AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52253

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52253.t1 MTR_7g077620 94.054 370 22 0 1 370 1 370 0.0 713
MS.gene52253.t1 MTR_7g077660 71.088 377 95 8 1 372 1 368 1.12e-176 496
MS.gene52253.t1 MTR_7g077650 69.393 379 102 7 1 372 1 372 1.13e-172 486
MS.gene52253.t1 MTR_7g076110 57.432 296 115 5 85 372 21 313 7.62e-104 308
MS.gene52253.t1 MTR_7g076100 67.089 237 76 2 137 372 65 300 2.83e-102 304
MS.gene52253.t1 MTR_7g076100 75.926 54 12 1 1 53 1 54 2.66e-20 90.5
MS.gene52253.t1 MTR_1g108740 44.211 380 166 15 1 370 1 344 6.32e-85 261
MS.gene52253.t1 MTR_5g038260 42.750 400 179 15 3 372 4 383 3.20e-84 261
MS.gene52253.t1 MTR_5g038230 41.730 393 159 14 5 370 4 353 2.32e-79 248
MS.gene52253.t1 MTR_1g064570 40.811 419 179 18 3 372 2 400 4.05e-76 241
MS.gene52253.t1 MTR_5g082770 46.624 311 130 7 5 305 4 288 1.48e-72 228
MS.gene52253.t1 MTR_1g016150 47.368 209 100 6 1 204 1 204 3.98e-50 168
MS.gene52253.t1 MTR_1g016150 37.097 124 67 4 201 318 117 235 8.43e-11 62.0
MS.gene52253.t1 MTR_7g076130 62.903 124 45 1 168 290 25 148 9.06e-45 151
MS.gene52253.t1 MTR_5g082780 43.668 229 93 10 114 327 1 208 5.51e-39 139
MS.gene52253.t1 MTR_1g108750 44.231 156 51 4 5 159 4 124 1.11e-26 103
MS.gene52253.t1 MTR_3g114970 26.203 374 201 17 4 347 3 331 2.31e-17 82.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 68 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCCAGAAGAATATTATTA+TGG 0.194741 7.4:-28574008 MS.gene52253:CDS
TATTCTTCTGGAAAATTATA+TGG 0.217616 7.4:+28574017 None:intergenic
TTCTCAAGGTAAGTAAAATT+AGG 0.221508 7.4:+28574053 None:intergenic
CAGATCAATCCCATTGAAAT+TGG 0.221701 7.4:+28573619 None:intergenic
TCAAGAGGATGTTACATCTT+TGG 0.236048 7.4:-28573650 MS.gene52253:CDS
GTTGCAGCGATTTACAATTT+TGG 0.255211 7.4:-28574245 MS.gene52253:CDS
TTCCCATAATAATATTCTTC+TGG 0.264764 7.4:+28574005 None:intergenic
AACATCCTCTTGAAGGAAAT+TGG 0.274037 7.4:+28573660 None:intergenic
ATTAAAAGTAAAACATGTTT+AGG 0.274585 7.4:-28574428 MS.gene52253:CDS
CAAGAGGATGTTACATCTTT+GGG 0.279656 7.4:-28573649 MS.gene52253:CDS
GGAGCTATACTGCTCTTAAA+AGG 0.328493 7.4:+28574347 None:intergenic
TAATCACTTGGGCTTGTAAT+GGG 0.338599 7.4:+28574272 None:intergenic
TTCCAGAAGAATATTATTAT+GGG 0.343297 7.4:-28574007 MS.gene52253:CDS
AAGAACACATAGATCATGTT+AGG 0.348741 7.4:-28574655 MS.gene52253:CDS
GAAGGATGGGATAAATGAAT+AGG 0.361300 7.4:+28574455 None:intergenic
TCTCAAGGTAAGTAAAATTA+GGG 0.370039 7.4:+28574054 None:intergenic
TTCGAGATGTGGCAGACTAA+TGG 0.372397 7.4:+28574325 None:intergenic
AGATTGCTACCCTCTTAGTT+TGG 0.376216 7.4:-28574693 MS.gene52253:CDS
GGGTTCTACCCCAATTTCAA+TGG 0.404683 7.4:-28573629 MS.gene52253:CDS
AGATCAATCCCATTGAAATT+GGG 0.410514 7.4:+28573620 None:intergenic
AAAAGGATTCACTAGAGTTA+TGG 0.411464 7.4:+28574364 None:intergenic
CACATAGATCATGTTAGGTT+TGG 0.419733 7.4:-28574650 MS.gene52253:CDS
TAGCAATGAGAAAGGTAGAT+TGG 0.422043 7.4:-28574724 None:intergenic
AGGAGGATTGTTGAATTTGA+AGG 0.434909 7.4:+28574094 None:intergenic
TCGAGATGTGGCAGACTAAT+GGG 0.436341 7.4:+28574326 None:intergenic
AAGATGTAACATCCTCTTGA+AGG 0.440096 7.4:+28573653 None:intergenic
TTGTTTCTCAAAGTTTGAAA+AGG 0.453913 7.4:-28573775 MS.gene52253:CDS
CCATGGTTGGCTTGCACTAG+TGG 0.460763 7.4:-28574399 MS.gene52253:CDS
AAGGATGGGATAAATGAATA+GGG 0.470406 7.4:+28574456 None:intergenic
TTATAAAGGCTTGGTATTTG+CGG 0.472828 7.4:-28574141 MS.gene52253:CDS
ATAATCACTTGGGCTTGTAA+TGG 0.476686 7.4:+28574271 None:intergenic
AGCAATGAGAAAGGTAGATT+GGG 0.477990 7.4:-28574723 None:intergenic
TCGTCAAGAACCAAACTAAG+AGG 0.484268 7.4:+28574683 None:intergenic
AATCATTGACCGGAGACATA+TGG 0.484616 7.4:-28573968 MS.gene52253:CDS
GGTTCTACCCCAATTTCAAT+GGG 0.486591 7.4:-28573628 MS.gene52253:CDS
GTTTAGGTTGTAGCCATGGT+TGG 0.497773 7.4:-28574412 MS.gene52253:CDS
TACAAGCCCAAGTGATTATG+TGG 0.499442 7.4:-28574267 MS.gene52253:CDS
ATAGGGTACTCTTTCTCACT+TGG 0.511489 7.4:+28574473 None:intergenic
CTTTACCAATTTCCTTCAAG+AGG 0.512890 7.4:-28573665 MS.gene52253:CDS
CAAATCTATAATGCGAAGGA+TGG 0.523156 7.4:-28573705 MS.gene52253:CDS
TTTCACCATCCATATGTCTC+CGG 0.527974 7.4:+28573959 None:intergenic
TACGAGACAATTTGTTTGAG+AGG 0.528949 7.4:+28574540 None:intergenic
TTTGAGAGGATCATTAACAT+AGG 0.529450 7.4:+28574554 None:intergenic
TAGTTTGGTTCTTGACGAGT+TGG 0.532019 7.4:-28574678 MS.gene52253:CDS
TTCAAACTTTGAGAAACAAG+AGG 0.532702 7.4:+28573779 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.549128 7.4:+28574260 None:intergenic
ACATGTTTAGGTTGTAGCCA+TGG 0.559363 7.4:-28574416 MS.gene52253:CDS
TGTAATGGGGTCAGCAGACA+AGG 0.568289 7.4:+28574286 None:intergenic
TTGGTGTGGTGTGCAAGAGT+TGG 0.569193 7.4:-28574631 MS.gene52253:CDS
AGTTTGTATGTAAGATTGTG+TGG 0.574270 7.4:+28573921 None:intergenic
TTGTTGAGAGATTCGAGATG+TGG 0.590451 7.4:+28574314 None:intergenic
TAGGGTACTCTTTCTCACTT+GGG 0.591906 7.4:+28574474 None:intergenic
GATCAATCCCATTGAAATTG+GGG 0.599101 7.4:+28573621 None:intergenic
GAGTACTAGCTATCTTCTCA+AGG 0.600472 7.4:+28574039 None:intergenic
CGTCAAGAACCAAACTAAGA+GGG 0.605996 7.4:+28574684 None:intergenic
AATCACTTGGGCTTGTAATG+GGG 0.606028 7.4:+28574273 None:intergenic
GTTACAAATCTATAATGCGA+AGG 0.615721 7.4:-28573709 MS.gene52253:CDS
CCACTAGTGCAAGCCAACCA+TGG 0.620481 7.4:+28574399 None:intergenic
CTGCAACCACATAATCACTT+GGG 0.636696 7.4:+28574261 None:intergenic
GTTTGTATGTAAGATTGTGT+GGG 0.646089 7.4:+28573922 None:intergenic
GAGAGGATCATTAACATAGG+TGG 0.648255 7.4:+28574557 None:intergenic
AGATCATGTTAGGTTTGGTG+TGG 0.661894 7.4:-28574645 MS.gene52253:CDS
GGGTCAATTGAGTCATCACA+AGG 0.675309 7.4:+28574074 None:intergenic
ACATCTCGAATCTCTCAACA+AGG 0.689831 7.4:-28574312 MS.gene52253:CDS
ATTGACCGGAGACATATGGA+TGG 0.696827 7.4:-28573964 MS.gene52253:CDS
GTAGACGTGCAAAATCAAAG+AGG 0.713785 7.4:-28574520 MS.gene52253:CDS
TTGGAACTGGATGCCCAGAG+CGG 0.723217 7.4:-28573885 MS.gene52253:CDS
TCAATTGAGTCATCACAAGG+AGG 0.741566 7.4:+28574077 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAAAGTAAAACATGTTT+AGG - chr7.4:28573914-28573933 MS.gene52253:CDS 15.0%
!!! ACTAATGTTGTATTTTATAA+AGG - chr7.4:28574187-28574206 MS.gene52253:CDS 15.0%
!!! TCAATTTATTTTATTTACGA+TGG - chr7.4:28574592-28574611 MS.gene52253:CDS 15.0%
!! ACCATAAAAATCATCAATTT+AGG - chr7.4:28573753-28573772 MS.gene52253:CDS 20.0%
!! TTCCAGAAGAATATTATTAT+GGG - chr7.4:28574335-28574354 MS.gene52253:CDS 20.0%
!! TTTCCAGAAGAATATTATTA+TGG - chr7.4:28574334-28574353 MS.gene52253:CDS 20.0%
!!! ACATGTTTTACTTTTAATGA+TGG + chr7.4:28573912-28573931 None:intergenic 20.0%
!!! TATTCTTCTGGAAAATTATA+TGG + chr7.4:28574328-28574347 None:intergenic 20.0%
!!! TCCTAAATTGATGATTTTTA+TGG + chr7.4:28573757-28573776 None:intergenic 20.0%
! TCTCAAGGTAAGTAAAATTA+GGG + chr7.4:28574291-28574310 None:intergenic 25.0%
! TTCCCATAATAATATTCTTC+TGG + chr7.4:28574340-28574359 None:intergenic 25.0%
! TTCTCAAGGTAAGTAAAATT+AGG + chr7.4:28574292-28574311 None:intergenic 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr7.4:28574364-28574383 MS.gene52253:CDS 25.0%
!! TGTTGTATTTTATAAAGGCT+TGG - chr7.4:28574192-28574211 MS.gene52253:CDS 25.0%
!! TTGTTTCTCAAAGTTTGAAA+AGG - chr7.4:28574567-28574586 MS.gene52253:CDS 25.0%
!!! AACATTTTATTTGTCGGAAT+CGG - chr7.4:28574520-28574539 MS.gene52253:CDS 25.0%
!!! GAGAACAACATTTTATTTGT+CGG - chr7.4:28574514-28574533 MS.gene52253:CDS 25.0%
!!! GTTTTACTTTTAATGATGGA+AGG + chr7.4:28573908-28573927 None:intergenic 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.4:28573981-28574000 None:intergenic 30.0%
AAGAACACATAGATCATGTT+AGG - chr7.4:28573687-28573706 MS.gene52253:CDS 30.0%
AAGGATGGGATAAATGAATA+GGG + chr7.4:28573889-28573908 None:intergenic 30.0%
AGTTTGTATGTAAGATTGTG+TGG + chr7.4:28574424-28574443 None:intergenic 30.0%
GTTACAAATCTATAATGCGA+AGG - chr7.4:28574633-28574652 MS.gene52253:CDS 30.0%
GTTTGTATGTAAGATTGTGT+GGG + chr7.4:28574423-28574442 None:intergenic 30.0%
TTTGAGAGGATCATTAACAT+AGG + chr7.4:28573791-28573810 None:intergenic 30.0%
! CAAACTCTACGTTTTCAAAT+TGG - chr7.4:28574438-28574457 MS.gene52253:CDS 30.0%
! TTATAAAGGCTTGGTATTTG+CGG - chr7.4:28574201-28574220 MS.gene52253:CDS 30.0%
! TTCAAACTTTGAGAAACAAG+AGG + chr7.4:28574566-28574585 None:intergenic 30.0%
!! ACTTTTAATGATGGAAGGAT+GGG + chr7.4:28573903-28573922 None:intergenic 30.0%
!! TACTTTTAATGATGGAAGGA+TGG + chr7.4:28573904-28573923 None:intergenic 30.0%
AACATCCTCTTGAAGGAAAT+TGG + chr7.4:28574685-28574704 None:intergenic 35.0%
AAGATGTAACATCCTCTTGA+AGG + chr7.4:28574692-28574711 None:intergenic 35.0%
AGGAGGATTGTTGAATTTGA+AGG + chr7.4:28574251-28574270 None:intergenic 35.0%
ATAATCACTTGGGCTTGTAA+TGG + chr7.4:28574074-28574093 None:intergenic 35.0%
CAAATCTATAATGCGAAGGA+TGG - chr7.4:28574637-28574656 MS.gene52253:CDS 35.0%
CAAGAGGATGTTACATCTTT+GGG - chr7.4:28574693-28574712 MS.gene52253:CDS 35.0%
CACATAGATCATGTTAGGTT+TGG - chr7.4:28573692-28573711 MS.gene52253:CDS 35.0%
CTTTACCAATTTCCTTCAAG+AGG - chr7.4:28574677-28574696 MS.gene52253:CDS 35.0%
GAAGGATGGGATAAATGAAT+AGG + chr7.4:28573890-28573909 None:intergenic 35.0%
TAATCACTTGGGCTTGTAAT+GGG + chr7.4:28574073-28574092 None:intergenic 35.0%
TCAAGAGGATGTTACATCTT+TGG - chr7.4:28574692-28574711 MS.gene52253:CDS 35.0%
! CTACGTTTTCAAATTGGAAC+TGG - chr7.4:28574444-28574463 MS.gene52253:CDS 35.0%
! GTTGCAGCGATTTACAATTT+TGG - chr7.4:28574097-28574116 MS.gene52253:CDS 35.0%
! TACGAGACAATTTGTTTGAG+AGG + chr7.4:28573805-28573824 None:intergenic 35.0%
AATCACTTGGGCTTGTAATG+GGG + chr7.4:28574072-28574091 None:intergenic 40.0%
AATCATTGACCGGAGACATA+TGG - chr7.4:28574374-28574393 MS.gene52253:CDS 40.0%
ACATCTCGAATCTCTCAACA+AGG - chr7.4:28574030-28574049 MS.gene52253:CDS 40.0%
AGATTGCTACCCTCTTAGTT+TGG - chr7.4:28573649-28573668 MS.gene52253:CDS 40.0%
CGTCAAGAACCAAACTAAGA+GGG + chr7.4:28573661-28573680 None:intergenic 40.0%
CTGCAACCACATAATCACTT+GGG + chr7.4:28574084-28574103 None:intergenic 40.0%
GAGAGGATCATTAACATAGG+TGG + chr7.4:28573788-28573807 None:intergenic 40.0%
GAGTACTAGCTATCTTCTCA+AGG + chr7.4:28574306-28574325 None:intergenic 40.0%
GGAGCTATACTGCTCTTAAA+AGG + chr7.4:28573998-28574017 None:intergenic 40.0%
GGTTCTACCCCAATTTCAAT+GGG - chr7.4:28574714-28574733 MS.gene52253:CDS 40.0%
GTAGACGTGCAAAATCAAAG+AGG - chr7.4:28573822-28573841 MS.gene52253:CDS 40.0%
TACAAGCCCAAGTGATTATG+TGG - chr7.4:28574075-28574094 MS.gene52253:CDS 40.0%
TCAATTGAGTCATCACAAGG+AGG + chr7.4:28574268-28574287 None:intergenic 40.0%
TCGTCAAGAACCAAACTAAG+AGG + chr7.4:28573662-28573681 None:intergenic 40.0%
TTGTTGAGAGATTCGAGATG+TGG + chr7.4:28574031-28574050 None:intergenic 40.0%
TTTCACCATCCATATGTCTC+CGG + chr7.4:28574386-28574405 None:intergenic 40.0%
! AAAGAGCAAGCCAGTCTTTT+TGG - chr7.4:28574134-28574153 MS.gene52253:CDS 40.0%
! ATAGGGTACTCTTTCTCACT+TGG + chr7.4:28573872-28573891 None:intergenic 40.0%
! TAGGGTACTCTTTCTCACTT+GGG + chr7.4:28573871-28573890 None:intergenic 40.0%
! TTGTTCAACTTTTCCGCTCT+GGG + chr7.4:28574473-28574492 None:intergenic 40.0%
! TTTGTTCAACTTTTCCGCTC+TGG + chr7.4:28574474-28574493 None:intergenic 40.0%
!! ACATGTTTAGGTTGTAGCCA+TGG - chr7.4:28573926-28573945 MS.gene52253:CDS 40.0%
!! AGATCATGTTAGGTTTGGTG+TGG - chr7.4:28573697-28573716 MS.gene52253:CDS 40.0%
!! TAGTTTGGTTCTTGACGAGT+TGG - chr7.4:28573664-28573683 MS.gene52253:CDS 40.0%
ATTGACCGGAGACATATGGA+TGG - chr7.4:28574378-28574397 MS.gene52253:CDS 45.0%
CTGCACGAATCCAAAAAGAC+TGG + chr7.4:28574147-28574166 None:intergenic 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.4:28574085-28574104 None:intergenic 45.0%
GGGTCAATTGAGTCATCACA+AGG + chr7.4:28574271-28574290 None:intergenic 45.0%
GGGTTCTACCCCAATTTCAA+TGG - chr7.4:28574713-28574732 MS.gene52253:CDS 45.0%
TCGAGATGTGGCAGACTAAT+GGG + chr7.4:28574019-28574038 None:intergenic 45.0%
TTCGAGATGTGGCAGACTAA+TGG + chr7.4:28574020-28574039 None:intergenic 45.0%
!! GTTTAGGTTGTAGCCATGGT+TGG - chr7.4:28573930-28573949 MS.gene52253:CDS 45.0%
TTGGTGTGGTGTGCAAGAGT+TGG - chr7.4:28573711-28573730 MS.gene52253:CDS 50.0%
! TGTAATGGGGTCAGCAGACA+AGG + chr7.4:28574059-28574078 None:intergenic 50.0%
CCACTAGTGCAAGCCAACCA+TGG + chr7.4:28573946-28573965 None:intergenic 55.0%
TTGGAACTGGATGCCCAGAG+CGG - chr7.4:28574457-28574476 MS.gene52253:CDS 55.0%
!! CCATGGTTGGCTTGCACTAG+TGG - chr7.4:28573943-28573962 MS.gene52253:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 28573623 28574741 28573623 ID=MS.gene52253
chr7.4 mRNA 28573623 28574741 28573623 ID=MS.gene52253.t1;Parent=MS.gene52253
chr7.4 exon 28573623 28574741 28573623 ID=MS.gene52253.t1.exon1;Parent=MS.gene52253.t1
chr7.4 CDS 28573623 28574741 28573623 ID=cds.MS.gene52253.t1;Parent=MS.gene52253.t1
Gene Sequence

>MS.gene52253

ATGAGAAAGGTAGATTGGGCAAATTTAGATTGCTACCCTCTTAGTTTGGTTCTTGACGAGTTGGAAGAACACATAGATCATGTTAGGTTTGGTGTGGTGTGCAAGAGTTGGCTATCAATTGCAAAGCTTAACCATAAAAATCATCAATTTAGGATTAATGTACCACCTATGTTAATGATCCTCTCAAACAAATTGTCTCGTAGACGTGCAAAATCAAAGAGGAAGATGAAATCGTTATATAGTATCCCAAGTGAGAAAGAGTACCCTATTCATTTATCCCATCCTTCCATCATTAAAAGTAAAACATGTTTAGGTTGTAGCCATGGTTGGCTTGCACTAGTGGATAAAAACAATGCCATAACTCTAGTGAATCCTTTTAAGAGCAGTATAGCTCCCATTAGTCTGCCACATCTCGAATCTCTCAACAAGGTTACCTTGTCTGCTGACCCCATTACAAGCCCAAGTGATTATGTGGTTGCAGCGATTTACAATTTTGGTTCTCTCGCTTTCAAAAGAGCAAGCCAGTCTTTTTGGATTCGTGCAGACACAAATGAATTTTCTTTCACTAATGTTGTATTTTATAAAGGCTTGGTATTTGCGGACAGCGAACAAGACTTCATTGTATCCTTCAAATTCAACAATCCTCCTTGTGATGACTCAATTGACCCTAATTTTACTTACCTTGAGAAGATAGCTAGTACTCCATATAATTTTCCAGAAGAATATTATTATGGGAATTCTTATTTTGTGAAATCATTGACCGGAGACATATGGATGGTGAAAAGATGTTTAATCGACCCACACAATCTTACATACAAACTCTACGTTTTCAAATTGGAACTGGATGCCCAGAGCGGAAAAGTTGAACAAATCAACAAACTTGTGAGTTTAGAGAACAACATTTTATTTGTCGGAATCGGCGATTCAATTTCTGTGTCAGCCTCTTGTTTCTCAAAGTTTGAAAAGGATTCAATTTATTTTATTTACGATGGCGATGAAGATGATTTAGAGTTACAAATCTATAATGCGAAGGATGGAAGTTATCGTAGTCAATCTTTACCAATTTCCTTCAAGAGGATGTTACATCTTTGGGTTCTACCCCAATTTCAATGGGATTGA
Protein sequence

>MS.gene52253.t1

MRKVDWANLDCYPLSLVLDELEEHIDHVRFGVVCKSWLSIAKLNHKNHQFRINVPPMLMILSNKLSRRRAKSKRKMKSLYSIPSEKEYPIHLSHPSIIKSKTCLGCSHGWLALVDKNNAITLVNPFKSSIAPISLPHLESLNKVTLSADPITSPSDYVVAAIYNFGSLAFKRASQSFWIRADTNEFSFTNVVFYKGLVFADSEQDFIVSFKFNNPPCDDSIDPNFTYLEKIASTPYNFPEEYYYGNSYFVKSLTGDIWMVKRCLIDPHNLTYKLYVFKLELDAQSGKVEQINKLVSLENNILFVGIGDSISVSASCFSKFEKDSIYFIYDGDEDDLELQIYNAKDGSYRSQSLPISFKRMLHLWVLPQFQWD