AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66661


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66661.t1 MTR_6g477950 81.481 81 15 0 171 251 64 144 5.19e-41 143
MS.gene66661.t1 MTR_5g071410 33.463 257 157 3 1 252 22 269 9.34e-31 115
MS.gene66661.t1 MTR_7g117585 44.660 103 57 0 150 252 44 146 1.65e-21 87.8
MS.gene66661.t1 MTR_8g069780 50.000 80 40 0 172 251 76 155 1.14e-18 80.9
MS.gene66661.t1 MTR_3g117130 50.000 80 40 0 172 251 199 278 6.22e-17 79.0
MS.gene66661.t1 MTR_2g437520 48.193 83 40 1 172 251 121 203 6.61e-15 71.6
MS.gene66661.t1 MTR_0131s0030 34.127 126 73 4 123 242 28 149 7.44e-14 67.8
MS.gene66661.t1 MTR_2g012700 29.565 115 77 2 139 251 7 119 1.02e-13 66.6
MS.gene66661.t1 MTR_2g062330 33.333 102 65 2 150 251 40 138 9.06e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 56 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAACGTCATCCACTTTCT+TGG 0.252631 4.3:+48727985 None:intergenic
CAAACTCATCTCTACCTAAC+TGG 0.330629 4.3:+48728720 None:intergenic
TGCTGATAAGTTTGAATTGA+AGG 0.332261 4.3:-48728669 MS.gene66661:CDS
CAAGATTGACATACCTCGTC+TGG 0.362427 4.3:+48729040 None:intergenic
CACTTTGTGTTCAAAGTGAT+AGG 0.388587 4.3:+48728391 None:intergenic
AGAGGTTGTTGACAACAAAA+AGG 0.410832 4.3:-48728510 MS.gene66661:CDS
TCCCAACTGTGTGTCTATAG+AGG 0.413228 4.3:-48728019 MS.gene66661:CDS
TCCGTTCAGCGGTGTTGAGC+CGG 0.427766 4.3:+48727932 None:intergenic
TGTTTGTTCGTGTGGTTCGT+AGG 0.430579 4.3:-48727801 MS.gene66661:CDS
AGAGGGATAGTTATCCAGTT+AGG 0.432165 4.3:-48728734 MS.gene66661:CDS
AGTCGAAAACAATGTGGAAT+TGG 0.434044 4.3:-48728567 MS.gene66661:CDS
GTTTGTTCGTGTGGTTCGTA+GGG 0.439333 4.3:-48727800 MS.gene66661:CDS
AGATGTTATTGATATAAGTT+CGG 0.453836 4.3:-48728480 MS.gene66661:CDS
GCTATGTCTAAGCGTGTTCT+CGG 0.457464 4.3:-48728362 MS.gene66661:CDS
CAGTTAGGTAGAGATGAGTT+TGG 0.459071 4.3:-48728719 MS.gene66661:CDS
GATTTCTTCATAAGAAATCA+AGG 0.490357 4.3:-48728803 MS.gene66661:CDS
GGTTGACATGGATACTGATA+AGG 0.495581 4.3:-48727965 MS.gene66661:CDS
AGGGTGGTCAAAATTTGTTA+AGG 0.509813 4.3:-48727884 MS.gene66661:CDS
AAATCAAGATGTCGAAGAAG+TGG 0.519141 4.3:-48728420 MS.gene66661:CDS
TTCATCTTTGTTCCGTTCAG+CGG 0.520880 4.3:+48727921 None:intergenic
ACCTCTATAGACACACAGTT+GGG 0.523029 4.3:+48728018 None:intergenic
CTCGCGAAATTTGAATATCT+CGG 0.529020 4.3:-48728638 MS.gene66661:CDS
CTCTTGTACGACATGTGCAT+TGG 0.540397 4.3:+48728529 None:intergenic
TCACCATTCCTAGCATATCC+AGG 0.541689 4.3:+48728761 None:intergenic
TGATATAAGTTCGGATGAAG+AGG 0.542008 4.3:-48728471 MS.gene66661:CDS
CGTAGGGGTAACATTGCTTG+AGG 0.546560 4.3:-48727784 None:intergenic
CAATGTGGAATTGGTCCCAC+AGG 0.547816 4.3:-48728558 MS.gene66661:CDS
GTGGATGACGTTGGTTGACA+TGG 0.551372 4.3:-48727977 MS.gene66661:CDS
TAAGGATCGCCGCTTAAAAG+AGG 0.551825 4.3:-48727866 MS.gene66661:CDS
TCTATTCTGATCAGCCAAGA+AGG 0.552897 4.3:+48728592 None:intergenic
TAGGAGAGGATACAAGTGGA+TGG 0.555529 4.3:-48728827 MS.gene66661:CDS
GTAGGGGTAACATTGCTTGA+GGG 0.558229 4.3:-48727783 None:intergenic
ACTTTGTGTTCAAAGTGATA+GGG 0.559481 4.3:+48728392 None:intergenic
TGTGCATTGGCAGCAGCCTG+TGG 0.560921 4.3:+48728542 None:intergenic
CTGATAAGGAATACAAGTGC+CGG 0.561599 4.3:-48727951 MS.gene66661:CDS
GCGTGTTCTCGGACAACCAA+TGG 0.563243 4.3:-48728351 MS.gene66661:intron
TAAACAAGCCTGGATATGCT+AGG 0.566021 4.3:-48728769 MS.gene66661:CDS
ACACGAACAAACAAAACTCT+AGG 0.566819 4.3:+48727811 None:intergenic
TTCAAACTTATCAGCAATTG+CGG 0.567663 4.3:+48728676 None:intergenic
AACCTCTATAGACACACAGT+TGG 0.572525 4.3:+48728017 None:intergenic
ATGCTTCAAATAAACAAGCC+TGG 0.574525 4.3:-48728779 MS.gene66661:CDS
CTAGGAATGGTGATTGCAGA+GGG 0.589160 4.3:-48728751 MS.gene66661:CDS
GCCGGCTCAACACCGCTGAA+CGG 0.601141 4.3:-48727933 MS.gene66661:CDS
AAGCCTGGATATGCTAGGAA+TGG 0.602016 4.3:-48728764 MS.gene66661:CDS
CAATGCACATGTCGTACAAG+AGG 0.602899 4.3:-48728528 MS.gene66661:CDS
AAGATTGACATACCTCGTCT+GGG 0.609292 4.3:+48729041 None:intergenic
AAGGATCGCCGCTTAAAAGA+GGG 0.619565 4.3:-48727865 MS.gene66661:CDS
TTTGTTCGTGTGGTTCGTAG+GGG 0.631032 4.3:-48727799 MS.gene66661:CDS
TATAAGTTCGGATGAAGAGG+TGG 0.631039 4.3:-48728468 MS.gene66661:CDS
GTGCATTGGCAGCAGCCTGT+GGG 0.640871 4.3:+48728543 None:intergenic
CGAACAAACAAAACTCTAGG+AGG 0.641317 4.3:+48727814 None:intergenic
GCTAGGAATGGTGATTGCAG+AGG 0.652278 4.3:-48728752 MS.gene66661:CDS
TCCAAGAAAGTGGATGACGT+TGG 0.665396 4.3:-48727986 MS.gene66661:CDS
TAGACAAGTCGAAAACAATG+TGG 0.686168 4.3:-48728573 MS.gene66661:CDS
AACCATGGTGAACCCAGACG+AGG 0.693320 4.3:-48729053 None:intergenic
TACCTCGTCTGGGTTCACCA+TGG 0.713572 4.3:+48729051 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTACTATTTATATTTGTA+TGG - chr4.3:48728566-48728585 MS.gene66661:CDS 10.0%
!! CATATGAAATTAATTAAAAT+AGG - chr4.3:48728592-48728611 MS.gene66661:CDS 10.0%
!!! TTATTTTGAAAAATATAATC+TGG - chr4.3:48728634-48728653 MS.gene66661:CDS 10.0%
!! ATATGAATGTTAATGATAAA+GGG + chr4.3:48728533-48728552 None:intergenic 15.0%
!! TTTCAAAATAAATTAGATGT+GGG + chr4.3:48728625-48728644 None:intergenic 15.0%
!!! TAATGTTTTTGTTCATTTTT+AGG - chr4.3:48727989-48728008 MS.gene66661:CDS 15.0%
!!! TTTTCAAAATAAATTAGATG+TGG + chr4.3:48728626-48728645 None:intergenic 15.0%
!!! TTTTTTATGGTTATTTGTTT+GGG - chr4.3:48727906-48727925 MS.gene66661:CDS 15.0%
!! AGATGTTATTGATATAAGTT+CGG - chr4.3:48728355-48728374 MS.gene66661:CDS 20.0%
!! CATATGAATGTTAATGATAA+AGG + chr4.3:48728534-48728553 None:intergenic 20.0%
!! CTTTATCATTAACATTCATA+TGG - chr4.3:48728532-48728551 MS.gene66661:CDS 20.0%
!! TTATTTGAATAACTAACCAT+TGG + chr4.3:48728503-48728522 None:intergenic 20.0%
!! TTCAAAATAAATTAGATGTG+GGG + chr4.3:48728624-48728643 None:intergenic 20.0%
!! TTTCTTATACATAGTGTATA+TGG - chr4.3:48728729-48728748 MS.gene66661:CDS 20.0%
!! TTTGAAAAATATAATCTGGA+AGG - chr4.3:48728638-48728657 MS.gene66661:CDS 20.0%
!!! GTTTTTTATGGTTATTTGTT+TGG - chr4.3:48727905-48727924 MS.gene66661:CDS 20.0%
! AAAGCAACAAACAACTAAAA+AGG + chr4.3:48728712-48728731 None:intergenic 25.0%
! AACAAAGATGAAAAAGCTTT+GGG - chr4.3:48728925-48728944 MS.gene66661:intron 25.0%
! GATTTCTTCATAAGAAATCA+AGG - chr4.3:48728032-48728051 MS.gene66661:intron 25.0%
! GTAACTAAAAACATGTTCAA+TGG + chr4.3:48728224-48728243 None:intergenic 25.0%
! GTAACTATATTATCGTCTAT+AGG + chr4.3:48728687-48728706 None:intergenic 25.0%
!! AAAAAAGCATAAGTAACTTC+TGG - chr4.3:48727955-48727974 MS.gene66661:CDS 25.0%
!! AAAAAGCATAAGTAACTTCT+GGG - chr4.3:48727956-48727975 MS.gene66661:CDS 25.0%
!! AACCATAAAAAACTTGTTTG+CGG + chr4.3:48727898-48727917 None:intergenic 25.0%
!! TTGATTTTGCTCTTCATTAT+CGG + chr4.3:48728402-48728421 None:intergenic 25.0%
!!! TGACAAGCTAATTTTTGATT+TGG - chr4.3:48728993-48729012 MS.gene66661:intron 25.0%
!!! TTTGGTTTTTTCATGAAGAA+CGG - chr4.3:48728134-48728153 MS.gene66661:intron 25.0%
!!! TTTTAAAACTTCCAAGAAAG+TGG - chr4.3:48728839-48728858 MS.gene66661:intron 25.0%
!!! TTTTTGTTCATTTTTAGGAG+AGG - chr4.3:48727994-48728013 MS.gene66661:CDS 25.0%
AAACAAACTACAGTAACCTT+AGG + chr4.3:48727837-48727856 None:intergenic 30.0%
ACTTTGTGTTCAAAGTGATA+GGG + chr4.3:48728446-48728465 None:intergenic 30.0%
ATTGAATGAAACTCTTCCTA+AGG - chr4.3:48727818-48727837 MS.gene66661:CDS 30.0%
GAACAAAGATGAAAAAGCTT+TGG - chr4.3:48728924-48728943 MS.gene66661:intron 30.0%
TGCTGATAAGTTTGAATTGA+AGG - chr4.3:48728166-48728185 MS.gene66661:intron 30.0%
TTCAAACTTATCAGCAATTG+CGG + chr4.3:48728162-48728181 None:intergenic 30.0%
TTTGTTTGGGTATATGTGTT+TGG - chr4.3:48727919-48727938 MS.gene66661:CDS 30.0%
! CGTCTATAGGTACTTAATTT+TGG + chr4.3:48728674-48728693 None:intergenic 30.0%
!!! CATGTTTTTAGTTACCTTCT+TGG - chr4.3:48728229-48728248 MS.gene66661:intron 30.0%
!!! TACCGCAAACAAGTTTTTTA+TGG - chr4.3:48727893-48727912 MS.gene66661:CDS 30.0%
AAATCAAGATGTCGAAGAAG+TGG - chr4.3:48728415-48728434 MS.gene66661:CDS 35.0%
ACACGAACAAACAAAACTCT+AGG + chr4.3:48729027-48729046 None:intergenic 35.0%
AGAGGTTGTTGACAACAAAA+AGG - chr4.3:48728325-48728344 MS.gene66661:intron 35.0%
AGTCGAAAACAATGTGGAAT+TGG - chr4.3:48728268-48728287 MS.gene66661:intron 35.0%
ATGCTTCAAATAAACAAGCC+TGG - chr4.3:48728056-48728075 MS.gene66661:intron 35.0%
CACTTTGTGTTCAAAGTGAT+AGG + chr4.3:48728447-48728466 None:intergenic 35.0%
CTCGCGAAATTTGAATATCT+CGG - chr4.3:48728197-48728216 MS.gene66661:intron 35.0%
TAGACAAGTCGAAAACAATG+TGG - chr4.3:48728262-48728281 MS.gene66661:intron 35.0%
TGATATAAGTTCGGATGAAG+AGG - chr4.3:48728364-48728383 MS.gene66661:CDS 35.0%
!! AGGGTGGTCAAAATTTGTTA+AGG - chr4.3:48728951-48728970 MS.gene66661:intron 35.0%
!! ATGAAAAAGCTTTGGGAAGA+GGG - chr4.3:48728932-48728951 MS.gene66661:intron 35.0%
!! GGTATATGTGTTTGGTGTTT+AGG - chr4.3:48727927-48727946 MS.gene66661:CDS 35.0%
!! TTTTTAGGAGAGGATACAAG+TGG - chr4.3:48728004-48728023 MS.gene66661:CDS 35.0%
!!! TAGAGTTTTGTTTGTTCGTG+TGG - chr4.3:48729026-48729045 MS.gene66661:intron 35.0%
AACCTCTATAGACACACAGT+TGG + chr4.3:48728821-48728840 None:intergenic 40.0%
AAGATTGACATACCTCGTCT+GGG + chr4.3:48727797-48727816 None:intergenic 40.0%
ACCTCTATAGACACACAGTT+GGG + chr4.3:48728820-48728839 None:intergenic 40.0%
AGAGGGATAGTTATCCAGTT+AGG - chr4.3:48728101-48728120 MS.gene66661:intron 40.0%
CAAACTCATCTCTACCTAAC+TGG + chr4.3:48728118-48728137 None:intergenic 40.0%
CAGTTAGGTAGAGATGAGTT+TGG - chr4.3:48728116-48728135 MS.gene66661:intron 40.0%
CGAACAAACAAAACTCTAGG+AGG + chr4.3:48729024-48729043 None:intergenic 40.0%
CTGATAAGGAATACAAGTGC+CGG - chr4.3:48728884-48728903 MS.gene66661:intron 40.0%
GGTTGACATGGATACTGATA+AGG - chr4.3:48728870-48728889 MS.gene66661:intron 40.0%
GGTTGTTGACAACAAAAAGG+TGG - chr4.3:48728328-48728347 MS.gene66661:intron 40.0%
TAAACAAGCCTGGATATGCT+AGG - chr4.3:48728066-48728085 MS.gene66661:intron 40.0%
TATAAGTTCGGATGAAGAGG+TGG - chr4.3:48728367-48728386 MS.gene66661:CDS 40.0%
TCTATTCTGATCAGCCAAGA+AGG + chr4.3:48728246-48728265 None:intergenic 40.0%
TTCATCTTTGTTCCGTTCAG+CGG + chr4.3:48728917-48728936 None:intergenic 40.0%
!! GATGAAAAAGCTTTGGGAAG+AGG - chr4.3:48728931-48728950 MS.gene66661:intron 40.0%
AAGCCTGGATATGCTAGGAA+TGG - chr4.3:48728071-48728090 MS.gene66661:intron 45.0%
AAGGATCGCCGCTTAAAAGA+GGG - chr4.3:48728970-48728989 MS.gene66661:intron 45.0%
ACCAACGTCATCCACTTTCT+TGG + chr4.3:48728853-48728872 None:intergenic 45.0%
CAAGATTGACATACCTCGTC+TGG + chr4.3:48727798-48727817 None:intergenic 45.0%
CAATGCACATGTCGTACAAG+AGG - chr4.3:48728307-48728326 MS.gene66661:intron 45.0%
CTAGGAATGGTGATTGCAGA+GGG - chr4.3:48728084-48728103 MS.gene66661:intron 45.0%
CTCTTGTACGACATGTGCAT+TGG + chr4.3:48728309-48728328 None:intergenic 45.0%
GCTATGTCTAAGCGTGTTCT+CGG - chr4.3:48728473-48728492 MS.gene66661:CDS 45.0%
GTTTGTTCGTGTGGTTCGTA+GGG - chr4.3:48729035-48729054 MS.gene66661:intron 45.0%
TAAGGATCGCCGCTTAAAAG+AGG - chr4.3:48728969-48728988 MS.gene66661:intron 45.0%
TAGGAGAGGATACAAGTGGA+TGG - chr4.3:48728008-48728027 MS.gene66661:CDS 45.0%
TCACCATTCCTAGCATATCC+AGG + chr4.3:48728077-48728096 None:intergenic 45.0%
TCCAAGAAAGTGGATGACGT+TGG - chr4.3:48728849-48728868 MS.gene66661:intron 45.0%
TCCCAACTGTGTGTCTATAG+AGG - chr4.3:48728816-48728835 MS.gene66661:CDS 45.0%
TGTTTGTTCGTGTGGTTCGT+AGG - chr4.3:48729034-48729053 MS.gene66661:intron 45.0%
TTTGTTCGTGTGGTTCGTAG+GGG - chr4.3:48729036-48729055 MS.gene66661:intron 45.0%
! GCTTGTCACCCTCTTTTAAG+CGG + chr4.3:48728981-48729000 None:intergenic 45.0%
!! AAAAAGCTTTGGGAAGAGGG+TGG - chr4.3:48728935-48728954 MS.gene66661:intron 45.0%
CAATGTGGAATTGGTCCCAC+AGG - chr4.3:48728277-48728296 MS.gene66661:intron 50.0%
GCTAGGAATGGTGATTGCAG+AGG - chr4.3:48728083-48728102 MS.gene66661:intron 50.0%
! GTGGATGACGTTGGTTGACA+TGG - chr4.3:48728858-48728877 MS.gene66661:intron 50.0%
GCGTGTTCTCGGACAACCAA+TGG - chr4.3:48728484-48728503 MS.gene66661:CDS 55.0%
! GTGCATTGGCAGCAGCCTGT+GGG + chr4.3:48728295-48728314 None:intergenic 60.0%
! TCCGTTCAGCGGTGTTGAGC+CGG + chr4.3:48728906-48728925 None:intergenic 60.0%
! TGTGCATTGGCAGCAGCCTG+TGG + chr4.3:48728296-48728315 None:intergenic 60.0%
! GCCGGCTCAACACCGCTGAA+CGG - chr4.3:48728902-48728921 MS.gene66661:intron 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 48727786 48729071 48727786 ID=MS.gene66661
chr4.3 mRNA 48727786 48729071 48727786 ID=MS.gene66661.t1;Parent=MS.gene66661
chr4.3 exon 48729054 48729071 48729054 ID=MS.gene66661.t1.exon1;Parent=MS.gene66661.t1
chr4.3 CDS 48729054 48729071 48729054 ID=cds.MS.gene66661.t1;Parent=MS.gene66661.t1
chr4.3 exon 48728352 48728846 48728352 ID=MS.gene66661.t1.exon2;Parent=MS.gene66661.t1
chr4.3 CDS 48728352 48728846 48728352 ID=cds.MS.gene66661.t1;Parent=MS.gene66661.t1
chr4.3 exon 48727786 48728046 48727786 ID=MS.gene66661.t1.exon3;Parent=MS.gene66661.t1
chr4.3 CDS 48727786 48728046 48727786 ID=cds.MS.gene66661.t1;Parent=MS.gene66661.t1
Gene Sequence

>MS.gene66661

ATGGTGAACCCAGACGAGGTATGTCAATCTTGATTGAATGAAACTCTTCCTAAGGTTACTGTAGTTTGTTTTGTTTCACATCATATTTGTTTTATTCGTTGTAAATATACCGCAAACAAGTTTTTTATGGTTATTTGTTTGGGTATATGTGTTTGGTGTTTAGGATTAAAAAAAAGCATAAGTAACTTCTGGGATTATAATTTTAATGTTTTTGTTCATTTTTAGGAGAGGATACAAGTGGATGGTGATTTCTTCATAAGAAATCAAGGCATGCTTCAAATAAACAAGCCTGGATATGCTAGGAATGGTGATTGCAGAGGGATAGTTATCCAGTTAGGTAGAGATGAGTTTGGTTTTTTCATGAAGAACGGTGCCGCAATTGCTGATAAGTTTGAATTGAAGGCACATACTCTCGCGAAATTTGAATATCTCGGACCATTGAACATGTTTTTAGTTACCTTCTTGGCTGATCAGAATAGACAAGTCGAAAACAATGTGGAATTGGTCCCACAGGCTGCTGCCAATGCACATGTCGTACAAGAGGTTGTTGACAACAAAAAGGTGGTTCAAGATGTTATTGATATAAGTTCGGATGAAGAGGTGGATGTGACATCCGATAATGAAGAGCAAAATCAAGATGTCGAAGAAGTGGAAGATCCCTATCACTTTGAACACAAAGTGTCTGCTGCTATGTCTAAGCGTGTTCTCGGACAACCAATGGTTAGTTATTCAAATAAATTTCTTCCCTTTATCATTAACATTCATATGGAGTATCAAAATAATTACTATTTATATTTGTATGGTGTCATATGAAATTAATTAAAATAGGTAATCACCCCACATCTAATTTATTTTGAAAAATATAATCTGGAAGGTCTTGAATTGCCAAAATTAAGTACCTATAGACGATAATATAGTTACTACCTTTTTAGTTGTTTGTTGCTTTCTTATACATAGTGTATATGGTGTCGATATCACTAAAAAGTTACTACTTAATCTAAGTTATTTTAATTTCTTTTTGCTAGCATTTTCCCAACTGTGTGTCTATAGAGGTTTTAAAACTTCCAAGAAAGTGGATGACGTTGGTTGACATGGATACTGATAAGGAATACAAGTGCCGGCTCAACACCGCTGAACGGAACAAAGATGAAAAAGCTTTGGGAAGAGGGTGGTCAAAATTTGTTAAGGATCGCCGCTTAAAAGAGGGTGACAAGCTAATTTTTGATTTGGATCGACCTCCTAGAGTTTTGTTTGTTCGTGTGGTTCGTAGGGGTAACATTGCTTGA

Protein sequence

>MS.gene66661.t1

MVNPDEERIQVDGDFFIRNQGMLQINKPGYARNGDCRGIVIQLGRDEFGFFMKNGAAIADKFELKAHTLAKFEYLGPLNMFLVTFLADQNRQVENNVELVPQAAANAHVVQEVVDNKKVVQDVIDISSDEEVDVTSDNEEQNQDVEEVEDPYHFEHKVSAAMSKRVLGQPMHFPNCVSIEVLKLPRKWMTLVDMDTDKEYKCRLNTAERNKDEKALGRGWSKFVKDRRLKEGDKLIFDLDRPPRVLFVRVVRRGNIA