AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85826

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85826.t1 MTR_7g077620 68.011 372 106 3 1 361 1 370 1.38e-172 486
MS.gene85826.t1 MTR_7g077650 65.526 380 106 10 1 363 1 372 6.37e-155 440
MS.gene85826.t1 MTR_7g077660 62.599 377 118 10 1 363 1 368 3.66e-146 418
MS.gene85826.t1 MTR_1g108740 43.968 373 168 15 1 361 1 344 1.13e-84 260
MS.gene85826.t1 MTR_7g076110 50.169 295 126 6 87 363 22 313 1.80e-82 254
MS.gene85826.t1 MTR_7g076100 58.475 236 86 3 139 363 66 300 2.02e-81 251
MS.gene85826.t1 MTR_7g076100 80.000 55 9 2 1 54 1 54 9.32e-20 89.0
MS.gene85826.t1 MTR_5g038260 40.351 399 181 15 3 363 4 383 1.22e-73 233
MS.gene85826.t1 MTR_1g064570 39.618 419 175 16 3 363 2 400 4.25e-71 227
MS.gene85826.t1 MTR_5g038230 40.310 387 164 15 5 361 4 353 1.75e-69 222
MS.gene85826.t1 MTR_5g082770 45.246 305 134 9 5 296 4 288 6.67e-67 213
MS.gene85826.t1 MTR_1g016150 45.217 230 108 7 1 216 1 226 4.12e-51 171
MS.gene85826.t1 MTR_5g082780 38.326 227 118 7 115 328 1 218 9.86e-31 117
MS.gene85826.t1 MTR_7g076130 51.538 130 48 5 169 284 25 153 5.93e-27 104
MS.gene85826.t1 MTR_1g108750 43.949 157 51 6 5 160 4 124 3.93e-21 88.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 74 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTTCCATCCTTCACATTA+TGG 0.195674 6.4:+14621503 None:intergenic
CAAACTCTACGTTTACAAAT+TGG 0.205980 6.4:-14621707 MS.gene85826:CDS
TTTCAACATACTTGAGAGTT+TGG 0.271304 6.4:-14621653 MS.gene85826:CDS
CAACCGGATGTCACATCTTT+GGG 0.283463 6.4:-14621452 MS.gene85826:CDS
GTTGAACCCGAAGCTTAAAA+TGG 0.296182 6.4:+14621876 None:intergenic
TCAACCGGATGTCACATCTT+TGG 0.300744 6.4:-14621453 MS.gene85826:CDS
TAATTACTCGGGCTTGTAAT+CGG 0.322229 6.4:+14622045 None:intergenic
GACATCCGGTTGAAGGAAAT+TGG 0.322776 6.4:+14621463 None:intergenic
TGGATTCGTGTAAACAGATA+TGG 0.324446 6.4:-14621961 MS.gene85826:CDS
CAATGAAATGACGGTGTGTT+TGG 0.335412 6.4:-14622202 MS.gene85826:CDS
AAGAACACATAGATCATGTT+AGG 0.348741 6.4:-14622431 MS.gene85826:CDS
AAACAGATTCGCTAGTGTTA+TGG 0.359880 6.4:+14622137 None:intergenic
ACACACCGTCATTTCATTGA+TGG 0.365745 6.4:+14622206 None:intergenic
AGAAGGTCTACCTCTTAGTT+TGG 0.383875 6.4:-14622469 MS.gene85826:CDS
CTACGTTTACAAATTGGAAC+TGG 0.389715 6.4:-14621701 MS.gene85826:CDS
CTTTACCAATTTCCTTCAAC+CGG 0.393860 6.4:-14621468 MS.gene85826:CDS
TTTCCAGAACAATATCATTA+CGG 0.401041 6.4:-14621814 MS.gene85826:CDS
CCATGGTTGGCTTGCATTGG+TGG 0.402911 6.4:-14622172 MS.gene85826:CDS
TTGGAGAGGTGGCAGACTAA+TGG 0.403671 6.4:+14622098 None:intergenic
GGGTTCTACCACAATTTCAA+TGG 0.406178 6.4:-14621432 MS.gene85826:CDS
AGTACTAGCCATCTCATAAC+AGG 0.421090 6.4:+14621846 None:intergenic
AGGCAATGAGGAAGGTAGAT+TGG 0.421191 6.4:-14622500 None:intergenic
AAAGAGCAAGTCAATCATCT+TGG 0.426179 6.4:-14621981 MS.gene85826:CDS
TGGAGAGGTGGCAGACTAAT+GGG 0.429349 6.4:+14622099 None:intergenic
CCTCCGTAATGATATTGTTC+TGG 0.431440 6.4:+14621811 None:intergenic
GTAGATTGGGCAAATTTAGA+AGG 0.435773 6.4:-14622486 MS.gene85826:CDS
TTGTTTCTCCAAGTTTGAAA+AGG 0.460734 6.4:-14621578 MS.gene85826:CDS
AATTACTCGGGCTTGTAATC+GGG 0.467266 6.4:+14622046 None:intergenic
AATGAAATGACGGTGTGTTT+GGG 0.468609 6.4:-14622201 MS.gene85826:CDS
GGCAATGAGGAAGGTAGATT+GGG 0.471328 6.4:-14622499 None:intergenic
TAGTTTGGTTCTTGAGAAGT+TGG 0.473111 6.4:-14622454 MS.gene85826:CDS
GGTTCTACCACAATTTCAAT+GGG 0.480142 6.4:-14621431 MS.gene85826:CDS
TAGCCATGGTTGGCTTGCAT+TGG 0.484269 6.4:-14622175 MS.gene85826:CDS
AATCATTGACCGGAGACATA+TGG 0.484616 6.4:-14621771 MS.gene85826:CDS
ACCTCTCCAATCTGTTTACA+AGG 0.490029 6.4:-14622085 MS.gene85826:CDS
TTCTCAAGAACCAAACTAAG+AGG 0.491952 6.4:+14622459 None:intergenic
CTGATATTTGCTGTTGGCAA+CGG 0.495311 6.4:-14621904 MS.gene85826:CDS
TCATTTCATTGATGGAAGGA+TGG 0.502472 6.4:+14622214 None:intergenic
AAGATGTGACATCCGGTTGA+AGG 0.515408 6.4:+14621456 None:intergenic
CAAATCCATAATGTGAAGGA+TGG 0.524725 6.4:-14621508 MS.gene85826:CDS
TTTCACCATCCATATGTCTC+CGG 0.527974 6.4:+14621762 None:intergenic
GATCAATCCCATTGAAATTG+TGG 0.531759 6.4:+14621424 None:intergenic
GTGTGTTTGGGCGTTAGCCA+TGG 0.536708 6.4:-14622189 MS.gene85826:CDS
AAAGGTCTGATATTTGCTGT+TGG 0.547450 6.4:-14621910 MS.gene85826:CDS
TACAAGCCCGAGTAATTATG+TGG 0.548444 6.4:-14622040 MS.gene85826:CDS
CATTTCATTGATGGAAGGAT+GGG 0.554300 6.4:+14622215 None:intergenic
GTTTGGGCGTTAGCCATGGT+TGG 0.554659 6.4:-14622185 MS.gene85826:CDS
AGGTAACCTTGTAAACAGAT+TGG 0.555212 6.4:+14622079 None:intergenic
GCTGCAACCACATAATTACT+CGG 0.560384 6.4:+14622033 None:intergenic
GAACCCAAAGATGTGACATC+CGG 0.561035 6.4:+14621449 None:intergenic
TTCGTGTGGTGTGCAAGACT+TGG 0.561436 6.4:-14622407 MS.gene85826:CDS
CAATTCTGCCTGTTATGAGA+TGG 0.570742 6.4:-14621854 MS.gene85826:CDS
TTCAAACTTGGAGAAACAAG+AGG 0.574529 6.4:+14621582 None:intergenic
AGAGGATCATCAACATAGGA+TGG 0.580233 6.4:+14622331 None:intergenic
CAGAACAATATCATTACGGA+GGG 0.584738 6.4:-14621810 MS.gene85826:CDS
TATGAGAATTATTGTATGAG+AGG 0.586159 6.4:+14622313 None:intergenic
TCCTTCCATCAATGAAATGA+CGG 0.587156 6.4:-14622211 MS.gene85826:CDS
ATTATGATAGGCAATGAGGA+AGG 0.591409 6.4:-14622508 None:intergenic
ACCGTCATTTCATTGATGGA+AGG 0.592100 6.4:+14622210 None:intergenic
TTGTAAACAGATTGGAGAGG+TGG 0.610040 6.4:+14622087 None:intergenic
GTTACAAATCCATAATGTGA+AGG 0.610111 6.4:-14621512 MS.gene85826:CDS
CTGCAACCACATAATTACTC+GGG 0.612955 6.4:+14622034 None:intergenic
AACTTGGAGAAACAAGAGGC+TGG 0.613015 6.4:+14621586 None:intergenic
TATGAGAGGATCATCAACAT+AGG 0.615056 6.4:+14622327 None:intergenic
CCAGAACAATATCATTACGG+AGG 0.624405 6.4:-14621811 MS.gene85826:CDS
AGTTTGCATAAATGCTTGCG+AGG 0.629904 6.4:+14621724 None:intergenic
AGATCATGTTAGGTTTCGTG+TGG 0.631367 6.4:-14622421 MS.gene85826:CDS
AAATTGGTAAAGATTGACTA+CGG 0.637052 6.4:+14621479 None:intergenic
TGTAATCGGGTCATCAGACA+AGG 0.645501 6.4:+14622059 None:intergenic
TTGGAACTGGACACTATGAG+TGG 0.646325 6.4:-14621688 MS.gene85826:CDS
CCACCAATGCAAGCCAACCA+TGG 0.665097 6.4:+14622172 None:intergenic
ATTGACCGGAGACATATGGA+TGG 0.696827 6.4:-14621767 MS.gene85826:CDS
GTTGCAGCGATTTACAACTG+TGG 0.706416 6.4:-14622018 MS.gene85826:CDS
ACCTTGTAAACAGATTGGAG+AGG 0.742777 6.4:+14622084 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCAATTTATTTTATTTATGA+TGG - chr6.4:14622368-14622387 MS.gene85826:CDS 10.0%
!! ACCATAAAAATCATCAATTT+AGG - chr6.4:14621559-14621578 MS.gene85826:CDS 20.0%
!!! AACATTTTATTTGTTGGAAT+CGG - chr6.4:14622296-14622315 MS.gene85826:CDS 20.0%
!!! ACTGATGTTGTATTTTATAA+AGG - chr6.4:14621993-14622012 MS.gene85826:CDS 20.0%
!!! TCCTAAATTGATGATTTTTA+TGG + chr6.4:14621563-14621582 None:intergenic 20.0%
! AAATTGGTAAAGATTGACTA+CGG + chr6.4:14622445-14622464 None:intergenic 25.0%
! TATGAGAATTATTGTATGAG+AGG + chr6.4:14621611-14621630 None:intergenic 25.0%
! TTTCCAGAACAATATCATTA+CGG - chr6.4:14622107-14622126 MS.gene85826:CDS 25.0%
!! AATTGAATCCTTTTCAAACT+TGG + chr6.4:14622354-14622373 None:intergenic 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr6.4:14622140-14622159 MS.gene85826:CDS 25.0%
!!! GAAAGCAACATTTTATTTGT+TGG - chr6.4:14622290-14622309 MS.gene85826:CDS 25.0%
!!! TATTTTATTTATGATGGCGA+CGG - chr6.4:14622374-14622393 MS.gene85826:CDS 25.0%
AAGAACACATAGATCATGTT+AGG - chr6.4:14621490-14621509 MS.gene85826:CDS 30.0%
CAAACTCTACGTTTACAAAT+TGG - chr6.4:14622214-14622233 MS.gene85826:CDS 30.0%
GTTACAAATCCATAATGTGA+AGG - chr6.4:14622409-14622428 MS.gene85826:CDS 30.0%
TTTCAACATACTTGAGAGTT+TGG - chr6.4:14622268-14622287 MS.gene85826:CDS 30.0%
! TTGTTTCTCCAAGTTTGAAA+AGG - chr6.4:14622343-14622362 MS.gene85826:CDS 30.0%
AAACAGATTCGCTAGTGTTA+TGG + chr6.4:14621787-14621806 None:intergenic 35.0%
AAAGAGCAAGTCAATCATCT+TGG - chr6.4:14621940-14621959 MS.gene85826:CDS 35.0%
AACTTCCATCCTTCACATTA+TGG + chr6.4:14622421-14622440 None:intergenic 35.0%
AATGAAATGACGGTGTGTTT+GGG - chr6.4:14621720-14621739 MS.gene85826:CDS 35.0%
AGGTAACCTTGTAAACAGAT+TGG + chr6.4:14621845-14621864 None:intergenic 35.0%
CAAATCCATAATGTGAAGGA+TGG - chr6.4:14622413-14622432 MS.gene85826:CDS 35.0%
CAGAACAATATCATTACGGA+GGG - chr6.4:14622111-14622130 MS.gene85826:CDS 35.0%
CATTTCATTGATGGAAGGAT+GGG + chr6.4:14621709-14621728 None:intergenic 35.0%
CTACGTTTACAAATTGGAAC+TGG - chr6.4:14622220-14622239 MS.gene85826:CDS 35.0%
CTTTACCAATTTCCTTCAAC+CGG - chr6.4:14622453-14622472 MS.gene85826:CDS 35.0%
GGTTCTACCACAATTTCAAT+GGG - chr6.4:14622490-14622509 MS.gene85826:CDS 35.0%
GTAGATTGGGCAAATTTAGA+AGG - chr6.4:14621435-14621454 MS.gene85826:CDS 35.0%
TAATTACTCGGGCTTGTAAT+CGG + chr6.4:14621879-14621898 None:intergenic 35.0%
TATGAGAGGATCATCAACAT+AGG + chr6.4:14621597-14621616 None:intergenic 35.0%
TCATTTCATTGATGGAAGGA+TGG + chr6.4:14621710-14621729 None:intergenic 35.0%
TCCTTCCATCAATGAAATGA+CGG - chr6.4:14621710-14621729 MS.gene85826:CDS 35.0%
TGGATTCGTGTAAACAGATA+TGG - chr6.4:14621960-14621979 MS.gene85826:CDS 35.0%
TTCAAACTTGGAGAAACAAG+AGG + chr6.4:14622342-14622361 None:intergenic 35.0%
TTCTCAAGAACCAAACTAAG+AGG + chr6.4:14621465-14621484 None:intergenic 35.0%
!! AAAGGTCTGATATTTGCTGT+TGG - chr6.4:14622011-14622030 MS.gene85826:CDS 35.0%
!! TAGTTTGGTTCTTGAGAAGT+TGG - chr6.4:14621467-14621486 MS.gene85826:CDS 35.0%
AATCATTGACCGGAGACATA+TGG - chr6.4:14622150-14622169 MS.gene85826:CDS 40.0%
AATTACTCGGGCTTGTAATC+GGG + chr6.4:14621878-14621897 None:intergenic 40.0%
ACACACCGTCATTTCATTGA+TGG + chr6.4:14621718-14621737 None:intergenic 40.0%
ACCGTCATTTCATTGATGGA+AGG + chr6.4:14621714-14621733 None:intergenic 40.0%
ACCTCTCCAATCTGTTTACA+AGG - chr6.4:14621836-14621855 MS.gene85826:CDS 40.0%
ACCTTGTAAACAGATTGGAG+AGG + chr6.4:14621840-14621859 None:intergenic 40.0%
AGAAGGTCTACCTCTTAGTT+TGG - chr6.4:14621452-14621471 MS.gene85826:CDS 40.0%
AGAGGATCATCAACATAGGA+TGG + chr6.4:14621593-14621612 None:intergenic 40.0%
AGATCATGTTAGGTTTCGTG+TGG - chr6.4:14621500-14621519 MS.gene85826:CDS 40.0%
AGTACTAGCCATCTCATAAC+AGG + chr6.4:14622078-14622097 None:intergenic 40.0%
AGTTTGCATAAATGCTTGCG+AGG + chr6.4:14622200-14622219 None:intergenic 40.0%
CAATGAAATGACGGTGTGTT+TGG - chr6.4:14621719-14621738 MS.gene85826:CDS 40.0%
CAATTCTGCCTGTTATGAGA+TGG - chr6.4:14622067-14622086 MS.gene85826:CDS 40.0%
CCAGAACAATATCATTACGG+AGG - chr6.4:14622110-14622129 MS.gene85826:CDS 40.0%
CCTCCGTAATGATATTGTTC+TGG + chr6.4:14622113-14622132 None:intergenic 40.0%
CTGCAACCACATAATTACTC+GGG + chr6.4:14621890-14621909 None:intergenic 40.0%
GCTGCAACCACATAATTACT+CGG + chr6.4:14621891-14621910 None:intergenic 40.0%
GGGTTCTACCACAATTTCAA+TGG - chr6.4:14622489-14622508 MS.gene85826:CDS 40.0%
GTTGAACCCGAAGCTTAAAA+TGG + chr6.4:14622048-14622067 None:intergenic 40.0%
TACAAGCCCGAGTAATTATG+TGG - chr6.4:14621881-14621900 MS.gene85826:CDS 40.0%
TTGTAAACAGATTGGAGAGG+TGG + chr6.4:14621837-14621856 None:intergenic 40.0%
TTTCACCATCCATATGTCTC+CGG + chr6.4:14622162-14622181 None:intergenic 40.0%
! GAGACACCATTTTAAGCTTC+GGG - chr6.4:14622039-14622058 MS.gene85826:CDS 40.0%
! GGAGACACCATTTTAAGCTT+CGG - chr6.4:14622038-14622057 MS.gene85826:CDS 40.0%
!! CTGATATTTGCTGTTGGCAA+CGG - chr6.4:14622017-14622036 MS.gene85826:CDS 40.0%
AACTTGGAGAAACAAGAGGC+TGG + chr6.4:14622338-14622357 None:intergenic 45.0%
AAGATGTGACATCCGGTTGA+AGG + chr6.4:14622468-14622487 None:intergenic 45.0%
ATTGACCGGAGACATATGGA+TGG - chr6.4:14622154-14622173 MS.gene85826:CDS 45.0%
CAACCGGATGTCACATCTTT+GGG - chr6.4:14622469-14622488 MS.gene85826:CDS 45.0%
GAACCCAAAGATGTGACATC+CGG + chr6.4:14622475-14622494 None:intergenic 45.0%
GACATCCGGTTGAAGGAAAT+TGG + chr6.4:14622461-14622480 None:intergenic 45.0%
GTTGCAGCGATTTACAACTG+TGG - chr6.4:14621903-14621922 MS.gene85826:CDS 45.0%
TCAACCGGATGTCACATCTT+TGG - chr6.4:14622468-14622487 MS.gene85826:CDS 45.0%
TGTAATCGGGTCATCAGACA+AGG + chr6.4:14621865-14621884 None:intergenic 45.0%
TTGGAACTGGACACTATGAG+TGG - chr6.4:14622233-14622252 MS.gene85826:CDS 45.0%
TGGAGAGGTGGCAGACTAAT+GGG + chr6.4:14621825-14621844 None:intergenic 50.0%
TTCGTGTGGTGTGCAAGACT+TGG - chr6.4:14621514-14621533 MS.gene85826:CDS 50.0%
TTGGAGAGGTGGCAGACTAA+TGG + chr6.4:14621826-14621845 None:intergenic 50.0%
!! TAGCCATGGTTGGCTTGCAT+TGG - chr6.4:14621746-14621765 MS.gene85826:CDS 50.0%
CCACCAATGCAAGCCAACCA+TGG + chr6.4:14621752-14621771 None:intergenic 55.0%
GTGTGTTTGGGCGTTAGCCA+TGG - chr6.4:14621732-14621751 MS.gene85826:CDS 55.0%
GTTTGGGCGTTAGCCATGGT+TGG - chr6.4:14621736-14621755 MS.gene85826:CDS 55.0%
!! CCATGGTTGGCTTGCATTGG+TGG - chr6.4:14621749-14621768 MS.gene85826:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 14621426 14622517 14621426 ID=MS.gene85826
chr6.4 mRNA 14621426 14622517 14621426 ID=MS.gene85826.t1;Parent=MS.gene85826
chr6.4 exon 14621426 14622517 14621426 ID=MS.gene85826.t1.exon1;Parent=MS.gene85826.t1
chr6.4 CDS 14621426 14622517 14621426 ID=cds.MS.gene85826.t1;Parent=MS.gene85826.t1
Gene Sequence

>MS.gene85826

ATGAGGAAGGTAGATTGGGCAAATTTAGAAGGTCTACCTCTTAGTTTGGTTCTTGAGAAGTTGGAAGAACACATAGATCATGTTAGGTTTCGTGTGGTGTGCAAGACTTGGCTATCAGTTGCAAATCATCTTAACCATAAAAATCATCAATTTAGGATTAATGTCCATCCTATGTTGATGATCCTCTCATACAATAATTCTCATATACGTACAATATCACAGACGAAGAAGAGATCTCTGTATAGTATTCTTAGTGAGAAAGAGTACGCTATTCAATTATCCCATCCTTCCATCAATGAAATGACGGTGTGTTTGGGCGTTAGCCATGGTTGGCTTGCATTGGTGGATGACAACAAAGCCATAACACTAGCGAATCTGTTTAAGTATAGTGTAGCTCCCATTAGTCTGCCACCTCTCCAATCTGTTTACAAGGTTACCTTGTCTGATGACCCGATTACAAGCCCGAGTAATTATGTGGTTGCAGCGATTTACAACTGTGGTTCTCTCGCTTTCAAAAGAGCAAGTCAATCATCTTGGATTCGTGTAAACAGATATGGATTTTATATCACTGATGTTGTATTTTATAAAGGTCTGATATTTGCTGTTGGCAACGGAGACACCATTTTAAGCTTCGGGTTCAACAATTCTGCCTGTTATGAGATGGCTAGTACTCATAATTTTTTTCCAGAACAATATCATTACGGAGGGCATGCTTATTTTGTGAAATCATTGACCGGAGACATATGGATGGTGAAAAGATGTTTAATTGATCCTCGCAAGCATTTATGCAAACTCTACGTTTACAAATTGGAACTGGACACTATGAGTGGAAAAGTTAAACATTTCAACATACTTGAGAGTTTGGAAAGCAACATTTTATTTGTTGGAATCGGAGATTCAATTTCTGTGCCAGCCTCTTGTTTCTCCAAGTTTGAAAAGGATTCAATTTATTTTATTTATGATGGCGACGGAGATGATTTAGAGTTACAAATCCATAATGTGAAGGATGGAAGTTTCCGTAGTCAATCTTTACCAATTTCCTTCAACCGGATGTCACATCTTTGGGTTCTACCACAATTTCAATGGGATTGA
Protein sequence

>MS.gene85826.t1

MRKVDWANLEGLPLSLVLEKLEEHIDHVRFRVVCKTWLSVANHLNHKNHQFRINVHPMLMILSYNNSHIRTISQTKKRSLYSILSEKEYAIQLSHPSINEMTVCLGVSHGWLALVDDNKAITLANLFKYSVAPISLPPLQSVYKVTLSDDPITSPSNYVVAAIYNCGSLAFKRASQSSWIRVNRYGFYITDVVFYKGLIFAVGNGDTILSFGFNNSACYEMASTHNFFPEQYHYGGHAYFVKSLTGDIWMVKRCLIDPRKHLCKLYVYKLELDTMSGKVKHFNILESLESNILFVGIGDSISVPASCFSKFEKDSIYFIYDGDGDDLELQIHNVKDGSFRSQSLPISFNRMSHLWVLPQFQWD