AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1410610


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1410610 MtrunA17_Chr6g0486171 70.238 252 43 3 10 231 4 253 3.05e-118 338
Msa1410610 MtrunA17_Chr6g0486151 32.000 175 82 5 101 239 124 297 5.80e-16 75.5
Msa1410610 MtrunA17_Chr6g0486131 50.633 79 29 2 70 140 1 77 5.17e-15 72.0
Msa1410610 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 tig0023681:-33128 Msa1410610:CDS
TAGAGTGTTAAACAATGATT+TGG 0.292646 tig0023681:-33348 Msa1410610:CDS
TCCTTATGAACACCCTTCTT+TGG 0.298019 tig0023681:-33309 Msa1410610:CDS
TCCTATAATCACACCTTGAT+TGG 0.339634 tig0023681:+33127 None:intergenic
TTAAAATTTGTTTCATAAAG+TGG 0.347789 tig0023681:+33586 None:intergenic
TCACGAAGATGGTCTCATTA+AGG 0.371609 tig0023681:-33716 Msa1410610:CDS
TGAGAATAATGGTGAAGAAA+TGG 0.383194 tig0023681:-33186 Msa1410610:CDS
AAGTATCGAGAACATGGATT+TGG 0.409114 tig0023681:-33265 Msa1410610:CDS
TGATTTGGATGTTTCAATGA+AGG 0.418905 tig0023681:-33333 Msa1410610:CDS
ACCAAAGAAGGGTGTTCATA+AGG 0.427204 tig0023681:+33308 None:intergenic
TTGTGCTGCTCAAACTCATA+TGG 0.442909 tig0023681:-33222 Msa1410610:CDS
ATTTGAAGCAATACCAAAGA+AGG 0.460237 tig0023681:+33296 None:intergenic
TAATGAGACTAAGAACCATT+GGG 0.460274 tig0023681:-33563 Msa1410610:CDS
CAATTTGAGACTGAGAATAA+TGG 0.473417 tig0023681:-33197 Msa1410610:CDS
GTGATTATAGGAAATAATAA+TGG 0.477144 tig0023681:-33116 Msa1410610:CDS
TATAACGAAGAATGTAAATA+CGG 0.485507 tig0023681:+33660 None:intergenic
ACACTACGTAGATGGTAAAT+CGG 0.499784 tig0023681:-33767 Msa1410610:CDS
ACAGTGTCACACTACGTAGA+TGG 0.500726 tig0023681:-33775 Msa1410610:CDS
ATAATGAGACTAAGAACCAT+TGG 0.500792 tig0023681:-33564 Msa1410610:CDS
GTTCCCACGCTCTTCTCCGA+TGG 0.501338 tig0023681:+33850 None:intergenic
GAACTGTCTAGGCAAACAAA+TGG 0.501490 tig0023681:-33164 Msa1410610:CDS
AAGAAACTTTCTGTTAGAAG+AGG 0.522872 tig0023681:-33080 Msa1410610:CDS
CGAGAACATGGATTTGGAAG+TGG 0.525089 tig0023681:-33259 Msa1410610:CDS
GTTTCATAAAGTGGATCGAT+GGG 0.528809 tig0023681:+33595 None:intergenic
TTGATAATATATCACGAAGA+TGG 0.534894 tig0023681:-33727 Msa1410610:CDS
GTGAAGAAATGGAACTGTCT+AGG 0.541494 tig0023681:-33175 Msa1410610:CDS
CGCAGTTTCAGTAGAGGGGA+AGG 0.543862 tig0023681:-33803 Msa1410610:CDS
GTGCAGCAGAAGAGAAAGAA+GGG 0.548287 tig0023681:-33478 Msa1410610:CDS
TTCAACAAGTATCGAGAACA+TGG 0.554270 tig0023681:-33271 Msa1410610:CDS
TGTTTCATAAAGTGGATCGA+TGG 0.554991 tig0023681:+33594 None:intergenic
TGTGCAGCAGAAGAGAAAGA+AGG 0.574995 tig0023681:-33479 Msa1410610:CDS
GAACACGCAGTTTCAGTAGA+GGG 0.589661 tig0023681:-33808 Msa1410610:CDS
AAAACGTATGTTGCATACCA+TGG 0.598167 tig0023681:-33529 Msa1410610:CDS
AACACGCAGTTTCAGTAGAG+GGG 0.607913 tig0023681:-33807 Msa1410610:CDS
AATGTAAATACGGATCCAGT+AGG 0.609266 tig0023681:+33670 None:intergenic
TTTCCATCGGAGAAGAGCGT+GGG 0.612805 tig0023681:-33853 Msa1410610:CDS
AGACTAAGAACCATTGGGGA+GGG 0.620733 tig0023681:-33558 Msa1410610:CDS
TTTGAAGCAATACCAAAGAA+GGG 0.625309 tig0023681:+33297 None:intergenic
TGAACACGCAGTTTCAGTAG+AGG 0.635989 tig0023681:-33809 Msa1410610:CDS
GAGACTAAGAACCATTGGGG+AGG 0.649630 tig0023681:-33559 Msa1410610:CDS
AACATGGATTTGGAAGTGGA+CGG 0.673745 tig0023681:-33255 Msa1410610:CDS
AATGAGACTAAGAACCATTG+GGG 0.684064 tig0023681:-33562 Msa1410610:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAAAATTTGTTTCATAAAG+TGG + tig0023681:33355-33374 None:intergenic 15.0%
!!! TTAAAATTTGTTTCATAAAG+TGG + tig0023681:33355-33374 None:intergenic 15.0%
!! TATAACGAAGAATGTAAATA+CGG + tig0023681:33281-33300 None:intergenic 20.0%
!! GTGATTATAGGAAATAATAA+TGG - tig0023681:33822-33841 Msa1410610:CDS 20.0%
!! TATAACGAAGAATGTAAATA+CGG + tig0023681:33281-33300 None:intergenic 20.0%
!! GTGATTATAGGAAATAATAA+TGG - tig0023681:33822-33841 Msa1410610:CDS 20.0%
!! TTGATAATATATCACGAAGA+TGG - tig0023681:33211-33230 Msa1410610:CDS 25.0%
!! GACTTAAATTTCGTTTTCTA+CGG - tig0023681:33244-33263 Msa1410610:CDS 25.0%
!!! GTAAACAATGCTTTTTAAGT+CGG - tig0023681:33530-33549 Msa1410610:CDS 25.0%
!! TAGAGTGTTAAACAATGATT+TGG - tig0023681:33590-33609 Msa1410610:CDS 25.0%
!! TTGATAATATATCACGAAGA+TGG - tig0023681:33211-33230 Msa1410610:CDS 25.0%
!! GACTTAAATTTCGTTTTCTA+CGG - tig0023681:33244-33263 Msa1410610:CDS 25.0%
!!! GTAAACAATGCTTTTTAAGT+CGG - tig0023681:33530-33549 Msa1410610:CDS 25.0%
!! TAGAGTGTTAAACAATGATT+TGG - tig0023681:33590-33609 Msa1410610:CDS 25.0%
ATAATGAGACTAAGAACCAT+TGG - tig0023681:33374-33393 Msa1410610:intron 30.0%
TAATGAGACTAAGAACCATT+GGG - tig0023681:33375-33394 Msa1410610:intron 30.0%
ATACCATGGAGATAAAAATG+AGG - tig0023681:33423-33442 Msa1410610:intron 30.0%
TACCATGGAGATAAAAATGA+GGG - tig0023681:33424-33443 Msa1410610:intron 30.0%
!! TTTTAAGTCGGAAAAAAGTG+AGG - tig0023681:33542-33561 Msa1410610:CDS 30.0%
! TGATTTGGATGTTTCAATGA+AGG - tig0023681:33605-33624 Msa1410610:CDS 30.0%
! TTTGAAGCAATACCAAAGAA+GGG + tig0023681:33644-33663 None:intergenic 30.0%
! ATTTGAAGCAATACCAAAGA+AGG + tig0023681:33645-33664 None:intergenic 30.0%
! CAATTTGAGACTGAGAATAA+TGG - tig0023681:33741-33760 Msa1410610:CDS 30.0%
TGAGAATAATGGTGAAGAAA+TGG - tig0023681:33752-33771 Msa1410610:CDS 30.0%
! AATAGTACTTTTGCCAATCA+AGG - tig0023681:33798-33817 Msa1410610:CDS 30.0%
AAGAAACTTTCTGTTAGAAG+AGG - tig0023681:33858-33877 Msa1410610:CDS 30.0%
ATAATGAGACTAAGAACCAT+TGG - tig0023681:33374-33393 Msa1410610:intron 30.0%
TAATGAGACTAAGAACCATT+GGG - tig0023681:33375-33394 Msa1410610:intron 30.0%
ATACCATGGAGATAAAAATG+AGG - tig0023681:33423-33442 Msa1410610:intron 30.0%
TACCATGGAGATAAAAATGA+GGG - tig0023681:33424-33443 Msa1410610:intron 30.0%
!! TTTTAAGTCGGAAAAAAGTG+AGG - tig0023681:33542-33561 Msa1410610:CDS 30.0%
! TGATTTGGATGTTTCAATGA+AGG - tig0023681:33605-33624 Msa1410610:CDS 30.0%
! TTTGAAGCAATACCAAAGAA+GGG + tig0023681:33644-33663 None:intergenic 30.0%
! ATTTGAAGCAATACCAAAGA+AGG + tig0023681:33645-33664 None:intergenic 30.0%
! CAATTTGAGACTGAGAATAA+TGG - tig0023681:33741-33760 Msa1410610:CDS 30.0%
TGAGAATAATGGTGAAGAAA+TGG - tig0023681:33752-33771 Msa1410610:CDS 30.0%
! AATAGTACTTTTGCCAATCA+AGG - tig0023681:33798-33817 Msa1410610:CDS 30.0%
AAGAAACTTTCTGTTAGAAG+AGG - tig0023681:33858-33877 Msa1410610:CDS 30.0%
ACACTACGTAGATGGTAAAT+CGG - tig0023681:33171-33190 Msa1410610:CDS 35.0%
AATGTAAATACGGATCCAGT+AGG + tig0023681:33271-33290 None:intergenic 35.0%
GTTTCATAAAGTGGATCGAT+GGG + tig0023681:33346-33365 None:intergenic 35.0%
TGTTTCATAAAGTGGATCGA+TGG + tig0023681:33347-33366 None:intergenic 35.0%
AATGAGACTAAGAACCATTG+GGG - tig0023681:33376-33395 Msa1410610:intron 35.0%
AAAACGTATGTTGCATACCA+TGG - tig0023681:33409-33428 Msa1410610:intron 35.0%
ACCATGGAGATAAAAATGAG+GGG - tig0023681:33425-33444 Msa1410610:intron 35.0%
TGAGGTTGGACTTTCAATAA+TGG - tig0023681:33560-33579 Msa1410610:CDS 35.0%
!! TTCAACAAGTATCGAGAACA+TGG - tig0023681:33667-33686 Msa1410610:CDS 35.0%
!! AAGTATCGAGAACATGGATT+TGG - tig0023681:33673-33692 Msa1410610:CDS 35.0%
TCCTATAATCACACCTTGAT+TGG + tig0023681:33814-33833 None:intergenic 35.0%
ACACTACGTAGATGGTAAAT+CGG - tig0023681:33171-33190 Msa1410610:CDS 35.0%
AATGTAAATACGGATCCAGT+AGG + tig0023681:33271-33290 None:intergenic 35.0%
GTTTCATAAAGTGGATCGAT+GGG + tig0023681:33346-33365 None:intergenic 35.0%
TGTTTCATAAAGTGGATCGA+TGG + tig0023681:33347-33366 None:intergenic 35.0%
AATGAGACTAAGAACCATTG+GGG - tig0023681:33376-33395 Msa1410610:intron 35.0%
AAAACGTATGTTGCATACCA+TGG - tig0023681:33409-33428 Msa1410610:intron 35.0%
ACCATGGAGATAAAAATGAG+GGG - tig0023681:33425-33444 Msa1410610:intron 35.0%
TGAGGTTGGACTTTCAATAA+TGG - tig0023681:33560-33579 Msa1410610:CDS 35.0%
!! TTCAACAAGTATCGAGAACA+TGG - tig0023681:33667-33686 Msa1410610:CDS 35.0%
!! AAGTATCGAGAACATGGATT+TGG - tig0023681:33673-33692 Msa1410610:CDS 35.0%
TCCTATAATCACACCTTGAT+TGG + tig0023681:33814-33833 None:intergenic 35.0%
TCACGAAGATGGTCTCATTA+AGG - tig0023681:33222-33241 Msa1410610:CDS 40.0%
!! TCCCCTCATTTTTATCTCCA+TGG + tig0023681:33429-33448 None:intergenic 40.0%
AAGTCGGAAAAAAGTGAGGT+TGG - tig0023681:33546-33565 Msa1410610:CDS 40.0%
TCCTTATGAACACCCTTCTT+TGG - tig0023681:33629-33648 Msa1410610:CDS 40.0%
!! ACCAAAGAAGGGTGTTCATA+AGG + tig0023681:33633-33652 None:intergenic 40.0%
AACATGGATTTGGAAGTGGA+CGG - tig0023681:33683-33702 Msa1410610:CDS 40.0%
! TTGTGCTGCTCAAACTCATA+TGG - tig0023681:33716-33735 Msa1410610:CDS 40.0%
GTGAAGAAATGGAACTGTCT+AGG - tig0023681:33763-33782 Msa1410610:CDS 40.0%
GAACTGTCTAGGCAAACAAA+TGG - tig0023681:33774-33793 Msa1410610:CDS 40.0%
GCCAATCAAGGTGTGATTAT+AGG - tig0023681:33810-33829 Msa1410610:CDS 40.0%
TCACGAAGATGGTCTCATTA+AGG - tig0023681:33222-33241 Msa1410610:CDS 40.0%
!! TCCCCTCATTTTTATCTCCA+TGG + tig0023681:33429-33448 None:intergenic 40.0%
AAGTCGGAAAAAAGTGAGGT+TGG - tig0023681:33546-33565 Msa1410610:CDS 40.0%
TCCTTATGAACACCCTTCTT+TGG - tig0023681:33629-33648 Msa1410610:CDS 40.0%
!! ACCAAAGAAGGGTGTTCATA+AGG + tig0023681:33633-33652 None:intergenic 40.0%
AACATGGATTTGGAAGTGGA+CGG - tig0023681:33683-33702 Msa1410610:CDS 40.0%
! TTGTGCTGCTCAAACTCATA+TGG - tig0023681:33716-33735 Msa1410610:CDS 40.0%
GTGAAGAAATGGAACTGTCT+AGG - tig0023681:33763-33782 Msa1410610:CDS 40.0%
GAACTGTCTAGGCAAACAAA+TGG - tig0023681:33774-33793 Msa1410610:CDS 40.0%
GCCAATCAAGGTGTGATTAT+AGG - tig0023681:33810-33829 Msa1410610:CDS 40.0%
TGAACACGCAGTTTCAGTAG+AGG - tig0023681:33129-33148 Msa1410610:CDS 45.0%
GAACACGCAGTTTCAGTAGA+GGG - tig0023681:33130-33149 Msa1410610:CDS 45.0%
AACACGCAGTTTCAGTAGAG+GGG - tig0023681:33131-33150 Msa1410610:CDS 45.0%
ACAGTGTCACACTACGTAGA+TGG - tig0023681:33163-33182 Msa1410610:CDS 45.0%
! TTCGTTTTCTACGGACCTAC+TGG - tig0023681:33253-33272 Msa1410610:CDS 45.0%
AGACTAAGAACCATTGGGGA+GGG - tig0023681:33380-33399 Msa1410610:intron 45.0%
! TTTTCGTAATCCCTCCCCAA+TGG + tig0023681:33393-33412 None:intergenic 45.0%
TGTGCAGCAGAAGAGAAAGA+AGG - tig0023681:33459-33478 Msa1410610:intron 45.0%
GTGCAGCAGAAGAGAAAGAA+GGG - tig0023681:33460-33479 Msa1410610:intron 45.0%
! AAAGCCTTGTGCAATCAGAG+TGG - tig0023681:33489-33508 Msa1410610:CDS 45.0%
CGAGAACATGGATTTGGAAG+TGG - tig0023681:33679-33698 Msa1410610:CDS 45.0%
TGAACACGCAGTTTCAGTAG+AGG - tig0023681:33129-33148 Msa1410610:CDS 45.0%
GAACACGCAGTTTCAGTAGA+GGG - tig0023681:33130-33149 Msa1410610:CDS 45.0%
AACACGCAGTTTCAGTAGAG+GGG - tig0023681:33131-33150 Msa1410610:CDS 45.0%
ACAGTGTCACACTACGTAGA+TGG - tig0023681:33163-33182 Msa1410610:CDS 45.0%
! TTCGTTTTCTACGGACCTAC+TGG - tig0023681:33253-33272 Msa1410610:CDS 45.0%
AGACTAAGAACCATTGGGGA+GGG - tig0023681:33380-33399 Msa1410610:intron 45.0%
! TTTTCGTAATCCCTCCCCAA+TGG + tig0023681:33393-33412 None:intergenic 45.0%
TGTGCAGCAGAAGAGAAAGA+AGG - tig0023681:33459-33478 Msa1410610:intron 45.0%
GTGCAGCAGAAGAGAAAGAA+GGG - tig0023681:33460-33479 Msa1410610:intron 45.0%
! AAAGCCTTGTGCAATCAGAG+TGG - tig0023681:33489-33508 Msa1410610:CDS 45.0%
CGAGAACATGGATTTGGAAG+TGG - tig0023681:33679-33698 Msa1410610:CDS 45.0%
! TTTTCCATCGGAGAAGAGCG+TGG - tig0023681:33084-33103 Msa1410610:CDS 50.0%
! TTTCCATCGGAGAAGAGCGT+GGG - tig0023681:33085-33104 Msa1410610:CDS 50.0%
GAGACTAAGAACCATTGGGG+AGG - tig0023681:33379-33398 Msa1410610:intron 50.0%
! TGTGCCACTCTGATTGCACA+AGG + tig0023681:33496-33515 None:intergenic 50.0%
! TTTTCCATCGGAGAAGAGCG+TGG - tig0023681:33084-33103 Msa1410610:CDS 50.0%
! TTTCCATCGGAGAAGAGCGT+GGG - tig0023681:33085-33104 Msa1410610:CDS 50.0%
GAGACTAAGAACCATTGGGG+AGG - tig0023681:33379-33398 Msa1410610:intron 50.0%
! TGTGCCACTCTGATTGCACA+AGG + tig0023681:33496-33515 None:intergenic 50.0%
CGCAGTTTCAGTAGAGGGGA+AGG - tig0023681:33135-33154 Msa1410610:CDS 55.0%
CGCAGTTTCAGTAGAGGGGA+AGG - tig0023681:33135-33154 Msa1410610:CDS 55.0%
GTTCCCACGCTCTTCTCCGA+TGG + tig0023681:33091-33110 None:intergenic 60.0%
GTTCCCACGCTCTTCTCCGA+TGG + tig0023681:33091-33110 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0023681 gene 33073 33887 33073 ID=Msa1410610;Name=Msa1410610
tig0023681 mRNA 33073 33887 33073 ID=Msa1410610-mRNA-1;Parent=Msa1410610;Name=Msa1410610-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|0|0|1|1|1|2|0|241
tig0023681 exon 33464 33887 33464 ID=Msa1410610-mRNA-1:exon:26679;Parent=Msa1410610-mRNA-1
tig0023681 exon 33073 33374 33073 ID=Msa1410610-mRNA-1:exon:26678;Parent=Msa1410610-mRNA-1
tig0023681 CDS 33464 33887 33464 ID=Msa1410610-mRNA-1:cds;Parent=Msa1410610-mRNA-1
tig0023681 CDS 33073 33374 33073 ID=Msa1410610-mRNA-1:cds;Parent=Msa1410610-mRNA-1
Gene Sequence

>Msa1410610

ATGGGAAATAGTTTTCCATCGGAGAAGAGCGTGGGAACGAATGCAAGCATCAAACTTGAACACGCAGTTTCAGTAGAGGGGAAGGCATATACAGTGTCACACTACGTAGATGGTAAATCGGTTGTTATACTCTACTTATTGATAATATATCACGAAGATGGTCTCATTAAGGACTTAAATTTCGTTTTCTACGGACCTACTGGATCCGTATTTACATTCTTCGTTATAAATAAAGCAGAAAACAATCTTCTTAATTGCTGTCATACTAATCCCATCGATCCACTTTATGAAACAAATTTTAATAATGAGACTAAGAACCATTGGGGAGGGATTACGAAAACGTATGTTGCATACCATGGAGATAAAAATGAGGGGAATCTTCTTGTTGTGCAGCAGAAGAGAAAGAAGGGAGTTGAAAAGCCTTATATTAGAGTGTTAAACAATGATTTGGATGTTTCAATGAAGGATCCTTATGAACACCCTTCTTTGGTATTGCTTCAAATGTTTCAACAAGTATCGAGAACATGGATTTGGAAGTGGACGGCATGCTCTCATTGTGCTGCTCAAACTCATATGGAACAATTTGAGACTGAGAATAATGGTGAAGAAATGGAACTGTCTAGGCAAACAAATGGAAATAGTACTTTTGCCAATCAAGGTGTGATTATAGGAAATAATAATGGTAATTTAGTTGTGAAGAAACTTTCTGTTAGAAGAGGCAACTAA

Protein sequence

>Msa1410610

MGNSFPSEKSVGTNASIKLEHAVSVEGKAYTVSHYVDGKSVVILYLLIIYHEDGLIKDLNFVFYGPTGSVFTFFVINKAENNLLNCCHTNPIDPLYETNFNNETKNHWGGITKTYVAYHGDKNEGNLLVVQQKRKKGVEKPYIRVLNNDLDVSMKDPYEHPSLVLLQMFQQVSRTWIWKWTACSHCAAQTHMEQFETENNGEEMELSRQTNGNSTFANQGVIIGNNNGNLVVKKLSVRRGN*