AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27747

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27747.t1 MTR_7g077620 93.514 370 24 0 1 370 1 370 0.0 709
MS.gene27747.t1 MTR_7g077660 70.557 377 97 8 1 372 1 368 6.66e-175 491
MS.gene27747.t1 MTR_7g077650 69.129 379 103 7 1 372 1 372 2.00e-171 483
MS.gene27747.t1 MTR_7g076110 58.246 285 111 4 96 372 29 313 1.32e-102 305
MS.gene27747.t1 MTR_7g076100 67.089 237 76 2 137 372 65 300 3.76e-102 304
MS.gene27747.t1 MTR_7g076100 74.074 54 13 1 1 53 1 54 9.66e-20 89.0
MS.gene27747.t1 MTR_5g038260 43.000 400 178 15 3 372 4 383 2.00e-85 264
MS.gene27747.t1 MTR_1g108740 44.211 380 166 15 1 370 1 344 4.15e-85 262
MS.gene27747.t1 MTR_5g038230 41.772 395 160 14 3 370 2 353 2.89e-80 250
MS.gene27747.t1 MTR_1g064570 40.573 419 180 18 3 372 2 400 2.50e-76 241
MS.gene27747.t1 MTR_5g082770 46.624 311 130 7 5 305 4 288 6.57e-73 229
MS.gene27747.t1 MTR_1g016150 47.368 209 100 6 1 204 1 204 2.74e-50 169
MS.gene27747.t1 MTR_1g016150 37.097 124 67 4 201 318 117 235 7.97e-11 62.0
MS.gene27747.t1 MTR_7g076130 62.903 124 45 1 168 290 25 148 8.23e-45 152
MS.gene27747.t1 MTR_5g082780 43.668 229 93 10 114 327 1 208 5.01e-39 139
MS.gene27747.t1 MTR_1g108750 44.231 156 51 4 5 159 4 124 1.12e-26 103
MS.gene27747.t1 MTR_3g114970 25.936 374 202 17 4 347 3 331 1.48e-17 83.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 69 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCCAGAAGAATATTATTA+TGG 0.194741 7.3:-29204206 MS.gene27747:CDS
TATTCTTCTGGAAAATTATA+TGG 0.217616 7.3:+29204215 None:intergenic
TTCTCAAGGTAAGTAAAATT+AGG 0.221508 7.3:+29204251 None:intergenic
CAGATCAATCCCATTGAAAT+TGG 0.221701 7.3:+29203817 None:intergenic
TCAAGAGGATGTTACATCTT+TGG 0.236048 7.3:-29203848 MS.gene27747:CDS
GTTGCAGCGATTTACAATTT+TGG 0.255211 7.3:-29204443 MS.gene27747:CDS
TTCCCATAATAATATTCTTC+TGG 0.264764 7.3:+29204203 None:intergenic
AACATCCTCTTGAAGGAAAT+TGG 0.274037 7.3:+29203858 None:intergenic
ATTAAAAGTAAAACATGTTT+AGG 0.274585 7.3:-29204626 MS.gene27747:CDS
CAAGAGGATGTTACATCTTT+GGG 0.279656 7.3:-29203847 MS.gene27747:CDS
GGTCAATGATTTCACAAAAT+AGG 0.308630 7.3:+29204178 None:intergenic
GGAGCTATACTGCTCTTAAA+AGG 0.328493 7.3:+29204545 None:intergenic
TAATCACTTGGGCTTGTAAT+GGG 0.338599 7.3:+29204470 None:intergenic
TTCCAGAAGAATATTATTAT+GGG 0.343297 7.3:-29204205 MS.gene27747:CDS
AAGAACACATAGATCATGTT+AGG 0.348741 7.3:-29204853 MS.gene27747:CDS
GAAGGATGGGATAAATGAAT+AGG 0.361300 7.3:+29204653 None:intergenic
TCTCAAGGTAAGTAAAATTA+GGG 0.370039 7.3:+29204252 None:intergenic
TTCGAGATGTGGCAGACTAA+TGG 0.372397 7.3:+29204523 None:intergenic
AGATTGCTACCCTCTTAGTT+TGG 0.376216 7.3:-29204891 MS.gene27747:CDS
GGGTTCTACCCCAATTTCAA+TGG 0.404683 7.3:-29203827 MS.gene27747:CDS
AGATCAATCCCATTGAAATT+GGG 0.410514 7.3:+29203818 None:intergenic
AAAAGGATTCACTAGAGTTA+TGG 0.411464 7.3:+29204562 None:intergenic
GGCAATGAGAAAGGCAGATT+GGG 0.416832 7.3:-29204921 None:intergenic
CACATAGATCATGTTAGGTT+TGG 0.419733 7.3:-29204848 MS.gene27747:CDS
AGGAGGATTGTTGAATTTGA+AGG 0.434909 7.3:+29204292 None:intergenic
TCGAGATGTGGCAGACTAAT+GGG 0.436341 7.3:+29204524 None:intergenic
AAGATGTAACATCCTCTTGA+AGG 0.440096 7.3:+29203851 None:intergenic
TTGTTTCTCAAAGTTTGAAA+AGG 0.453913 7.3:-29203973 MS.gene27747:CDS
CCATGGTTGGCTTGCACTAG+TGG 0.460763 7.3:-29204597 MS.gene27747:CDS
TGGCAATGAGAAAGGCAGAT+TGG 0.466930 7.3:-29204922 None:intergenic
AAGGATGGGATAAATGAATA+GGG 0.470406 7.3:+29204654 None:intergenic
TTATAAAGGCTTGGTATTTG+CGG 0.472828 7.3:-29204339 MS.gene27747:CDS
ATAATCACTTGGGCTTGTAA+TGG 0.476686 7.3:+29204469 None:intergenic
TCGTCAAGAACCAAACTAAG+AGG 0.484268 7.3:+29204881 None:intergenic
AATCATTGACCGGAGACATA+TGG 0.484616 7.3:-29204166 MS.gene27747:CDS
GGTTCTACCCCAATTTCAAT+GGG 0.486591 7.3:-29203826 MS.gene27747:CDS
GTTTAGGTTGTAGCCATGGT+TGG 0.497773 7.3:-29204610 MS.gene27747:CDS
TACAAGCCCAAGTGATTATG+TGG 0.499442 7.3:-29204465 MS.gene27747:CDS
CTTTACCAATTTCCTTCAAG+AGG 0.512890 7.3:-29203863 MS.gene27747:CDS
CAAATCTATAATGCGAAGGA+TGG 0.523156 7.3:-29203903 MS.gene27747:CDS
ATAGGGTACACTTTCTCACT+TGG 0.523908 7.3:+29204671 None:intergenic
TTTCACCATCCATATGTCTC+CGG 0.527974 7.3:+29204157 None:intergenic
TACGAGACAATTTGTTTGAG+AGG 0.528949 7.3:+29204738 None:intergenic
TTTGAGAGGATCATTAACAT+AGG 0.529450 7.3:+29204752 None:intergenic
TAGTTTGGTTCTTGACGAGT+TGG 0.532019 7.3:-29204876 MS.gene27747:CDS
TTCAAACTTTGAGAAACAAG+AGG 0.532702 7.3:+29203977 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.549128 7.3:+29204458 None:intergenic
ACATGTTTAGGTTGTAGCCA+TGG 0.559363 7.3:-29204614 MS.gene27747:CDS
TGTAATGGGGTCAGCAGACA+AGG 0.568289 7.3:+29204484 None:intergenic
TTGGTGTGGTGTGCAAGAGT+TGG 0.569193 7.3:-29204829 MS.gene27747:CDS
AGTTTGTATGTAAGATTGTG+TGG 0.574270 7.3:+29204119 None:intergenic
TTGTTGAGAGATTCGAGATG+TGG 0.590451 7.3:+29204512 None:intergenic
GATCAATCCCATTGAAATTG+GGG 0.599101 7.3:+29203819 None:intergenic
GAGTACTAGCTATCTTCTCA+AGG 0.600472 7.3:+29204237 None:intergenic
CGTCAAGAACCAAACTAAGA+GGG 0.605996 7.3:+29204882 None:intergenic
AATCACTTGGGCTTGTAATG+GGG 0.606028 7.3:+29204471 None:intergenic
TAGGGTACACTTTCTCACTT+GGG 0.606994 7.3:+29204672 None:intergenic
GTTACAAATCTATAATGCGA+AGG 0.615721 7.3:-29203907 MS.gene27747:CDS
CCACTAGTGCAAGCCAACCA+TGG 0.620481 7.3:+29204597 None:intergenic
CTGCAACCACATAATCACTT+GGG 0.636696 7.3:+29204459 None:intergenic
GTTTGTATGTAAGATTGTGT+GGG 0.646089 7.3:+29204120 None:intergenic
GAGAGGATCATTAACATAGG+TGG 0.648255 7.3:+29204755 None:intergenic
AGATCATGTTAGGTTTGGTG+TGG 0.661894 7.3:-29204843 MS.gene27747:CDS
GGGTCAATTGAGTCATCACA+AGG 0.675309 7.3:+29204272 None:intergenic
ACATCTCGAATCTCTCAACA+AGG 0.689831 7.3:-29204510 MS.gene27747:CDS
ATTGACCGGAGACATATGGA+TGG 0.696827 7.3:-29204162 MS.gene27747:CDS
GTAGACGTGCAAAATCAAAG+AGG 0.713785 7.3:-29204718 MS.gene27747:CDS
TTGGAACTGGATGCCCAGAG+CGG 0.723217 7.3:-29204083 MS.gene27747:CDS
TCAATTGAGTCATCACAAGG+AGG 0.741566 7.3:+29204275 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAAAGTAAAACATGTTT+AGG - chr7.3:29204112-29204131 MS.gene27747:CDS 15.0%
!!! ACTAATGTTGTATTTTATAA+AGG - chr7.3:29204385-29204404 MS.gene27747:CDS 15.0%
!!! TCAATTTATTTTATTTACGA+TGG - chr7.3:29204790-29204809 MS.gene27747:CDS 15.0%
!! ACCATAAAAATCATCAATTT+AGG - chr7.3:29203951-29203970 MS.gene27747:CDS 20.0%
!! TTCCAGAAGAATATTATTAT+GGG - chr7.3:29204533-29204552 MS.gene27747:CDS 20.0%
!! TTTCCAGAAGAATATTATTA+TGG - chr7.3:29204532-29204551 MS.gene27747:CDS 20.0%
!!! ACATGTTTTACTTTTAATGA+TGG + chr7.3:29204110-29204129 None:intergenic 20.0%
!!! TATTCTTCTGGAAAATTATA+TGG + chr7.3:29204526-29204545 None:intergenic 20.0%
!!! TCCTAAATTGATGATTTTTA+TGG + chr7.3:29203955-29203974 None:intergenic 20.0%
! TCTCAAGGTAAGTAAAATTA+GGG + chr7.3:29204489-29204508 None:intergenic 25.0%
! TTCCCATAATAATATTCTTC+TGG + chr7.3:29204538-29204557 None:intergenic 25.0%
! TTCTCAAGGTAAGTAAAATT+AGG + chr7.3:29204490-29204509 None:intergenic 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr7.3:29204562-29204581 MS.gene27747:CDS 25.0%
!! TGTTGTATTTTATAAAGGCT+TGG - chr7.3:29204390-29204409 MS.gene27747:CDS 25.0%
!! TTGTTTCTCAAAGTTTGAAA+AGG - chr7.3:29204765-29204784 MS.gene27747:CDS 25.0%
!!! AACATTTTATTTGTCGGAAT+CGG - chr7.3:29204718-29204737 MS.gene27747:CDS 25.0%
!!! GAGAACAACATTTTATTTGT+CGG - chr7.3:29204712-29204731 MS.gene27747:CDS 25.0%
!!! GTTTTACTTTTAATGATGGA+AGG + chr7.3:29204106-29204125 None:intergenic 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.3:29204179-29204198 None:intergenic 30.0%
AAGAACACATAGATCATGTT+AGG - chr7.3:29203885-29203904 MS.gene27747:CDS 30.0%
AAGGATGGGATAAATGAATA+GGG + chr7.3:29204087-29204106 None:intergenic 30.0%
AGTTTGTATGTAAGATTGTG+TGG + chr7.3:29204622-29204641 None:intergenic 30.0%
GGTCAATGATTTCACAAAAT+AGG + chr7.3:29204563-29204582 None:intergenic 30.0%
GTTACAAATCTATAATGCGA+AGG - chr7.3:29204831-29204850 MS.gene27747:CDS 30.0%
GTTTGTATGTAAGATTGTGT+GGG + chr7.3:29204621-29204640 None:intergenic 30.0%
TTTGAGAGGATCATTAACAT+AGG + chr7.3:29203989-29204008 None:intergenic 30.0%
! CAAACTCTACGTTTTCAAAT+TGG - chr7.3:29204636-29204655 MS.gene27747:CDS 30.0%
! TTATAAAGGCTTGGTATTTG+CGG - chr7.3:29204399-29204418 MS.gene27747:CDS 30.0%
! TTCAAACTTTGAGAAACAAG+AGG + chr7.3:29204764-29204783 None:intergenic 30.0%
!! ACTTTTAATGATGGAAGGAT+GGG + chr7.3:29204101-29204120 None:intergenic 30.0%
!! TACTTTTAATGATGGAAGGA+TGG + chr7.3:29204102-29204121 None:intergenic 30.0%
AACATCCTCTTGAAGGAAAT+TGG + chr7.3:29204883-29204902 None:intergenic 35.0%
AAGATGTAACATCCTCTTGA+AGG + chr7.3:29204890-29204909 None:intergenic 35.0%
AGGAGGATTGTTGAATTTGA+AGG + chr7.3:29204449-29204468 None:intergenic 35.0%
ATAATCACTTGGGCTTGTAA+TGG + chr7.3:29204272-29204291 None:intergenic 35.0%
CAAATCTATAATGCGAAGGA+TGG - chr7.3:29204835-29204854 MS.gene27747:CDS 35.0%
CAAGAGGATGTTACATCTTT+GGG - chr7.3:29204891-29204910 MS.gene27747:CDS 35.0%
CACATAGATCATGTTAGGTT+TGG - chr7.3:29203890-29203909 MS.gene27747:CDS 35.0%
CTTTACCAATTTCCTTCAAG+AGG - chr7.3:29204875-29204894 MS.gene27747:CDS 35.0%
GAAGGATGGGATAAATGAAT+AGG + chr7.3:29204088-29204107 None:intergenic 35.0%
TAATCACTTGGGCTTGTAAT+GGG + chr7.3:29204271-29204290 None:intergenic 35.0%
TCAAGAGGATGTTACATCTT+TGG - chr7.3:29204890-29204909 MS.gene27747:CDS 35.0%
! CTACGTTTTCAAATTGGAAC+TGG - chr7.3:29204642-29204661 MS.gene27747:CDS 35.0%
! GTTGCAGCGATTTACAATTT+TGG - chr7.3:29204295-29204314 MS.gene27747:CDS 35.0%
! TACGAGACAATTTGTTTGAG+AGG + chr7.3:29204003-29204022 None:intergenic 35.0%
AATCACTTGGGCTTGTAATG+GGG + chr7.3:29204270-29204289 None:intergenic 40.0%
AATCATTGACCGGAGACATA+TGG - chr7.3:29204572-29204591 MS.gene27747:CDS 40.0%
ACATCTCGAATCTCTCAACA+AGG - chr7.3:29204228-29204247 MS.gene27747:CDS 40.0%
AGATTGCTACCCTCTTAGTT+TGG - chr7.3:29203847-29203866 MS.gene27747:CDS 40.0%
ATAGGGTACACTTTCTCACT+TGG + chr7.3:29204070-29204089 None:intergenic 40.0%
CGTCAAGAACCAAACTAAGA+GGG + chr7.3:29203859-29203878 None:intergenic 40.0%
CTGCAACCACATAATCACTT+GGG + chr7.3:29204282-29204301 None:intergenic 40.0%
GAGAGGATCATTAACATAGG+TGG + chr7.3:29203986-29204005 None:intergenic 40.0%
GAGTACTAGCTATCTTCTCA+AGG + chr7.3:29204504-29204523 None:intergenic 40.0%
GGAGCTATACTGCTCTTAAA+AGG + chr7.3:29204196-29204215 None:intergenic 40.0%
GGTTCTACCCCAATTTCAAT+GGG - chr7.3:29204912-29204931 MS.gene27747:CDS 40.0%
GTAGACGTGCAAAATCAAAG+AGG - chr7.3:29204020-29204039 MS.gene27747:CDS 40.0%
TACAAGCCCAAGTGATTATG+TGG - chr7.3:29204273-29204292 MS.gene27747:CDS 40.0%
TAGGGTACACTTTCTCACTT+GGG + chr7.3:29204069-29204088 None:intergenic 40.0%
TCAATTGAGTCATCACAAGG+AGG + chr7.3:29204466-29204485 None:intergenic 40.0%
TCGTCAAGAACCAAACTAAG+AGG + chr7.3:29203860-29203879 None:intergenic 40.0%
TTGTTGAGAGATTCGAGATG+TGG + chr7.3:29204229-29204248 None:intergenic 40.0%
TTTCACCATCCATATGTCTC+CGG + chr7.3:29204584-29204603 None:intergenic 40.0%
! AAAGAGCAAGCCAGTCTTTT+TGG - chr7.3:29204332-29204351 MS.gene27747:CDS 40.0%
! TTGTTCAACTTTTCCGCTCT+GGG + chr7.3:29204671-29204690 None:intergenic 40.0%
! TTTGTTCAACTTTTCCGCTC+TGG + chr7.3:29204672-29204691 None:intergenic 40.0%
!! ACATGTTTAGGTTGTAGCCA+TGG - chr7.3:29204124-29204143 MS.gene27747:CDS 40.0%
!! AGATCATGTTAGGTTTGGTG+TGG - chr7.3:29203895-29203914 MS.gene27747:CDS 40.0%
!! TAGTTTGGTTCTTGACGAGT+TGG - chr7.3:29203862-29203881 MS.gene27747:CDS 40.0%
ATTGACCGGAGACATATGGA+TGG - chr7.3:29204576-29204595 MS.gene27747:CDS 45.0%
CTGCACGAATCCAAAAAGAC+TGG + chr7.3:29204345-29204364 None:intergenic 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.3:29204283-29204302 None:intergenic 45.0%
GGGTCAATTGAGTCATCACA+AGG + chr7.3:29204469-29204488 None:intergenic 45.0%
GGGTTCTACCCCAATTTCAA+TGG - chr7.3:29204911-29204930 MS.gene27747:CDS 45.0%
TCGAGATGTGGCAGACTAAT+GGG + chr7.3:29204217-29204236 None:intergenic 45.0%
TTCGAGATGTGGCAGACTAA+TGG + chr7.3:29204218-29204237 None:intergenic 45.0%
!! GTTTAGGTTGTAGCCATGGT+TGG - chr7.3:29204128-29204147 MS.gene27747:CDS 45.0%
TTGGTGTGGTGTGCAAGAGT+TGG - chr7.3:29203909-29203928 MS.gene27747:CDS 50.0%
! TGTAATGGGGTCAGCAGACA+AGG + chr7.3:29204257-29204276 None:intergenic 50.0%
CCACTAGTGCAAGCCAACCA+TGG + chr7.3:29204144-29204163 None:intergenic 55.0%
TTGGAACTGGATGCCCAGAG+CGG - chr7.3:29204655-29204674 MS.gene27747:CDS 55.0%
!! CCATGGTTGGCTTGCACTAG+TGG - chr7.3:29204141-29204160 MS.gene27747:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 29203821 29204939 29203821 ID=MS.gene27747
chr7.3 mRNA 29203821 29204939 29203821 ID=MS.gene27747.t1;Parent=MS.gene27747
chr7.3 exon 29203821 29204939 29203821 ID=MS.gene27747.t1.exon1;Parent=MS.gene27747.t1
chr7.3 CDS 29203821 29204939 29203821 ID=cds.MS.gene27747.t1;Parent=MS.gene27747.t1
Gene Sequence

>MS.gene27747

ATGAGAAAGGCAGATTGGGCAAATTTAGATTGCTACCCTCTTAGTTTGGTTCTTGACGAGTTGGAAGAACACATAGATCATGTTAGGTTTGGTGTGGTGTGCAAGAGTTGGCTATCAATTGCAAAGCTTAACCATAAAAATCATCAATTTAGGATTAATGTACCACCTATGTTAATGATCCTCTCAAACAAATTGTCTCGTAGACGTGCAAAATCAAAGAGGAAGATGAAATCGTTATATAGTATCCCAAGTGAGAAAGTGTACCCTATTCATTTATCCCATCCTTCCATCATTAAAAGTAAAACATGTTTAGGTTGTAGCCATGGTTGGCTTGCACTAGTGGATAAAAACAATGCCATAACTCTAGTGAATCCTTTTAAGAGCAGTATAGCTCCCATTAGTCTGCCACATCTCGAATCTCTCAACAAGGTTACCTTGTCTGCTGACCCCATTACAAGCCCAAGTGATTATGTGGTTGCAGCGATTTACAATTTTGGTTCTCTCGCTTTCAAAAGAGCAAGCCAGTCTTTTTGGATTCGTGCAGACACAAATGAATTTTCTTTCACTAATGTTGTATTTTATAAAGGCTTGGTATTTGCGGACAGCGAACAAGACTTCATTGTATCCTTCAAATTCAACAATCCTCCTTGTGATGACTCAATTGACCCTAATTTTACTTACCTTGAGAAGATAGCTAGTACTCCATATAATTTTCCAGAAGAATATTATTATGGGAATTCCTATTTTGTGAAATCATTGACCGGAGACATATGGATGGTGAAAAGATGTTTAATCGACCCACACAATCTTACATACAAACTCTACGTTTTCAAATTGGAACTGGATGCCCAGAGCGGAAAAGTTGAACAAATCAACAAACTTGTGAGTTTAGAGAACAACATTTTATTTGTCGGAATCGGCGATTCAATTTCTGTGTCAGCCTCTTGTTTCTCAAAGTTTGAAAAGGATTCAATTTATTTTATTTACGATGGCGATGAAGATGATTTAGAGTTACAAATCTATAATGCGAAGGATGGAAGTTATCGTAGTCAATCTTTACCAATTTCCTTCAAGAGGATGTTACATCTTTGGGTTCTACCCCAATTTCAATGGGATTGA
Protein sequence

>MS.gene27747.t1

MRKADWANLDCYPLSLVLDELEEHIDHVRFGVVCKSWLSIAKLNHKNHQFRINVPPMLMILSNKLSRRRAKSKRKMKSLYSIPSEKVYPIHLSHPSIIKSKTCLGCSHGWLALVDKNNAITLVNPFKSSIAPISLPHLESLNKVTLSADPITSPSDYVVAAIYNFGSLAFKRASQSFWIRADTNEFSFTNVVFYKGLVFADSEQDFIVSFKFNNPPCDDSIDPNFTYLEKIASTPYNFPEEYYYGNSYFVKSLTGDIWMVKRCLIDPHNLTYKLYVFKLELDAQSGKVEQINKLVSLENNILFVGIGDSISVSASCFSKFEKDSIYFIYDGDEDDLELQIYNAKDGSYRSQSLPISFKRMLHLWVLPQFQWD