AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24464


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24464.t1 MTR_1g018420 95.339 236 6 3 1 235 1 232 2.68e-167 461
MS.gene24464.t1 MTR_3g102980 60.324 247 71 10 1 233 1 234 1.83e-82 246
MS.gene24464.t1 MTR_1g106730 43.396 265 84 13 1 224 3 242 1.01e-47 158
MS.gene24464.t1 MTR_1g062780 35.567 194 89 7 43 203 81 271 2.34e-21 90.5
MS.gene24464.t1 MTR_4g027440 51.190 84 41 0 80 163 220 303 1.97e-20 89.0
MS.gene24464.t1 MTR_0160s0030 38.849 139 60 5 71 209 231 344 1.61e-17 80.5
MS.gene24464.t1 MTR_4g109340 39.490 157 57 9 73 199 341 489 1.38e-16 78.6
MS.gene24464.t1 MTR_7g100100 35.294 119 68 1 80 198 34 143 3.84e-16 73.6
MS.gene24464.t1 MTR_5g062300 48.352 91 40 3 79 162 118 208 5.23e-16 75.1
MS.gene24464.t1 MTR_1g090703 30.180 222 107 8 21 196 81 300 6.84e-16 75.9
MS.gene24464.t1 MTR_1g067650 29.412 170 89 4 32 194 3 148 6.52e-15 70.5
MS.gene24464.t1 MTR_5g099040 43.119 109 37 3 80 164 130 237 8.48e-15 72.0
MS.gene24464.t1 MTR_1g067640 29.412 170 89 4 32 194 2 147 9.34e-15 70.1
MS.gene24464.t1 MTR_1g115345 43.902 82 37 2 80 160 45 118 1.63e-14 70.1
MS.gene24464.t1 MTR_7g023560 33.577 137 67 5 32 167 2 115 1.08e-13 67.4
MS.gene24464.t1 MTR_1g067660 33.582 134 66 3 38 171 6 116 2.52e-13 66.2
MS.gene24464.t1 MTR_4g057230 29.878 164 68 4 44 160 67 230 6.86e-12 63.9
MS.gene24464.t1 MTR_4g100860 28.788 198 100 6 14 196 130 301 3.95e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24464.t1 AT1G27730 50.202 247 87 11 1 231 1 227 2.50e-59 187
MS.gene24464.t1 AT5G04340 51.092 229 96 8 1 215 1 227 3.77e-53 171
MS.gene24464.t1 AT3G19580 40.945 254 102 7 1 212 1 248 9.30e-47 156
MS.gene24464.t1 AT3G19580 40.945 254 102 7 1 212 1 248 9.30e-47 156
MS.gene24464.t1 AT5G43170 45.106 235 74 10 1 223 1 192 3.19e-43 145
MS.gene24464.t1 AT5G67450 40.249 241 95 8 1 196 1 237 3.87e-36 128
MS.gene24464.t1 AT3G49930 43.500 200 69 8 25 209 36 206 6.25e-36 127
MS.gene24464.t1 AT2G28200 37.629 194 89 7 37 199 70 262 4.32e-25 100
MS.gene24464.t1 AT3G60580 37.912 182 83 5 38 209 122 283 4.86e-24 97.4
MS.gene24464.t1 AT2G45120 38.554 166 84 4 38 196 146 300 6.74e-23 95.1
MS.gene24464.t1 AT1G49900 52.809 89 34 2 80 167 193 274 4.81e-21 92.0
MS.gene24464.t1 AT1G49900 47.059 102 43 2 79 179 749 840 2.07e-20 90.1
MS.gene24464.t1 AT5G03510 32.292 192 98 4 39 199 69 259 8.17e-20 86.3
MS.gene24464.t1 AT5G04390 29.310 232 110 8 39 231 96 312 8.31e-18 81.6
MS.gene24464.t1 AT1G02040 32.812 192 90 8 5 161 61 248 1.88e-17 80.1
MS.gene24464.t1 AT5G56200 43.956 91 40 1 82 161 344 434 1.47e-16 78.6
MS.gene24464.t1 AT2G37430 37.594 133 61 4 32 160 2 116 5.23e-16 73.6
MS.gene24464.t1 AT4G35280 35.938 128 59 4 39 162 138 246 5.44e-16 75.5
MS.gene24464.t1 AT3G46090 35.385 130 59 3 38 167 11 115 1.92e-15 72.0
MS.gene24464.t1 AT1G02030 45.679 81 35 1 80 160 160 231 4.68e-15 72.8
MS.gene24464.t1 AT3G53600 31.361 169 90 6 32 194 2 150 1.02e-14 70.1
MS.gene24464.t1 AT2G28710 35.593 118 45 3 43 160 14 100 2.97e-14 68.6
MS.gene24464.t1 AT2G17180 30.675 163 77 5 39 196 121 252 1.10e-13 68.9
MS.gene24464.t1 AT3G46080 44.048 84 37 2 77 160 34 107 2.15e-13 66.2
MS.gene24464.t1 AT5G61470 40.000 85 33 2 80 161 228 297 1.41e-12 66.2
MS.gene24464.t1 AT5G59820 34.091 132 55 6 46 174 18 120 3.55e-12 62.8
MS.gene24464.t1 AT3G10470 30.000 180 68 5 39 160 104 283 5.67e-12 65.1
MS.gene24464.t1 AT3G46070 36.667 90 49 2 71 160 27 108 1.82e-11 61.2

Find 58 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCATCGAAGGTGAATTT+AGG 0.257514 1.1:+4499195 None:intergenic
CGTTTAGTCCATGGAAGATT+TGG 0.286174 1.1:+4499174 None:intergenic
AAAATTCGGAATTTCAATCT+TGG 0.317164 1.1:+4498555 None:intergenic
AGAACATTTGTAACTGAGTT+TGG 0.333314 1.1:+4499008 None:intergenic
CCGGAGTTTGCTAATAAGAT+TGG 0.334097 1.1:-4498643 MS.gene24464:CDS
ATTATTCATCACTGAAAATT+CGG 0.339013 1.1:+4498541 None:intergenic
TTGTCAATGGTTGTTGGTGG+TGG 0.368111 1.1:+4499042 None:intergenic
TTTCCGACAGGACAAGCTTT+GGG 0.386450 1.1:-4498796 MS.gene24464:CDS
AACTCCGTCGGTGGCGGTGT+TGG 0.405927 1.1:-4498922 MS.gene24464:CDS
AGTGCATGAACGTGAACGTT+TGG 0.411256 1.1:+4499143 None:intergenic
AAATTCGGAATTTCAATCTT+GGG 0.411878 1.1:+4498556 None:intergenic
TCTGAATATCCCGGCTTATC+CGG 0.414206 1.1:-4498662 MS.gene24464:CDS
GTTTCCGACAGGACAAGCTT+TGG 0.428305 1.1:-4498797 MS.gene24464:CDS
GATTCAAAGGCTTGAAATCA+TGG 0.448405 1.1:+4499064 None:intergenic
TTCTTCATCATCACAGGATG+AGG 0.458403 1.1:+4498601 None:intergenic
TTGTTGTTGTCAATGGTTGT+TGG 0.473433 1.1:+4499036 None:intergenic
AATTTAGGAGTAGTAGAAGT+GGG 0.488875 1.1:+4499210 None:intergenic
CACTACGAAGGTGTTGTTGG+TGG 0.490444 1.1:-4498757 MS.gene24464:CDS
GCTTTCTTCTTCATCATCAC+AGG 0.490449 1.1:+4498595 None:intergenic
TCCGTCGGTGGCGGTGTTGG+TGG 0.493089 1.1:-4498919 MS.gene24464:CDS
TGAGCTTGTGGTTGCAGCTG+AGG 0.495728 1.1:+4498876 None:intergenic
TTAGCAAACTCCGGATAAGC+CGG 0.495798 1.1:+4498652 None:intergenic
GAATTTAGGAGTAGTAGAAG+TGG 0.499359 1.1:+4499209 None:intergenic
ATGAGTGTTCGATTTGTCAT+AGG 0.501927 1.1:-4498822 MS.gene24464:CDS
ACTTGCTTTGTGTCCACCGA+GGG 0.502207 1.1:+4498954 None:intergenic
ACTACGAAGGTGTTGTTGGT+GGG 0.505453 1.1:-4498756 MS.gene24464:CDS
TGTCATAGGTCGTTTCCGAC+AGG 0.511441 1.1:-4498808 MS.gene24464:CDS
TTGTTGTCAATGGTTGTTGG+TGG 0.511574 1.1:+4499039 None:intergenic
CTACGAAGGTGTTGTTGGTG+GGG 0.511916 1.1:-4498755 MS.gene24464:CDS
GTTGCAGCTGAGGAAGTTGA+TGG 0.514028 1.1:+4498886 None:intergenic
GAACGTTTACGTTTAGTCCA+TGG 0.532372 1.1:+4499165 None:intergenic
GTTGTTGGTGGTGGATTCAA+AGG 0.535966 1.1:+4499051 None:intergenic
TGTCACTACGAAGGTGTTGT+TGG 0.546239 1.1:-4498760 MS.gene24464:CDS
TCGATGAACCAAATCTTCCA+TGG 0.550148 1.1:-4499182 MS.gene24464:CDS
TACGAAGGTGTTGTTGGTGG+GGG 0.550558 1.1:-4498754 MS.gene24464:CDS
CCAATCTTATTAGCAAACTC+CGG 0.554584 1.1:+4498643 None:intergenic
CCACCCAAAGCTTGTCCTGT+CGG 0.557784 1.1:+4498793 None:intergenic
TGATTTCGATCTGAATATCC+CGG 0.576158 1.1:-4498671 MS.gene24464:CDS
CCGACAGGACAAGCTTTGGG+TGG 0.581171 1.1:-4498793 MS.gene24464:CDS
AGCTCAGCCAACACAAACGC+TGG 0.582947 1.1:-4498859 MS.gene24464:CDS
TGAAATCATGGCGGTTGGTG+TGG 0.583151 1.1:+4499076 None:intergenic
TAGCAAACTCCGGATAAGCC+GGG 0.583949 1.1:+4498653 None:intergenic
AGGCTTGAAATCATGGCGGT+TGG 0.583949 1.1:+4499071 None:intergenic
TCTGCTATAACTGTCTCTGA+AGG 0.590024 1.1:-4498721 MS.gene24464:CDS
TGTCTCATCATGCTCGCTCG+TGG 0.591916 1.1:-4499099 MS.gene24464:CDS
TATAACTGTCTCTGAAGGTG+TGG 0.592472 1.1:-4498716 MS.gene24464:CDS
GTTTGTGTTGGCTGAGCTTG+TGG 0.592566 1.1:+4498864 None:intergenic
TGGAAGATTTGGTTCATCGA+AGG 0.595055 1.1:+4499185 None:intergenic
AACACCGCCAGCGTTTGTGT+TGG 0.599705 1.1:+4498852 None:intergenic
ATAACTGTCTCTGAAGGTGT+GGG 0.609017 1.1:-4498715 MS.gene24464:CDS
GACTTGCTTTGTGTCCACCG+AGG 0.621099 1.1:+4498953 None:intergenic
TCTTCTTATCAAGCCCTCGG+TGG 0.636904 1.1:-4498967 MS.gene24464:CDS
ACCACCAACACCGCCACCGA+CGG 0.639061 1.1:+4498918 None:intergenic
ATCACGTTGATGACTATGTG+TGG 0.647702 1.1:+4498690 None:intergenic
TCAGCCAACACAAACGCTGG+CGG 0.666871 1.1:-4498856 MS.gene24464:CDS
TTGCAGCTGAGGAAGTTGAT+GGG 0.673304 1.1:+4498887 None:intergenic
CACAAACGTTGTCACTACGA+AGG 0.683725 1.1:-4498769 MS.gene24464:CDS
TCAAAGGCTTGAAATCATGG+CGG 0.753429 1.1:+4499067 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATTCGGAATTTCAATCT+TGG + chr1.1:4499231-4499250 None:intergenic 25.0%
! AAATTCGGAATTTCAATCTT+GGG + chr1.1:4499230-4499249 None:intergenic 25.0%
AATTTAGGAGTAGTAGAAGT+GGG + chr1.1:4498576-4498595 None:intergenic 30.0%
AGAACATTTGTAACTGAGTT+TGG + chr1.1:4498778-4498797 None:intergenic 30.0%
CCAATCTTATTAGCAAACTC+CGG + chr1.1:4499143-4499162 None:intergenic 35.0%
GAATTTAGGAGTAGTAGAAG+TGG + chr1.1:4498577-4498596 None:intergenic 35.0%
GATTCAAAGGCTTGAAATCA+TGG + chr1.1:4498722-4498741 None:intergenic 35.0%
TGATTTCGATCTGAATATCC+CGG - chr1.1:4499112-4499131 MS.gene24464:CDS 35.0%
! ATGAGTGTTCGATTTGTCAT+AGG - chr1.1:4498961-4498980 MS.gene24464:CDS 35.0%
! TTGTTGTTGTCAATGGTTGT+TGG + chr1.1:4498750-4498769 None:intergenic 35.0%
! TTTTCTTCTTATCAAGCCCT+CGG - chr1.1:4498813-4498832 MS.gene24464:CDS 35.0%
CGTTTAGTCCATGGAAGATT+TGG + chr1.1:4498612-4498631 None:intergenic 40.0%
GAACGTTTACGTTTAGTCCA+TGG + chr1.1:4498621-4498640 None:intergenic 40.0%
GCTTTCTTCTTCATCATCAC+AGG + chr1.1:4499191-4499210 None:intergenic 40.0%
GGTTCATCGAAGGTGAATTT+AGG + chr1.1:4498591-4498610 None:intergenic 40.0%
TCAAAGGCTTGAAATCATGG+CGG + chr1.1:4498719-4498738 None:intergenic 40.0%
TCGATGAACCAAATCTTCCA+TGG - chr1.1:4498601-4498620 MS.gene24464:CDS 40.0%
TCTGCTATAACTGTCTCTGA+AGG - chr1.1:4499062-4499081 MS.gene24464:CDS 40.0%
TTCTTCATCATCACAGGATG+AGG + chr1.1:4499185-4499204 None:intergenic 40.0%
TTGTTGTCAATGGTTGTTGG+TGG + chr1.1:4498747-4498766 None:intergenic 40.0%
! ATAACTGTCTCTGAAGGTGT+GGG - chr1.1:4499068-4499087 MS.gene24464:CDS 40.0%
! TATAACTGTCTCTGAAGGTG+TGG - chr1.1:4499067-4499086 MS.gene24464:CDS 40.0%
! TGGAAGATTTGGTTCATCGA+AGG + chr1.1:4498601-4498620 None:intergenic 40.0%
!! ATCACGTTGATGACTATGTG+TGG + chr1.1:4499096-4499115 None:intergenic 40.0%
!! CCGGAGTTTGCTAATAAGAT+TGG - chr1.1:4499140-4499159 MS.gene24464:CDS 40.0%
!! GGTGTTGTTGTTGTTGTCAA+TGG + chr1.1:4498757-4498776 None:intergenic 40.0%
AGTGCATGAACGTGAACGTT+TGG + chr1.1:4498643-4498662 None:intergenic 45.0%
CACAAACGTTGTCACTACGA+AGG - chr1.1:4499014-4499033 MS.gene24464:CDS 45.0%
TCTGAATATCCCGGCTTATC+CGG - chr1.1:4499121-4499140 MS.gene24464:CDS 45.0%
TTAGCAAACTCCGGATAAGC+CGG + chr1.1:4499134-4499153 None:intergenic 45.0%
TTTCCGACAGGACAAGCTTT+GGG - chr1.1:4498987-4499006 MS.gene24464:CDS 45.0%
! GAAGAAAGCTCGTGTTTTCG+TGG - chr1.1:4499202-4499221 MS.gene24464:CDS 45.0%
! TTGCAGCTGAGGAAGTTGAT+GGG + chr1.1:4498899-4498918 None:intergenic 45.0%
! TTGTCAATGGTTGTTGGTGG+TGG + chr1.1:4498744-4498763 None:intergenic 45.0%
!! ACTACGAAGGTGTTGTTGGT+GGG - chr1.1:4499027-4499046 MS.gene24464:CDS 45.0%
!! GTTGTTGGTGGTGGATTCAA+AGG + chr1.1:4498735-4498754 None:intergenic 45.0%
!! TGTCACTACGAAGGTGTTGT+TGG - chr1.1:4499023-4499042 MS.gene24464:CDS 45.0%
ACTTGCTTTGTGTCCACCGA+GGG + chr1.1:4498832-4498851 None:intergenic 50.0%
AGGCTTGAAATCATGGCGGT+TGG + chr1.1:4498715-4498734 None:intergenic 50.0%
AGTCACCGCAAAAACTCCGT+CGG - chr1.1:4498849-4498868 MS.gene24464:CDS 50.0%
GTTGCAGCTGAGGAAGTTGA+TGG + chr1.1:4498900-4498919 None:intergenic 50.0%
GTTTCCGACAGGACAAGCTT+TGG - chr1.1:4498986-4499005 MS.gene24464:CDS 50.0%
TAGCAAACTCCGGATAAGCC+GGG + chr1.1:4499133-4499152 None:intergenic 50.0%
TCTTCTTATCAAGCCCTCGG+TGG - chr1.1:4498816-4498835 MS.gene24464:CDS 50.0%
TGTCATAGGTCGTTTCCGAC+AGG - chr1.1:4498975-4498994 MS.gene24464:CDS 50.0%
! TGAAATCATGGCGGTTGGTG+TGG + chr1.1:4498710-4498729 None:intergenic 50.0%
!! CACTACGAAGGTGTTGTTGG+TGG - chr1.1:4499026-4499045 MS.gene24464:CDS 50.0%
!! CTACGAAGGTGTTGTTGGTG+GGG - chr1.1:4499028-4499047 MS.gene24464:CDS 50.0%
!! GTTTGTGTTGGCTGAGCTTG+TGG + chr1.1:4498922-4498941 None:intergenic 50.0%
!! TACGAAGGTGTTGTTGGTGG+GGG - chr1.1:4499029-4499048 MS.gene24464:CDS 50.0%
AACACCGCCAGCGTTTGTGT+TGG + chr1.1:4498934-4498953 None:intergenic 55.0%
AGCTCAGCCAACACAAACGC+TGG - chr1.1:4498924-4498943 MS.gene24464:CDS 55.0%
CCACCCAAAGCTTGTCCTGT+CGG + chr1.1:4498993-4499012 None:intergenic 55.0%
TCAGCCAACACAAACGCTGG+CGG - chr1.1:4498927-4498946 MS.gene24464:CDS 55.0%
TGAGCTTGTGGTTGCAGCTG+AGG + chr1.1:4498910-4498929 None:intergenic 55.0%
TGTCTCATCATGCTCGCTCG+TGG - chr1.1:4498684-4498703 MS.gene24464:CDS 55.0%
! GACTTGCTTTGTGTCCACCG+AGG + chr1.1:4498833-4498852 None:intergenic 55.0%
CACCGCAAAAACTCCGTCGG+TGG - chr1.1:4498852-4498871 MS.gene24464:CDS 60.0%
CGCAAAAACTCCGTCGGTGG+CGG - chr1.1:4498855-4498874 MS.gene24464:CDS 60.0%
! CGCCACCGACGGAGTTTTTG+CGG + chr1.1:4498857-4498876 None:intergenic 60.0%
!! CCGACAGGACAAGCTTTGGG+TGG - chr1.1:4498990-4499009 MS.gene24464:CDS 60.0%
ACCACCAACACCGCCACCGA+CGG + chr1.1:4498868-4498887 None:intergenic 65.0%
! AACTCCGTCGGTGGCGGTGT+TGG - chr1.1:4498861-4498880 MS.gene24464:CDS 65.0%
! TCCGTCGGTGGCGGTGTTGG+TGG - chr1.1:4498864-4498883 MS.gene24464:CDS 70.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 4498549 4499256 4498549 ID=MS.gene24464
chr1.1 mRNA 4498549 4499256 4498549 ID=MS.gene24464.t1;Parent=MS.gene24464
chr1.1 exon 4498549 4499256 4498549 ID=MS.gene24464.t1.exon1;Parent=MS.gene24464.t1
chr1.1 CDS 4498549 4499256 4498549 ID=cds.MS.gene24464.t1;Parent=MS.gene24464.t1
Gene Sequence

>MS.gene24464

ATGGCTCTAGAAGCACTTAACTCACCCACTTCTACTACTCCTAAATTCACCTTCGATGAACCAAATCTTCCATGGACTAAACGTAAACGTTCCAAACGTTCACGTTCATGCACTGAAGAAGAATATCTCGCTCTCTGTCTCATCATGCTCGCTCGTGGCCACACCAACCGCCATGATTTCAAGCCTTTGAATCCACCACCAACAACCATTGACAACAACAACAACACCAAACTCAGTTACAAATGTTCTGTCTGTAACAAAGAGTTTTCTTCTTATCAAGCCCTCGGTGGACACAAAGCAAGTCACCGCAAAAACTCCGTCGGTGGCGGTGTTGGTGGTGATGATCACCCATCAACTTCCTCAGCTGCAACCACAAGCTCAGCCAACACAAACGCTGGCGGTGTTAGATCTCATGAGTGTTCGATTTGTCATAGGTCGTTTCCGACAGGACAAGCTTTGGGTGGACACAAACGTTGTCACTACGAAGGTGTTGTTGGTGGGGGTGCTTCTGCTTCTGCTATAACTGTCTCTGAAGGTGTGGGATCCACACATAGTCATCAACGTGATTTCGATCTGAATATCCCGGCTTATCCGGAGTTTGCTAATAAGATTGGAGAAGATGAAGTTGAAAGTCCTCATCCTGTGATGATGAAGAAGAAAGCTCGTGTTTTCGTGGTGCCCAAGATTGAAATTCCGAATTTTCAGTGA

Protein sequence

>MS.gene24464.t1

MALEALNSPTSTTPKFTFDEPNLPWTKRKRSKRSRSCTEEEYLALCLIMLARGHTNRHDFKPLNPPPTTIDNNNNTKLSYKCSVCNKEFSSYQALGGHKASHRKNSVGGGVGGDDHPSTSSAATTSSANTNAGGVRSHECSICHRSFPTGQALGGHKRCHYEGVVGGGASASAITVSEGVGSTHSHQRDFDLNIPAYPEFANKIGEDEVESPHPVMMKKKARVFVVPKIEIPNFQ