AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0657970


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 113 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATTAATGGACTACAAAAT+AGG 0.300456 4_3:+67955122 None:intergenic
AATCAAGAAAAGTCTTTGTT+TGG 0.318002 4_3:+67956897 None:intergenic
TTTATGATTCATATTCATAA+TGG 0.350792 4_3:-67956697 Msa0657970:CDS
TGCCCTTGAACTTTATCTCT+TGG 0.367137 4_3:+67956923 None:intergenic
CAGAGTTGTTGATGAAGGTT+AGG 0.413011 4_3:-67957903 Msa0657970:CDS
GATTAATGGACTACAAAATA+GGG 0.417116 4_3:+67955123 None:intergenic
ATTCATGCCGCCACACTCAT+AGG 0.484038 4_3:-67956633 Msa0657970:CDS
CGACCAAGAGATAAAGTTCA+AGG 0.484816 4_3:-67956926 Msa0657970:CDS
GTCTTTATCTGAGATAAAGT+TGG 0.491471 4_3:-67956968 Msa0657970:CDS
GTTGATGAAGGTTAGGAATG+AGG 0.513138 4_3:-67957896 Msa0657970:intron
GATTCATATTCATAATGGCA+TGG 0.515799 4_3:-67956692 Msa0657970:CDS
GTGGGAATAGATAACTTGAT+AGG 0.521772 4_3:-67956661 Msa0657970:CDS
AGGCTCAGAGTTGTTGATGA+AGG 0.526366 4_3:-67957908 Msa0657970:CDS
TGTTTGCATATTATTGAGAG+TGG 0.529375 4_3:+67955148 None:intergenic
ATTCATATTCATAATGGCAT+GGG 0.540099 4_3:-67956691 Msa0657970:CDS
TAATGGCATGGGATCTCGTG+TGG 0.565661 4_3:-67956680 Msa0657970:CDS
AATGGCATGGGATCTCGTGT+GGG 0.632770 4_3:-67956679 Msa0657970:CDS
GACCAAGAGATAAAGTTCAA+GGG 0.637923 4_3:-67956925 Msa0657970:CDS
TCAATTCTGACCTATGAGTG+TGG 0.668878 4_3:+67956623 None:intergenic
ATTCTGACCTATGAGTGTGG+CGG 0.701306 4_3:+67956626 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATATTTTTTTTAAACAAAA+GGG + chr4_3:67956142-67956161 None:intergenic 10.0%
!!! ACATATTTTTTTTAAACAAA+AGG + chr4_3:67956143-67956162 None:intergenic 10.0%
!! TAAACAAAAGAAAAATAAAT+TGG + chr4_3:67957266-67957285 None:intergenic 10.0%
!!! ATAAACTAATTTTTTTTGTT+TGG + chr4_3:67957528-67957547 None:intergenic 10.0%
!!! TATAAACTATAGATTATTTT+CGG + chr4_3:67957643-67957662 None:intergenic 10.0%
!! TCAATTAATGAAATACAAAT+AGG + chr4_3:67955261-67955280 None:intergenic 15.0%
!!! TTTATTATTATTTTGACAAG+AGG - chr4_3:67956414-67956433 Msa0657970:intron 15.0%
!!! TTATTATTATTTTGACAAGA+GGG - chr4_3:67956415-67956434 Msa0657970:intron 15.0%
!! TTTATGATTCATATTCATAA+TGG - chr4_3:67956528-67956547 Msa0657970:intron 15.0%
!! TTTACAGTCTAATAAATATT+TGG + chr4_3:67957578-67957597 None:intergenic 15.0%
!! TTGATTGTATGTAAATTTGA+AGG - chr4_3:67955437-67955456 Msa0657970:intron 20.0%
!!! GTTATATTATTAGCTCTTAA+TGG - chr4_3:67955637-67955656 Msa0657970:intron 20.0%
!! TTGAAATATTAATGGTAAAC+AGG + chr4_3:67955716-67955735 None:intergenic 20.0%
!! TGTTTACCATTAATATTTCA+AGG - chr4_3:67955715-67955734 Msa0657970:intron 20.0%
!!! ATTAATATTTCAAGGCTTTT+GGG - chr4_3:67955723-67955742 Msa0657970:intron 20.0%
!!! ACTTGGTTTCTTTTTTAATT+TGG - chr4_3:67955893-67955912 Msa0657970:intron 20.0%
!!! TTTGAGATAAAAAAATGCTT+TGG + chr4_3:67955959-67955978 None:intergenic 20.0%
!!! AAAGTTTTTTGTTTTGCTTA+AGG - chr4_3:67956072-67956091 Msa0657970:intron 20.0%
!!! TTTAGAATAACATAGTACAA+AGG - chr4_3:67956170-67956189 Msa0657970:intron 20.0%
!! TTCTTGATTAATTCTATTGT+AGG - chr4_3:67956342-67956361 Msa0657970:intron 20.0%
!! ATATGTGTAAATATCTAAAG+TGG - chr4_3:67956688-67956707 Msa0657970:CDS 20.0%
!!! CTATTTTCTACTTTTATAAG+TGG - chr4_3:67957042-67957061 Msa0657970:intron 20.0%
!!! ACTGATTTTATTATTGAAAC+TGG - chr4_3:67957190-67957209 Msa0657970:intron 20.0%
!!! ATTTTATTATTGAAACTGGT+GGG - chr4_3:67957194-67957213 Msa0657970:intron 20.0%
!! TGTTTGAGGATTAAAATAAT+AGG - chr4_3:67957294-67957313 Msa0657970:intron 20.0%
!!! ATTTGAAATGAAGCTAAAAA+TGG + chr4_3:67957350-67957369 None:intergenic 20.0%
!! TAAATATACGATAGACAATT+AGG - chr4_3:67957484-67957503 Msa0657970:intron 20.0%
!!! TCAATTTTATTGTTTCATTG+TGG - chr4_3:67957718-67957737 Msa0657970:intron 20.0%
!!! CTTCTAAAAGAGATATTATA+TGG - chr4_3:67957867-67957886 Msa0657970:intron 20.0%
! TGTCTCAATATGTATTAAGT+AGG - chr4_3:67955212-67955231 Msa0657970:intron 25.0%
!! CGTTTTTCTCTAATATTACT+TGG - chr4_3:67955293-67955312 Msa0657970:intron 25.0%
! ATTTGATGCATAAGTCTTTA+AGG + chr4_3:67955687-67955706 None:intergenic 25.0%
! CAAAAGCCTTGAAATATTAA+TGG + chr4_3:67955724-67955743 None:intergenic 25.0%
!! CATTAATATTTCAAGGCTTT+TGG - chr4_3:67955722-67955741 Msa0657970:intron 25.0%
! TTGGGTATAATAGCATTATT+AGG - chr4_3:67955741-67955760 Msa0657970:intron 25.0%
! TAAAAAAGAAACCAAGTTAG+AGG + chr4_3:67955890-67955909 None:intergenic 25.0%
!!! AAATGCTTTGGAATTTAAAG+TGG + chr4_3:67955947-67955966 None:intergenic 25.0%
! TTAAACAAAAGGGAAAACTA+TGG + chr4_3:67956132-67956151 None:intergenic 25.0%
! TCAGATAAAGACTACAAAAT+AGG + chr4_3:67956249-67956268 None:intergenic 25.0%
! AATCAAGAAAAGTCTTTGTT+TGG + chr4_3:67956331-67956350 None:intergenic 25.0%
! ATTCATATTCATAATGGCAT+GGG - chr4_3:67956534-67956553 Msa0657970:intron 25.0%
!! AATACCAATTTTGCAAAAGA+AGG - chr4_3:67956626-67956645 Msa0657970:CDS 25.0%
!! AAAACCTTCTTTTGCAAAAT+TGG + chr4_3:67956633-67956652 None:intergenic 25.0%
!! TGTAAATATCTAAAGTGGAT+TGG - chr4_3:67956693-67956712 Msa0657970:CDS 25.0%
! GTGTGTTAAATTAAAATGAG+TGG + chr4_3:67956766-67956785 None:intergenic 25.0%
! AATCAGTCTAGTTAATGATT+TGG + chr4_3:67957177-67957196 None:intergenic 25.0%
!! GATTTTATTATTGAAACTGG+TGG - chr4_3:67957193-67957212 Msa0657970:intron 25.0%
! TGTTTAAGAGATTATGTTTG+AGG - chr4_3:67957280-67957299 Msa0657970:intron 25.0%
! CATGCTAATTGTATTAGTAT+TGG - chr4_3:67957317-67957336 Msa0657970:intron 25.0%
! CGCATTTATTAAATTTAGAG+TGG - chr4_3:67957419-67957438 Msa0657970:intron 25.0%
!!! TTTTTTTGTTTGGATCAATG+TGG + chr4_3:67957518-67957537 None:intergenic 25.0%
! AAATATTTGGCTGATGTTAT+TGG + chr4_3:67957565-67957584 None:intergenic 25.0%
! TGAATCATAGATCAGAAATA+AGG + chr4_3:67957790-67957809 None:intergenic 25.0%
! TAGAAGTTAGAAAACTGTTA+TGG + chr4_3:67957853-67957872 None:intergenic 25.0%
!!! TATATGGTTTTGCATATACT+TGG - chr4_3:67957883-67957902 Msa0657970:intron 25.0%
! AAATGAAAAGAACTCGTTAT+AGG + chr4_3:67957960-67957979 None:intergenic 25.0%
! ACTGAAAATAAACTATCTAG+AGG + chr4_3:67958054-67958073 None:intergenic 25.0%
TTTCTCTAATATTACTTGGC+AGG - chr4_3:67955297-67955316 Msa0657970:intron 30.0%
CTCTTAGAACTATACATAGA+CGG + chr4_3:67955386-67955405 None:intergenic 30.0%
! TTCTAAGAGAATTCAGAACT+AGG - chr4_3:67955397-67955416 Msa0657970:intron 30.0%
ATTATGATCGAAGATTCACA+TGG - chr4_3:67955506-67955525 Msa0657970:intron 30.0%
! TATGAGCAGTTTGAAATGTT+TGG + chr4_3:67955548-67955567 None:intergenic 30.0%
!! TAGTCTTATAACTCTCTTCA+AGG - chr4_3:67955767-67955786 Msa0657970:intron 30.0%
! ACTCATTTTCCATTTACCAT+GGG - chr4_3:67956005-67956024 Msa0657970:intron 30.0%
TTTCTATATCCCATGGTAAA+TGG + chr4_3:67956017-67956036 None:intergenic 30.0%
TACATACACTTAGTAGATTG+TGG - chr4_3:67956194-67956213 Msa0657970:intron 30.0%
! GTCTTTATCTGAGATAAAGT+TGG - chr4_3:67956257-67956276 Msa0657970:intron 30.0%
GATTCATATTCATAATGGCA+TGG - chr4_3:67956533-67956552 Msa0657970:intron 30.0%
TAAAATGAGTGGTTCAATGT+TGG + chr4_3:67956755-67956774 None:intergenic 30.0%
CAAATCAATGTTCTCTAGTT+AGG + chr4_3:67956927-67956946 None:intergenic 30.0%
! CTAACTAGAGAACATTGATT+TGG - chr4_3:67956925-67956944 Msa0657970:CDS 30.0%
TATGAACGTAAAACACTACA+CGG - chr4_3:67958009-67958028 Msa0657970:intron 30.0%
TGTTTGCATATTATTGAGAG+TGG + chr4_3:67958080-67958099 None:intergenic 30.0%
! TACATAGACGGACATTTTGT+AGG + chr4_3:67955374-67955393 None:intergenic 35.0%
! ACTCTCTTCAAGGTTTTCAT+TGG - chr4_3:67955777-67955796 Msa0657970:intron 35.0%
AGAAAACGTGCAAGTAAGTT+TGG - chr4_3:67955864-67955883 Msa0657970:intron 35.0%
! GACTCATTTTCCATTTACCA+TGG - chr4_3:67956004-67956023 Msa0657970:intron 35.0%
! CATAGCTTTTCTATATCCCA+TGG + chr4_3:67956024-67956043 None:intergenic 35.0%
ACCTATCTTACTCTTTCAGA+TGG + chr4_3:67956098-67956117 None:intergenic 35.0%
ACAAAAGGGAAAACTATGGA+TGG + chr4_3:67956128-67956147 None:intergenic 35.0%
GACCAAGAGATAAAGTTCAA+GGG - chr4_3:67956300-67956319 Msa0657970:intron 35.0%
GTGGGAATAGATAACTTGAT+AGG - chr4_3:67956564-67956583 Msa0657970:intron 35.0%
!! AATATCTAAAGTGGATTGGC+AGG - chr4_3:67956697-67956716 Msa0657970:CDS 35.0%
!! ATATCTAAAGTGGATTGGCA+GGG - chr4_3:67956698-67956717 Msa0657970:CDS 35.0%
TCCAAATTATCGATGGCAAT+GGG + chr4_3:67956900-67956919 None:intergenic 35.0%
ATCCAAATTATCGATGGCAA+TGG + chr4_3:67956901-67956920 None:intergenic 35.0%
ATTGCCATCGATAATTTGGA+TGG - chr4_3:67956900-67956919 Msa0657970:CDS 35.0%
GTATCCTGTTTGAGAAACTT+GGG + chr4_3:67957145-67957164 None:intergenic 35.0%
TGTATCCTGTTTGAGAAACT+TGG + chr4_3:67957146-67957165 None:intergenic 35.0%
!! AGAGTGGAAAGTGTCTATAT+AGG - chr4_3:67957435-67957454 Msa0657970:intron 35.0%
GATGATGTAAGCTAGAATCA+AGG + chr4_3:67957685-67957704 None:intergenic 35.0%
ATGAACGTAAAACACTACAC+GGG - chr4_3:67958010-67958029 Msa0657970:intron 35.0%
! CAGAGTTGTTGATGAAGGTT+AGG - chr4_3:67955322-67955341 Msa0657970:intron 40.0%
! GTTGATGAAGGTTAGGAATG+AGG - chr4_3:67955329-67955348 Msa0657970:intron 40.0%
! GGTTTTCATTGGACAAAGAG+AGG - chr4_3:67955788-67955807 Msa0657970:intron 40.0%
AGTAAGTTTGGCCTCTAACT+TGG - chr4_3:67955876-67955895 Msa0657970:intron 40.0%
GCCATCTGAAAGAGTAAGAT+AGG - chr4_3:67956094-67956113 Msa0657970:intron 40.0%
CGACCAAGAGATAAAGTTCA+AGG - chr4_3:67956299-67956318 Msa0657970:intron 40.0%
TGCCCTTGAACTTTATCTCT+TGG + chr4_3:67956305-67956324 None:intergenic 40.0%
TCAATTCTGACCTATGAGTG+TGG + chr4_3:67956605-67956624 None:intergenic 40.0%
CCAAATTATCGATGGCAATG+GGG + chr4_3:67956899-67956918 None:intergenic 40.0%
AGGACCATCCAAATTATCGA+TGG + chr4_3:67956907-67956926 None:intergenic 40.0%
TTATTGAAACTGGTGGGACA+AGG - chr4_3:67957200-67957219 Msa0657970:intron 40.0%
TATTGAAACTGGTGGGACAA+GGG - chr4_3:67957201-67957220 Msa0657970:intron 40.0%
! GTGAGCGCTCTAAATGTTTG+AGG - chr4_3:67955186-67955205 Msa0657970:intron 45.0%
! AGGCTCAGAGTTGTTGATGA+AGG - chr4_3:67955317-67955336 Msa0657970:intron 45.0%
ATTCTGACCTATGAGTGTGG+CGG + chr4_3:67956602-67956621 None:intergenic 45.0%
CCCCATTGCCATCGATAATT+TGG - chr4_3:67956896-67956915 Msa0657970:CDS 45.0%
ACCACCCAAGTTTCTCAAAC+AGG - chr4_3:67957138-67957157 Msa0657970:intron 45.0%
TCCTGTTTGAGAAACTTGGG+TGG + chr4_3:67957142-67957161 None:intergenic 45.0%
TAATGGCATGGGATCTCGTG+TGG - chr4_3:67956545-67956564 Msa0657970:intron 50.0%
AATGGCATGGGATCTCGTGT+GGG - chr4_3:67956546-67956565 Msa0657970:intron 50.0%
ATTCATGCCGCCACACTCAT+AGG - chr4_3:67956592-67956611 Msa0657970:intron 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 67955133 67958114 67955133 ID=Msa0657970;Name=Msa0657970
chr4_3 mRNA 67955133 67958114 67955133 ID=Msa0657970-mRNA-1;Parent=Msa0657970;Name=Msa0657970-mRNA-1;_AED=0.47;_eAED=0.48;_QI=0|0.25|0.2|0.8|0|0.2|5|0|116
chr4_3 exon 67958108 67958114 67958108 ID=Msa0657970-mRNA-1:exon:19639;Parent=Msa0657970-mRNA-1
chr4_3 exon 67957897 67957928 67957897 ID=Msa0657970-mRNA-1:exon:19638;Parent=Msa0657970-mRNA-1
chr4_3 exon 67956888 67956989 67956888 ID=Msa0657970-mRNA-1:exon:19637;Parent=Msa0657970-mRNA-1
chr4_3 exon 67956600 67956767 67956600 ID=Msa0657970-mRNA-1:exon:19636;Parent=Msa0657970-mRNA-1
chr4_3 exon 67955133 67955174 67955133 ID=Msa0657970-mRNA-1:exon:19635;Parent=Msa0657970-mRNA-1
chr4_3 CDS 67958108 67958114 67958108 ID=Msa0657970-mRNA-1:cds;Parent=Msa0657970-mRNA-1
chr4_3 CDS 67957897 67957928 67957897 ID=Msa0657970-mRNA-1:cds;Parent=Msa0657970-mRNA-1
chr4_3 CDS 67956888 67956989 67956888 ID=Msa0657970-mRNA-1:cds;Parent=Msa0657970-mRNA-1
chr4_3 CDS 67956600 67956767 67956600 ID=Msa0657970-mRNA-1:cds;Parent=Msa0657970-mRNA-1
chr4_3 CDS 67955133 67955174 67955133 ID=Msa0657970-mRNA-1:cds;Parent=Msa0657970-mRNA-1
Gene Sequence

>Msa0657970

ATGAATGGCTCAGAGTTGTTGATGAAGGTTAGGAATGAGTCTTTATCTGAGATAAAGTTGGAGCTAAAGAACAAGCAGAGCGACCAAGAGATAAAGTTCAAGGGCAATGCCAAACAAAGACTTTTCTTGATTAATTCTATTACTTTAGATAAAGTGATTGTGAGTATTTTGCTCATCTTTGTAAATAATTTTATGATTCATATTCATAATGGCATGGGATCTCGTGTGGGAATAGATAACTTGATAGGTCAGAATTCATGCCGCCACACTCATAGGTCAGAATTGAGAATACCAATTTTGCAAAAGAAGTCTTCCACTCTCAATAATATGCAAACACTCCCTATTTTGTAG

Protein sequence

>Msa0657970

MNGSELLMKVRNESLSEIKLELKNKQSDQEIKFKGNAKQRLFLINSITLDKVIVSILLIFVNNFMIHIHNGMGSRVGIDNLIGQNSCRHTHRSELRIPILQKKSSTLNNMQTLPIL*