AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052065

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052065.t1 MTR_4g093740 70.213 94 13 2 156 247 432 512 1.18e-30 120
MS.gene052065.t1 MTR_8g005930 45.732 164 59 5 120 269 33 180 2.58e-29 110
MS.gene052065.t1 MTR_5g034920 53.030 132 37 5 156 283 365 475 2.21e-21 93.6
MS.gene052065.t1 MTR_6g044410 34.444 180 57 7 68 207 157 315 3.66e-16 78.2
MS.gene052065.t1 MTR_7g056053 44.262 122 24 3 165 283 273 353 6.09e-12 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 77 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGAATTTGCACACTCTTT+AGG 0.178653 2.2:+4724395 None:intergenic
AAGAATTTGCACACTCTTTA+GGG 0.199120 2.2:+4724396 None:intergenic
AGGATTTGAAAGTAGGAATT+TGG 0.210954 2.2:+4724437 None:intergenic
TCATCATGAGAAGTGATATT+TGG 0.224790 2.2:+4724889 None:intergenic
CTCAACAAATCAAGATGTTT+TGG 0.243154 2.2:-4724803 MS.gene052065:CDS
ACAAAACTCATTTGACATAT+TGG 0.248642 2.2:-4724761 MS.gene052065:CDS
GCAAATTCTTTCTAAACTTT+GGG 0.254754 2.2:-4724383 MS.gene052065:CDS
TGCAAATTCTTTCTAAACTT+TGG 0.269634 2.2:-4724384 MS.gene052065:CDS
CTAGCATAACTAGTAGTTAT+AGG 0.290714 2.2:+4724487 None:intergenic
GGAGCAGCTGCAGCCTTAAC+AGG 0.292026 2.2:+4724835 None:intergenic
TGAGGCTTTGCTTGGTGATT+TGG 0.298661 2.2:-4724710 MS.gene052065:CDS
ACCCAAGCAGCAACCTTAAC+TGG 0.299272 2.2:+4724595 None:intergenic
TCCAGTTAAGGTTGCTGCTT+GGG 0.317202 2.2:-4724596 MS.gene052065:CDS
AGGGACATTGGAACACTTAC+TGG 0.329272 2.2:+4724855 None:intergenic
GTAACATTGGGAGAATTTCT+AGG 0.345387 2.2:+4724652 None:intergenic
GAGGCTTTGCTTGGTGATTT+GGG 0.369101 2.2:-4724709 MS.gene052065:CDS
TTGAGCACGGGTCCTCATTC+CGG 0.381998 2.2:+4724171 None:intergenic
GGTTGCTGCCCCTAAGGCTT+TGG 0.384694 2.2:-4724620 MS.gene052065:CDS
TAAGGCTTTGGATCCAGTTA+AGG 0.398021 2.2:-4724608 MS.gene052065:CDS
TTAACTGGATCCAAAGCCTT+AGG 0.407727 2.2:+4724610 None:intergenic
TCCACCTCAATTCTCTTGCT+AGG 0.415455 2.2:+4724322 None:intergenic
AGGGGCAGCAACCTTATCTA+TGG 0.418278 2.2:+4724630 None:intergenic
CCACCTCAATTCTCTTGCTA+GGG 0.430436 2.2:+4724323 None:intergenic
AAAGTAGGAATTTGGCTTGA+AGG 0.434500 2.2:+4724445 None:intergenic
GGTACATTGGAGGTTCCTAC+TGG 0.435652 2.2:-4724688 MS.gene052065:CDS
TGGAGAGAGGATTTGAAAGT+AGG 0.440008 2.2:+4724430 None:intergenic
ATCCAGTTAAGGTTGCTGCT+TGG 0.455056 2.2:-4724597 MS.gene052065:CDS
ACCTTATCTATGGTAACATT+GGG 0.459533 2.2:+4724640 None:intergenic
CAAGAGAATTGAGGTGGAAG+AGG 0.460449 2.2:-4724317 MS.gene052065:CDS
GTGTTCCAATGTCCCTGTTA+AGG 0.463859 2.2:-4724848 MS.gene052065:CDS
GTATCTCAAAGTCAGATATG+AGG 0.464590 2.2:+4724281 None:intergenic
AACCTTATCTATGGTAACAT+TGG 0.469442 2.2:+4724639 None:intergenic
TAACTGGATCCAAAGCCTTA+GGG 0.471677 2.2:+4724611 None:intergenic
TCATACATAGATTGTGTGAC+AGG 0.474470 2.2:+4724529 None:intergenic
TGAAGTAGAAGAGGTGATGG+AGG 0.475774 2.2:-4724356 MS.gene052065:CDS
TGTAGCTGTGAGGACAACTT+TGG 0.478225 2.2:+4724138 None:intergenic
TCCCAATGTTACCATAGATA+AGG 0.485035 2.2:-4724641 MS.gene052065:CDS
TGATGATAGGTGTTTAAAAC+TGG 0.485631 2.2:+4724553 None:intergenic
GTAGTTATAGGTTGAGGCAT+AGG 0.496023 2.2:+4724499 None:intergenic
AAGTAGGAATTTGGCTTGAA+GGG 0.499401 2.2:+4724446 None:intergenic
GGATGAAGTAGAAGAGGTGA+TGG 0.507065 2.2:-4724359 MS.gene052065:CDS
GCTTGGTGATTTGGGTACAT+TGG 0.511450 2.2:-4724701 MS.gene052065:CDS
GCGGAAGGTGAGGCTTTGCT+TGG 0.518364 2.2:-4724718 MS.gene052065:CDS
AGATAAGGTTGCTGCCCCTA+AGG 0.521048 2.2:-4724626 MS.gene052065:CDS
AAACTCATTTGACATATTGG+TGG 0.525267 2.2:-4724758 MS.gene052065:CDS
TGGTGATTTGGGTACATTGG+AGG 0.525374 2.2:-4724698 MS.gene052065:CDS
CAAATTCTTTCTAAACTTTG+GGG 0.525703 2.2:-4724382 MS.gene052065:CDS
AATTCTTTCTAAACTTTGGG+GGG 0.530607 2.2:-4724380 MS.gene052065:CDS
TAACTAGTAGTTATAGGTTG+AGG 0.537172 2.2:+4724493 None:intergenic
TGATTTGTTGAGTATGTACA+TGG 0.541524 2.2:+4724814 None:intergenic
TTGTGTGACAGGCTGATGAT+AGG 0.542472 2.2:+4724540 None:intergenic
CAACCCTAGCAAGAGAATTG+AGG 0.542893 2.2:-4724326 MS.gene052065:CDS
TCTGCTAGCTTTAACTCAGC+CGG 0.545712 2.2:-4724190 MS.gene052065:CDS
ATAAAATAAATATAGAATTG+AGG 0.554825 2.2:-4724941 MS.gene052065:intron
TCTTTAGGGCTGCAGCAGAA+TGG 0.555193 2.2:+4724410 None:intergenic
GCTTTAACTCAGCCGGAATG+AGG 0.558162 2.2:-4724183 MS.gene052065:CDS
TTAGCGCTCTCCGATAGACT+TGG 0.564999 2.2:+4724253 None:intergenic
TTTAAAACTGGTGACAGCAC+AGG 0.574153 2.2:+4724565 None:intergenic
TATCTCAAAGTCAGATATGA+GGG 0.577352 2.2:+4724282 None:intergenic
AATTGAGGTCAACACGAAAG+AGG 0.580175 2.2:-4724926 MS.gene052065:CDS
AAGTCTATCGGAGAGCGCTA+AGG 0.582780 2.2:-4724251 MS.gene052065:CDS
AACTGGATCCAAAGCCTTAG+GGG 0.588469 2.2:+4724612 None:intergenic
TGCAGCCTTAACAGGGACAT+TGG 0.589744 2.2:+4724843 None:intergenic
GATACATTATCCAAGTCTAT+CGG 0.591665 2.2:-4724263 MS.gene052065:CDS
GGGACATTGGAACACTTACT+GGG 0.593421 2.2:+4724856 None:intergenic
AAATTCTTTCTAAACTTTGG+GGG 0.600695 2.2:-4724381 MS.gene052065:CDS
AGAAGCTCGTGCACAAAGTG+AGG 0.605104 2.2:-4724213 MS.gene052065:CDS
TACTGAGATAGCGGAAGGTG+AGG 0.607347 2.2:-4724728 MS.gene052065:CDS
CCCTAGCAAGAGAATTGAGG+TGG 0.609973 2.2:-4724323 MS.gene052065:CDS
AACTGGTGACAGCACAGGAG+TGG 0.620216 2.2:+4724570 None:intergenic
GAGCAGCTGCAGCCTTAACA+GGG 0.636334 2.2:+4724836 None:intergenic
GATGTTACTGAGATAGCGGA+AGG 0.640760 2.2:-4724733 MS.gene052065:CDS
GGCTGCAGCAGAATGGAGAG+AGG 0.646190 2.2:+4724417 None:intergenic
GGCGCATCATGCAAACCAGT+AGG 0.682683 2.2:+4724673 None:intergenic
GGATGATGTTACTGAGATAG+CGG 0.719553 2.2:-4724737 MS.gene052065:CDS
CCAACTATTCTGTAGCTGTG+AGG 0.740276 2.2:+4724128 None:intergenic
TATAGGTTGAGGCATAGGAG+CGG 0.740893 2.2:+4724504 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAATAAATATAGAATTG+AGG - chr2.2:4724329-4724348 MS.gene052065:CDS 10.0%
!!! AAATGTTATAAATATTTTCA+AGG - chr2.2:4724146-4724165 MS.gene052065:CDS 10.0%
!!! AATGTTATAAATATTTTCAA+GGG - chr2.2:4724147-4724166 MS.gene052065:CDS 10.0%
!!! ATGTTATAAATATTTTCAAG+GGG - chr2.2:4724148-4724167 MS.gene052065:CDS 15.0%
!!! TTGAAATATTGATTTTGAAA+AGG - chr2.2:4724213-4724232 MS.gene052065:CDS 15.0%
!!! AGTTTTGTAAATCAAGATTT+TGG + chr2.2:4724497-4724516 None:intergenic 20.0%
!!! TAATTTTTTTTTCATGTCGA+AGG - chr2.2:4724267-4724286 MS.gene052065:CDS 20.0%
! AAATTCTTTCTAAACTTTGG+GGG - chr2.2:4724889-4724908 MS.gene052065:CDS 25.0%
! ACAAAACTCATTTGACATAT+TGG - chr2.2:4724509-4724528 MS.gene052065:CDS 25.0%
! CAAATTCTTTCTAAACTTTG+GGG - chr2.2:4724888-4724907 MS.gene052065:CDS 25.0%
! GCAAATTCTTTCTAAACTTT+GGG - chr2.2:4724887-4724906 MS.gene052065:CDS 25.0%
! TGCAAATTCTTTCTAAACTT+TGG - chr2.2:4724886-4724905 MS.gene052065:CDS 25.0%
!!! ATTGTTATTTATGCTCAACA+TGG + chr2.2:4724301-4724320 None:intergenic 25.0%
!!! TTGTTATTTATGCTCAACAT+GGG + chr2.2:4724300-4724319 None:intergenic 25.0%
AAACTCATTTGACATATTGG+TGG - chr2.2:4724512-4724531 MS.gene052065:CDS 30.0%
AAAGAATTTGCACACTCTTT+AGG + chr2.2:4724878-4724897 None:intergenic 30.0%
AACCTTATCTATGGTAACAT+TGG + chr2.2:4724634-4724653 None:intergenic 30.0%
AAGAATTTGCACACTCTTTA+GGG + chr2.2:4724877-4724896 None:intergenic 30.0%
AATTCTTTCTAAACTTTGGG+GGG - chr2.2:4724890-4724909 MS.gene052065:CDS 30.0%
ACCTTATCTATGGTAACATT+GGG + chr2.2:4724633-4724652 None:intergenic 30.0%
AGGATTTGAAAGTAGGAATT+TGG + chr2.2:4724836-4724855 None:intergenic 30.0%
CTAGCATAACTAGTAGTTAT+AGG + chr2.2:4724786-4724805 None:intergenic 30.0%
GATACATTATCCAAGTCTAT+CGG - chr2.2:4725007-4725026 MS.gene052065:intron 30.0%
TAACTAGTAGTTATAGGTTG+AGG + chr2.2:4724780-4724799 None:intergenic 30.0%
TATCTCAAAGTCAGATATGA+GGG + chr2.2:4724991-4725010 None:intergenic 30.0%
TCATCATGAGAAGTGATATT+TGG + chr2.2:4724384-4724403 None:intergenic 30.0%
! CTCAACAAATCAAGATGTTT+TGG - chr2.2:4724467-4724486 MS.gene052065:CDS 30.0%
! TGATGATAGGTGTTTAAAAC+TGG + chr2.2:4724720-4724739 None:intergenic 30.0%
!! TGATTTGTTGAGTATGTACA+TGG + chr2.2:4724459-4724478 None:intergenic 30.0%
GTAACATTGGGAGAATTTCT+AGG + chr2.2:4724621-4724640 None:intergenic 35.0%
GTATCTCAAAGTCAGATATG+AGG + chr2.2:4724992-4725011 None:intergenic 35.0%
TCATACATAGATTGTGTGAC+AGG + chr2.2:4724744-4724763 None:intergenic 35.0%
TCCCAATGTTACCATAGATA+AGG - chr2.2:4724629-4724648 MS.gene052065:CDS 35.0%
!! AAAGTAGGAATTTGGCTTGA+AGG + chr2.2:4724828-4724847 None:intergenic 35.0%
!! AAGTAGGAATTTGGCTTGAA+GGG + chr2.2:4724827-4724846 None:intergenic 35.0%
AATTGAGGTCAACACGAAAG+AGG - chr2.2:4724344-4724363 MS.gene052065:CDS 40.0%
GGATGATGTTACTGAGATAG+CGG - chr2.2:4724533-4724552 MS.gene052065:CDS 40.0%
TAACTGGATCCAAAGCCTTA+GGG + chr2.2:4724662-4724681 None:intergenic 40.0%
TGGAGAGAGGATTTGAAAGT+AGG + chr2.2:4724843-4724862 None:intergenic 40.0%
TTAACTGGATCCAAAGCCTT+AGG + chr2.2:4724663-4724682 None:intergenic 40.0%
! GTAGTTATAGGTTGAGGCAT+AGG + chr2.2:4724774-4724793 None:intergenic 40.0%
! TGGAGTTACTCTTTTGAGCA+CGG + chr2.2:4725115-4725134 None:intergenic 40.0%
! TTTAAAACTGGTGACAGCAC+AGG + chr2.2:4724708-4724727 None:intergenic 40.0%
!! TAAGGCTTTGGATCCAGTTA+AGG - chr2.2:4724662-4724681 MS.gene052065:CDS 40.0%
AACTGGATCCAAAGCCTTAG+GGG + chr2.2:4724661-4724680 None:intergenic 45.0%
AGGGACATTGGAACACTTAC+TGG + chr2.2:4724418-4724437 None:intergenic 45.0%
ATCCAGTTAAGGTTGCTGCT+TGG - chr2.2:4724673-4724692 MS.gene052065:CDS 45.0%
CAACCCTAGCAAGAGAATTG+AGG - chr2.2:4724944-4724963 MS.gene052065:intron 45.0%
CAAGAGAATTGAGGTGGAAG+AGG - chr2.2:4724953-4724972 MS.gene052065:intron 45.0%
CCACCTCAATTCTCTTGCTA+GGG + chr2.2:4724950-4724969 None:intergenic 45.0%
GGATGAAGTAGAAGAGGTGA+TGG - chr2.2:4724911-4724930 MS.gene052065:CDS 45.0%
GGGACATTGGAACACTTACT+GGG + chr2.2:4724417-4724436 None:intergenic 45.0%
GTGTTCCAATGTCCCTGTTA+AGG - chr2.2:4724422-4724441 MS.gene052065:CDS 45.0%
TCCACCTCAATTCTCTTGCT+AGG + chr2.2:4724951-4724970 None:intergenic 45.0%
TGTAGCTGTGAGGACAACTT+TGG + chr2.2:4725135-4725154 None:intergenic 45.0%
TTGTGTGACAGGCTGATGAT+AGG + chr2.2:4724733-4724752 None:intergenic 45.0%
! GAGGCTTTGCTTGGTGATTT+GGG - chr2.2:4724561-4724580 MS.gene052065:CDS 45.0%
! GCTTGGTGATTTGGGTACAT+TGG - chr2.2:4724569-4724588 MS.gene052065:CDS 45.0%
! GGAGTTACTCTTTTGAGCAC+GGG + chr2.2:4725114-4725133 None:intergenic 45.0%
! TATAGGTTGAGGCATAGGAG+CGG + chr2.2:4724769-4724788 None:intergenic 45.0%
! TCCAGTTAAGGTTGCTGCTT+GGG - chr2.2:4724674-4724693 MS.gene052065:CDS 45.0%
! TGAAGTAGAAGAGGTGATGG+AGG - chr2.2:4724914-4724933 MS.gene052065:CDS 45.0%
! TGAGGCTTTGCTTGGTGATT+TGG - chr2.2:4724560-4724579 MS.gene052065:CDS 45.0%
! TGGTGATTTGGGTACATTGG+AGG - chr2.2:4724572-4724591 MS.gene052065:CDS 45.0%
!! GATGTTACTGAGATAGCGGA+AGG - chr2.2:4724537-4724556 MS.gene052065:CDS 45.0%
!! TCTGCTAGCTTTAACTCAGC+CGG - chr2.2:4725080-4725099 MS.gene052065:intron 45.0%
ACCCAAGCAGCAACCTTAAC+TGG + chr2.2:4724678-4724697 None:intergenic 50.0%
AGAAGCTCGTGCACAAAGTG+AGG - chr2.2:4725057-4725076 MS.gene052065:intron 50.0%
AGATAAGGTTGCTGCCCCTA+AGG - chr2.2:4724644-4724663 MS.gene052065:CDS 50.0%
AGGGGCAGCAACCTTATCTA+TGG + chr2.2:4724643-4724662 None:intergenic 50.0%
CCCTAGCAAGAGAATTGAGG+TGG - chr2.2:4724947-4724966 MS.gene052065:intron 50.0%
GCTTTAACTCAGCCGGAATG+AGG - chr2.2:4725087-4725106 MS.gene052065:intron 50.0%
GGTACATTGGAGGTTCCTAC+TGG - chr2.2:4724582-4724601 MS.gene052065:CDS 50.0%
TGCAGCCTTAACAGGGACAT+TGG + chr2.2:4724430-4724449 None:intergenic 50.0%
TTAGCGCTCTCCGATAGACT+TGG + chr2.2:4725020-4725039 None:intergenic 50.0%
TTGGGGGGATGAAGTAGAAG+AGG - chr2.2:4724905-4724924 MS.gene052065:CDS 50.0%
!! AAGTCTATCGGAGAGCGCTA+AGG - chr2.2:4725019-4725038 MS.gene052065:intron 50.0%
!! TACTGAGATAGCGGAAGGTG+AGG - chr2.2:4724542-4724561 MS.gene052065:CDS 50.0%
!! TCTTTAGGGCTGCAGCAGAA+TGG + chr2.2:4724863-4724882 None:intergenic 50.0%
AACTGGTGACAGCACAGGAG+TGG + chr2.2:4724703-4724722 None:intergenic 55.0%
GAGCAGCTGCAGCCTTAACA+GGG + chr2.2:4724437-4724456 None:intergenic 55.0%
GGCGCATCATGCAAACCAGT+AGG + chr2.2:4724600-4724619 None:intergenic 55.0%
TTGAGCACGGGTCCTCATTC+CGG + chr2.2:4725102-4725121 None:intergenic 55.0%
GCGGAAGGTGAGGCTTTGCT+TGG - chr2.2:4724552-4724571 MS.gene052065:CDS 60.0%
GGAGCAGCTGCAGCCTTAAC+AGG + chr2.2:4724438-4724457 None:intergenic 60.0%
GGCTGCAGCAGAATGGAGAG+AGG + chr2.2:4724856-4724875 None:intergenic 60.0%
GGTTGCTGCCCCTAAGGCTT+TGG - chr2.2:4724650-4724669 MS.gene052065:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 4724132 4725160 4724132 ID=MS.gene052065
chr2.2 mRNA 4724132 4725160 4724132 ID=MS.gene052065.t1;Parent=MS.gene052065
chr2.2 exon 4725123 4725160 4725123 ID=MS.gene052065.t1.exon1;Parent=MS.gene052065.t1
chr2.2 CDS 4725123 4725160 4725123 ID=cds.MS.gene052065.t1;Parent=MS.gene052065.t1
chr2.2 exon 4724132 4724948 4724132 ID=MS.gene052065.t1.exon2;Parent=MS.gene052065.t1
chr2.2 CDS 4724132 4724948 4724132 ID=cds.MS.gene052065.t1;Parent=MS.gene052065.t1
Gene Sequence

>MS.gene052065

ATGAGTGTTTTGAAAAATGTTATAAATATTTTCAAGGGGTTTTTTAAACTTAATTTATATTATGTGATCTTTGTTTTCTATTTGAAATATTGATTTTGAAAAGGTGCGTTTGAAAAGTTTTTTTTGTTGAAAATATAATTTTTTTTTCATGTCGAAGGTGTTGCGCCCATGTTGAGCATAAATAACAATGACATGCGATAAAATAAATATAGAATTGAGGTCAACACGAAAGAGGACACTACTAGCAATCCAAATATCACTTCTCATGATGATGTCAATCTGCCCAGTAAGTGTTCCAATGTCCCTGTTAAGGCTGCAGCTGCTCCATGTACATACTCAACAAATCAAGATGTTTTGGTTGACCAAAATCTTGATTTACAAAACTCATTTGACATATTGGTGGATGATGTTACTGAGATAGCGGAAGGTGAGGCTTTGCTTGGTGATTTGGGTACATTGGAGGTTCCTACTGGTTTGCATGATGCGCCTAGAAATTCTCCCAATGTTACCATAGATAAGGTTGCTGCCCCTAAGGCTTTGGATCCAGTTAAGGTTGCTGCTTGGGTAGCCACTCCTGTGCTGTCACCAGTTTTAAACACCTATCATCAGCCTGTCACACAATCTATGTATGAAACCGCTCCTATGCCTCAACCTATAACTACTAGTTATGCTAGTTTGACAAGTGACAAGCTCCCTTCAAGCCAAATTCCTACTTTCAAATCCTCTCTCCATTCTGCTGCAGCCCTAAAGAGTGTGCAAATTCTTTCTAAACTTTGGGGGGATGAAGTAGAAGAGGTGATGGAGGATACTCTCAACCCTAGCAAGAGAATTGAGGTGGAAGAGGACAATGTTGAAGCCCTCATATCTGACTTTGAGATACATTATCCAAGTCTATCGGAGAGCGCTAAGGCAGAGAAAAAGAAGAAGAAGCTCGTGCACAAAGTGAGGTCTGCTAGCTTTAACTCAGCCGGAATGAGGACCCGTGCTCAAAAGAGTAACTCCAAAGTTGTCCTCACAGCTACAGAATAG
Protein sequence

>MS.gene052065.t1

MSVLKNVINIFKGIEVNTKEDTTSNPNITSHDDVNLPSKCSNVPVKAAAAPCTYSTNQDVLVDQNLDLQNSFDILVDDVTEIAEGEALLGDLGTLEVPTGLHDAPRNSPNVTIDKVAAPKALDPVKVAAWVATPVLSPVLNTYHQPVTQSMYETAPMPQPITTSYASLTSDKLPSSQIPTFKSSLHSAAALKSVQILSKLWGDEVEEVMEDTLNPSKRIEVEEDNVEALISDFEIHYPSLSESAKAEKKKKKLVHKVRSASFNSAGMRTRAQKSNSKVVLTATE