AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene026867

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026867.t1 MTR_2g075910 98.043 460 9 0 1 460 1 460 0.0 936
MS.gene026867.t1 MTR_8g059485 59.870 461 156 10 1 455 1 438 1.25e-179 510
MS.gene026867.t1 MTR_8g059485 59.870 461 156 10 1 455 10 447 3.36e-179 509
MS.gene026867.t1 MTR_8g087400 45.140 463 239 7 1 453 1 458 6.00e-126 374
MS.gene026867.t1 MTR_4g025420 41.103 399 217 5 62 453 25 412 1.99e-99 304
MS.gene026867.t1 MTR_0178s0030 31.738 397 246 5 69 453 139 522 1.87e-57 198
MS.gene026867.t1 MTR_5g075180 31.990 397 232 8 64 455 78 441 3.21e-50 177
MS.gene026867.t1 MTR_3g462150 30.941 404 246 11 73 457 92 481 4.88e-50 177
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026867.t1 AT1G53380 52.288 459 204 7 1 453 1 450 3.50e-167 478
MS.gene026867.t1 AT1G53380 52.288 459 204 7 1 453 1 450 3.50e-167 478
MS.gene026867.t1 AT1G53380 52.288 459 204 7 1 453 1 450 3.50e-167 478
MS.gene026867.t1 AT1G53380 52.288 459 204 7 1 453 1 450 3.50e-167 478
MS.gene026867.t1 AT1G53380 52.288 459 204 7 1 453 1 450 3.50e-167 478
MS.gene026867.t1 AT3G14870 50.318 471 216 5 1 458 2 467 1.84e-164 472
MS.gene026867.t1 AT3G14870 50.318 471 216 5 1 458 5 470 2.15e-164 472
MS.gene026867.t1 AT3G14870 50.318 471 216 5 1 458 1 466 2.44e-164 472
MS.gene026867.t1 AT3G14870 50.318 471 216 5 1 458 1 466 2.44e-164 472
MS.gene026867.t1 AT3G14870 50.318 471 216 5 1 458 1 466 2.44e-164 472
MS.gene026867.t1 AT1G29300 42.050 478 233 9 1 457 1 455 7.33e-111 335
MS.gene026867.t1 AT2G45260 39.905 421 237 4 43 453 4 418 7.59e-102 311
MS.gene026867.t1 AT3G60680 31.969 391 250 4 74 459 120 499 1.13e-59 203
MS.gene026867.t1 AT4G34080 37.500 280 168 2 62 334 2 281 3.27e-56 188
MS.gene026867.t1 AT2G30380 32.804 378 211 4 76 453 76 410 6.99e-54 186
MS.gene026867.t1 AT4G33320 35.664 286 176 3 62 339 2 287 4.60e-50 172
MS.gene026867.t1 AT5G58960 29.087 416 245 10 73 456 86 483 9.01e-47 169
MS.gene026867.t1 AT5G58960 29.087 416 245 10 73 456 86 483 9.01e-47 169
MS.gene026867.t1 AT5G58960 30.000 410 249 11 73 456 161 558 2.37e-46 169
MS.gene026867.t1 AT2G32130 44.355 124 69 0 73 196 34 157 1.36e-26 105
MS.gene026867.t1 AT4G36100 46.078 102 52 1 62 160 2 103 1.24e-20 90.9

Find 46 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATGTTTGTTTCATCCTT+TGG 0.256313 2.4:-21333421 None:intergenic
TCATTTGGAAGATTGAAATT+AGG 0.272865 2.4:-21334153 None:intergenic
GCTAGCATTTCAACGGTTAA+AGG 0.286606 2.4:+21333547 MS.gene026867:CDS
GATAATGTTGTTCACATATC+AGG 0.291769 2.4:+21333913 MS.gene026867:CDS
AGCTGAATCGAAGGAGATAA+AGG 0.344297 2.4:+21333729 MS.gene026867:CDS
ATGAAATGAGATCTGCAAAA+TGG 0.347278 2.4:+21334013 MS.gene026867:CDS
TTCCTAGCTAATTTCTTGCT+TGG 0.381111 2.4:-21333337 None:intergenic
GACGAAGAACAGTAGCAAAA+TGG 0.401046 2.4:-21333948 None:intergenic
GAAATCTTTCAAGTGGGAAA+AGG 0.412349 2.4:+21334483 MS.gene026867:CDS
TCAGAAGCTTCAATTCCATC+AGG 0.419938 2.4:-21333610 None:intergenic
TCATCTGGAAGTGACTCATT+TGG 0.420184 2.4:-21334168 None:intergenic
TTGCTTGGTGTCACTGCTGA+AGG 0.427239 2.4:-21333322 None:intergenic
GTTTCTTAAAGAGAAATTAG+TGG 0.430754 2.4:+21333825 MS.gene026867:CDS
TCAGAAGAAGAACCAGTTGT+TGG 0.431414 2.4:+21334582 MS.gene026867:CDS
AATTGCGCAAACGATGATCT+TGG 0.434932 2.4:-21334273 None:intergenic
AGCTTGAACTTCAAAAGAAA+AGG 0.445286 2.4:-21334460 None:intergenic
GAAACTCTCCACCACTCAAA+AGG 0.448344 2.4:-21334371 None:intergenic
CGAGGTTACCGCGAAGAAGT+TGG 0.455237 2.4:+21333768 MS.gene026867:CDS
CATCGTTTGCGCAATTCTGC+AGG 0.469810 2.4:+21334280 MS.gene026867:CDS
CGCGAAGAAGTTGGAATCAC+AGG 0.476006 2.4:+21333777 MS.gene026867:CDS
TGCTCTAAGATGAAGAACTT+TGG 0.476082 2.4:-21333365 None:intergenic
AAATCTTTCAAGTGGGAAAA+GGG 0.495316 2.4:+21334484 MS.gene026867:CDS
CTGTGATTCCAACTTCTTCG+CGG 0.496048 2.4:-21333776 None:intergenic
TCAATTCCATCAGGGTCAAA+AGG 0.497708 2.4:-21333601 None:intergenic
GCTGCGAGTATCGCTTTCTC+TGG 0.498611 2.4:-21333709 None:intergenic
ACAACAGCAAAACCAACAAC+TGG 0.503833 2.4:-21334594 None:intergenic
TGAAATGAGATCTGCAAAAT+GGG 0.517744 2.4:+21334014 MS.gene026867:CDS
GCTGAATCGAAGGAGATAAA+GGG 0.535338 2.4:+21333730 MS.gene026867:CDS
CTTCTTCGCGGTAACCTCGT+AGG 0.541450 2.4:-21333764 None:intergenic
TCAAGCTGAAATCTTTCAAG+TGG 0.545340 2.4:+21334476 MS.gene026867:CDS
GAGAAGAGATTGAATCAAAG+TGG 0.546796 2.4:+21333874 MS.gene026867:CDS
TGGAAAAGACTACAATAACT+TGG 0.552801 2.4:+21333440 MS.gene026867:CDS
TGAGTTGATTCTTCTGCATG+AGG 0.560321 2.4:-21334662 None:intergenic
CAAGCTGAAATCTTTCAAGT+GGG 0.598623 2.4:+21334477 MS.gene026867:CDS
TCCAAAGGATGAAACAAACA+TGG 0.604906 2.4:+21333420 MS.gene026867:CDS
GATACTCGCAGCTGAATCGA+AGG 0.611880 2.4:+21333720 MS.gene026867:CDS
CAGAAGCTTCAATTCCATCA+GGG 0.612641 2.4:-21333609 None:intergenic
AGTATCGCTTTCTCTGGTGA+AGG 0.613880 2.4:-21333703 None:intergenic
TGCTACTGTTCTTCGTCACG+CGG 0.615594 2.4:+21333954 MS.gene026867:CDS
TATATCTGATACAAATCCAA+AGG 0.615715 2.4:+21333405 MS.gene026867:CDS
GATCGATTCGAAACTTTGTG+AGG 0.630009 2.4:+21333980 MS.gene026867:CDS
CACCAAGCAAGAAATTAGCT+AGG 0.637970 2.4:+21333335 MS.gene026867:CDS
AGAACAGTAGCAAAATGGCT+AGG 0.639681 2.4:-21333943 None:intergenic
GCATGAGGTAAACTTGACAC+TGG 0.642471 2.4:-21334647 None:intergenic
CATGCAGAAGAATCAACTCA+AGG 0.660821 2.4:+21334665 MS.gene026867:CDS
TGATGCTATTGAACACAATG+TGG 0.709156 2.4:+21334053 MS.gene026867:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAAAAAATCAACAAAAT+TGG + chr2.4:21334190-21334209 MS.gene026867:CDS 15.0%
! GTTTCTTAAAGAGAAATTAG+TGG + chr2.4:21333825-21333844 MS.gene026867:CDS 25.0%
! TATATCTGATACAAATCCAA+AGG + chr2.4:21333405-21333424 MS.gene026867:CDS 25.0%
! TCATTTGGAAGATTGAAATT+AGG - chr2.4:21334156-21334175 None:intergenic 25.0%
!! AAAAATGATGACTCCATTTT+TGG - chr2.4:21334330-21334349 None:intergenic 25.0%
!!! AAAATGGAGTCATCATTTTT+TGG + chr2.4:21334330-21334349 MS.gene026867:CDS 25.0%
!!! GATGCAAAAAAATCACTTTT+TGG - chr2.4:21334396-21334415 None:intergenic 25.0%
!!! TGTTGATTTTTTCTATCATC+TGG - chr2.4:21334186-21334205 None:intergenic 25.0%
AGCTTGAACTTCAAAAGAAA+AGG - chr2.4:21334463-21334482 None:intergenic 30.0%
ATGAAATGAGATCTGCAAAA+TGG + chr2.4:21334013-21334032 MS.gene026867:CDS 30.0%
GATAATGTTGTTCACATATC+AGG + chr2.4:21333913-21333932 MS.gene026867:CDS 30.0%
TGAAATGAGATCTGCAAAAT+GGG + chr2.4:21334014-21334033 MS.gene026867:CDS 30.0%
TGGAAAAGACTACAATAACT+TGG + chr2.4:21333440-21333459 MS.gene026867:CDS 30.0%
! AAATCTTTCAAGTGGGAAAA+GGG + chr2.4:21334484-21334503 MS.gene026867:CDS 30.0%
! GATTTTTGCTAGCATTTCAA+CGG + chr2.4:21333540-21333559 MS.gene026867:CDS 30.0%
! TAGATTTTCTGATGTGTACA+TGG + chr2.4:21334509-21334528 MS.gene026867:CDS 30.0%
! TTTTGCATCTTTTGCTGAAA+TGG + chr2.4:21334407-21334426 MS.gene026867:CDS 30.0%
GAGAAGAGATTGAATCAAAG+TGG + chr2.4:21333874-21333893 MS.gene026867:CDS 35.0%
TCAAGCTGAAATCTTTCAAG+TGG + chr2.4:21334476-21334495 MS.gene026867:CDS 35.0%
TCCAAAGGATGAAACAAACA+TGG + chr2.4:21333420-21333439 MS.gene026867:CDS 35.0%
TCCATGTTTGTTTCATCCTT+TGG - chr2.4:21333424-21333443 None:intergenic 35.0%
TGATGCTATTGAACACAATG+TGG + chr2.4:21334053-21334072 MS.gene026867:CDS 35.0%
TTCCTAGCTAATTTCTTGCT+TGG - chr2.4:21333340-21333359 None:intergenic 35.0%
! CAAGCTGAAATCTTTCAAGT+GGG + chr2.4:21334477-21334496 MS.gene026867:CDS 35.0%
! GAAATCTTTCAAGTGGGAAA+AGG + chr2.4:21334483-21334502 MS.gene026867:CDS 35.0%
! GAGACTTGTTCATCCAAAAA+TGG + chr2.4:21334314-21334333 MS.gene026867:CDS 35.0%
! GTTTTACCAATCCTAAAACC+AGG - chr2.4:21334621-21334640 None:intergenic 35.0%
! TTTTGCTGAAATGGCTAAGA+GGG + chr2.4:21334416-21334435 MS.gene026867:CDS 35.0%
!! TGCTCTAAGATGAAGAACTT+TGG - chr2.4:21333368-21333387 None:intergenic 35.0%
!! TTTTTGGCAACATGATTCAC+AGG + chr2.4:21334346-21334365 MS.gene026867:CDS 35.0%
AATTGCGCAAACGATGATCT+TGG - chr2.4:21334276-21334295 None:intergenic 40.0%
ACAACAGCAAAACCAACAAC+TGG - chr2.4:21334597-21334616 None:intergenic 40.0%
AGAACAGTAGCAAAATGGCT+AGG - chr2.4:21333946-21333965 None:intergenic 40.0%
AGCTGAATCGAAGGAGATAA+AGG + chr2.4:21333729-21333748 MS.gene026867:CDS 40.0%
CACCAAGCAAGAAATTAGCT+AGG + chr2.4:21333335-21333354 MS.gene026867:CDS 40.0%
CAGAAGCTTCAATTCCATCA+GGG - chr2.4:21333612-21333631 None:intergenic 40.0%
GACGAAGAACAGTAGCAAAA+TGG - chr2.4:21333951-21333970 None:intergenic 40.0%
GCTAGCATTTCAACGGTTAA+AGG + chr2.4:21333547-21333566 MS.gene026867:CDS 40.0%
GCTGAATCGAAGGAGATAAA+GGG + chr2.4:21333730-21333749 MS.gene026867:CDS 40.0%
TCAATTCCATCAGGGTCAAA+AGG - chr2.4:21333604-21333623 None:intergenic 40.0%
TCAGAAGAAGAACCAGTTGT+TGG + chr2.4:21334582-21334601 MS.gene026867:CDS 40.0%
TCAGAAGCTTCAATTCCATC+AGG - chr2.4:21333613-21333632 None:intergenic 40.0%
TCATCTGGAAGTGACTCATT+TGG - chr2.4:21334171-21334190 None:intergenic 40.0%
! ATTCACAGGAACCTTTTGAG+TGG + chr2.4:21334360-21334379 MS.gene026867:CDS 40.0%
! CTTTTGCTGAAATGGCTAAG+AGG + chr2.4:21334415-21334434 MS.gene026867:CDS 40.0%
!! GATCGATTCGAAACTTTGTG+AGG + chr2.4:21333980-21333999 MS.gene026867:CDS 40.0%
!! TGAGTTGATTCTTCTGCATG+AGG - chr2.4:21334665-21334684 None:intergenic 40.0%
!! TTGCTGTTGTTCCTGGTTTT+AGG + chr2.4:21334607-21334626 MS.gene026867:CDS 40.0%
!!! GTTGTTCCTGGTTTTAGGAT+TGG + chr2.4:21334612-21334631 MS.gene026867:CDS 40.0%
AGTATCGCTTTCTCTGGTGA+AGG - chr2.4:21333706-21333725 None:intergenic 45.0%
CTGTGATTCCAACTTCTTCG+CGG - chr2.4:21333779-21333798 None:intergenic 45.0%
GAAACTCTCCACCACTCAAA+AGG - chr2.4:21334374-21334393 None:intergenic 45.0%
GCATGAGGTAAACTTGACAC+TGG - chr2.4:21334650-21334669 None:intergenic 45.0%
! GGGTGTCATAAAAACCTACG+AGG + chr2.4:21333750-21333769 MS.gene026867:CDS 45.0%
!!! GTTGGTTTTGCTGTTGTTCC+TGG + chr2.4:21334600-21334619 MS.gene026867:CDS 45.0%
CATCGTTTGCGCAATTCTGC+AGG + chr2.4:21334280-21334299 MS.gene026867:CDS 50.0%
CGCGAAGAAGTTGGAATCAC+AGG + chr2.4:21333777-21333796 MS.gene026867:CDS 50.0%
GATACTCGCAGCTGAATCGA+AGG + chr2.4:21333720-21333739 MS.gene026867:CDS 50.0%
TGCTACTGTTCTTCGTCACG+CGG + chr2.4:21333954-21333973 MS.gene026867:CDS 50.0%
! CAGACACCTTTTGACCCTGA+TGG + chr2.4:21333595-21333614 MS.gene026867:CDS 50.0%
!! CACAGGAACCTTTTGAGTGG+TGG + chr2.4:21334363-21334382 MS.gene026867:CDS 50.0%
!! TTGCTTGGTGTCACTGCTGA+AGG - chr2.4:21333325-21333344 None:intergenic 50.0%
CGAGGTTACCGCGAAGAAGT+TGG + chr2.4:21333768-21333787 MS.gene026867:CDS 55.0%
CTTCTTCGCGGTAACCTCGT+AGG - chr2.4:21333767-21333786 None:intergenic 55.0%
! GCTGCGAGTATCGCTTTCTC+TGG - chr2.4:21333712-21333731 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 21333307 21334686 21333307 ID=MS.gene026867
chr2.4 mRNA 21333307 21334686 21333307 ID=MS.gene026867.t1;Parent=MS.gene026867
chr2.4 exon 21333307 21334686 21333307 ID=MS.gene026867.t1.exon1;Parent=MS.gene026867.t1
chr2.4 CDS 21333307 21334686 21333307 ID=cds.MS.gene026867.t1;Parent=MS.gene026867.t1
Gene Sequence

>MS.gene026867

ATGGAATCAATGAAACCTTCAGCAGTGACACCAAGCAAGAAATTAGCTAGGAATTTCGCCAAAGTTCTTCATCTTAGAGCATTTTTGAAGAATGTTACTATATCTGATACAAATCCAAAGGATGAAACAAACATGGAAAAGACTACAATAACTTGGTCTGAATCATTCAAAAAAGTTGATGAAGATGAAGAGATTGAAGAACAAAGAGTTGCAACAGAAGCACTTCTTTCAAAGATTTTTGCTAGCATTTCAACGGTTAAAGGTGCATATGCTGAACTGCAACATTTTCAGACACCTTTTGACCCTGATGGAATTGAAGCTTCTGATAAACTACTAGTTTCTGAGTTGAAGCATTTATCTGAGCTAAAACAATGTTACTTGAAGAAACAATTTGATCCTTCACCAGAGAAAGCGATACTCGCAGCTGAATCGAAGGAGATAAAGGGTGTCATAAAAACCTACGAGGTTACCGCGAAGAAGTTGGAATCACAGGTAAGACTCAAAGATTCTGAGATTATGTTTCTTAAAGAGAAATTAGTGGAAGCTAATAGTCATAACAAGTTGATTGAGAAGAGATTGAATCAAAGTGGAACATTATCAGTACTTGATAATGTTGTTCACATATCAGGATTAAGTCCTAGCCATTTTGCTACTGTTCTTCGTCACGCGGTTAGATCGATTCGAAACTTTGTGAGGTTAATTGTTGATGAAATGAGATCTGCAAAATGGGATATTGATGCTGCTGTTGATGCTATTGAACACAATGTGGTTTATATGATAGAAGATCACAAGTGTTTCACAATTGAATCTTTTGTTTGCAAAGAAATGTTTGATGCATTTCACTTTCCTAATTTCAATCTTCCAAATGAGTCACTTCCAGATGATAGAAAAAATCAACAAAATTGGTTCTTTGAGAAGTTCAATGAGTTGAAATCAACGAAAGCTAAAGACTTTCTTGCTGAGAAACCAAGATCATCGTTTGCGCAATTCTGCAGGAACAAGTATTTGAGACTTGTTCATCCAAAAATGGAGTCATCATTTTTTGGCAACATGATTCACAGGAACCTTTTGAGTGGTGGAGAGTTTCCAAAAAGTGATTTTTTTGCATCTTTTGCTGAAATGGCTAAGAGGGTTTTTCTCTTACATTGTTTAGCCTTTTCTTTTGAAGTTCAAGCTGAAATCTTTCAAGTGGGAAAAGGGTGTAGATTTTCTGATGTGTACATGGAAAGTGTGAATGATGAAATGTTTGTGTTTTCAGACAAGACAGTTGTTGAATCAGAAGAAGAACCAGTTGTTGGTTTTGCTGTTGTTCCTGGTTTTAGGATTGGTAAAACTGTTTTCCAGTGTCAAGTTTACCTCATGCAGAAGAATCAACTCAAG
Protein sequence

>MS.gene026867.t1

MESMKPSAVTPSKKLARNFAKVLHLRAFLKNVTISDTNPKDETNMEKTTITWSESFKKVDEDEEIEEQRVATEALLSKIFASISTVKGAYAELQHFQTPFDPDGIEASDKLLVSELKHLSELKQCYLKKQFDPSPEKAILAAESKEIKGVIKTYEVTAKKLESQVRLKDSEIMFLKEKLVEANSHNKLIEKRLNQSGTLSVLDNVVHISGLSPSHFATVLRHAVRSIRNFVRLIVDEMRSAKWDIDAAVDAIEHNVVYMIEDHKCFTIESFVCKEMFDAFHFPNFNLPNESLPDDRKNQQNWFFEKFNELKSTKAKDFLAEKPRSSFAQFCRNKYLRLVHPKMESSFFGNMIHRNLLSGGEFPKSDFFASFAEMAKRVFLLHCLAFSFEVQAEIFQVGKGCRFSDVYMESVNDEMFVFSDKTVVESEEEPVVGFAVVPGFRIGKTVFQCQVYLMQKNQLK