AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0926980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0926980 MtrunA17_Chr6g0486171 70.238 252 43 3 10 231 4 253 3.05e-118 338
Msa0926980 MtrunA17_Chr6g0486151 32.000 175 82 5 101 239 124 297 5.80e-16 75.5
Msa0926980 MtrunA17_Chr6g0486131 50.633 79 29 2 70 140 1 77 5.17e-15 72.0
Msa0926980 MtrunA17_Chr6g0486181 30.045 223 115 7 1 185 1 220 8.79e-14 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 42 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCAATCAAGGTGTGATTAT+AGG 0.272186 6_2:+71039523 Msa0926980:CDS
TAGAGTGTTAAACAATGATT+TGG 0.292646 6_2:+71039303 Msa0926980:CDS
TCCTTATGAACACCCTTCTT+TGG 0.298019 6_2:+71039342 Msa0926980:CDS
TCCTATAATCACACCTTGAT+TGG 0.339634 6_2:-71039524 None:intergenic
TTAAAATTTGTTTCATAAAG+TGG 0.347789 6_2:-71039065 None:intergenic
TCACGAAGATGGTCTCATTA+AGG 0.371609 6_2:+71038935 Msa0926980:CDS
TGAGAATAATGGTGAAGAAA+TGG 0.383194 6_2:+71039465 Msa0926980:CDS
AAGTATCGAGAACATGGATT+TGG 0.409114 6_2:+71039386 Msa0926980:CDS
TGATTTGGATGTTTCAATGA+AGG 0.418905 6_2:+71039318 Msa0926980:CDS
ACCAAAGAAGGGTGTTCATA+AGG 0.427204 6_2:-71039343 None:intergenic
TTGTGCTGCTCAAACTCATA+TGG 0.442909 6_2:+71039429 Msa0926980:CDS
ATTTGAAGCAATACCAAAGA+AGG 0.460237 6_2:-71039355 None:intergenic
TAATGAGACTAAGAACCATT+GGG 0.460274 6_2:+71039088 Msa0926980:CDS
CAATTTGAGACTGAGAATAA+TGG 0.473417 6_2:+71039454 Msa0926980:CDS
GTGATTATAGGAAATAATAA+TGG 0.477144 6_2:+71039535 Msa0926980:CDS
TATAACGAAGAATGTAAATA+CGG 0.485507 6_2:-71038991 None:intergenic
ACACTACGTAGATGGTAAAT+CGG 0.499784 6_2:+71038884 Msa0926980:CDS
ACAGTGTCACACTACGTAGA+TGG 0.500726 6_2:+71038876 Msa0926980:CDS
ATAATGAGACTAAGAACCAT+TGG 0.500792 6_2:+71039087 Msa0926980:CDS
GTTCCCACGCTCTTCTCCGA+TGG 0.501338 6_2:-71038801 None:intergenic
GAACTGTCTAGGCAAACAAA+TGG 0.501490 6_2:+71039487 Msa0926980:CDS
AAGAAACTTTCTGTTAGAAG+AGG 0.522872 6_2:+71039571 Msa0926980:CDS
CGAGAACATGGATTTGGAAG+TGG 0.525089 6_2:+71039392 Msa0926980:CDS
GTTTCATAAAGTGGATCGAT+GGG 0.528809 6_2:-71039056 None:intergenic
TTGATAATATATCACGAAGA+TGG 0.534894 6_2:+71038924 Msa0926980:CDS
GTGAAGAAATGGAACTGTCT+AGG 0.541494 6_2:+71039476 Msa0926980:CDS
CGCAGTTTCAGTAGAGGGGA+AGG 0.543862 6_2:+71038848 Msa0926980:CDS
GTGCAGCAGAAGAGAAAGAA+GGG 0.548287 6_2:+71039173 Msa0926980:CDS
TTCAACAAGTATCGAGAACA+TGG 0.554270 6_2:+71039380 Msa0926980:CDS
TGTTTCATAAAGTGGATCGA+TGG 0.554991 6_2:-71039057 None:intergenic
TGTGCAGCAGAAGAGAAAGA+AGG 0.574995 6_2:+71039172 Msa0926980:CDS
GAACACGCAGTTTCAGTAGA+GGG 0.589661 6_2:+71038843 Msa0926980:CDS
AAAACGTATGTTGCATACCA+TGG 0.598167 6_2:+71039122 Msa0926980:CDS
AACACGCAGTTTCAGTAGAG+GGG 0.607913 6_2:+71038844 Msa0926980:CDS
AATGTAAATACGGATCCAGT+AGG 0.609266 6_2:-71038981 None:intergenic
TTTCCATCGGAGAAGAGCGT+GGG 0.612805 6_2:+71038798 Msa0926980:CDS
AGACTAAGAACCATTGGGGA+GGG 0.620733 6_2:+71039093 Msa0926980:CDS
TTTGAAGCAATACCAAAGAA+GGG 0.625309 6_2:-71039354 None:intergenic
TGAACACGCAGTTTCAGTAG+AGG 0.635989 6_2:+71038842 Msa0926980:CDS
GAGACTAAGAACCATTGGGG+AGG 0.649630 6_2:+71039092 Msa0926980:CDS
AACATGGATTTGGAAGTGGA+CGG 0.673745 6_2:+71039396 Msa0926980:CDS
AATGAGACTAAGAACCATTG+GGG 0.684064 6_2:+71039089 Msa0926980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAAAATTTGTTTCATAAAG+TGG - chr6_2:71039068-71039087 None:intergenic 15.0%
!!! TTAAAATTTGTTTCATAAAG+TGG - chr6_2:71039068-71039087 None:intergenic 15.0%
!! TATAACGAAGAATGTAAATA+CGG - chr6_2:71038994-71039013 None:intergenic 20.0%
!! GTGATTATAGGAAATAATAA+TGG + chr6_2:71039535-71039554 Msa0926980:CDS 20.0%
!! TATAACGAAGAATGTAAATA+CGG - chr6_2:71038994-71039013 None:intergenic 20.0%
!! GTGATTATAGGAAATAATAA+TGG + chr6_2:71039535-71039554 Msa0926980:CDS 20.0%
!! TTGATAATATATCACGAAGA+TGG + chr6_2:71038924-71038943 Msa0926980:CDS 25.0%
!! GACTTAAATTTCGTTTTCTA+CGG + chr6_2:71038957-71038976 Msa0926980:CDS 25.0%
!!! GTAAACAATGCTTTTTAAGT+CGG + chr6_2:71039243-71039262 Msa0926980:intron 25.0%
!! TAGAGTGTTAAACAATGATT+TGG + chr6_2:71039303-71039322 Msa0926980:CDS 25.0%
!! TTGATAATATATCACGAAGA+TGG + chr6_2:71038924-71038943 Msa0926980:CDS 25.0%
!! GACTTAAATTTCGTTTTCTA+CGG + chr6_2:71038957-71038976 Msa0926980:CDS 25.0%
!!! GTAAACAATGCTTTTTAAGT+CGG + chr6_2:71039243-71039262 Msa0926980:intron 25.0%
!! TAGAGTGTTAAACAATGATT+TGG + chr6_2:71039303-71039322 Msa0926980:CDS 25.0%
ATAATGAGACTAAGAACCAT+TGG + chr6_2:71039087-71039106 Msa0926980:CDS 30.0%
TAATGAGACTAAGAACCATT+GGG + chr6_2:71039088-71039107 Msa0926980:CDS 30.0%
ATACCATGGAGATAAAAATG+AGG + chr6_2:71039136-71039155 Msa0926980:CDS 30.0%
TACCATGGAGATAAAAATGA+GGG + chr6_2:71039137-71039156 Msa0926980:CDS 30.0%
!! TTTTAAGTCGGAAAAAAGTG+AGG + chr6_2:71039255-71039274 Msa0926980:intron 30.0%
! TGATTTGGATGTTTCAATGA+AGG + chr6_2:71039318-71039337 Msa0926980:CDS 30.0%
! TTTGAAGCAATACCAAAGAA+GGG - chr6_2:71039357-71039376 None:intergenic 30.0%
! ATTTGAAGCAATACCAAAGA+AGG - chr6_2:71039358-71039377 None:intergenic 30.0%
! CAATTTGAGACTGAGAATAA+TGG + chr6_2:71039454-71039473 Msa0926980:CDS 30.0%
TGAGAATAATGGTGAAGAAA+TGG + chr6_2:71039465-71039484 Msa0926980:CDS 30.0%
! AATAGTACTTTTGCCAATCA+AGG + chr6_2:71039511-71039530 Msa0926980:CDS 30.0%
AAGAAACTTTCTGTTAGAAG+AGG + chr6_2:71039571-71039590 Msa0926980:CDS 30.0%
ATAATGAGACTAAGAACCAT+TGG + chr6_2:71039087-71039106 Msa0926980:CDS 30.0%
TAATGAGACTAAGAACCATT+GGG + chr6_2:71039088-71039107 Msa0926980:CDS 30.0%
ATACCATGGAGATAAAAATG+AGG + chr6_2:71039136-71039155 Msa0926980:CDS 30.0%
TACCATGGAGATAAAAATGA+GGG + chr6_2:71039137-71039156 Msa0926980:CDS 30.0%
!! TTTTAAGTCGGAAAAAAGTG+AGG + chr6_2:71039255-71039274 Msa0926980:intron 30.0%
! TGATTTGGATGTTTCAATGA+AGG + chr6_2:71039318-71039337 Msa0926980:CDS 30.0%
! TTTGAAGCAATACCAAAGAA+GGG - chr6_2:71039357-71039376 None:intergenic 30.0%
! ATTTGAAGCAATACCAAAGA+AGG - chr6_2:71039358-71039377 None:intergenic 30.0%
! CAATTTGAGACTGAGAATAA+TGG + chr6_2:71039454-71039473 Msa0926980:CDS 30.0%
TGAGAATAATGGTGAAGAAA+TGG + chr6_2:71039465-71039484 Msa0926980:CDS 30.0%
! AATAGTACTTTTGCCAATCA+AGG + chr6_2:71039511-71039530 Msa0926980:CDS 30.0%
AAGAAACTTTCTGTTAGAAG+AGG + chr6_2:71039571-71039590 Msa0926980:CDS 30.0%
ACACTACGTAGATGGTAAAT+CGG + chr6_2:71038884-71038903 Msa0926980:CDS 35.0%
AATGTAAATACGGATCCAGT+AGG - chr6_2:71038984-71039003 None:intergenic 35.0%
GTTTCATAAAGTGGATCGAT+GGG - chr6_2:71039059-71039078 None:intergenic 35.0%
TGTTTCATAAAGTGGATCGA+TGG - chr6_2:71039060-71039079 None:intergenic 35.0%
AATGAGACTAAGAACCATTG+GGG + chr6_2:71039089-71039108 Msa0926980:CDS 35.0%
AAAACGTATGTTGCATACCA+TGG + chr6_2:71039122-71039141 Msa0926980:CDS 35.0%
ACCATGGAGATAAAAATGAG+GGG + chr6_2:71039138-71039157 Msa0926980:CDS 35.0%
TGAGGTTGGACTTTCAATAA+TGG + chr6_2:71039273-71039292 Msa0926980:intron 35.0%
!! TTCAACAAGTATCGAGAACA+TGG + chr6_2:71039380-71039399 Msa0926980:CDS 35.0%
!! AAGTATCGAGAACATGGATT+TGG + chr6_2:71039386-71039405 Msa0926980:CDS 35.0%
TCCTATAATCACACCTTGAT+TGG - chr6_2:71039527-71039546 None:intergenic 35.0%
ACACTACGTAGATGGTAAAT+CGG + chr6_2:71038884-71038903 Msa0926980:CDS 35.0%
AATGTAAATACGGATCCAGT+AGG - chr6_2:71038984-71039003 None:intergenic 35.0%
GTTTCATAAAGTGGATCGAT+GGG - chr6_2:71039059-71039078 None:intergenic 35.0%
TGTTTCATAAAGTGGATCGA+TGG - chr6_2:71039060-71039079 None:intergenic 35.0%
AATGAGACTAAGAACCATTG+GGG + chr6_2:71039089-71039108 Msa0926980:CDS 35.0%
AAAACGTATGTTGCATACCA+TGG + chr6_2:71039122-71039141 Msa0926980:CDS 35.0%
ACCATGGAGATAAAAATGAG+GGG + chr6_2:71039138-71039157 Msa0926980:CDS 35.0%
TGAGGTTGGACTTTCAATAA+TGG + chr6_2:71039273-71039292 Msa0926980:intron 35.0%
!! TTCAACAAGTATCGAGAACA+TGG + chr6_2:71039380-71039399 Msa0926980:CDS 35.0%
!! AAGTATCGAGAACATGGATT+TGG + chr6_2:71039386-71039405 Msa0926980:CDS 35.0%
TCCTATAATCACACCTTGAT+TGG - chr6_2:71039527-71039546 None:intergenic 35.0%
TCACGAAGATGGTCTCATTA+AGG + chr6_2:71038935-71038954 Msa0926980:CDS 40.0%
!! TCCCCTCATTTTTATCTCCA+TGG - chr6_2:71039142-71039161 None:intergenic 40.0%
AAGTCGGAAAAAAGTGAGGT+TGG + chr6_2:71039259-71039278 Msa0926980:intron 40.0%
TCCTTATGAACACCCTTCTT+TGG + chr6_2:71039342-71039361 Msa0926980:CDS 40.0%
!! ACCAAAGAAGGGTGTTCATA+AGG - chr6_2:71039346-71039365 None:intergenic 40.0%
AACATGGATTTGGAAGTGGA+CGG + chr6_2:71039396-71039415 Msa0926980:CDS 40.0%
! TTGTGCTGCTCAAACTCATA+TGG + chr6_2:71039429-71039448 Msa0926980:CDS 40.0%
GTGAAGAAATGGAACTGTCT+AGG + chr6_2:71039476-71039495 Msa0926980:CDS 40.0%
GAACTGTCTAGGCAAACAAA+TGG + chr6_2:71039487-71039506 Msa0926980:CDS 40.0%
GCCAATCAAGGTGTGATTAT+AGG + chr6_2:71039523-71039542 Msa0926980:CDS 40.0%
TCACGAAGATGGTCTCATTA+AGG + chr6_2:71038935-71038954 Msa0926980:CDS 40.0%
!! TCCCCTCATTTTTATCTCCA+TGG - chr6_2:71039142-71039161 None:intergenic 40.0%
AAGTCGGAAAAAAGTGAGGT+TGG + chr6_2:71039259-71039278 Msa0926980:intron 40.0%
TCCTTATGAACACCCTTCTT+TGG + chr6_2:71039342-71039361 Msa0926980:CDS 40.0%
!! ACCAAAGAAGGGTGTTCATA+AGG - chr6_2:71039346-71039365 None:intergenic 40.0%
AACATGGATTTGGAAGTGGA+CGG + chr6_2:71039396-71039415 Msa0926980:CDS 40.0%
! TTGTGCTGCTCAAACTCATA+TGG + chr6_2:71039429-71039448 Msa0926980:CDS 40.0%
GTGAAGAAATGGAACTGTCT+AGG + chr6_2:71039476-71039495 Msa0926980:CDS 40.0%
GAACTGTCTAGGCAAACAAA+TGG + chr6_2:71039487-71039506 Msa0926980:CDS 40.0%
GCCAATCAAGGTGTGATTAT+AGG + chr6_2:71039523-71039542 Msa0926980:CDS 40.0%
TGAACACGCAGTTTCAGTAG+AGG + chr6_2:71038842-71038861 Msa0926980:CDS 45.0%
GAACACGCAGTTTCAGTAGA+GGG + chr6_2:71038843-71038862 Msa0926980:CDS 45.0%
AACACGCAGTTTCAGTAGAG+GGG + chr6_2:71038844-71038863 Msa0926980:CDS 45.0%
ACAGTGTCACACTACGTAGA+TGG + chr6_2:71038876-71038895 Msa0926980:CDS 45.0%
! TTCGTTTTCTACGGACCTAC+TGG + chr6_2:71038966-71038985 Msa0926980:CDS 45.0%
AGACTAAGAACCATTGGGGA+GGG + chr6_2:71039093-71039112 Msa0926980:CDS 45.0%
! TTTTCGTAATCCCTCCCCAA+TGG - chr6_2:71039106-71039125 None:intergenic 45.0%
TGTGCAGCAGAAGAGAAAGA+AGG + chr6_2:71039172-71039191 Msa0926980:CDS 45.0%
GTGCAGCAGAAGAGAAAGAA+GGG + chr6_2:71039173-71039192 Msa0926980:CDS 45.0%
! AAAGCCTTGTGCAATCAGAG+TGG + chr6_2:71039202-71039221 Msa0926980:intron 45.0%
CGAGAACATGGATTTGGAAG+TGG + chr6_2:71039392-71039411 Msa0926980:CDS 45.0%
TGAACACGCAGTTTCAGTAG+AGG + chr6_2:71038842-71038861 Msa0926980:CDS 45.0%
GAACACGCAGTTTCAGTAGA+GGG + chr6_2:71038843-71038862 Msa0926980:CDS 45.0%
AACACGCAGTTTCAGTAGAG+GGG + chr6_2:71038844-71038863 Msa0926980:CDS 45.0%
ACAGTGTCACACTACGTAGA+TGG + chr6_2:71038876-71038895 Msa0926980:CDS 45.0%
! TTCGTTTTCTACGGACCTAC+TGG + chr6_2:71038966-71038985 Msa0926980:CDS 45.0%
AGACTAAGAACCATTGGGGA+GGG + chr6_2:71039093-71039112 Msa0926980:CDS 45.0%
! TTTTCGTAATCCCTCCCCAA+TGG - chr6_2:71039106-71039125 None:intergenic 45.0%
TGTGCAGCAGAAGAGAAAGA+AGG + chr6_2:71039172-71039191 Msa0926980:CDS 45.0%
GTGCAGCAGAAGAGAAAGAA+GGG + chr6_2:71039173-71039192 Msa0926980:CDS 45.0%
! AAAGCCTTGTGCAATCAGAG+TGG + chr6_2:71039202-71039221 Msa0926980:intron 45.0%
CGAGAACATGGATTTGGAAG+TGG + chr6_2:71039392-71039411 Msa0926980:CDS 45.0%
! TTTTCCATCGGAGAAGAGCG+TGG + chr6_2:71038797-71038816 Msa0926980:CDS 50.0%
! TTTCCATCGGAGAAGAGCGT+GGG + chr6_2:71038798-71038817 Msa0926980:CDS 50.0%
GAGACTAAGAACCATTGGGG+AGG + chr6_2:71039092-71039111 Msa0926980:CDS 50.0%
! TGTGCCACTCTGATTGCACA+AGG - chr6_2:71039209-71039228 None:intergenic 50.0%
! TTTTCCATCGGAGAAGAGCG+TGG + chr6_2:71038797-71038816 Msa0926980:CDS 50.0%
! TTTCCATCGGAGAAGAGCGT+GGG + chr6_2:71038798-71038817 Msa0926980:CDS 50.0%
GAGACTAAGAACCATTGGGG+AGG + chr6_2:71039092-71039111 Msa0926980:CDS 50.0%
! TGTGCCACTCTGATTGCACA+AGG - chr6_2:71039209-71039228 None:intergenic 50.0%
CGCAGTTTCAGTAGAGGGGA+AGG + chr6_2:71038848-71038867 Msa0926980:CDS 55.0%
CGCAGTTTCAGTAGAGGGGA+AGG + chr6_2:71038848-71038867 Msa0926980:CDS 55.0%
GTTCCCACGCTCTTCTCCGA+TGG - chr6_2:71038804-71038823 None:intergenic 60.0%
GTTCCCACGCTCTTCTCCGA+TGG - chr6_2:71038804-71038823 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 71038786 71039600 71038786 ID=Msa0926980;Name=Msa0926980
chr6_2 mRNA 71038786 71039600 71038786 ID=Msa0926980-mRNA-1;Parent=Msa0926980;Name=Msa0926980-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|0|0|1|1|1|2|0|241
chr6_2 exon 71038786 71039209 71038786 ID=Msa0926980-mRNA-1:exon:11721;Parent=Msa0926980-mRNA-1
chr6_2 exon 71039299 71039600 71039299 ID=Msa0926980-mRNA-1:exon:11722;Parent=Msa0926980-mRNA-1
chr6_2 CDS 71038786 71039209 71038786 ID=Msa0926980-mRNA-1:cds;Parent=Msa0926980-mRNA-1
chr6_2 CDS 71039299 71039600 71039299 ID=Msa0926980-mRNA-1:cds;Parent=Msa0926980-mRNA-1
Gene Sequence

>Msa0926980

ATGGGAAATAGTTTTCCATCGGAGAAGAGCGTGGGAACGAATGCAAGCATCAAACTTGAACACGCAGTTTCAGTAGAGGGGAAGGCATATACAGTGTCACACTACGTAGATGGTAAATCGGTTGTTATACTCTACTTATTGATAATATATCACGAAGATGGTCTCATTAAGGACTTAAATTTCGTTTTCTACGGACCTACTGGATCCGTATTTACATTCTTCGTTATAAATAAAGCAGAAAACAATCTTCTTAATTGCTGTCATACTAATCCCATCGATCCACTTTATGAAACAAATTTTAATAATGAGACTAAGAACCATTGGGGAGGGATTACGAAAACGTATGTTGCATACCATGGAGATAAAAATGAGGGGAATCTTCTTGTTGTGCAGCAGAAGAGAAAGAAGGGAGTTGAAAAGCCTTATATTAGAGTGTTAAACAATGATTTGGATGTTTCAATGAAGGATCCTTATGAACACCCTTCTTTGGTATTGCTTCAAATGTTTCAACAAGTATCGAGAACATGGATTTGGAAGTGGACGGCATGCTCTCATTGTGCTGCTCAAACTCATATGGAACAATTTGAGACTGAGAATAATGGTGAAGAAATGGAACTGTCTAGGCAAACAAATGGAAATAGTACTTTTGCCAATCAAGGTGTGATTATAGGAAATAATAATGGTAATTTAGTTGTGAAGAAACTTTCTGTTAGAAGAGGCAACTAA

Protein sequence

>Msa0926980

MGNSFPSEKSVGTNASIKLEHAVSVEGKAYTVSHYVDGKSVVILYLLIIYHEDGLIKDLNFVFYGPTGSVFTFFVINKAENNLLNCCHTNPIDPLYETNFNNETKNHWGGITKTYVAYHGDKNEGNLLVVQQKRKKGVEKPYIRVLNNDLDVSMKDPYEHPSLVLLQMFQQVSRTWIWKWTACSHCAAQTHMEQFETENNGEEMELSRQTNGNSTFANQGVIIGNNNGNLVVKKLSVRRGN*