AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene50209

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50209.t1 MTR_5g072510 95.556 225 10 0 1 225 1 225 2.42e-128 361
MS.gene50209.t1 MTR_4g094428 63.830 188 52 2 33 204 42 229 1.70e-81 243
MS.gene50209.t1 MTR_3g031830 85.915 142 20 0 37 178 42 183 1.77e-81 243
MS.gene50209.t1 MTR_1g442860 79.200 125 26 0 37 161 65 189 3.74e-77 231
MS.gene50209.t1 MTR_1g075990 77.305 141 32 0 27 167 43 183 7.98e-74 222
MS.gene50209.t1 MTR_2g016110 70.423 142 41 1 26 167 25 165 1.43e-71 216
MS.gene50209.t1 MTR_2g076400 72.593 135 37 0 36 170 32 166 2.10e-70 213
MS.gene50209.t1 MTR_7g097030 78.358 134 29 0 34 167 61 194 2.98e-70 214
MS.gene50209.t1 MTR_7g115700 67.568 148 42 4 36 180 26 170 3.46e-70 212
MS.gene50209.t1 MTR_1g069825 79.389 131 27 0 37 167 52 182 2.40e-69 212
MS.gene50209.t1 MTR_2g092950 71.654 127 36 0 34 160 20 146 2.50e-69 210
MS.gene50209.t1 MTR_4g079930 69.291 127 39 0 34 160 26 152 8.59e-69 209
MS.gene50209.t1 MTR_1g080210 72.727 143 39 0 37 179 40 182 7.29e-67 204
MS.gene50209.t1 MTR_8g086350 72.800 125 34 0 36 160 30 154 1.07e-58 183
MS.gene50209.t1 MTR_1g114020 66.000 50 17 0 31 80 65 114 9.34e-20 83.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50209.t1 AT1G07090 66.489 188 53 2 1 186 1 180 5.63e-89 261
MS.gene50209.t1 AT5G58500 68.715 179 42 3 35 212 17 182 1.02e-83 247
MS.gene50209.t1 AT2G31160 73.248 157 41 1 13 168 29 185 1.05e-71 218
MS.gene50209.t1 AT2G42610 72.059 136 38 0 34 169 22 157 1.14e-70 214
MS.gene50209.t1 AT2G42610 72.059 136 38 0 34 169 22 157 1.14e-70 214
MS.gene50209.t1 AT3G23290 80.952 126 24 0 36 161 47 172 3.62e-68 208
MS.gene50209.t1 AT5G28490 69.737 152 41 1 15 166 8 154 6.61e-68 207
MS.gene50209.t1 AT3G04510 75.385 130 32 0 37 166 33 162 7.07e-66 202
MS.gene50209.t1 AT1G78815 70.400 125 37 0 36 160 39 163 8.55e-66 202
MS.gene50209.t1 AT1G16910 66.165 133 45 0 33 165 19 151 9.86e-63 193
MS.gene50209.t1 AT4G18610 66.667 126 41 1 36 160 36 161 4.22e-62 192

Find 73 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCAAGTATCTTGATCAATT+TGG 0.199090 5.2:+60810984 MS.gene50209:CDS
ACGCTCTCATCGGACGTCTT+AGG 0.202990 5.2:+60811105 MS.gene50209:CDS
CTGCATAGTGCTAGGGTTAA+TGG 0.263262 5.2:-60810939 None:intergenic
CGGCTTGGTGTTGGTGTTGC+TGG 0.267162 5.2:-60810852 None:intergenic
GGGTTAGGTTGTCCGAAATA+TGG 0.338434 5.2:-60811035 None:intergenic
CTTCCCCACGCTTGCTTAAG+AGG 0.344190 5.2:-60811077 None:intergenic
CGAGGAAAACGGTGGTAAAC+TGG 0.347252 5.2:+60811136 MS.gene50209:CDS
CGCTCTCATCGGACGTCTTA+GGG 0.360799 5.2:+60811106 MS.gene50209:CDS
GTGATAGGTTGTCCATATTT+CGG 0.376674 5.2:+60811023 MS.gene50209:CDS
GTTGGTGTTGCTGGTGATGA+AGG 0.383238 5.2:-60810843 None:intergenic
GATTTATCTGAGGGAAGTTA+AGG 0.397608 5.2:+60811190 MS.gene50209:CDS
TGTGACGGTGGTAGTATTAT+TGG 0.411712 5.2:-60811387 None:intergenic
GATGGTAACACCGAGAGAAT+TGG 0.417561 5.2:+60811344 MS.gene50209:CDS
AAAACTAAGGTGCACGTGAT+AGG 0.426316 5.2:+60811008 MS.gene50209:CDS
ACGTCTTAGGGCTGCTTTCG+AGG 0.442268 5.2:+60811118 MS.gene50209:CDS
AGTCACAAAAGCGACGAGAC+TGG 0.455576 5.2:+60810880 MS.gene50209:CDS
GCGCAAGGAGAAGGTGGGTT+AGG 0.457008 5.2:-60811050 None:intergenic
GTGCTCCACTGCATAGTGCT+AGG 0.463475 5.2:-60810947 None:intergenic
AGAGTAATCCGTTTGGAACT+CGG 0.465602 5.2:+60811159 MS.gene50209:CDS
CGTTTGGAACTCGGGCGGTA+AGG 0.468516 5.2:+60811168 MS.gene50209:CDS
TGTGGTTACGTAGATATTGT+TGG 0.476151 5.2:-60810911 None:intergenic
GAGTAATCCGTTTGGAACTC+GGG 0.476931 5.2:+60811160 MS.gene50209:CDS
GGTGACGGTGGTGGTATTGA+TGG 0.478331 5.2:+60811326 MS.gene50209:CDS
GCCTCCAGTGGTGTTTCTGA+TGG 0.496541 5.2:-60810807 None:intergenic
TCGGTAATGGAAGCTGCATC+TGG 0.501540 5.2:+60810759 None:intergenic
ACCTATTGTTAGTGTTAGTA+CGG 0.504598 5.2:+60811409 MS.gene50209:CDS
GACTCGTAGCGGCTTGGTGT+TGG 0.507637 5.2:-60810861 None:intergenic
GCCGTACTAACACTAACAAT+AGG 0.510181 5.2:-60811410 None:intergenic
GTTGCTGGTGATGAAGGTTG+TGG 0.519042 5.2:-60810837 None:intergenic
CTTGTCCTCTTAAGCAAGCG+TGG 0.521556 5.2:+60811072 MS.gene50209:CDS
AGGGCTGCTTTCGAGGAAAA+CGG 0.523449 5.2:+60811125 MS.gene50209:CDS
AGAGGACAAGCGCAAGGAGA+AGG 0.525742 5.2:-60811059 None:intergenic
GGACAAGCGCAAGGAGAAGG+TGG 0.534211 5.2:-60811056 None:intergenic
CTTACCGCCCGAGTTCCAAA+CGG 0.537176 5.2:-60811167 None:intergenic
AAACTGGAGAGTAATCCGTT+TGG 0.544575 5.2:+60811152 MS.gene50209:CDS
GGTGTTTCTGATGGTATTGA+CGG 0.548053 5.2:-60810798 None:intergenic
CTAGGGTTAATGGTGGTTTG+TGG 0.548564 5.2:-60810929 None:intergenic
GATGGTATTGACGGTGGTGG+TGG 0.551307 5.2:-60810789 None:intergenic
TGCTCCACTGCATAGTGCTA+GGG 0.553244 5.2:-60810946 None:intergenic
GCGGTGAATAGTAGTGGACT+TGG 0.557889 5.2:+60811305 MS.gene50209:CDS
TTGTCCTCTTAAGCAAGCGT+GGG 0.563836 5.2:+60811073 MS.gene50209:CDS
AACACCAGCTCCAATTCTCT+CGG 0.568073 5.2:-60811354 None:intergenic
GGAAGTCTTGACGCTCTCAT+CGG 0.568235 5.2:+60811095 MS.gene50209:CDS
GACGGTGGTAGTATTATTGG+TGG 0.568631 5.2:-60811384 None:intergenic
AGTGGACTTGGTGACGGTGG+TGG 0.574244 5.2:+60811317 MS.gene50209:CDS
GGCGGTAAGGATTTATCTGA+GGG 0.577139 5.2:+60811181 MS.gene50209:CDS
GGGCGGTAAGGATTTATCTG+AGG 0.579521 5.2:+60811180 MS.gene50209:CDS
TGTGGTTGTGCTGCCTCCAG+TGG 0.594979 5.2:-60810819 None:intergenic
ATTGCAGCAGCGGTGACAGT+GGG 0.601286 5.2:-60811266 None:intergenic
GATGGTCAAGCTAAAGCTAG+AGG 0.604205 5.2:+60811212 MS.gene50209:CDS
TCTGATGGTATTGACGGTGG+TGG 0.606284 5.2:-60810792 None:intergenic
AACACTAACAATAGGTGTGA+CGG 0.607101 5.2:-60811402 None:intergenic
TATTGCAGCAGCGGTGACAG+TGG 0.608654 5.2:-60811267 None:intergenic
TATCTGAGGGAAGTTAAGGA+TGG 0.611775 5.2:+60811194 MS.gene50209:CDS
GTAATGGAAGCTGCATCTGG+TGG 0.611925 5.2:+60810762 None:intergenic
GACAAGCGCAAGGAGAAGGT+GGG 0.614541 5.2:-60811055 None:intergenic
ACAGCAGCGGTGAATAGTAG+TGG 0.615069 5.2:+60811299 MS.gene50209:CDS
GAGAGAATTGGAGCTGGTGT+TGG 0.623654 5.2:+60811356 MS.gene50209:CDS
AGTTGATATTATTGCAGCAG+CGG 0.629514 5.2:-60811276 None:intergenic
ACCATCAGAAACACCACTGG+AGG 0.636743 5.2:+60810806 MS.gene50209:CDS
AATACCATCAGAAACACCAC+TGG 0.637868 5.2:+60810803 MS.gene50209:CDS
CATAGTGCTAGGGTTAATGG+TGG 0.640579 5.2:-60810936 None:intergenic
AATAGTAGTGGACTTGGTGA+CGG 0.643866 5.2:+60811311 MS.gene50209:CDS
TGCTTAAGAGGACAAGCGCA+AGG 0.646571 5.2:-60811065 None:intergenic
AACACCGAGAGAATTGGAGC+TGG 0.649987 5.2:+60811350 MS.gene50209:CDS
AATAATATCAACTACAGCAG+CGG 0.669859 5.2:+60811286 MS.gene50209:CDS
AGTAGTGGACTTGGTGACGG+TGG 0.690950 5.2:+60811314 MS.gene50209:CDS
TTAACCCTAGCACTATGCAG+TGG 0.696826 5.2:+60810942 MS.gene50209:CDS
GTTTCTGATGGTATTGACGG+TGG 0.698342 5.2:-60810795 None:intergenic
TGTCCTCTTAAGCAAGCGTG+GGG 0.708587 5.2:+60811074 MS.gene50209:CDS
ACTAACAATAGGTGTGACGG+TGG 0.726512 5.2:-60811399 None:intergenic
TAATCCGTTTGGAACTCGGG+CGG 0.729170 5.2:+60811163 MS.gene50209:CDS
GCTGCTTTCGAGGAAAACGG+TGG 0.733556 5.2:+60811128 MS.gene50209:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGATCAATTTGGAAAAACTA+AGG + chr5.2:60810995-60811014 MS.gene50209:CDS 25.0%
! TTCCTTATGAGAAAAAGAAA+CGG + chr5.2:60811237-60811256 MS.gene50209:CDS 25.0%
AATAATATCAACTACAGCAG+CGG + chr5.2:60811286-60811305 MS.gene50209:CDS 30.0%
ACCTATTGTTAGTGTTAGTA+CGG + chr5.2:60811409-60811428 MS.gene50209:CDS 30.0%
CTCAAGTATCTTGATCAATT+TGG + chr5.2:60810984-60811003 MS.gene50209:CDS 30.0%
! TTCCGTTTCTTTTTCTCATA+AGG - chr5.2:60811242-60811261 None:intergenic 30.0%
AACACTAACAATAGGTGTGA+CGG - chr5.2:60811405-60811424 None:intergenic 35.0%
ATGAGAAAAAGAAACGGAAG+AGG + chr5.2:60811243-60811262 MS.gene50209:CDS 35.0%
GATTTATCTGAGGGAAGTTA+AGG + chr5.2:60811190-60811209 MS.gene50209:CDS 35.0%
GTGATAGGTTGTCCATATTT+CGG + chr5.2:60811023-60811042 MS.gene50209:CDS 35.0%
TGTGGTTACGTAGATATTGT+TGG - chr5.2:60810914-60810933 None:intergenic 35.0%
! AGTTGATATTATTGCAGCAG+CGG - chr5.2:60811279-60811298 None:intergenic 35.0%
AAAACTAAGGTGCACGTGAT+AGG + chr5.2:60811008-60811027 MS.gene50209:CDS 40.0%
AAACTGGAGAGTAATCCGTT+TGG + chr5.2:60811152-60811171 MS.gene50209:CDS 40.0%
AATACCATCAGAAACACCAC+TGG + chr5.2:60810803-60810822 MS.gene50209:CDS 40.0%
GCCGTACTAACACTAACAAT+AGG - chr5.2:60811413-60811432 None:intergenic 40.0%
TATCTGAGGGAAGTTAAGGA+TGG + chr5.2:60811194-60811213 MS.gene50209:CDS 40.0%
TGTGACGGTGGTAGTATTAT+TGG - chr5.2:60811390-60811409 None:intergenic 40.0%
! AGAGTAATCCGTTTGGAACT+CGG + chr5.2:60811159-60811178 MS.gene50209:CDS 40.0%
! GGTGTTTCTGATGGTATTGA+CGG - chr5.2:60810801-60810820 None:intergenic 40.0%
!! AATAGTAGTGGACTTGGTGA+CGG + chr5.2:60811311-60811330 MS.gene50209:CDS 40.0%
AACACCAGCTCCAATTCTCT+CGG - chr5.2:60811357-60811376 None:intergenic 45.0%
ACTAACAATAGGTGTGACGG+TGG - chr5.2:60811402-60811421 None:intergenic 45.0%
CATAGTGCTAGGGTTAATGG+TGG - chr5.2:60810939-60810958 None:intergenic 45.0%
CTAGGGTTAATGGTGGTTTG+TGG - chr5.2:60810932-60810951 None:intergenic 45.0%
CTGCATAGTGCTAGGGTTAA+TGG - chr5.2:60810942-60810961 None:intergenic 45.0%
GACGGTGGTAGTATTATTGG+TGG - chr5.2:60811387-60811406 None:intergenic 45.0%
GATGGTAACACCGAGAGAAT+TGG + chr5.2:60811344-60811363 MS.gene50209:CDS 45.0%
GATGGTCAAGCTAAAGCTAG+AGG + chr5.2:60811212-60811231 MS.gene50209:CDS 45.0%
GGCGGTAAGGATTTATCTGA+GGG + chr5.2:60811181-60811200 MS.gene50209:CDS 45.0%
TTAACCCTAGCACTATGCAG+TGG + chr5.2:60810942-60810961 MS.gene50209:CDS 45.0%
TTGTCCTCTTAAGCAAGCGT+GGG + chr5.2:60811073-60811092 MS.gene50209:CDS 45.0%
! GAGTAATCCGTTTGGAACTC+GGG + chr5.2:60811160-60811179 MS.gene50209:CDS 45.0%
! GGGTTAGGTTGTCCGAAATA+TGG - chr5.2:60811038-60811057 None:intergenic 45.0%
!! GTTTCTGATGGTATTGACGG+TGG - chr5.2:60810798-60810817 None:intergenic 45.0%
AACACCGAGAGAATTGGAGC+TGG + chr5.2:60811350-60811369 MS.gene50209:CDS 50.0%
ACAGCAGCGGTGAATAGTAG+TGG + chr5.2:60811299-60811318 MS.gene50209:CDS 50.0%
ACCATCAGAAACACCACTGG+AGG + chr5.2:60810806-60810825 MS.gene50209:CDS 50.0%
AGTCACAAAAGCGACGAGAC+TGG + chr5.2:60810880-60810899 MS.gene50209:CDS 50.0%
CGAGGAAAACGGTGGTAAAC+TGG + chr5.2:60811136-60811155 MS.gene50209:CDS 50.0%
CTTGTCCTCTTAAGCAAGCG+TGG + chr5.2:60811072-60811091 MS.gene50209:CDS 50.0%
GAGAGAATTGGAGCTGGTGT+TGG + chr5.2:60811356-60811375 MS.gene50209:CDS 50.0%
GGAAGTCTTGACGCTCTCAT+CGG + chr5.2:60811095-60811114 MS.gene50209:CDS 50.0%
GGGCGGTAAGGATTTATCTG+AGG + chr5.2:60811180-60811199 MS.gene50209:CDS 50.0%
TGCTCCACTGCATAGTGCTA+GGG - chr5.2:60810949-60810968 None:intergenic 50.0%
TGCTTAAGAGGACAAGCGCA+AGG - chr5.2:60811068-60811087 None:intergenic 50.0%
TGTCCTCTTAAGCAAGCGTG+GGG + chr5.2:60811074-60811093 MS.gene50209:CDS 50.0%
! AGGGCTGCTTTCGAGGAAAA+CGG + chr5.2:60811125-60811144 MS.gene50209:CDS 50.0%
! GTTGCTGGTGATGAAGGTTG+TGG - chr5.2:60810840-60810859 None:intergenic 50.0%
! TAATCCGTTTGGAACTCGGG+CGG + chr5.2:60811163-60811182 MS.gene50209:CDS 50.0%
! TTTTGTGACTCGTAGCGGCT+TGG - chr5.2:60810870-60810889 None:intergenic 50.0%
!! GCGGTGAATAGTAGTGGACT+TGG + chr5.2:60811305-60811324 MS.gene50209:CDS 50.0%
!! GTTGGTGTTGCTGGTGATGA+AGG - chr5.2:60810846-60810865 None:intergenic 50.0%
!! TCTGATGGTATTGACGGTGG+TGG - chr5.2:60810795-60810814 None:intergenic 50.0%
!!! GTCGCTTTTGTGACTCGTAG+CGG - chr5.2:60810875-60810894 None:intergenic 50.0%
ACGCTCTCATCGGACGTCTT+AGG + chr5.2:60811105-60811124 MS.gene50209:CDS 55.0%
AGAGGACAAGCGCAAGGAGA+AGG - chr5.2:60811062-60811081 None:intergenic 55.0%
ATTGCAGCAGCGGTGACAGT+GGG - chr5.2:60811269-60811288 None:intergenic 55.0%
CGCTCTCATCGGACGTCTTA+GGG + chr5.2:60811106-60811125 MS.gene50209:CDS 55.0%
CTTACCGCCCGAGTTCCAAA+CGG - chr5.2:60811170-60811189 None:intergenic 55.0%
CTTCCCCACGCTTGCTTAAG+AGG - chr5.2:60811080-60811099 None:intergenic 55.0%
GACAAGCGCAAGGAGAAGGT+GGG - chr5.2:60811058-60811077 None:intergenic 55.0%
GTGCTCCACTGCATAGTGCT+AGG - chr5.2:60810950-60810969 None:intergenic 55.0%
TATTGCAGCAGCGGTGACAG+TGG - chr5.2:60811270-60811289 None:intergenic 55.0%
! ACGTCTTAGGGCTGCTTTCG+AGG + chr5.2:60811118-60811137 MS.gene50209:CDS 55.0%
! GCCTCCAGTGGTGTTTCTGA+TGG - chr5.2:60810810-60810829 None:intergenic 55.0%
! GCTGCTTTCGAGGAAAACGG+TGG + chr5.2:60811128-60811147 MS.gene50209:CDS 55.0%
! GGTGACGGTGGTGGTATTGA+TGG + chr5.2:60811326-60811345 MS.gene50209:CDS 55.0%
!! AGTAGTGGACTTGGTGACGG+TGG + chr5.2:60811314-60811333 MS.gene50209:CDS 55.0%
!! GATGGTATTGACGGTGGTGG+TGG - chr5.2:60810792-60810811 None:intergenic 55.0%
GGACAAGCGCAAGGAGAAGG+TGG - chr5.2:60811059-60811078 None:intergenic 60.0%
TGTGGTTGTGCTGCCTCCAG+TGG - chr5.2:60810822-60810841 None:intergenic 60.0%
! CGTTTGGAACTCGGGCGGTA+AGG + chr5.2:60811168-60811187 MS.gene50209:CDS 60.0%
! GCGCAAGGAGAAGGTGGGTT+AGG - chr5.2:60811053-60811072 None:intergenic 60.0%
!! AGTGGACTTGGTGACGGTGG+TGG + chr5.2:60811317-60811336 MS.gene50209:CDS 60.0%
!! CGGCTTGGTGTTGGTGTTGC+TGG - chr5.2:60810855-60810874 None:intergenic 60.0%
!! GACTCGTAGCGGCTTGGTGT+TGG - chr5.2:60810864-60810883 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 60810765 60811442 60810765 ID=MS.gene50209
chr5.2 mRNA 60810765 60811442 60810765 ID=MS.gene50209.t1;Parent=MS.gene50209
chr5.2 exon 60810765 60811442 60810765 ID=MS.gene50209.t1.exon1;Parent=MS.gene50209.t1
chr5.2 CDS 60810765 60811442 60810765 ID=cds.MS.gene50209.t1;Parent=MS.gene50209.t1
Gene Sequence

>MS.gene50209

ATGGAAGCTGCATCTGGTGGAGAACCACCACCACCGTCAATACCATCAGAAACACCACTGGAGGCAGCACAACCACAACCTTCATCACCAGCAACACCAACACCAAGCCGCTACGAGTCACAAAAGCGACGAGACTGGAACACGTTCCAACAATATCTACGTAACCACAAACCACCATTAACCCTAGCACTATGCAGTGGAGCACACGTGATCGAGTTTCTCAAGTATCTTGATCAATTTGGAAAAACTAAGGTGCACGTGATAGGTTGTCCATATTTCGGACAACCTAACCCACCTTCTCCTTGCGCTTGTCCTCTTAAGCAAGCGTGGGGAAGTCTTGACGCTCTCATCGGACGTCTTAGGGCTGCTTTCGAGGAAAACGGTGGTAAACTGGAGAGTAATCCGTTTGGAACTCGGGCGGTAAGGATTTATCTGAGGGAAGTTAAGGATGGTCAAGCTAAAGCTAGAGGAGTTCCTTATGAGAAAAAGAAACGGAAGAGGCCCACTGTCACCGCTGCTGCAATAATATCAACTACAGCAGCGGTGAATAGTAGTGGACTTGGTGACGGTGGTGGTATTGATGGTAACACCGAGAGAATTGGAGCTGGTGTTGGTGTTACCACCAATAATACTACCACCGTCACACCTATTGTTAGTGTTAGTACGGCTATAGTATAG
Protein sequence

>MS.gene50209.t1

MEAASGGEPPPPSIPSETPLEAAQPQPSSPATPTPSRYESQKRRDWNTFQQYLRNHKPPLTLALCSGAHVIEFLKYLDQFGKTKVHVIGCPYFGQPNPPSPCACPLKQAWGSLDALIGRLRAAFEENGGKLESNPFGTRAVRIYLREVKDGQAKARGVPYEKKKRKRPTVTAAAIISTTAAVNSSGLGDGGGIDGNTERIGAGVGVTTNNTTTVTPIVSVSTAIV