AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27754

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27754.t1 MTR_7g077650 78.610 374 71 4 1 367 1 372 0.0 576
MS.gene27754.t1 MTR_7g077660 72.654 373 91 6 1 367 1 368 0.0 521
MS.gene27754.t1 MTR_7g077620 66.935 372 114 4 1 365 1 370 2.15e-173 488
MS.gene27754.t1 MTR_7g076110 53.691 298 116 8 86 367 22 313 2.65e-97 292
MS.gene27754.t1 MTR_1g108740 45.119 379 159 15 1 365 1 344 5.40e-89 271
MS.gene27754.t1 MTR_7g076100 52.688 279 120 6 97 367 26 300 6.08e-87 265
MS.gene27754.t1 MTR_7g076100 70.370 54 15 1 1 53 1 54 4.10e-17 81.3
MS.gene27754.t1 MTR_5g038260 41.353 399 181 14 3 367 4 383 1.49e-77 244
MS.gene27754.t1 MTR_5g038230 41.509 371 140 13 5 343 4 329 9.37e-72 228
MS.gene27754.t1 MTR_5g082770 45.048 313 129 10 5 303 4 287 5.87e-70 221
MS.gene27754.t1 MTR_1g064570 39.480 423 174 19 3 367 2 400 5.21e-69 222
MS.gene27754.t1 MTR_1g016150 48.958 192 93 4 1 188 1 191 1.35e-49 167
MS.gene27754.t1 MTR_7g076130 56.098 123 50 2 170 289 27 148 4.11e-38 134
MS.gene27754.t1 MTR_5g082780 39.224 232 107 10 114 331 1 212 3.77e-34 126
MS.gene27754.t1 MTR_1g108750 41.667 156 55 6 5 159 4 124 2.52e-19 83.2
MS.gene27754.t1 MTR_3g114970 23.387 372 213 13 4 344 3 333 2.49e-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 70 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTATATTGTTAATGATTT+AGG 0.039594 7.3:-29139677 MS.gene27754:CDS
AAAGACCAAGCCAATCATTT+TGG 0.213196 7.3:-29140138 MS.gene27754:CDS
TTTATATTGTTAATGATTTA+GGG 0.247410 7.3:-29139676 MS.gene27754:CDS
ACAAAATTTCATTGTATTGA+TGG 0.259868 7.3:+29140363 None:intergenic
CCATGATAACGACGTAGTTT+TGG 0.306817 7.3:+29139935 None:intergenic
AATGACCAAACTTGAGAGTT+TGG 0.311921 7.3:-29139783 MS.gene27754:CDS
AATTACAACTTTCCTACAAC+TGG 0.317321 7.3:-29139610 MS.gene27754:CDS
GTCTTCCAAACTCTCAAGTT+TGG 0.322441 7.3:+29139778 None:intergenic
GTTGCAGCAATTTACAAGTT+TGG 0.322860 7.3:-29140175 MS.gene27754:CDS
GGAGGTACACTATACTTAAA+AGG 0.322941 7.3:+29140277 None:intergenic
TTGTAGGAAAGTTGTAATTT+TGG 0.337038 7.3:+29139614 None:intergenic
AGAAGAACTTCCTCTTAGTT+TGG 0.345468 7.3:-29140623 MS.gene27754:CDS
AAGTACAAACAGACTATGTT+AGG 0.349616 7.3:-29140585 MS.gene27754:CDS
GAAGGATGGGACAATTGAAT+AGG 0.359686 7.3:+29140385 None:intergenic
GGGTTCTACCACAACTTCAT+TGG 0.363398 7.3:-29139574 MS.gene27754:CDS
TTCGAGAGGTGGCAGACTAA+TGG 0.384467 7.3:+29140255 None:intergenic
CCATGGTTGGCTTGCATTGG+TGG 0.397590 7.3:-29140329 MS.gene27754:CDS
TAGAAATGAGGAAGGTTGAT+TGG 0.411376 7.3:-29140654 None:intergenic
AGGAGGATTGTTTAGCTTGA+AGG 0.413972 7.3:+29140024 None:intergenic
AGCCTCTTGTTTCTCCAAGT+TGG 0.414433 7.3:-29139711 MS.gene27754:CDS
AAAACGTTGCATCCAGTTGT+AGG 0.414803 7.3:+29139598 None:intergenic
AAAAGGATTCACTAGAGTTA+TGG 0.416187 7.3:+29140294 None:intergenic
AATCATTGACCGGAGAAATA+TGG 0.417114 7.3:-29139895 MS.gene27754:CDS
TAGGGTACTCTTTCTTACTT+AGG 0.417568 7.3:+29140404 None:intergenic
TTGTTTCTCCAAGTTGGAAA+AGG 0.437802 7.3:-29139705 MS.gene27754:CDS
TCGAGAGGTGGCAGACTAAT+GGG 0.438780 7.3:+29140256 None:intergenic
ACTAGCCATCTTCTCATAGT+AGG 0.443005 7.3:+29139973 None:intergenic
GGTTCTACCACAACTTCATT+GGG 0.443765 7.3:-29139573 MS.gene27754:CDS
TAGCCATGGTTGGCTTGCAT+TGG 0.461010 7.3:-29140332 MS.gene27754:CDS
CAAACAGACTATGTTAGGTT+TGG 0.468455 7.3:-29140580 MS.gene27754:CDS
TTGGTGTTGTGTGTAAGAAT+TGG 0.484526 7.3:-29140561 MS.gene27754:CDS
TAGTTTGGTTCTTGAAAAGT+TGG 0.485672 7.3:-29140608 MS.gene27754:CDS
AGAAATGAGGAAGGTTGATT+GGG 0.494917 7.3:-29140653 None:intergenic
TCATTGTATTGATGGAAGGA+TGG 0.495017 7.3:+29140371 None:intergenic
AAGGATGGGACAATTGAATA+GGG 0.496366 7.3:+29140386 None:intergenic
CATTGTATTGATGGAAGGAT+GGG 0.497806 7.3:+29140372 None:intergenic
GTTTGGGCTGTAGCCATGGT+TGG 0.500900 7.3:-29140342 MS.gene27754:CDS
CTACGCGAATCCAAAATGAT+TGG 0.502017 7.3:+29140128 None:intergenic
TAATCACTTGGATTTGTCAC+GGG 0.505018 7.3:+29140202 None:intergenic
CCAAAACTACGTCGTTATCA+TGG 0.509352 7.3:-29139935 MS.gene27754:CDS
TCTCATCAACCATATTTCTC+CGG 0.510997 7.3:+29139886 None:intergenic
CGAATCCAAAATGATTGGCT+TGG 0.520142 7.3:+29140133 None:intergenic
AATTTCATTGTATTGATGGA+AGG 0.524624 7.3:+29140367 None:intergenic
CCAGTTCCAATTTGAAAACG+TGG 0.529346 7.3:+29139831 None:intergenic
CAGTTCCAATTTGAAAACGT+GGG 0.532083 7.3:+29139832 None:intergenic
ACCTCTCGAATCTGTTTCCA+AGG 0.534304 7.3:-29140242 MS.gene27754:CDS
GAGATCTTTAACGTCAAGGA+TGG 0.538671 7.3:-29139650 MS.gene27754:CDS
GTCAGCAGACAAGGTAACCT+TGG 0.544724 7.3:+29140225 None:intergenic
GTTAGAGATCTTTAACGTCA+AGG 0.568886 7.3:-29139654 MS.gene27754:CDS
TGTCACGGGGTCAGCAGACA+AGG 0.572198 7.3:+29140216 None:intergenic
TTGGAACTGGATGCCGAGAG+TGG 0.572302 7.3:-29139818 MS.gene27754:CDS
ATGAGAAGATGCTTAATCGA+CGG 0.575214 7.3:-29139869 MS.gene27754:CDS
GTGAGGATCATCAGCATAGG+TGG 0.578217 7.3:+29140487 None:intergenic
GGATCATTTGAGTCATGAGA+AGG 0.579857 7.3:+29140004 None:intergenic
ATAATCACTTGGATTTGTCA+CGG 0.582648 7.3:+29140201 None:intergenic
GTTTAGCTTGAAGGATACAA+TGG 0.589118 7.3:+29140033 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.591162 7.3:+29140190 None:intergenic
TTTGTGAGGATCATCAGCAT+AGG 0.591672 7.3:+29140484 None:intergenic
TTCCAACTTGGAGAAACAAG+AGG 0.597328 7.3:+29139709 None:intergenic
TCATTTGAGTCATGAGAAGG+AGG 0.598538 7.3:+29140007 None:intergenic
CTCTTACCTAGAAATGAGGA+AGG 0.603852 7.3:-29140662 None:intergenic
GACAAATCCAAGTGATTATG+TGG 0.609021 7.3:-29140197 MS.gene27754:CDS
GCTCAATCCCAATGAAGTTG+TGG 0.625686 7.3:+29139566 None:intergenic
TTGGAAACAGATTCGAGAGG+TGG 0.643460 7.3:+29140244 None:intergenic
AGTTCCAATTTGAAAACGTG+GGG 0.649411 7.3:+29139833 None:intergenic
AATCACTTGGATTTGTCACG+GGG 0.664381 7.3:+29140203 None:intergenic
CCACCAATGCAAGCCAACCA+TGG 0.665097 7.3:+29140329 None:intergenic
TGTGATATTGTATGTATACG+CGG 0.730158 7.3:+29140454 None:intergenic
AGAGGTGGCAGACTAATGGG+AGG 0.733529 7.3:+29140259 None:intergenic
ACCTTGGAAACAGATTCGAG+AGG 0.760909 7.3:+29140241 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATATTGTTAATGATTT+AGG - chr7.3:29140540-29140559 MS.gene27754:CDS 10.0%
!! TTTATATTGTTAATGATTTA+GGG - chr7.3:29140541-29140560 MS.gene27754:CDS 10.0%
!!! AATACAATGAAATTTTGTTT+GGG - chr7.3:29139859-29139878 MS.gene27754:CDS 15.0%
!! ACAAAATTTCATTGTATTGA+TGG + chr7.3:29139857-29139876 None:intergenic 20.0%
!! ACCATAAAAATCATCAATTT+AGG - chr7.3:29139698-29139717 MS.gene27754:CDS 20.0%
!!! ACGAATATTGTGTTTTATAA+AGG - chr7.3:29140132-29140151 MS.gene27754:CDS 20.0%
!!! CAATACAATGAAATTTTGTT+TGG - chr7.3:29139858-29139877 MS.gene27754:CDS 20.0%
!!! TCCTAAATTGATGATTTTTA+TGG + chr7.3:29139702-29139721 None:intergenic 20.0%
! TTCTCATAGTAGGAAAAATT+AGG + chr7.3:29140237-29140256 None:intergenic 25.0%
!! AATTTCATTGTATTGATGGA+AGG + chr7.3:29139853-29139872 None:intergenic 25.0%
!! TATTGTGTTTTATAAAGGCA+TGG - chr7.3:29140137-29140156 MS.gene27754:CDS 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr7.3:29140312-29140331 MS.gene27754:CDS 25.0%
!! TTGTAGGAAAGTTGTAATTT+TGG + chr7.3:29140606-29140625 None:intergenic 25.0%
!!! ATTTTATTTGTCAGAAGTGT+TGG - chr7.3:29140465-29140484 MS.gene27754:CDS 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.3:29139926-29139945 None:intergenic 30.0%
AAGTACAAACAGACTATGTT+AGG - chr7.3:29139632-29139651 MS.gene27754:CDS 30.0%
AATTACAACTTTCCTACAAC+TGG - chr7.3:29140607-29140626 MS.gene27754:CDS 30.0%
ATAATCACTTGGATTTGTCA+CGG + chr7.3:29140019-29140038 None:intergenic 30.0%
TGTGATATTGTATGTATACG+CGG + chr7.3:29139766-29139785 None:intergenic 30.0%
! AATTGAATCCTTTTCCAACT+TGG + chr7.3:29140523-29140542 None:intergenic 30.0%
! TTTTTCCTACTATGAGAAGA+TGG - chr7.3:29140239-29140258 MS.gene27754:CDS 30.0%
!! TAGTTTGGTTCTTGAAAAGT+TGG - chr7.3:29139609-29139628 MS.gene27754:CDS 30.0%
!! TTTTCAAGAACCAAACTAAG+AGG + chr7.3:29139607-29139626 None:intergenic 30.0%
!!! CGTAGTTTTGGAATCATATA+TGG + chr7.3:29140273-29140292 None:intergenic 30.0%
AAGGATGGGACAATTGAATA+GGG + chr7.3:29139834-29139853 None:intergenic 35.0%
AATCATTGACCGGAGAAATA+TGG - chr7.3:29140322-29140341 MS.gene27754:CDS 35.0%
AATGACCAAACTTGAGAGTT+TGG - chr7.3:29140434-29140453 MS.gene27754:CDS 35.0%
AGAAGAACTTCCTCTTAGTT+TGG - chr7.3:29139594-29139613 MS.gene27754:CDS 35.0%
AGTTCCAATTTGAAAACGTG+GGG + chr7.3:29140387-29140406 None:intergenic 35.0%
ATGAGAAGATGCTTAATCGA+CGG - chr7.3:29140348-29140367 MS.gene27754:CDS 35.0%
CAAACAGACTATGTTAGGTT+TGG - chr7.3:29139637-29139656 MS.gene27754:CDS 35.0%
CAGTTCCAATTTGAAAACGT+GGG + chr7.3:29140388-29140407 None:intergenic 35.0%
GACAAATCCAAGTGATTATG+TGG - chr7.3:29140020-29140039 MS.gene27754:CDS 35.0%
GTTAGAGATCTTTAACGTCA+AGG - chr7.3:29140563-29140582 MS.gene27754:CDS 35.0%
GTTGCAGCAATTTACAAGTT+TGG - chr7.3:29140042-29140061 MS.gene27754:CDS 35.0%
TAATCACTTGGATTTGTCAC+GGG + chr7.3:29140018-29140037 None:intergenic 35.0%
TCTCATCAACCATATTTCTC+CGG + chr7.3:29140334-29140353 None:intergenic 35.0%
! AAAGACCAAGCCAATCATTT+TGG - chr7.3:29140079-29140098 MS.gene27754:CDS 35.0%
! CATTGTATTGATGGAAGGAT+GGG + chr7.3:29139848-29139867 None:intergenic 35.0%
! GGAGGTACACTATACTTAAA+AGG + chr7.3:29139943-29139962 None:intergenic 35.0%
! TAGGGTACTCTTTCTTACTT+AGG + chr7.3:29139816-29139835 None:intergenic 35.0%
! TCATTGTATTGATGGAAGGA+TGG + chr7.3:29139849-29139868 None:intergenic 35.0%
! TTGTTTCTCCAAGTTGGAAA+AGG - chr7.3:29140512-29140531 MS.gene27754:CDS 35.0%
!! GTTTAGCTTGAAGGATACAA+TGG + chr7.3:29140187-29140206 None:intergenic 35.0%
!! TTGGTGTTGTGTGTAAGAAT+TGG - chr7.3:29139656-29139675 MS.gene27754:CDS 35.0%
!! TTGTTCAAGTTTTCCACTCT+CGG + chr7.3:29140415-29140434 None:intergenic 35.0%
AAAACGTTGCATCCAGTTGT+AGG + chr7.3:29140622-29140641 None:intergenic 40.0%
AATCACTTGGATTTGTCACG+GGG + chr7.3:29140017-29140036 None:intergenic 40.0%
ACTAGCCATCTTCTCATAGT+AGG + chr7.3:29140247-29140266 None:intergenic 40.0%
CCAAAACTACGTCGTTATCA+TGG - chr7.3:29140282-29140301 MS.gene27754:CDS 40.0%
CCAGTTCCAATTTGAAAACG+TGG + chr7.3:29140389-29140408 None:intergenic 40.0%
CTACGCGAATCCAAAATGAT+TGG + chr7.3:29140092-29140111 None:intergenic 40.0%
GAAGGATGGGACAATTGAAT+AGG + chr7.3:29139835-29139854 None:intergenic 40.0%
GAGATCTTTAACGTCAAGGA+TGG - chr7.3:29140567-29140586 MS.gene27754:CDS 40.0%
GGATCATTTGAGTCATGAGA+AGG + chr7.3:29140216-29140235 None:intergenic 40.0%
GGTTCTACCACAACTTCATT+GGG - chr7.3:29140644-29140663 MS.gene27754:CDS 40.0%
GTCTTCCAAACTCTCAAGTT+TGG + chr7.3:29140442-29140461 None:intergenic 40.0%
TCATTTGAGTCATGAGAAGG+AGG + chr7.3:29140213-29140232 None:intergenic 40.0%
TTCCAACTTGGAGAAACAAG+AGG + chr7.3:29140511-29140530 None:intergenic 40.0%
TTTGTGAGGATCATCAGCAT+AGG + chr7.3:29139736-29139755 None:intergenic 40.0%
! ACAACTGGATGCAACGTTTT+TGG - chr7.3:29140622-29140641 MS.gene27754:CDS 40.0%
! CAAACCCCACGTTTTCAAAT+TGG - chr7.3:29140380-29140399 MS.gene27754:CDS 40.0%
! CAACTGGATGCAACGTTTTT+GGG - chr7.3:29140623-29140642 MS.gene27754:CDS 40.0%
! CCACGTTTTCAAATTGGAAC+TGG - chr7.3:29140386-29140405 MS.gene27754:CDS 40.0%
! CGAATCCAAAATGATTGGCT+TGG + chr7.3:29140087-29140106 None:intergenic 40.0%
!! AGGAGGATTGTTTAGCTTGA+AGG + chr7.3:29140196-29140215 None:intergenic 40.0%
!! CCATGATAACGACGTAGTTT+TGG + chr7.3:29140285-29140304 None:intergenic 40.0%
!!! TACGCGGCAATTTTTTTGTG+AGG + chr7.3:29139750-29139769 None:intergenic 40.0%
ACCTCTCGAATCTGTTTCCA+AGG - chr7.3:29139975-29139994 MS.gene27754:CDS 45.0%
ACCTTGGAAACAGATTCGAG+AGG + chr7.3:29139979-29139998 None:intergenic 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.3:29140030-29140049 None:intergenic 45.0%
GGGTTCTACCACAACTTCAT+TGG - chr7.3:29140643-29140662 MS.gene27754:CDS 45.0%
TTGGAAACAGATTCGAGAGG+TGG + chr7.3:29139976-29139995 None:intergenic 45.0%
! AGCCTCTTGTTTCTCCAAGT+TGG - chr7.3:29140506-29140525 MS.gene27754:CDS 45.0%
!! TTTTGTTTGGGCTGTAGCCA+TGG - chr7.3:29139871-29139890 MS.gene27754:CDS 45.0%
GTCAGCAGACAAGGTAACCT+TGG + chr7.3:29139995-29140014 None:intergenic 50.0%
GTGAGGATCATCAGCATAGG+TGG + chr7.3:29139733-29139752 None:intergenic 50.0%
TCGAGAGGTGGCAGACTAAT+GGG + chr7.3:29139964-29139983 None:intergenic 50.0%
TTCGAGAGGTGGCAGACTAA+TGG + chr7.3:29139965-29139984 None:intergenic 50.0%
!! TAGCCATGGTTGGCTTGCAT+TGG - chr7.3:29139885-29139904 MS.gene27754:CDS 50.0%
AGAGGTGGCAGACTAATGGG+AGG + chr7.3:29139961-29139980 None:intergenic 55.0%
CCACCAATGCAAGCCAACCA+TGG + chr7.3:29139891-29139910 None:intergenic 55.0%
GTTTGGGCTGTAGCCATGGT+TGG - chr7.3:29139875-29139894 MS.gene27754:CDS 55.0%
TTGGAACTGGATGCCGAGAG+TGG - chr7.3:29140399-29140418 MS.gene27754:CDS 55.0%
!! CCATGGTTGGCTTGCATTGG+TGG - chr7.3:29139888-29139907 MS.gene27754:CDS 55.0%
TGTCACGGGGTCAGCAGACA+AGG + chr7.3:29140004-29140023 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 29139568 29140671 29139568 ID=MS.gene27754
chr7.3 mRNA 29139568 29140671 29139568 ID=MS.gene27754.t1;Parent=MS.gene27754
chr7.3 exon 29139568 29140671 29139568 ID=MS.gene27754.t1.exon1;Parent=MS.gene27754.t1
chr7.3 CDS 29139568 29140671 29139568 ID=cds.MS.gene27754.t1;Parent=MS.gene27754.t1
Gene Sequence

>MS.gene27754

ATGAGGAAGGTTGATTGGGCATATTTAGAAGAACTTCCTCTTAGTTTGGTTCTTGAAAAGTTGGAAGTACAAACAGACTATGTTAGGTTTGGTGTTGTGTGTAAGAATTGGCTACAAATTGCAAAGCTTAACCATAAAAATCATCAATTTAGGATTAATGTACCACCTATGCTGATGATCCTCACAAAAAAATTGCCGCGTATACATACAATATCACAGACAAAGAAGATATCATTGTATAATATCCTAAGTAAGAAAGAGTACCCTATTCAATTGTCCCATCCTTCCATCAATACAATGAAATTTTGTTTGGGCTGTAGCCATGGTTGGCTTGCATTGGTGGATGATAACAATGCCATAACTCTAGTGAATCCTTTTAAGTATAGTGTACCTCCCATTAGTCTGCCACCTCTCGAATCTGTTTCCAAGGTTACCTTGTCTGCTGACCCCGTGACAAATCCAAGTGATTATGTGGTTGCAGCAATTTACAAGTTTGGTTATCTCGCTTTCAAAAGACCAAGCCAATCATTTTGGATTCGCGTAGACACAAATGAATTTACTTTCACGAATATTGTGTTTTATAAAGGCATGGTATTTGCTGATAGCTGCAGAGATACCATTGTATCCTTCAAGCTAAACAATCCTCCTTCTCATGACTCAAATGATCCTAATTTTTCCTACTATGAGAAGATGGCTAGTACTCCATATATGATTCCAAAACTACGTCGTTATCATGGACTTGCTTATTTTGTGAAATCATTGACCGGAGAAATATGGTTGATGAGAAGATGCTTAATCGACGGTTTTTCACTCAAACCCCACGTTTTCAAATTGGAACTGGATGCCGAGAGTGGAAAACTTGAACAAATGACCAAACTTGAGAGTTTGGAAGACAACATTTTATTTGTCAGAAGTGTTGGTGATTCAATTTCTGTGTCAGCCTCTTGTTTCTCCAAGTTGGAAAAGGATTCAATTTATATTGTTAATGATTTAGGGTTAGAGATCTTTAACGTCAAGGATGGAAGCTTTCAGAGACCAAAATTACAACTTTCCTACAACTGGATGCAACGTTTTTGGGTTCTACCACAACTTCATTGGGATTGA
Protein sequence

>MS.gene27754.t1

MRKVDWAYLEELPLSLVLEKLEVQTDYVRFGVVCKNWLQIAKLNHKNHQFRINVPPMLMILTKKLPRIHTISQTKKISLYNILSKKEYPIQLSHPSINTMKFCLGCSHGWLALVDDNNAITLVNPFKYSVPPISLPPLESVSKVTLSADPVTNPSDYVVAAIYKFGYLAFKRPSQSFWIRVDTNEFTFTNIVFYKGMVFADSCRDTIVSFKLNNPPSHDSNDPNFSYYEKMASTPYMIPKLRRYHGLAYFVKSLTGEIWLMRRCLIDGFSLKPHVFKLELDAESGKLEQMTKLESLEDNILFVRSVGDSISVSASCFSKLEKDSIYIVNDLGLEIFNVKDGSFQRPKLQLSYNWMQRFWVLPQLHWD