS.gene032616.t1 AT1G31320 69.318 88 27 0 8 95 12 99 7.45e-44 142
MS.gene032616.t1 AT1G07900 54.783 115 52 0 8 122 32 146 1.31e-43 142
MS.gene032616.t1 AT2G30340 55.752 113 50 0 8 120 51 163 1.90e-43 144
MS.gene032616.t1 AT2G30340 55.752 113 50 0 8 120 52 164 1.91e-43 144
MS.gene032616.t1 AT1G16530 62.617 107 39 1 8 113 13 119 2.91e-43 140
MS.gene032616.t1 AT2G28500 55.652 115 51 0 8 122 54 168 1.07e-42 141
MS.gene032616.t1 AT3G11090 58.559 111 44 1 6 116 8 116 1.26e-41 136
MS.gene032616.t1 AT2G40470 60.185 108 43 0 8 115 19 126 1.21e-40 135
MS.gene032616.t1 AT2G40470 60.185 108 43 0 8 115 44 151 2.45e-40 135
MS.gene032616.t1 AT3G26660 55.000 100 45 0 10 109 6 105 1.96e-38 127
MS.gene032616.t1 AT3G26620 55.000 100 45 0 10 109 6 105 2.16e-38 127
MS.gene032616.t1 AT2G42430 52.500 120 54 2 6 124 12 129 1.05e-35 124
MS.gene032616.t1 AT3G03760 54.808 104 46 1 8 110 50 153 1.97e-35 124
MS.gene032616.t1 AT4G00220 56.311 103 44 1 12 113 20 122 4.79e-34 119
MS.gene032616.t1 AT5G06080 54.639 97 43 1 8 103 6 102 1.82e-33 116
MS.gene032616.t1 AT4G00210 54.717 106 47 1 9 113 11 116 2.00e-33 117
MS.gene032616.t1 AT2G45420 55.340 103 45 1 12 113 40 142 5.32e-33 117
MS.gene032616.t1 AT3G58190 52.083 96 45 1 9 103 11 106 2.48e-31 112
MS.gene032616.t1 AT2G31310 52.083 96 45 1 8 102 6 101 2.63e-31 111
MS.gene032616.t1 AT2G45410 56.566 99 42 1 12 109 19 117 3.53e-31 110
MS.gene032616.t1 AT2G42440 49.495 99 49 1 6 103 4 102 9.01e-31 111
MS.gene032616.t1 AT3G50510 46.602 103 55 0 7 109 10 112 9.65e-30 107
MS.gene032616.t1 AT3G50510 46.602 103 55 0 7 109 10 112 9.65e-30 107
MS.gene032616.t1 AT3G13850 43.617 94 53 0 10 103 37 130 2.97e-25 97.4
MS.gene032616.t1 AT5G35900 45.000 100 55 0 10 109 6 105 3.57e-25 95.9
MS.gene032616.t1 AT3G47870 39.423 104 63 0 6 109 33 136 9.68e-25 97.4
MS.gene032616.t1 AT1G72980 41.346 104 61 0 6 109 10 113 2.03e-22 89.0
MS.gene032616.t1 AT1G06280 45.161 93 50 1 10 102 25 116 4.96e-21 85.1
MS.gene032616.t1 AT4G22700 34.921 126 71 4 10 134 6 121 6.64e-17 73.9
MS.gene032616.t1 AT2G19820 38.542 96 57 2 6 100 9 103 2.29e-16 70.9
MS.gene032616.t1 AT5G15060 36.986 73 44 1 10 80 18 90 1.19e-12 61.6
MS.gene032616.t1 AT3G27940 37.879 66 41 0 9 74 5 70 9.79e-11 57.0
MS.gene032616.t1 AT3G27940 37.879 66 41 0 9 74 5 70 9.79e-11 57.0
MS.gene032616.t1 AT3G27940 37.879 66 41 0 9 74 5 70 9.79e-11 57.0

Find 25 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAATGTTCACAAAATATT+TGG 0.192290 6.3:+1162034 MS.gene032616:CDS
GCAAACTTATGAGGCTCTTC+TGG 0.277156 6.3:-1162013 None:intergenic
GGCTCTTCTGGTGGGAAATA+AGG 0.304156 6.3:-1162001 None:intergenic
GGTTCTTCTTCTCTTGGTCT+TGG 0.305065 6.3:+1162265 MS.gene032616:CDS
CATCAAGGTTCTTCTTCTCT+TGG 0.331910 6.3:+1162259 MS.gene032616:CDS
TTATATATCACCTTTGTTGT+AGG 0.350339 6.3:-1162353 None:intergenic
TGAACATTTGCAAACTTATG+AGG 0.383834 6.3:-1162022 None:intergenic
GAATCATTGCTCAAATTAGA+TGG 0.418926 6.3:-1162319 None:intergenic
CTTGGACATGTTCATTCTGA+TGG 0.439607 6.3:+1162283 MS.gene032616:CDS
ATGATTTAAGCGAATCAAAT+CGG 0.450299 6.3:-1162239 None:intergenic
ATTTGAGCAATGATTCTTGT+GGG 0.463152 6.3:+1162326 MS.gene032616:CDS
TTGATTCGCTTAAATCATCA+AGG 0.486236 6.3:+1162244 MS.gene032616:CDS
ACAACTCATTAAGCTTCAAA+AGG 0.501141 6.3:+1162198 MS.gene032616:CDS
TGTGGGGATTCCTACAACAA+AGG 0.509877 6.3:+1162343 MS.gene032616:CDS
AGGATTAAAGATCCAGTGTA+TGG 0.525146 6.3:+1162145 MS.gene032616:CDS
AACTTATGAGGCTCTTCTGG+TGG 0.540828 6.3:-1162010 None:intergenic
AATTTGAGCAATGATTCTTG+TGG 0.553273 6.3:+1162325 MS.gene032616:CDS
ACTGTATCTTCTCTTTGATG+AGG 0.567592 6.3:-1162094 None:intergenic
GATCCAGTGTATGGTTGTGT+TGG 0.578362 6.3:+1162154 MS.gene032616:CDS
AGAAACTTGCAAGCAGCACA+TGG 0.591215 6.3:-1161944 None:intergenic
ACTTATGAGGCTCTTCTGGT+GGG 0.610191 6.3:-1162009 None:intergenic
TTTGAGCAATGATTCTTGTG+GGG 0.613138 6.3:+1162327 MS.gene032616:CDS
TAGCTTATGAAGCTGAAGCA+AGG 0.625096 6.3:+1162125 MS.gene032616:CDS
TGGAGAATTTGAGTAGCTTG+AGG 0.626001 6.3:-1161924 None:intergenic
GCTCCAACACAACCATACAC+TGG 0.629286 6.3:-1162157 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGATTTAAGCGAATCAAAT+CGG - chr6.3:1162242-1162261 None:intergenic 25.0%
! GCAAATGTTCACAAAATATT+TGG + chr6.3:1162034-1162053 MS.gene032616:CDS 25.0%
!! TTATATATCACCTTTGTTGT+AGG - chr6.3:1162356-1162375 None:intergenic 25.0%
AATTTGAGCAATGATTCTTG+TGG + chr6.3:1162325-1162344 MS.gene032616:CDS 30.0%
ACAACTCATTAAGCTTCAAA+AGG + chr6.3:1162198-1162217 MS.gene032616:CDS 30.0%
ATTTGAGCAATGATTCTTGT+GGG + chr6.3:1162326-1162345 MS.gene032616:CDS 30.0%
GAATCATTGCTCAAATTAGA+TGG - chr6.3:1162322-1162341 None:intergenic 30.0%
TGAACATTTGCAAACTTATG+AGG - chr6.3:1162025-1162044 None:intergenic 30.0%
! TTGATTCGCTTAAATCATCA+AGG + chr6.3:1162244-1162263 MS.gene032616:CDS 30.0%
AAGGTGCAAAAATGCAATCT+TGG - chr6.3:1161985-1162004 None:intergenic 35.0%
ACTGTATCTTCTCTTTGATG+AGG - chr6.3:1162097-1162116 None:intergenic 35.0%
AGGATTAAAGATCCAGTGTA+TGG + chr6.3:1162145-1162164 MS.gene032616:CDS 35.0%
TTTGAGCAATGATTCTTGTG+GGG + chr6.3:1162327-1162346 MS.gene032616:CDS 35.0%
CATCAAGGTTCTTCTTCTCT+TGG + chr6.3:1162259-1162278 MS.gene032616:CDS 40.0%
CTTGGACATGTTCATTCTGA+TGG + chr6.3:1162283-1162302 MS.gene032616:CDS 40.0%
TAGCTTATGAAGCTGAAGCA+AGG + chr6.3:1162125-1162144 MS.gene032616:CDS 40.0%
TGGAGAATTTGAGTAGCTTG+AGG - chr6.3:1161927-1161946 None:intergenic 40.0%
AACTTATGAGGCTCTTCTGG+TGG - chr6.3:1162013-1162032 None:intergenic 45.0%
ACTTATGAGGCTCTTCTGGT+GGG - chr6.3:1162012-1162031 None:intergenic 45.0%
AGAAACTTGCAAGCAGCACA+TGG - chr6.3:1161947-1161966 None:intergenic 45.0%
GATCCAGTGTATGGTTGTGT+TGG + chr6.3:1162154-1162173 MS.gene032616:CDS 45.0%
GCAAACTTATGAGGCTCTTC+TGG - chr6.3:1162016-1162035 None:intergenic 45.0%
GGTTCTTCTTCTCTTGGTCT+TGG + chr6.3:1162265-1162284 MS.gene032616:CDS 45.0%
TGTGGGGATTCCTACAACAA+AGG + chr6.3:1162343-1162362 MS.gene032616:CDS 45.0%
GCTCCAACACAACCATACAC+TGG - chr6.3:1162160-1162179 None:intergenic 50.0%
GGCTCTTCTGGTGGGAAATA+AGG - chr6.3:1162004-1162023 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 1161920 1162375 1161920 ID=MS.gene032616
chr6.3 mRNA 1161920 1162375 1161920 ID=MS.gene032616.t1;Parent=MS.gene032616
chr6.3 exon 1161920 1162375 1161920 ID=MS.gene032616.t1.exon1;Parent=MS.gene032616.t1
chr6.3 CDS 1161920 1162375 1161920 ID=cds.MS.gene032616.t1;Parent=MS.gene032616.t1
Gene Sequence

>MS.gene032616

ATGGCCTCAAGCTACTCAAATTCTCCATGTGCTGCTTGCAAGTTTCTAAGAAGAAAATGCAACCAAGATTGCATTTTTGCACCTTATTTCCCACCAGAAGAGCCTCATAAGTTTGCAAATGTTCACAAAATATTTGGTGCAAGCAATGTTAGCAAAATTCTTAATGAAGTTTTACCTCATCAAAGAGAAGATACAGTGAATTCTCTAGCTTATGAAGCTGAAGCAAGGATTAAAGATCCAGTGTATGGTTGTGTTGGAGCTATTTCAGTGCTTCAAAGACAACTCATTAAGCTTCAAAAGGAACTTGATGCTACAAATGCCGATTTGATTCGCTTAAATCATCAAGGTTCTTCTTCTCTTGGTCTTGGACATGTTCATTCTGATGGTTTTTTTAATTGTCCATCTAATTTGAGCAATGATTCTTGTGGGGATTCCTACAACAAAGGTGATATATAA
Protein sequence

>MS.gene032616.t1

MASSYSNSPCAACKFLRRKCNQDCIFAPYFPPEEPHKFANVHKIFGASNVSKILNEVLPHQREDTVNSLAYEAEARIKDPVYGCVGAISVLQRQLIKLQKELDATNADLIRLNHQGSSSLGLGHVHSDGFFNCPSNLSNDSCGDSYNKGDI