AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068677

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068677.t1 MTR_2g070310 96.479 284 10 0 1 284 1 284 0.0 565
MS.gene068677.t1 MTR_1g084050 49.438 267 135 0 15 281 38 304 1.17e-92 278
MS.gene068677.t1 MTR_7g112130 47.940 267 139 0 15 281 5 271 4.31e-90 270
MS.gene068677.t1 MTR_2g034240 47.955 269 138 2 15 281 5 273 2.70e-86 259
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068677.t1 AT5G56080 52.030 271 125 3 15 281 5 274 1.97e-91 274
MS.gene068677.t1 AT5G04950 49.815 271 132 2 15 281 5 275 4.35e-91 273
MS.gene068677.t1 AT1G09240 51.292 271 127 4 15 281 5 274 1.32e-88 266
MS.gene068677.t1 AT1G56430 48.881 268 132 4 18 281 9 275 2.66e-88 266

Find 54 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCACTAAGTTCAATTATAT+TGG 0.247107 2.2:-21512504 MS.gene068677:CDS
TAGCTTATCGATCAAGCTTT+AGG 0.325153 2.2:+21512086 None:intergenic
TTTCTAAGCTAGAATCTCTT+AGG 0.328740 2.2:-21512844 MS.gene068677:CDS
TCCTTCTGCTTTGCCACAAA+GGG 0.365628 2.2:+21512703 None:intergenic
CAGCTTCAAAATTGAAGGAT+TGG 0.377323 2.2:+21512918 None:intergenic
ATTTGTGACACAAGATATAA+TGG 0.377553 2.2:-21512369 MS.gene068677:CDS
TGCTAGCAAGATTGTGGCTT+CGG 0.391793 2.2:-21512417 MS.gene068677:CDS
CATTCACAACACCATTCTCT+TGG 0.394956 2.2:+21512561 None:intergenic
TTAACATAGTTTCCATGGTA+AGG 0.396731 2.2:+21512611 None:intergenic
GCCAATATAATTGAACTTAG+TGG 0.399358 2.2:+21512503 None:intergenic
AATGGAAGCTAAGGAGAGAT+TGG 0.401099 2.2:-21512351 MS.gene068677:CDS
AAAGTAGCATTTATAGGATC+TGG 0.401897 2.2:-21512533 MS.gene068677:CDS
ATATCATTCTCCTCAACAAT+AGG 0.407208 2.2:+21512182 None:intergenic
GAAAGCCTCATTCCCCTTTG+TGG 0.425154 2.2:-21512716 MS.gene068677:CDS
AAGAGATTCTAGCTTAGAAA+TGG 0.430571 2.2:+21512847 None:intergenic
CGCATTGTCTTAACCTCTTG+TGG 0.432545 2.2:+21512740 None:intergenic
TTGCTTGTAAGAAGTGCAAA+AGG 0.435002 2.2:-21512224 MS.gene068677:CDS
ATCTCTTAGGCCTTCAAAGC+AGG 0.436005 2.2:-21512831 MS.gene068677:CDS
AGGGTGTTAACCTGCTTTGA+AGG 0.438492 2.2:+21512821 None:intergenic
ATAATTGAACTTAGTGGCAT+TGG 0.438717 2.2:+21512509 None:intergenic
ATGGAAGCTAAGGAGAGATT+GGG 0.443348 2.2:-21512350 MS.gene068677:CDS
TGTCTTAACCTCTTGTGGTA+AGG 0.449698 2.2:+21512745 None:intergenic
TATTGTTGAGGAGAATGATA+TGG 0.461887 2.2:-21512180 MS.gene068677:CDS
AATTTCAGCTTCAAAATTGA+AGG 0.464475 2.2:+21512913 None:intergenic
GTTTGACTAAGTGAGTCAAA+AGG 0.470350 2.2:+21512801 None:intergenic
AACAAAATCCTCCAAGAGAA+TGG 0.470902 2.2:-21512572 MS.gene068677:CDS
CTTTGCCACAAAGGGGAATG+AGG 0.471873 2.2:+21512711 None:intergenic
CTAGTTTAACATAGTTTCCA+TGG 0.475050 2.2:+21512606 None:intergenic
TCACAACACCATTCTCTTGG+AGG 0.492086 2.2:+21512564 None:intergenic
GTCCTTCTGCTTTGCCACAA+AGG 0.493701 2.2:+21512702 None:intergenic
TAACATAGTTTCCATGGTAA+GGG 0.496507 2.2:+21512612 None:intergenic
ACAAGATATAATGGAAGCTA+AGG 0.502646 2.2:-21512360 MS.gene068677:CDS
TGGTAAGGCTTCAATCTCAA+TGG 0.508290 2.2:+21512760 None:intergenic
GCTTCAATCTCAATGGATGA+AGG 0.509882 2.2:+21512767 None:intergenic
CCCCTTTGTGGCAAAGCAGA+AGG 0.513729 2.2:-21512704 MS.gene068677:CDS
AAGGATTGGAAAGATGCCAT+TGG 0.518413 2.2:+21512932 None:intergenic
CGGATAAAGCACTTGAAAAG+AGG 0.520656 2.2:-21512397 MS.gene068677:CDS
TTTGACTAAGTGAGTCAAAA+GGG 0.523641 2.2:+21512802 None:intergenic
GATTGAAGCCTTACCACAAG+AGG 0.528285 2.2:-21512753 MS.gene068677:CDS
ATAAGAAAGTATATGAAGGA+AGG 0.551950 2.2:-21512254 MS.gene068677:CDS
TGAGATATGAGAAGCTCTTG+TGG 0.560483 2.2:+21512890 None:intergenic
TGCTTGTAAGAAGTGCAAAA+GGG 0.561089 2.2:-21512223 MS.gene068677:CDS
TGAGGTTGCTAGCAAGATTG+TGG 0.575623 2.2:-21512423 MS.gene068677:CDS
ACATATAAGAAAGTATATGA+AGG 0.575751 2.2:-21512258 MS.gene068677:CDS
TATTGATGAGAAAGCTAATG+AGG 0.589845 2.2:-21512441 MS.gene068677:CDS
CTTCAATCTCAATGGATGAA+GGG 0.591587 2.2:+21512768 None:intergenic
AGAAAGTATATGAAGGAAGG+TGG 0.592605 2.2:-21512251 MS.gene068677:CDS
TATATTGGCAACTCATCACA+TGG 0.625569 2.2:-21512489 MS.gene068677:CDS
AACGGATGATGTTATCAACT+CGG 0.627733 2.2:-21512126 MS.gene068677:CDS
CTGCACTTGTTGGTATGCGT+AGG 0.635388 2.2:-21512304 MS.gene068677:CDS
TGGAAGCTAAGGAGAGATTG+GGG 0.651928 2.2:-21512349 MS.gene068677:CDS
CCTTCTGCTTTGCCACAAAG+GGG 0.652708 2.2:+21512704 None:intergenic
CAATCTCAATGGATGAAGGG+AGG 0.659476 2.2:+21512771 None:intergenic
GAGTTGATAACATCATCCGT+TGG 0.686377 2.2:+21512128 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAGTGTTAAATTTTTCAC+TGG + chr2.2:21512394-21512413 None:intergenic 20.0%
!!! ACATATAAGAAAGTATATGA+AGG - chr2.2:21512768-21512787 MS.gene068677:CDS 20.0%
! AATTTCAGCTTCAAAATTGA+AGG + chr2.2:21512116-21512135 None:intergenic 25.0%
! ATTTGTGACACAAGATATAA+TGG - chr2.2:21512657-21512676 MS.gene068677:CDS 25.0%
! GCAAAAAAAGTAGCATTTAT+AGG - chr2.2:21512487-21512506 MS.gene068677:CDS 25.0%
!! AGTGAAAAAGTGAAGATTTT+GGG - chr2.2:21512745-21512764 MS.gene068677:CDS 25.0%
!! ATAAGAAAGTATATGAAGGA+AGG - chr2.2:21512772-21512791 MS.gene068677:CDS 25.0%
!! GAATGATATGGTAAATTTTG+AGG - chr2.2:21512858-21512877 MS.gene068677:CDS 25.0%
!! GTTAAATTTTTCACTGGATT+TGG + chr2.2:21512388-21512407 None:intergenic 25.0%
!!! GCAATATGATTGCATTTTTT+TGG - chr2.2:21512699-21512718 MS.gene068677:CDS 25.0%
!!! TTTTTTGTATCCTATTGTTG+AGG - chr2.2:21512834-21512853 MS.gene068677:CDS 25.0%
AAAGTAGCATTTATAGGATC+TGG - chr2.2:21512493-21512512 MS.gene068677:CDS 30.0%
ATAATTGAACTTAGTGGCAT+TGG + chr2.2:21512520-21512539 None:intergenic 30.0%
ATATCATTCTCCTCAACAAT+AGG + chr2.2:21512847-21512866 None:intergenic 30.0%
CTAGTTTAACATAGTTTCCA+TGG + chr2.2:21512423-21512442 None:intergenic 30.0%
GCCAATATAATTGAACTTAG+TGG + chr2.2:21512526-21512545 None:intergenic 30.0%
GCCACTAAGTTCAATTATAT+TGG - chr2.2:21512522-21512541 MS.gene068677:CDS 30.0%
TAACATAGTTTCCATGGTAA+GGG + chr2.2:21512417-21512436 None:intergenic 30.0%
TATTGATGAGAAAGCTAATG+AGG - chr2.2:21512585-21512604 MS.gene068677:CDS 30.0%
TATTGTTGAGGAGAATGATA+TGG - chr2.2:21512846-21512865 MS.gene068677:CDS 30.0%
TTAACATAGTTTCCATGGTA+AGG + chr2.2:21512418-21512437 None:intergenic 30.0%
TTTCTAAGCTAGAATCTCTT+AGG - chr2.2:21512182-21512201 MS.gene068677:CDS 30.0%
TTTGACTAAGTGAGTCAAAA+GGG + chr2.2:21512227-21512246 None:intergenic 30.0%
! ACAAGATATAATGGAAGCTA+AGG - chr2.2:21512666-21512685 MS.gene068677:CDS 30.0%
! GAGTGAAAAAGTGAAGATTT+TGG - chr2.2:21512744-21512763 MS.gene068677:CDS 30.0%
! GCTTACAATTTTTCATCCAA+CGG - chr2.2:21512882-21512901 MS.gene068677:CDS 30.0%
!! AAGAGATTCTAGCTTAGAAA+TGG + chr2.2:21512182-21512201 None:intergenic 30.0%
AACAAAATCCTCCAAGAGAA+TGG - chr2.2:21512454-21512473 MS.gene068677:CDS 35.0%
AACGGATGATGTTATCAACT+CGG - chr2.2:21512900-21512919 MS.gene068677:CDS 35.0%
CAGCTTCAAAATTGAAGGAT+TGG + chr2.2:21512111-21512130 None:intergenic 35.0%
CTTCAATCTCAATGGATGAA+GGG + chr2.2:21512261-21512280 None:intergenic 35.0%
GTTTGACTAAGTGAGTCAAA+AGG + chr2.2:21512228-21512247 None:intergenic 35.0%
TATATTGGCAACTCATCACA+TGG - chr2.2:21512537-21512556 MS.gene068677:CDS 35.0%
! AGAAAGTATATGAAGGAAGG+TGG - chr2.2:21512775-21512794 MS.gene068677:CDS 35.0%
! TGCTTGTAAGAAGTGCAAAA+GGG - chr2.2:21512803-21512822 MS.gene068677:CDS 35.0%
! TTAACACTTTTCCCTTACCA+TGG - chr2.2:21512403-21512422 MS.gene068677:CDS 35.0%
! TTGCTTGTAAGAAGTGCAAA+AGG - chr2.2:21512802-21512821 MS.gene068677:CDS 35.0%
!!! ATTTTTTTGGCTGCACTTGT+TGG - chr2.2:21512712-21512731 MS.gene068677:CDS 35.0%
!!! TTTTCACTGGATTTGGTGTT+TGG + chr2.2:21512381-21512400 None:intergenic 35.0%
AATGGAAGCTAAGGAGAGAT+TGG - chr2.2:21512675-21512694 MS.gene068677:CDS 40.0%
ATGGAAGCTAAGGAGAGATT+GGG - chr2.2:21512676-21512695 MS.gene068677:CDS 40.0%
CATTCACAACACCATTCTCT+TGG + chr2.2:21512468-21512487 None:intergenic 40.0%
GCTTCAATCTCAATGGATGA+AGG + chr2.2:21512262-21512281 None:intergenic 40.0%
TGAGATATGAGAAGCTCTTG+TGG + chr2.2:21512139-21512158 None:intergenic 40.0%
TGGTAAGGCTTCAATCTCAA+TGG + chr2.2:21512269-21512288 None:intergenic 40.0%
TGTCTTAACCTCTTGTGGTA+AGG + chr2.2:21512284-21512303 None:intergenic 40.0%
! CGGATAAAGCACTTGAAAAG+AGG - chr2.2:21512629-21512648 MS.gene068677:CDS 40.0%
!! GAGTTGATAACATCATCCGT+TGG + chr2.2:21512901-21512920 None:intergenic 40.0%
ATCTCTTAGGCCTTCAAAGC+AGG - chr2.2:21512195-21512214 MS.gene068677:CDS 45.0%
CAATCTCAATGGATGAAGGG+AGG + chr2.2:21512258-21512277 None:intergenic 45.0%
CGCATTGTCTTAACCTCTTG+TGG + chr2.2:21512289-21512308 None:intergenic 45.0%
GATTGAAGCCTTACCACAAG+AGG - chr2.2:21512273-21512292 MS.gene068677:CDS 45.0%
TCACAACACCATTCTCTTGG+AGG + chr2.2:21512465-21512484 None:intergenic 45.0%
TCCTTCTGCTTTGCCACAAA+GGG + chr2.2:21512326-21512345 None:intergenic 45.0%
TGAGGTTGCTAGCAAGATTG+TGG - chr2.2:21512603-21512622 MS.gene068677:CDS 45.0%
TGCTAGCAAGATTGTGGCTT+CGG - chr2.2:21512609-21512628 MS.gene068677:CDS 45.0%
TGGAAGCTAAGGAGAGATTG+GGG - chr2.2:21512677-21512696 MS.gene068677:CDS 45.0%
! AGGGTGTTAACCTGCTTTGA+AGG + chr2.2:21512208-21512227 None:intergenic 45.0%
CCTTCTGCTTTGCCACAAAG+GGG + chr2.2:21512325-21512344 None:intergenic 50.0%
CTTTGCCACAAAGGGGAATG+AGG + chr2.2:21512318-21512337 None:intergenic 50.0%
GAAAGCCTCATTCCCCTTTG+TGG - chr2.2:21512310-21512329 MS.gene068677:CDS 50.0%
GTCCTTCTGCTTTGCCACAA+AGG + chr2.2:21512327-21512346 None:intergenic 50.0%
! CTGCACTTGTTGGTATGCGT+AGG - chr2.2:21512722-21512741 MS.gene068677:CDS 50.0%
CCCCTTTGTGGCAAAGCAGA+AGG - chr2.2:21512322-21512341 MS.gene068677:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 21512097 21512951 21512097 ID=MS.gene068677
chr2.2 mRNA 21512097 21512951 21512097 ID=MS.gene068677.t1;Parent=MS.gene068677
chr2.2 exon 21512097 21512951 21512097 ID=MS.gene068677.t1.exon1;Parent=MS.gene068677.t1
chr2.2 CDS 21512097 21512951 21512097 ID=cds.MS.gene068677.t1;Parent=MS.gene068677.t1
Gene Sequence

>MS.gene068677

ATGGCATCTTTCCAATCCTTCAATTTTGAAGCTGAAATTCCACAAGAGCTTCTCATATCTCAAATCATGCAAATTCATGCAACCATTTCTAAGCTAGAATCTCTTAGGCCTTCAAAGCAGGTTAACACCCTTTTGACTCACTTAGTCAAACTTTGCATCCTCCCTTCATCCATTGAGATTGAAGCCTTACCACAAGAGGTTAAGACAATGCGTGAAAGCCTCATTCCCCTTTGTGGCAAAGCAGAAGGACTTTTAGAGCTTGAATTCTCAACTTTCATTAGCCAAACACCAAATCCAGTGAAAAATTTAACACTTTTCCCTTACCATGGAAACTATGTTAAACTAGCAAACTATGAGAACAAAATCCTCCAAGAGAATGGTGTTGTGAATGCAAAAAAAGTAGCATTTATAGGATCTGGTCCAATGCCACTAAGTTCAATTATATTGGCAACTCATCACATGGAATCAACTCACTTTGATAATTTTGATATTGATGAGAAAGCTAATGAGGTTGCTAGCAAGATTGTGGCTTCGGATAAAGCACTTGAAAAGAGGATGAAATTTGTGACACAAGATATAATGGAAGCTAAGGAGAGATTGGGGCAATATGATTGCATTTTTTTGGCTGCACTTGTTGGTATGCGTAGGAGTGAAAAAGTGAAGATTTTGGGACATATAAGAAAGTATATGAAGGAAGGTGGTGTTTTGCTTGTAAGAAGTGCAAAAGGGAGTAGAGCTTTTTTGTATCCTATTGTTGAGGAGAATGATATGGTAAATTTTGAGGTGCTTACAATTTTTCATCCAACGGATGATGTTATCAACTCGGTTGTTCTTCTTCGCAAGCCTAAAGCTTGA
Protein sequence

>MS.gene068677.t1

MASFQSFNFEAEIPQELLISQIMQIHATISKLESLRPSKQVNTLLTHLVKLCILPSSIEIEALPQEVKTMRESLIPLCGKAEGLLELEFSTFISQTPNPVKNLTLFPYHGNYVKLANYENKILQENGVVNAKKVAFIGSGPMPLSSIILATHHMESTHFDNFDIDEKANEVASKIVASDKALEKRMKFVTQDIMEAKERLGQYDCIFLAALVGMRRSEKVKILGHIRKYMKEGGVLLVRSAKGSRAFLYPIVEENDMVNFEVLTIFHPTDDVINSVVLLRKPKA