AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42433

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42433.t1 MTR_7g077620 93.514 370 24 0 1 370 1 370 0.0 711
MS.gene42433.t1 MTR_7g077660 70.557 377 97 8 1 372 1 368 1.52e-175 493
MS.gene42433.t1 MTR_7g077650 68.865 379 104 7 1 372 1 372 1.08e-171 483
MS.gene42433.t1 MTR_7g076110 57.095 296 116 5 85 372 21 313 3.42e-103 307
MS.gene42433.t1 MTR_7g076100 66.667 237 77 2 137 372 65 300 1.07e-101 303
MS.gene42433.t1 MTR_7g076100 74.074 54 13 1 1 53 1 54 9.03e-20 89.0
MS.gene42433.t1 MTR_1g108740 43.947 380 167 15 1 370 1 344 1.15e-84 261
MS.gene42433.t1 MTR_5g038260 42.500 400 180 15 3 372 4 383 4.72e-84 260
MS.gene42433.t1 MTR_5g038230 41.266 395 162 14 3 370 2 353 9.96e-79 246
MS.gene42433.t1 MTR_1g064570 40.334 419 181 18 3 372 2 400 6.77e-75 238
MS.gene42433.t1 MTR_5g082770 46.302 311 131 7 5 305 4 288 5.94e-72 226
MS.gene42433.t1 MTR_1g016150 46.890 209 101 6 1 204 1 204 1.31e-49 167
MS.gene42433.t1 MTR_1g016150 37.097 124 67 4 201 318 117 235 8.28e-11 62.0
MS.gene42433.t1 MTR_7g076130 62.903 124 45 1 168 290 25 148 8.06e-45 152
MS.gene42433.t1 MTR_5g082780 43.231 229 94 10 114 327 1 208 1.72e-38 138
MS.gene42433.t1 MTR_1g108750 43.590 156 52 4 5 159 4 124 4.59e-26 101
MS.gene42433.t1 MTR_3g114970 25.668 374 203 17 4 347 3 331 3.03e-16 79.3
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 7.2:-28498835 MS.gene42433:CDS
TATTCTTCTGGAAAATTATA+TGG 0.217616 7.2:+28498844 None:intergenic
TTCTCAAGGTAAGTAAAATT+AGG 0.221508 7.2:+28498880 None:intergenic
CAGATCAATCCCATTGAAAT+TGG 0.221701 7.2:+28498446 None:intergenic
TCAAGAGGATGTTACATCTT+TGG 0.236048 7.2:-28498477 MS.gene42433:CDS
GTTGCAGCGATTTACAATTT+TGG 0.255211 7.2:-28499072 MS.gene42433:CDS
TTCCCATAATAATATTCTTC+TGG 0.264764 7.2:+28498832 None:intergenic
AACATCCTCTTGAAGGAAAT+TGG 0.274037 7.2:+28498487 None:intergenic
ATTAAAAGTAAAACATGTTT+AGG 0.274585 7.2:-28499255 MS.gene42433:CDS
CAAGAGGATGTTACATCTTT+GGG 0.279656 7.2:-28498476 MS.gene42433:CDS
GGAGCTATACTGCTCTTAAA+AGG 0.328493 7.2:+28499174 None:intergenic
TAATCACTTGGGCTTGTAAT+GGG 0.338599 7.2:+28499099 None:intergenic
TTCCAGAAGAATATTATTAT+GGG 0.343297 7.2:-28498834 MS.gene42433:CDS
AAGAACACATAGATCATGTT+AGG 0.348741 7.2:-28499482 MS.gene42433:CDS
GAAGGATGGGATAAATGAAT+AGG 0.361300 7.2:+28499282 None:intergenic
TCTCAAGGTAAGTAAAATTA+GGG 0.370039 7.2:+28498881 None:intergenic
AGATTGCTACCCTCTTAGTT+TGG 0.376216 7.2:-28499520 MS.gene42433:CDS
TTCAAGATGTGGCAGACTAA+TGG 0.379731 7.2:+28499152 None:intergenic
GGGTTCTACCCCAATTTCAA+TGG 0.404683 7.2:-28498456 MS.gene42433:CDS
TCAAGATGTGGCAGACTAAT+GGG 0.407261 7.2:+28499153 None:intergenic
AGATCAATCCCATTGAAATT+GGG 0.410514 7.2:+28498447 None:intergenic
AAAAGGATTCACTAGAGTTA+TGG 0.411464 7.2:+28499191 None:intergenic
CACATAGATCATGTTAGGTT+TGG 0.419733 7.2:-28499477 MS.gene42433:CDS
AGGAGGATTGTTGAATTTGA+AGG 0.434909 7.2:+28498921 None:intergenic
AAGATGTAACATCCTCTTGA+AGG 0.440096 7.2:+28498480 None:intergenic
TTGTTTCTCAAAGTTTGAAA+AGG 0.453913 7.2:-28498602 MS.gene42433:CDS
AGCAATGAGAAAGGCAGATT+GGG 0.457389 7.2:-28499550 None:intergenic
CCATGGTTGGCTTGCACTAG+TGG 0.460763 7.2:-28499226 MS.gene42433:CDS
TAGCAATGAGAAAGGCAGAT+TGG 0.467073 7.2:-28499551 None:intergenic
AAGGATGGGATAAATGAATA+GGG 0.470406 7.2:+28499283 None:intergenic
TTATAAAGGCTTGGTATTTG+CGG 0.472828 7.2:-28498968 MS.gene42433:CDS
ATAATCACTTGGGCTTGTAA+TGG 0.476686 7.2:+28499098 None:intergenic
TCGTCAAGAACCAAACTAAG+AGG 0.484268 7.2:+28499510 None:intergenic
AATCATTGACCGGAGACATA+TGG 0.484616 7.2:-28498795 MS.gene42433:CDS
GGTTCTACCCCAATTTCAAT+GGG 0.486591 7.2:-28498455 MS.gene42433:CDS
GTTTAGGTTGTAGCCATGGT+TGG 0.497773 7.2:-28499239 MS.gene42433:CDS
TACAAGCCCAAGTGATTATG+TGG 0.499442 7.2:-28499094 MS.gene42433:CDS
ATAGGGTACTCTTTCTCACT+TGG 0.511489 7.2:+28499300 None:intergenic
CTTTACCAATTTCCTTCAAG+AGG 0.512890 7.2:-28498492 MS.gene42433:CDS
CAAATCTATAATGCGAAGGA+TGG 0.523156 7.2:-28498532 MS.gene42433:CDS
TTTCACCATCCATATGTCTC+CGG 0.527974 7.2:+28498786 None:intergenic
TACGAGACAATTTGTTTGAG+AGG 0.528949 7.2:+28499367 None:intergenic
TTTGAGAGGATCATTAACAT+AGG 0.529450 7.2:+28499381 None:intergenic
TAGTTTGGTTCTTGACGAGT+TGG 0.532019 7.2:-28499505 MS.gene42433:CDS
TTCAAACTTTGAGAAACAAG+AGG 0.532702 7.2:+28498606 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.549128 7.2:+28499087 None:intergenic
ACATGTTTAGGTTGTAGCCA+TGG 0.559363 7.2:-28499243 MS.gene42433:CDS
TGTAATGGGGTCAGCAGACA+AGG 0.568289 7.2:+28499113 None:intergenic
TTGGTGTGGTGTGCAAGAGT+TGG 0.569193 7.2:-28499458 MS.gene42433:CDS
AGTTTGTATGTAAGATTGTG+TGG 0.574270 7.2:+28498748 None:intergenic
TAGGGTACTCTTTCTCACTT+GGG 0.591906 7.2:+28499301 None:intergenic
GATCAATCCCATTGAAATTG+GGG 0.599101 7.2:+28498448 None:intergenic
GAGTACTAGCTATCTTCTCA+AGG 0.600472 7.2:+28498866 None:intergenic
TTGTTGAGAGATTCAAGATG+TGG 0.603045 7.2:+28499141 None:intergenic
CGTCAAGAACCAAACTAAGA+GGG 0.605996 7.2:+28499511 None:intergenic
AATCACTTGGGCTTGTAATG+GGG 0.606028 7.2:+28499100 None:intergenic
GTTACAAATCTATAATGCGA+AGG 0.615721 7.2:-28498536 MS.gene42433:CDS
CCACTAGTGCAAGCCAACCA+TGG 0.620481 7.2:+28499226 None:intergenic
CTGCAACCACATAATCACTT+GGG 0.636696 7.2:+28499088 None:intergenic
GTTTGTATGTAAGATTGTGT+GGG 0.646089 7.2:+28498749 None:intergenic
GAGAGGATCATTAACATAGG+TGG 0.648255 7.2:+28499384 None:intergenic
AGATCATGTTAGGTTTGGTG+TGG 0.661894 7.2:-28499472 MS.gene42433:CDS
GGGTCAATTGAGTCATCACA+AGG 0.675309 7.2:+28498901 None:intergenic
ACATCTTGAATCTCTCAACA+AGG 0.676210 7.2:-28499139 MS.gene42433:CDS
ATTGACCGGAGACATATGGA+TGG 0.696827 7.2:-28498791 MS.gene42433:CDS
GTAGACGTGCAAAATCAAAG+AGG 0.713785 7.2:-28499347 MS.gene42433:CDS
TTGGAACTGGATGCCCAGAG+CGG 0.723217 7.2:-28498712 MS.gene42433:CDS
TCAATTGAGTCATCACAAGG+AGG 0.741566 7.2:+28498904 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAAAGTAAAACATGTTT+AGG - chr7.2:28498741-28498760 MS.gene42433:CDS 15.0%
!!! ACTAATGTTGTATTTTATAA+AGG - chr7.2:28499014-28499033 MS.gene42433:CDS 15.0%
!!! TCAATTTATTTTATTTACGA+TGG - chr7.2:28499419-28499438 MS.gene42433:CDS 15.0%
!! ACCATAAAAATCATCAATTT+AGG - chr7.2:28498580-28498599 MS.gene42433:CDS 20.0%
!! TTCCAGAAGAATATTATTAT+GGG - chr7.2:28499162-28499181 MS.gene42433:CDS 20.0%
!! TTTCCAGAAGAATATTATTA+TGG - chr7.2:28499161-28499180 MS.gene42433:CDS 20.0%
!!! ACATGTTTTACTTTTAATGA+TGG + chr7.2:28498739-28498758 None:intergenic 20.0%
!!! TATTCTTCTGGAAAATTATA+TGG + chr7.2:28499155-28499174 None:intergenic 20.0%
!!! TCCTAAATTGATGATTTTTA+TGG + chr7.2:28498584-28498603 None:intergenic 20.0%
! TCTCAAGGTAAGTAAAATTA+GGG + chr7.2:28499118-28499137 None:intergenic 25.0%
! TTCCCATAATAATATTCTTC+TGG + chr7.2:28499167-28499186 None:intergenic 25.0%
! TTCTCAAGGTAAGTAAAATT+AGG + chr7.2:28499119-28499138 None:intergenic 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr7.2:28499191-28499210 MS.gene42433:CDS 25.0%
!! TGTTGTATTTTATAAAGGCT+TGG - chr7.2:28499019-28499038 MS.gene42433:CDS 25.0%
!! TTGTTTCTCAAAGTTTGAAA+AGG - chr7.2:28499394-28499413 MS.gene42433:CDS 25.0%
!!! AACATTTTATTTGTCGGAAT+CGG - chr7.2:28499347-28499366 MS.gene42433:CDS 25.0%
!!! GAGAACAACATTTTATTTGT+CGG - chr7.2:28499341-28499360 MS.gene42433:CDS 25.0%
!!! GTTTTACTTTTAATGATGGA+AGG + chr7.2:28498735-28498754 None:intergenic 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.2:28498808-28498827 None:intergenic 30.0%
AAGAACACATAGATCATGTT+AGG - chr7.2:28498514-28498533 MS.gene42433:CDS 30.0%
AAGGATGGGATAAATGAATA+GGG + chr7.2:28498716-28498735 None:intergenic 30.0%
AGTTTGTATGTAAGATTGTG+TGG + chr7.2:28499251-28499270 None:intergenic 30.0%
GTTACAAATCTATAATGCGA+AGG - chr7.2:28499460-28499479 MS.gene42433:CDS 30.0%
GTTTGTATGTAAGATTGTGT+GGG + chr7.2:28499250-28499269 None:intergenic 30.0%
TTTGAGAGGATCATTAACAT+AGG + chr7.2:28498618-28498637 None:intergenic 30.0%
! CAAACTCTACGTTTTCAAAT+TGG - chr7.2:28499265-28499284 MS.gene42433:CDS 30.0%
! TTATAAAGGCTTGGTATTTG+CGG - chr7.2:28499028-28499047 MS.gene42433:CDS 30.0%
! TTCAAACTTTGAGAAACAAG+AGG + chr7.2:28499393-28499412 None:intergenic 30.0%
!! ACTTTTAATGATGGAAGGAT+GGG + chr7.2:28498730-28498749 None:intergenic 30.0%
!! TACTTTTAATGATGGAAGGA+TGG + chr7.2:28498731-28498750 None:intergenic 30.0%
AACATCCTCTTGAAGGAAAT+TGG + chr7.2:28499512-28499531 None:intergenic 35.0%
AAGATGTAACATCCTCTTGA+AGG + chr7.2:28499519-28499538 None:intergenic 35.0%
ACATCTTGAATCTCTCAACA+AGG - chr7.2:28498857-28498876 MS.gene42433:CDS 35.0%
AGGAGGATTGTTGAATTTGA+AGG + chr7.2:28499078-28499097 None:intergenic 35.0%
ATAATCACTTGGGCTTGTAA+TGG + chr7.2:28498901-28498920 None:intergenic 35.0%
CAAATCTATAATGCGAAGGA+TGG - chr7.2:28499464-28499483 MS.gene42433:CDS 35.0%
CAAGAGGATGTTACATCTTT+GGG - chr7.2:28499520-28499539 MS.gene42433:CDS 35.0%
CACATAGATCATGTTAGGTT+TGG - chr7.2:28498519-28498538 MS.gene42433:CDS 35.0%
CTTTACCAATTTCCTTCAAG+AGG - chr7.2:28499504-28499523 MS.gene42433:CDS 35.0%
GAAGGATGGGATAAATGAAT+AGG + chr7.2:28498717-28498736 None:intergenic 35.0%
TAATCACTTGGGCTTGTAAT+GGG + chr7.2:28498900-28498919 None:intergenic 35.0%
TCAAGAGGATGTTACATCTT+TGG - chr7.2:28499519-28499538 MS.gene42433:CDS 35.0%
TTGTTGAGAGATTCAAGATG+TGG + chr7.2:28498858-28498877 None:intergenic 35.0%
! CTACGTTTTCAAATTGGAAC+TGG - chr7.2:28499271-28499290 MS.gene42433:CDS 35.0%
! GTTGCAGCGATTTACAATTT+TGG - chr7.2:28498924-28498943 MS.gene42433:CDS 35.0%
! TACGAGACAATTTGTTTGAG+AGG + chr7.2:28498632-28498651 None:intergenic 35.0%
AATCACTTGGGCTTGTAATG+GGG + chr7.2:28498899-28498918 None:intergenic 40.0%
AATCATTGACCGGAGACATA+TGG - chr7.2:28499201-28499220 MS.gene42433:CDS 40.0%
AGATTGCTACCCTCTTAGTT+TGG - chr7.2:28498476-28498495 MS.gene42433:CDS 40.0%
CGTCAAGAACCAAACTAAGA+GGG + chr7.2:28498488-28498507 None:intergenic 40.0%
CTGCAACCACATAATCACTT+GGG + chr7.2:28498911-28498930 None:intergenic 40.0%
GAGAGGATCATTAACATAGG+TGG + chr7.2:28498615-28498634 None:intergenic 40.0%
GAGTACTAGCTATCTTCTCA+AGG + chr7.2:28499133-28499152 None:intergenic 40.0%
GGAGCTATACTGCTCTTAAA+AGG + chr7.2:28498825-28498844 None:intergenic 40.0%
GGTTCTACCCCAATTTCAAT+GGG - chr7.2:28499541-28499560 MS.gene42433:CDS 40.0%
GTAGACGTGCAAAATCAAAG+AGG - chr7.2:28498649-28498668 MS.gene42433:CDS 40.0%
TACAAGCCCAAGTGATTATG+TGG - chr7.2:28498902-28498921 MS.gene42433:CDS 40.0%
TCAAGATGTGGCAGACTAAT+GGG + chr7.2:28498846-28498865 None:intergenic 40.0%
TCAATTGAGTCATCACAAGG+AGG + chr7.2:28499095-28499114 None:intergenic 40.0%
TCGTCAAGAACCAAACTAAG+AGG + chr7.2:28498489-28498508 None:intergenic 40.0%
TTCAAGATGTGGCAGACTAA+TGG + chr7.2:28498847-28498866 None:intergenic 40.0%
TTTCACCATCCATATGTCTC+CGG + chr7.2:28499213-28499232 None:intergenic 40.0%
! AAAGAGCAAGCCAGTCTTTT+TGG - chr7.2:28498961-28498980 MS.gene42433:CDS 40.0%
! ATAGGGTACTCTTTCTCACT+TGG + chr7.2:28498699-28498718 None:intergenic 40.0%
! TAGGGTACTCTTTCTCACTT+GGG + chr7.2:28498698-28498717 None:intergenic 40.0%
! TTGTTCAACTTTTCCGCTCT+GGG + chr7.2:28499300-28499319 None:intergenic 40.0%
! TTTGTTCAACTTTTCCGCTC+TGG + chr7.2:28499301-28499320 None:intergenic 40.0%
!! ACATGTTTAGGTTGTAGCCA+TGG - chr7.2:28498753-28498772 MS.gene42433:CDS 40.0%
!! AGATCATGTTAGGTTTGGTG+TGG - chr7.2:28498524-28498543 MS.gene42433:CDS 40.0%
!! TAGTTTGGTTCTTGACGAGT+TGG - chr7.2:28498491-28498510 MS.gene42433:CDS 40.0%
ATTGACCGGAGACATATGGA+TGG - chr7.2:28499205-28499224 MS.gene42433:CDS 45.0%
CTGCACGAATCCAAAAAGAC+TGG + chr7.2:28498974-28498993 None:intergenic 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.2:28498912-28498931 None:intergenic 45.0%
GGGTCAATTGAGTCATCACA+AGG + chr7.2:28499098-28499117 None:intergenic 45.0%
GGGTTCTACCCCAATTTCAA+TGG - chr7.2:28499540-28499559 MS.gene42433:CDS 45.0%
!! GTTTAGGTTGTAGCCATGGT+TGG - chr7.2:28498757-28498776 MS.gene42433:CDS 45.0%
TTGGTGTGGTGTGCAAGAGT+TGG - chr7.2:28498538-28498557 MS.gene42433:CDS 50.0%
! TGTAATGGGGTCAGCAGACA+AGG + chr7.2:28498886-28498905 None:intergenic 50.0%
CCACTAGTGCAAGCCAACCA+TGG + chr7.2:28498773-28498792 None:intergenic 55.0%
TTGGAACTGGATGCCCAGAG+CGG - chr7.2:28499284-28499303 MS.gene42433:CDS 55.0%
!! CCATGGTTGGCTTGCACTAG+TGG - chr7.2:28498770-28498789 MS.gene42433:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 28498450 28499568 28498450 ID=MS.gene42433
chr7.2 mRNA 28498450 28499568 28498450 ID=MS.gene42433.t1;Parent=MS.gene42433
chr7.2 exon 28498450 28499568 28498450 ID=MS.gene42433.t1.exon1;Parent=MS.gene42433.t1
chr7.2 CDS 28498450 28499568 28498450 ID=cds.MS.gene42433.t1;Parent=MS.gene42433.t1
Gene Sequence

>MS.gene42433

ATGAGAAAGGCAGATTGGGCAAATTTAGATTGCTACCCTCTTAGTTTGGTTCTTGACGAGTTGGAAGAACACATAGATCATGTTAGGTTTGGTGTGGTGTGCAAGAGTTGGCTATCAATTGCAAAGCTTAACCATAAAAATCATCAATTTAGGATTAATGTACCACCTATGTTAATGATCCTCTCAAACAAATTGTCTCGTAGACGTGCAAAATCAAAGAGGAAGATGAAATCGTTATATAGTATCCCAAGTGAGAAAGAGTACCCTATTCATTTATCCCATCCTTCCATCATTAAAAGTAAAACATGTTTAGGTTGTAGCCATGGTTGGCTTGCACTAGTGGATAAAAACAATGCCATAACTCTAGTGAATCCTTTTAAGAGCAGTATAGCTCCCATTAGTCTGCCACATCTTGAATCTCTCAACAAGGCTACCTTGTCTGCTGACCCCATTACAAGCCCAAGTGATTATGTGGTTGCAGCGATTTACAATTTTGGTTCTCTCGCTTTCAAAAGAGCAAGCCAGTCTTTTTGGATTCGTGCAGACACAAATGAATTTTCTTTCACTAATGTTGTATTTTATAAAGGCTTGGTATTTGCGGACAGCGAACAAGACTTCATTGTATCCTTCAAATTCAACAATCCTCCTTGTGATGACTCAATTGACCCTAATTTTACTTACCTTGAGAAGATAGCTAGTACTCCATATAATTTTCCAGAAGAATATTATTATGGGAATTCTTATTTTGTGAAATCATTGACCGGAGACATATGGATGGTGAAAAGATGTTTAATCGACCCACACAATCTTACATACAAACTCTACGTTTTCAAATTGGAACTGGATGCCCAGAGCGGAAAAGTTGAACAAATCAACAAGCTTGTGAGTTTAGAGAACAACATTTTATTTGTCGGAATCGGCGATTCAATTTCTGTGTCAGCCTCTTGTTTCTCAAAGTTTGAAAAGGATTCAATTTATTTTATTTACGATGGCGATGAAGATGATTTAGAGTTACAAATCTATAATGCGAAGGATGGAAGTTATCGTAGTCAATCTTTACCAATTTCCTTCAAGAGGATGTTACATCTTTGGGTTCTACCCCAATTTCAATGGGATTGA
Protein sequence

>MS.gene42433.t1

MRKADWANLDCYPLSLVLDELEEHIDHVRFGVVCKSWLSIAKLNHKNHQFRINVPPMLMILSNKLSRRRAKSKRKMKSLYSIPSEKEYPIHLSHPSIIKSKTCLGCSHGWLALVDKNNAITLVNPFKSSIAPISLPHLESLNKATLSADPITSPSDYVVAAIYNFGSLAFKRASQSFWIRADTNEFSFTNVVFYKGLVFADSEQDFIVSFKFNNPPCDDSIDPNFTYLEKIASTPYNFPEEYYYGNSYFVKSLTGDIWMVKRCLIDPHNLTYKLYVFKLELDAQSGKVEQINKLVSLENNILFVGIGDSISVSASCFSKFEKDSIYFIYDGDEDDLELQIYNAKDGSYRSQSLPISFKRMLHLWVLPQFQWD