AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29651

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29651.t1 MTR_5g082780 78.879 232 36 2 25 244 1 231 3.26e-126 358
MS.gene29651.t1 MTR_1g064570 42.073 328 133 10 1 277 79 400 1.13e-73 231
MS.gene29651.t1 MTR_5g082770 56.757 222 81 6 1 212 74 290 3.27e-71 221
MS.gene29651.t1 MTR_5g038260 45.548 292 127 9 15 277 95 383 5.61e-68 216
MS.gene29651.t1 MTR_5g038230 45.907 281 112 9 15 275 93 353 5.51e-64 204
MS.gene29651.t1 MTR_1g108740 42.435 271 124 8 15 275 96 344 7.20e-57 186
MS.gene29651.t1 MTR_7g077660 42.958 284 122 13 16 277 103 368 1.40e-54 181
MS.gene29651.t1 MTR_7g077620 41.118 304 128 14 2 275 88 370 1.24e-49 168
MS.gene29651.t1 MTR_7g077650 40.070 287 129 14 16 277 104 372 3.79e-47 161
MS.gene29651.t1 MTR_7g076110 39.041 292 139 14 13 277 34 313 2.11e-43 150
MS.gene29651.t1 MTR_7g076100 43.515 239 105 10 61 277 70 300 1.06e-41 145
MS.gene29651.t1 MTR_1g016150 40.777 103 45 4 2 99 88 179 1.78e-13 68.6
MS.gene29651.t1 MTR_1g016150 41.584 101 53 3 125 224 141 236 2.04e-13 68.6
MS.gene29651.t1 MTR_3g114990 26.667 330 174 18 1 273 90 408 9.25e-13 68.2
MS.gene29651.t1 MTR_6g023955 44.706 85 44 2 50 134 64 145 8.60e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 57 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTAATCCCATTGGAAATT+TGG 0.111032 5.1:+64854194 None:intergenic
GAGCTGGCTTCATTCCTTTA+TGG 0.175035 5.1:-64854693 MS.gene29651:CDS
TAAGAATTTGGCAATTTAAA+TGG 0.183830 5.1:+64855001 None:intergenic
AGCAGGACCCACAACCTTTC+TGG 0.187221 5.1:-64854223 MS.gene29651:CDS
TAATCATTTGGTCTTGTTAT+AGG 0.187600 5.1:+64854803 None:intergenic
TTTATGGATGTTATGTTCTA+TGG 0.218295 5.1:-64854677 MS.gene29651:CDS
TAAATATGGTAATAAGAATT+TGG 0.257178 5.1:+64854989 None:intergenic
AATCATTTGGTCTTGTTATA+GGG 0.294407 5.1:+64854804 None:intergenic
GGCTAAATCCACAATAAATA+TGG 0.298457 5.1:+64854975 None:intergenic
ATAGGAGCAACATTCTTAAA+AGG 0.302714 5.1:+64854902 None:intergenic
AACAAGACCAAATGATTATA+TGG 0.314220 5.1:-64854798 MS.gene29651:CDS
TTCACGGTCCATTTCATATA+GGG 0.322905 5.1:-64854307 MS.gene29651:CDS
CAAATTTCCAATGGGATTAG+TGG 0.338785 5.1:-64854193 None:intergenic
TCGAGGGTTGGAAGACTAAT+AGG 0.340960 5.1:+64854884 None:intergenic
GCTATGTCCTGAATTGGATT+TGG 0.346401 5.1:+64854584 None:intergenic
TGAAAAGCTATGTCCTGAAT+TGG 0.358033 5.1:+64854578 None:intergenic
ATTCACGGTCCATTTCATAT+AGG 0.364892 5.1:-64854308 MS.gene29651:CDS
GATAACTCCAAATCCAATTC+AGG 0.366133 5.1:-64854591 MS.gene29651:CDS
GCCACAACCATATAATCATT+TGG 0.389176 5.1:+64854791 None:intergenic
GCATCAGGTTCATACTTCTC+TGG 0.392853 5.1:-64854359 MS.gene29651:CDS
ACTGATTCAATTTCTGCATC+AGG 0.401480 5.1:-64854374 MS.gene29651:CDS
GCAGGACCCACAACCTTTCT+GGG 0.410798 5.1:-64854222 MS.gene29651:CDS
AAAAGGATGCAATAGTGTTA+TGG 0.423581 5.1:+64854919 None:intergenic
GATTCAATTTATTACATTCA+CGG 0.424146 5.1:-64854323 MS.gene29651:CDS
TTATATATCCCTATATGAAA+TGG 0.424795 5.1:+64854299 None:intergenic
TTGGAATTCGATGTTGAGAC+TGG 0.428338 5.1:-64854458 MS.gene29651:CDS
TTATCTTGTGAAGTCATTAG+AGG 0.436221 5.1:-64854540 MS.gene29651:CDS
GCAATTCACACTAACATTGA+TGG 0.439424 5.1:-64854770 MS.gene29651:CDS
ATAGAACATAACATCCATAA+AGG 0.458967 5.1:+64854679 None:intergenic
GGTCCTGCTTGTTGAAGAAA+TGG 0.463160 5.1:+64854237 None:intergenic
GGTAAAACCCAGAAAGGTTG+TGG 0.463897 5.1:+64854215 None:intergenic
ATGCTAAAGCTTGAGAGTCT+TGG 0.465110 5.1:-64854422 MS.gene29651:CDS
CTTATGTATGGTTCTCGAGC+TGG 0.466024 5.1:-64854709 MS.gene29651:CDS
ATTGTGGATTTAGCCATGGT+TGG 0.471805 5.1:-64854967 MS.gene29651:CDS
TCTTATTACCATATTTATTG+TGG 0.472815 5.1:-64854983 MS.gene29651:CDS
ACCAAATGATTATATGGTTG+TGG 0.479866 5.1:-64854792 MS.gene29651:CDS
TTTACCTGTGGTCGGGTACA+AGG 0.489187 5.1:-64854843 MS.gene29651:CDS
AAATTTGGTAAAACCCAGAA+AGG 0.519503 5.1:+64854209 None:intergenic
CAACCATTTCTTCAACAAGC+AGG 0.520003 5.1:-64854240 MS.gene29651:CDS
AATCATGCTGGACTTATGTA+TGG 0.521933 5.1:-64854721 MS.gene29651:CDS
ATTTATTGTGGATTTAGCCA+TGG 0.534223 5.1:-64854971 MS.gene29651:CDS
GGGATATATAATGTAAGAGA+TGG 0.535003 5.1:-64854287 MS.gene29651:CDS
AGTTGAACCACTAATCCCAT+TGG 0.545273 5.1:+64854186 None:intergenic
ATGGATGTTATGTTCTATGG+AGG 0.548376 5.1:-64854674 MS.gene29651:CDS
GTAAAACCCAGAAAGGTTGT+GGG 0.553567 5.1:+64854216 None:intergenic
ATACAAGTTTACCTGTGGTC+GGG 0.554481 5.1:-64854850 MS.gene29651:CDS
TAAAAGCGGGACAATCATGC+TGG 0.564345 5.1:-64854733 MS.gene29651:CDS
TATACAAGTTTACCTGTGGT+CGG 0.569637 5.1:-64854851 MS.gene29651:CDS
TATCTTGTGAAGTCATTAGA+GGG 0.571586 5.1:-64854539 MS.gene29651:CDS
TATGATCGATAATCGAGGGT+TGG 0.575237 5.1:+64854872 None:intergenic
GTGAAGAGTATGATGATCAA+AGG 0.582000 5.1:+64854262 None:intergenic
GTGACCTTGTACCCGACCAC+AGG 0.582047 5.1:+64854839 None:intergenic
CTATTGTTGCAAGCCAACCA+TGG 0.611822 5.1:+64854954 None:intergenic
TGTATATGATCGATAATCGA+GGG 0.630019 5.1:+64854868 None:intergenic
ATCATATACAAGTTTACCTG+TGG 0.632668 5.1:-64854855 MS.gene29651:CDS
AGTCATTAGAGGGAGACTTG+TGG 0.643188 5.1:-64854529 MS.gene29651:CDS
TTGTATATGATCGATAATCG+AGG 0.645288 5.1:+64854867 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAGATTTTTTACTTTTAA+GGG - chr5.1:64854703-64854722 MS.gene29651:CDS 10.0%
!! TAAATATGGTAATAAGAATT+TGG + chr5.1:64854217-64854236 None:intergenic 15.0%
!!! GAAAAGATTTTTTACTTTTA+AGG - chr5.1:64854702-64854721 MS.gene29651:CDS 15.0%
!! GATTCAATTTATTACATTCA+CGG - chr5.1:64854880-64854899 MS.gene29651:CDS 20.0%
!! TAAGAATTTGGCAATTTAAA+TGG + chr5.1:64854205-64854224 None:intergenic 20.0%
!! TCTTATTACCATATTTATTG+TGG - chr5.1:64854220-64854239 MS.gene29651:CDS 20.0%
!! TTATATATCCCTATATGAAA+TGG + chr5.1:64854907-64854926 None:intergenic 20.0%
! AACAAGACCAAATGATTATA+TGG - chr5.1:64854405-64854424 MS.gene29651:CDS 25.0%
! ATAGAACATAACATCCATAA+AGG + chr5.1:64854527-64854546 None:intergenic 25.0%
! TTTATGGATGTTATGTTCTA+TGG - chr5.1:64854526-64854545 MS.gene29651:CDS 25.0%
!! AGTATAGTATCTTTTAATCC+TGG - chr5.1:64854580-64854599 MS.gene29651:CDS 25.0%
!!! AATCATTTGGTCTTGTTATA+GGG + chr5.1:64854402-64854421 None:intergenic 25.0%
!!! TAATCATTTGGTCTTGTTAT+AGG + chr5.1:64854403-64854422 None:intergenic 25.0%
AAAAGGATGCAATAGTGTTA+TGG + chr5.1:64854287-64854306 None:intergenic 30.0%
AAATTTGGTAAAACCCAGAA+AGG + chr5.1:64854997-64855016 None:intergenic 30.0%
ACCAAATGATTATATGGTTG+TGG - chr5.1:64854411-64854430 MS.gene29651:CDS 30.0%
ATAGGAGCAACATTCTTAAA+AGG + chr5.1:64854304-64854323 None:intergenic 30.0%
ATCATATACAAGTTTACCTG+TGG - chr5.1:64854348-64854367 MS.gene29651:CDS 30.0%
ATTTATTGTGGATTTAGCCA+TGG - chr5.1:64854232-64854251 MS.gene29651:CDS 30.0%
GGCTAAATCCACAATAAATA+TGG + chr5.1:64854231-64854250 None:intergenic 30.0%
GGGATATATAATGTAAGAGA+TGG - chr5.1:64854916-64854935 MS.gene29651:CDS 30.0%
TATCTTGTGAAGTCATTAGA+GGG - chr5.1:64854664-64854683 MS.gene29651:CDS 30.0%
TGTATATGATCGATAATCGA+GGG + chr5.1:64854338-64854357 None:intergenic 30.0%
TTATCTTGTGAAGTCATTAG+AGG - chr5.1:64854663-64854682 MS.gene29651:CDS 30.0%
TTGTATATGATCGATAATCG+AGG + chr5.1:64854339-64854358 None:intergenic 30.0%
! CTTTTAATCCTGGTCATAAA+AGG - chr5.1:64854590-64854609 MS.gene29651:CDS 30.0%
! GGTTTTACCAAATTTCCAAT+GGG - chr5.1:64855002-64855021 MS.gene29651:CDS 30.0%
!! ACGTTTCGCTTTTATAAAAG+CGG - chr5.1:64854456-64854475 MS.gene29651:CDS 30.0%
!!! TGATTTTCAAGTGTACAAGT+TGG - chr5.1:64854726-64854745 MS.gene29651:CDS 30.0%
AATCATGCTGGACTTATGTA+TGG - chr5.1:64854482-64854501 MS.gene29651:CDS 35.0%
ATGGATGTTATGTTCTATGG+AGG - chr5.1:64854529-64854548 MS.gene29651:CDS 35.0%
ATTCACGGTCCATTTCATAT+AGG - chr5.1:64854895-64854914 MS.gene29651:CDS 35.0%
GATAACTCCAAATCCAATTC+AGG - chr5.1:64854612-64854631 MS.gene29651:CDS 35.0%
GCAATTCACACTAACATTGA+TGG - chr5.1:64854433-64854452 MS.gene29651:CDS 35.0%
GCCACAACCATATAATCATT+TGG + chr5.1:64854415-64854434 None:intergenic 35.0%
TATACAAGTTTACCTGTGGT+CGG - chr5.1:64854352-64854371 MS.gene29651:CDS 35.0%
TGAAAAGCTATGTCCTGAAT+TGG + chr5.1:64854628-64854647 None:intergenic 35.0%
TTCACGGTCCATTTCATATA+GGG - chr5.1:64854896-64854915 MS.gene29651:CDS 35.0%
! ACTGATTCAATTTCTGCATC+AGG - chr5.1:64854829-64854848 MS.gene29651:CDS 35.0%
! ATTCAGGACATAGCTTTTCA+TGG - chr5.1:64854628-64854647 MS.gene29651:CDS 35.0%
! GGGTTTTACCAAATTTCCAA+TGG - chr5.1:64855001-64855020 MS.gene29651:CDS 35.0%
! GTGAAGAGTATGATGATCAA+AGG + chr5.1:64854944-64854963 None:intergenic 35.0%
!! CGTTTCGCTTTTATAAAAGC+GGG - chr5.1:64854457-64854476 MS.gene29651:CDS 35.0%
!! GGAGACAATGTTTTGTTCTT+GGG - chr5.1:64854802-64854821 MS.gene29651:CDS 35.0%
!! TGGAGACAATGTTTTGTTCT+TGG - chr5.1:64854801-64854820 MS.gene29651:CDS 35.0%
ATACAAGTTTACCTGTGGTC+GGG - chr5.1:64854353-64854372 MS.gene29651:CDS 40.0%
ATGCTAAAGCTTGAGAGTCT+TGG - chr5.1:64854781-64854800 MS.gene29651:CDS 40.0%
ATTGTGGATTTAGCCATGGT+TGG - chr5.1:64854236-64854255 MS.gene29651:CDS 40.0%
CAACCATTTCTTCAACAAGC+AGG - chr5.1:64854963-64854982 MS.gene29651:CDS 40.0%
GCTATGTCCTGAATTGGATT+TGG + chr5.1:64854622-64854641 None:intergenic 40.0%
GTAAAACCCAGAAAGGTTGT+GGG + chr5.1:64854990-64855009 None:intergenic 40.0%
TATGATCGATAATCGAGGGT+TGG + chr5.1:64854334-64854353 None:intergenic 40.0%
TTGGAATTCGATGTTGAGAC+TGG - chr5.1:64854745-64854764 MS.gene29651:CDS 40.0%
! GGAGTTATCCTTTTATGACC+AGG + chr5.1:64854601-64854620 None:intergenic 40.0%
!! GCTTTTCATGGAAGCTCTAA+AGG - chr5.1:64854640-64854659 MS.gene29651:CDS 40.0%
AGTCATTAGAGGGAGACTTG+TGG - chr5.1:64854674-64854693 MS.gene29651:CDS 45.0%
CTATTGTTGCAAGCCAACCA+TGG + chr5.1:64854252-64854271 None:intergenic 45.0%
CTTATGTATGGTTCTCGAGC+TGG - chr5.1:64854494-64854513 MS.gene29651:CDS 45.0%
GCATCAGGTTCATACTTCTC+TGG - chr5.1:64854844-64854863 MS.gene29651:CDS 45.0%
GGTAAAACCCAGAAAGGTTG+TGG + chr5.1:64854991-64855010 None:intergenic 45.0%
TAAAAGCGGGACAATCATGC+TGG - chr5.1:64854470-64854489 MS.gene29651:CDS 45.0%
TCGAGGGTTGGAAGACTAAT+AGG + chr5.1:64854322-64854341 None:intergenic 45.0%
! GAGCTGGCTTCATTCCTTTA+TGG - chr5.1:64854510-64854529 MS.gene29651:CDS 45.0%
! GGTCCTGCTTGTTGAAGAAA+TGG + chr5.1:64854969-64854988 None:intergenic 45.0%
TTTACCTGTGGTCGGGTACA+AGG - chr5.1:64854360-64854379 MS.gene29651:CDS 50.0%
AGCAGGACCCACAACCTTTC+TGG - chr5.1:64854980-64854999 MS.gene29651:CDS 55.0%
GCAGGACCCACAACCTTTCT+GGG - chr5.1:64854981-64855000 MS.gene29651:CDS 55.0%
GTGACCTTGTACCCGACCAC+AGG + chr5.1:64854367-64854386 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 64854196 64855029 64854196 ID=MS.gene29651
chr5.1 mRNA 64854196 64855029 64854196 ID=MS.gene29651.t1;Parent=MS.gene29651
chr5.1 exon 64854196 64855029 64854196 ID=MS.gene29651.t1.exon1;Parent=MS.gene29651.t1
chr5.1 CDS 64854196 64855029 64854196 ID=cds.MS.gene29651.t1;Parent=MS.gene29651.t1
Gene Sequence

>MS.gene29651

ATGTATCCATTTAAATTGCCAAATTCTTATTACCATATTTATTGTGGATTTAGCCATGGTTGGCTTGCAACAATAGATAAAAGTCATGCCATAACACTATTGCATCCTTTTAAGAATGTTGCTCCTATTAGTCTTCCAACCCTCGATTATCGATCATATACAAGTTTACCTGTGGTCGGGTACAAGGTCACTCTTTCTGCTGACCCTATAACAAGACCAAATGATTATATGGTTGTGGCAATTCACACTAACATTGATGGACGTTTCGCTTTTATAAAAGCGGGACAATCATGCTGGACTTATGTATGGTTCTCGAGCTGGCTTCATTCCTTTATGGATGTTATGTTCTATGGAGGTTTAGTTTATGCTGTGAGTAAATATCACAGTATAGTATCTTTTAATCCTGGTCATAAAAGGATAACTCCAAATCCAATTCAGGACATAGCTTTTCATGGAAGCTCTAAAGGTTATCTTGTGAAGTCATTAGAGGGAGACTTGTGGATAGTGAAAAGATTTTTTACTTTTAAGGGTGATTTTCAAGTGTACAAGTTGGAATTCGATGTTGAGACTGGAAAGTTTAAACAAATGCTAAAGCTTGAGAGTCTTGGAGACAATGTTTTGTTCTTGGGAGACACTGATTCAATTTCTGCATCAGGTTCATACTTCTCTGGTTGTTTGAAAAAAGATTCAATTTATTACATTCACGGTCCATTTCATATAGGGATATATAATGTAAGAGATGGAACCTTTGATCATCATACTCTTCACAACCATTTCTTCAACAAGCAGGACCCACAACCTTTCTGGGTTTTACCAAATTTCCAATGGGATTAG
Protein sequence

>MS.gene29651.t1

MYPFKLPNSYYHIYCGFSHGWLATIDKSHAITLLHPFKNVAPISLPTLDYRSYTSLPVVGYKVTLSADPITRPNDYMVVAIHTNIDGRFAFIKAGQSCWTYVWFSSWLHSFMDVMFYGGLVYAVSKYHSIVSFNPGHKRITPNPIQDIAFHGSSKGYLVKSLEGDLWIVKRFFTFKGDFQVYKLEFDVETGKFKQMLKLESLGDNVLFLGDTDSISASGSYFSGCLKKDSIYYIHGPFHIGIYNVRDGTFDHHTLHNHFFNKQDPQPFWVLPNFQWD