AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66480

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66480.t1 MTR_1g017570 96.552 145 5 0 1 145 1 145 7.81e-101 285
MS.gene66480.t1 MTR_3g103360 58.333 144 56 2 1 144 1 140 7.60e-50 156
MS.gene66480.t1 MTR_4g097440 47.154 123 47 3 22 128 23 143 8.90e-20 80.9
MS.gene66480.t1 MTR_5g015090 45.082 122 51 3 31 139 22 140 5.84e-18 75.9
MS.gene66480.t1 MTR_8g086020 41.584 101 53 2 45 143 18 114 1.15e-14 67.4
MS.gene66480.t1 MTR_1g087040 37.273 110 62 2 34 143 4 106 1.71e-13 63.9
MS.gene66480.t1 MTR_1g022495 41.111 90 51 1 35 124 7 94 2.47e-12 61.2
MS.gene66480.t1 MTR_3g117120 43.902 82 44 1 43 124 15 94 2.55e-12 60.8
MS.gene66480.t1 MTR_4g070860 43.750 80 43 1 45 124 17 94 3.08e-12 60.8
MS.gene66480.t1 MTR_7g029400 44.156 77 43 0 59 135 83 159 1.55e-11 59.7
MS.gene66480.t1 MTR_8g015250 39.000 100 57 1 40 135 50 149 2.38e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66480.t1 AT3G49760 37.594 133 76 1 14 139 19 151 2.97e-20 81.6
MS.gene66480.t1 AT2G22850 45.783 83 45 0 57 139 126 208 2.74e-15 70.1
MS.gene66480.t1 AT2G22850 45.783 83 45 0 57 139 126 208 2.74e-15 70.1
MS.gene66480.t1 AT2G18160 43.750 80 45 0 45 124 16 95 5.63e-14 65.9
MS.gene66480.t1 AT1G75390 41.667 84 49 0 45 128 26 109 3.42e-13 63.5
MS.gene66480.t1 AT4G37730 51.471 68 33 0 57 124 194 261 4.06e-13 65.1
MS.gene66480.t1 AT1G75390 41.463 82 48 0 43 124 24 105 1.04e-12 61.2
MS.gene66480.t1 AT5G15830 38.835 103 59 2 26 128 44 142 9.81e-12 60.1
MS.gene66480.t1 AT1G59530 39.344 122 68 2 18 139 14 129 1.01e-11 59.3
MS.gene66480.t1 AT4G34590 43.939 66 37 0 59 124 26 91 9.35e-11 57.0

Find 45 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCCCTCATGGCAACACTTT+TGG 0.232653 1.4:+5200322 MS.gene66480:CDS
CGATTTGAACCGGTTGAGAA+TGG 0.382249 1.4:+5200208 MS.gene66480:CDS
TTGTGAACCGGACCCTGGAC+TGG 0.414459 1.4:-5200066 None:intergenic
ACCGGTTGAGAATGGAAAAC+CGG 0.420192 1.4:+5200216 MS.gene66480:CDS
TAAGGAGAATGCAATCAAAC+CGG 0.448119 1.4:+5200129 MS.gene66480:CDS
ACCTCACGAACGATTTGAAC+CGG 0.459693 1.4:+5200198 MS.gene66480:CDS
GGTCCGGCTCATGTGTGTTC+CGG 0.472124 1.4:+5199971 MS.gene66480:CDS
ATTGCATGGTTAACCCTAGC+TGG 0.474346 1.4:-5200250 None:intergenic
GGACCGGATACTCCTCTTCA+TGG 0.477097 1.4:-5199953 None:intergenic
ACGACTTGATCCTTGTGAAC+CGG 0.478619 1.4:-5200078 None:intergenic
GTGAACATGGTTTCATGAAC+CGG 0.479700 1.4:-5199990 None:intergenic
CCTGGACTGGATGGATCAAC+CGG 0.484260 1.4:-5200053 None:intergenic
CCGGTTGATCCATCCAGTCC+AGG 0.489171 1.4:+5200053 MS.gene66480:CDS
GATCCTTGTGAACCGGACCC+TGG 0.490890 1.4:-5200071 None:intergenic
GATCAACCGGTTGGTTAATG+AGG 0.507162 1.4:-5200040 None:intergenic
GATCCATCCAGTCCAGGGTC+CGG 0.524687 1.4:+5200059 MS.gene66480:CDS
CTTCCATGAAGAGGAGTATC+CGG 0.526400 1.4:+5199950 MS.gene66480:CDS
GTTCACACAAGGCGAAATAG+AGG 0.540753 1.4:+5200007 MS.gene66480:CDS
ATCCAAAAGTGTTGCCATGA+GGG 0.543780 1.4:-5200324 None:intergenic
TATTTCGCCTTGTGTGAACA+TGG 0.548387 1.4:-5200003 None:intergenic
GAACCGGAACACACATGAGC+CGG 0.554047 1.4:-5199974 None:intergenic
CCGGTTGAGAATGGAAAACC+GGG 0.557045 1.4:+5200217 MS.gene66480:CDS
GGAACACACATGAGCCGGAC+CGG 0.558056 1.4:-5199969 None:intergenic
AATCAAACCGGGAGTCGGCT+AGG 0.560261 1.4:+5200141 MS.gene66480:CDS
ATCAGAATCAATGTCCCTCA+TGG 0.566320 1.4:+5200310 MS.gene66480:CDS
AGCAATGTCCTTCCATGAAG+AGG 0.571717 1.4:+5199941 None:intergenic
GAACCGGACCCTGGACTGGA+TGG 0.582397 1.4:-5200062 None:intergenic
ATGAAGAGGAGTATCCGGTC+CGG 0.588642 1.4:+5199955 MS.gene66480:CDS
AGTCCAGGGTCCGGTTCACA+AGG 0.591544 1.4:+5200068 MS.gene66480:CDS
ACCGGTTCAAATCGTTCGTG+AGG 0.594738 1.4:-5200199 None:intergenic
CGGATACTCCTCTTCATGGA+AGG 0.596073 1.4:-5199949 None:intergenic
CGGTTGATCCATCCAGTCCA+GGG 0.598027 1.4:+5200054 MS.gene66480:CDS
GACTGGATGGATCAACCGGT+TGG 0.601414 1.4:-5200049 None:intergenic
GTGACCGCCTAGCCGACTCC+CGG 0.602249 1.4:-5200148 None:intergenic
TAATATGAGATTGTATTGCA+TGG 0.609971 1.4:-5200264 None:intergenic
ATCAACCGGTTGGTTAATGA+GGG 0.611428 1.4:-5200039 None:intergenic
AATGCAATCAAACCGGGAGT+CGG 0.621410 1.4:+5200136 MS.gene66480:CDS
ATACAATCTCATATTATCAA+CGG 0.623568 1.4:+5200271 MS.gene66480:CDS
AAGGAGAATGCAATCAAACC+GGG 0.631263 1.4:+5200130 MS.gene66480:CDS
CATGAAACCATGTTCACACA+AGG 0.636957 1.4:+5199996 MS.gene66480:CDS
GATCCAAAAGTGTTGCCATG+AGG 0.664933 1.4:-5200325 None:intergenic
TTCACAAGGATCAAGTCGTG+CGG 0.675020 1.4:+5200082 MS.gene66480:CDS
AGTCGGCTAGGCGGTCACGT+TGG 0.676204 1.4:+5200153 MS.gene66480:CDS
GGTCACGTTGGAGAAAGAAG+CGG 0.707696 1.4:+5200165 MS.gene66480:CDS
CAAACCGGGAGTCGGCTAGG+CGG 0.728540 1.4:+5200144 MS.gene66480:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATACAATCTCATATTATCAA+CGG + chr1.4:5200271-5200290 MS.gene66480:CDS 20.0%
! TAATATGAGATTGTATTGCA+TGG - chr1.4:5200267-5200286 None:intergenic 25.0%
! CAACACTTTTGGATCTATAT+CGG + chr1.4:5200333-5200352 MS.gene66480:CDS 30.0%
!!! TTCTCCTTATTTTTCTCTCA+CGG - chr1.4:5200118-5200137 None:intergenic 30.0%
TAAGGAGAATGCAATCAAAC+CGG + chr1.4:5200129-5200148 MS.gene66480:CDS 35.0%
! ATTTTCCCTCATTAACCAAC+CGG + chr1.4:5200034-5200053 MS.gene66480:CDS 35.0%
!!! TCTCCTTATTTTTCTCTCAC+GGG - chr1.4:5200117-5200136 None:intergenic 35.0%
AAGGAGAATGCAATCAAACC+GGG + chr1.4:5200130-5200149 MS.gene66480:CDS 40.0%
ATCAGAATCAATGTCCCTCA+TGG + chr1.4:5200310-5200329 MS.gene66480:CDS 40.0%
CATGAAACCATGTTCACACA+AGG + chr1.4:5199996-5200015 MS.gene66480:CDS 40.0%
GGGAACTAAAAAACCAGCTA+GGG + chr1.4:5200237-5200256 MS.gene66480:CDS 40.0%
GTGAACATGGTTTCATGAAC+CGG - chr1.4:5199993-5200012 None:intergenic 40.0%
TATTTCGCCTTGTGTGAACA+TGG - chr1.4:5200006-5200025 None:intergenic 40.0%
! ATCAACCGGTTGGTTAATGA+GGG - chr1.4:5200042-5200061 None:intergenic 40.0%
!! ATCCAAAAGTGTTGCCATGA+GGG - chr1.4:5200327-5200346 None:intergenic 40.0%
!!! CTAGCTGGTTTTTTAGTTCC+CGG - chr1.4:5200238-5200257 None:intergenic 40.0%
AATGCAATCAAACCGGGAGT+CGG + chr1.4:5200136-5200155 MS.gene66480:CDS 45.0%
ACCGGTTGAGAATGGAAAAC+CGG + chr1.4:5200216-5200235 MS.gene66480:CDS 45.0%
ACCTCACGAACGATTTGAAC+CGG + chr1.4:5200198-5200217 MS.gene66480:CDS 45.0%
ACGACTTGATCCTTGTGAAC+CGG - chr1.4:5200081-5200100 None:intergenic 45.0%
ATTGCATGGTTAACCCTAGC+TGG - chr1.4:5200253-5200272 None:intergenic 45.0%
CGACCCGTGAGAGAAAAATA+AGG + chr1.4:5200111-5200130 MS.gene66480:CDS 45.0%
CGATTTGAACCGGTTGAGAA+TGG + chr1.4:5200208-5200227 MS.gene66480:CDS 45.0%
CGGGAACTAAAAAACCAGCT+AGG + chr1.4:5200236-5200255 MS.gene66480:CDS 45.0%
GTTCACACAAGGCGAAATAG+AGG + chr1.4:5200007-5200026 MS.gene66480:CDS 45.0%
TTCACAAGGATCAAGTCGTG+CGG + chr1.4:5200082-5200101 MS.gene66480:CDS 45.0%
! GATCAACCGGTTGGTTAATG+AGG - chr1.4:5200043-5200062 None:intergenic 45.0%
!! CTTCCATGAAGAGGAGTATC+CGG + chr1.4:5199950-5199969 MS.gene66480:CDS 45.0%
!! GATCCAAAAGTGTTGCCATG+AGG - chr1.4:5200328-5200347 None:intergenic 45.0%
CCGGTTGAGAATGGAAAACC+GGG + chr1.4:5200217-5200236 MS.gene66480:CDS 50.0%
CGGATACTCCTCTTCATGGA+AGG - chr1.4:5199952-5199971 None:intergenic 50.0%
GGTCACGTTGGAGAAAGAAG+CGG + chr1.4:5200165-5200184 MS.gene66480:CDS 50.0%
! ACCGGTTCAAATCGTTCGTG+AGG - chr1.4:5200202-5200221 None:intergenic 50.0%
! CCCGGTTTTCCATTCTCAAC+CGG - chr1.4:5200220-5200239 None:intergenic 50.0%
! GTCCCTCATGGCAACACTTT+TGG + chr1.4:5200322-5200341 MS.gene66480:CDS 50.0%
!! ATGAAGAGGAGTATCCGGTC+CGG + chr1.4:5199955-5199974 MS.gene66480:CDS 50.0%
AATCAAACCGGGAGTCGGCT+AGG + chr1.4:5200141-5200160 MS.gene66480:CDS 55.0%
CGGTTGATCCATCCAGTCCA+GGG + chr1.4:5200054-5200073 MS.gene66480:CDS 55.0%
GAACCGGAACACACATGAGC+CGG - chr1.4:5199977-5199996 None:intergenic 55.0%
GACTGGATGGATCAACCGGT+TGG - chr1.4:5200052-5200071 None:intergenic 55.0%
GGACCGGATACTCCTCTTCA+TGG - chr1.4:5199956-5199975 None:intergenic 55.0%
! CCTGGACTGGATGGATCAAC+CGG - chr1.4:5200056-5200075 None:intergenic 55.0%
AGTCCAGGGTCCGGTTCACA+AGG + chr1.4:5200068-5200087 MS.gene66480:CDS 60.0%
CCGGTTGATCCATCCAGTCC+AGG + chr1.4:5200053-5200072 MS.gene66480:CDS 60.0%
GATCCATCCAGTCCAGGGTC+CGG + chr1.4:5200059-5200078 MS.gene66480:CDS 60.0%
GATCCTTGTGAACCGGACCC+TGG - chr1.4:5200074-5200093 None:intergenic 60.0%
GGAACACACATGAGCCGGAC+CGG - chr1.4:5199972-5199991 None:intergenic 60.0%
GGTCCGGCTCATGTGTGTTC+CGG + chr1.4:5199971-5199990 MS.gene66480:CDS 60.0%
TTGTGAACCGGACCCTGGAC+TGG - chr1.4:5200069-5200088 None:intergenic 60.0%
AGTCGGCTAGGCGGTCACGT+TGG + chr1.4:5200153-5200172 MS.gene66480:CDS 65.0%
CAAACCGGGAGTCGGCTAGG+CGG + chr1.4:5200144-5200163 MS.gene66480:CDS 65.0%
! GAACCGGACCCTGGACTGGA+TGG - chr1.4:5200065-5200084 None:intergenic 65.0%
! GTGACCGCCTAGCCGACTCC+CGG - chr1.4:5200151-5200170 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 5199945 5200382 5199945 ID=MS.gene66480
chr1.4 mRNA 5199945 5200382 5199945 ID=MS.gene66480.t1;Parent=MS.gene66480
chr1.4 exon 5199945 5200382 5199945 ID=MS.gene66480.t1.exon1;Parent=MS.gene66480.t1
chr1.4 CDS 5199945 5200382 5199945 ID=cds.MS.gene66480.t1;Parent=MS.gene66480.t1
Gene Sequence

>MS.gene66480

ATGTCCTTCCATGAAGAGGAGTATCCGGTCCGGCTCATGTGTGTTCCGGTTCATGAAACCATGTTCACACAAGGCGAAATAGAGGAGTTATTTTCCCTCATTAACCAACCGGTTGATCCATCCAGTCCAGGGTCCGGTTCACAAGGATCAAGTCGTGCGGTTTACTCGACCCGTGAGAGAAAAATAAGGAGAATGCAATCAAACCGGGAGTCGGCTAGGCGGTCACGTTGGAGAAAGAAGCGGCACGTAGAGAACCTCACGAACGATTTGAACCGGTTGAGAATGGAAAACCGGGAACTAAAAAACCAGCTAGGGTTAACCATGCAATACAATCTCATATTATCAACGGAGAATGAACGTCTAAGATCAGAATCAATGTCCCTCATGGCAACACTTTTGGATCTATATCGGACTTTAGAGACAATAATTTCACAATAG
Protein sequence

>MS.gene66480.t1

MSFHEEEYPVRLMCVPVHETMFTQGEIEELFSLINQPVDPSSPGSGSQGSSRAVYSTRERKIRRMQSNRESARRSRWRKKRHVENLTNDLNRLRMENRELKNQLGLTMQYNLILSTENERLRSESMSLMATLLDLYRTLETIISQ