AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0090950


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 8 sgRNAs with CRISPR-Local

Find 149 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATTGATCTTGAAGGATTT+TGG 0.241356 1_2:+73085544 Msa0090950:CDS
GAGCTTGCTAAACCTGAATT+AGG 0.258702 1_2:+73084414 Msa0090950:CDS
GCTACAATATGATTTGGTTT+TGG 0.292771 1_2:+73085505 Msa0090950:CDS
ATTCCAGCTACAATATGATT+TGG 0.322208 1_2:+73085499 Msa0090950:CDS
GTGTTCTCAAAACCTAATTC+AGG 0.330796 1_2:-73084426 None:intergenic
AAACCAAATCATATTGTAGC+TGG 0.444443 1_2:-73085502 None:intergenic
GGTAGGCATATTGATCTTGA+AGG 0.492825 1_2:+73085537 Msa0090950:CDS
TCAGAGAAAGACTGATGGAA+TGG 0.562153 1_2:+73082893 Msa0090950:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTGATTTTTTGTATTCAAT+TGG - chr1_2:73083273-73083292 None:intergenic 15.0%
!!! ATTTGTTTAATTTGGTTTTT+TGG + chr1_2:73083733-73083752 Msa0090950:intron 15.0%
!! AGTTCATTGTAATTAAATAA+TGG + chr1_2:73084930-73084949 Msa0090950:intron 15.0%
!! TTGAAATTCAAATTTGTAAG+AGG + chr1_2:73083041-73083060 Msa0090950:intron 20.0%
!! TGAAATTCAAATTTGTAAGA+GGG + chr1_2:73083042-73083061 Msa0090950:intron 20.0%
!! AATCTTTATATCTAATCCAA+AGG - chr1_2:73083108-73083127 None:intergenic 20.0%
!! ATTCAAACTAAAAGACAATT+GGG - chr1_2:73083136-73083155 None:intergenic 20.0%
!!! TAGTTTTCCATAGATTTTTT+AGG + chr1_2:73083679-73083698 Msa0090950:intron 20.0%
!! GTAAGATCATTTGTTTAATT+TGG + chr1_2:73083725-73083744 Msa0090950:intron 20.0%
!! ACTACAAATTCAATAGAAAA+TGG - chr1_2:73084482-73084501 None:intergenic 20.0%
!! AGTAACATAAATTAAGTGTT+TGG + chr1_2:73084743-73084762 Msa0090950:intron 20.0%
!!! ATAATAAGAGTGTAAAGTAA+AGG - chr1_2:73084824-73084843 None:intergenic 20.0%
!!! AGTACTCAATTTTTTTTTGT+TGG + chr1_2:73084969-73084988 Msa0090950:intron 20.0%
! ATGGAATGGTAAATAAAAGA+TGG + chr1_2:73082907-73082926 Msa0090950:intron 25.0%
!!! CTTCAACTTATTTTTTGCAT+CGG - chr1_2:73083016-73083035 None:intergenic 25.0%
!! GATGCAAAAAATAAGTTGAA+GGG + chr1_2:73083015-73083034 Msa0090950:intron 25.0%
! GATTCAAACTAAAAGACAAT+TGG - chr1_2:73083137-73083156 None:intergenic 25.0%
! TGATTGAGAATAGAAATCAA+AGG + chr1_2:73083560-73083579 Msa0090950:intron 25.0%
! GATTGAGAATAGAAATCAAA+GGG + chr1_2:73083561-73083580 Msa0090950:intron 25.0%
! TGAACAACAAATGAATTGAA+AGG - chr1_2:73083656-73083675 None:intergenic 25.0%
! AAAGAAGCCTAAAAAATCTA+TGG - chr1_2:73083689-73083708 None:intergenic 25.0%
! TTCTTTCAAAATCAAGGTAA+TGG + chr1_2:73083703-73083722 Msa0090950:intron 25.0%
!!! TTTTGGTTATTTGTAATCTG+AGG + chr1_2:73083750-73083769 Msa0090950:intron 25.0%
!! TTTTCCATTAGTGTTCTATA+AGG + chr1_2:73083821-73083840 Msa0090950:intron 25.0%
! TTTCCATTAGTGTTCTATAA+GGG + chr1_2:73083822-73083841 Msa0090950:intron 25.0%
! TACAGTTTAATGCATATGAT+TGG + chr1_2:73083975-73083994 Msa0090950:intron 25.0%
!!! TTTGTTTTCCTCTTCTTTTT+GGG + chr1_2:73084002-73084021 Msa0090950:intron 25.0%
! TTACAAAAAAAGAAGAAGCT+AGG - chr1_2:73084324-73084343 None:intergenic 25.0%
!!! GCTTCTTCTTTTTTTGTAAA+AGG + chr1_2:73084325-73084344 Msa0090950:intron 25.0%
! TAAAAGGATATCTCATGAAT+TGG + chr1_2:73084341-73084360 Msa0090950:intron 25.0%
!! CTATTGAATTTGTAGTCTTA+TGG + chr1_2:73084486-73084505 Msa0090950:intron 25.0%
! AACTTCATTTGATAAACACA+TGG + chr1_2:73084571-73084590 Msa0090950:intron 25.0%
! CATAAAATAAAGCTCATGTA+AGG - chr1_2:73084852-73084871 None:intergenic 25.0%
! ATCTATACAATTAGGTTTCA+TGG - chr1_2:73084881-73084900 None:intergenic 25.0%
! ATGAAACCTAATTGTATAGA+TGG + chr1_2:73084880-73084899 Msa0090950:intron 25.0%
!!! TAAAGGTGTTTTGTATTGTT+AGG + chr1_2:73085114-73085133 Msa0090950:intron 25.0%
!!! AAAGGTGTTTTGTATTGTTA+GGG + chr1_2:73085115-73085134 Msa0090950:intron 25.0%
!!! GCTTTAGAAACAATTCTATT+AGG + chr1_2:73085140-73085159 Msa0090950:intron 25.0%
! ATCGTGTGATTTGAAAATTA+AGG + chr1_2:73085172-73085191 Msa0090950:intron 25.0%
! ATAGAATCTTCAAGAAATCA+TGG - chr1_2:73085324-73085343 None:intergenic 25.0%
!!! ATTTGTTTTGACTTTTGATG+TGG + chr1_2:73085355-73085374 Msa0090950:intron 25.0%
! AAACAACATCACAAATTAGA+CGG - chr1_2:73085402-73085421 None:intergenic 25.0%
! TTCTGCATCAAAATAAAGTA+AGG - chr1_2:73085459-73085478 None:intergenic 25.0%
!!! TGATTTGGTTTTGGAATAAT+AGG + chr1_2:73085514-73085533 Msa0090950:CDS 25.0%
!!! GATTTGGTTTTGGAATAATA+GGG + chr1_2:73085515-73085534 Msa0090950:CDS 25.0%
!!! ATTTGGTTTTGGAATAATAG+GGG + chr1_2:73085516-73085535 Msa0090950:CDS 25.0%
!! ATATTGATCTTGAAGGATTT+TGG + chr1_2:73085544-73085563 Msa0090950:CDS 25.0%
AAAAATCAGAGAAAGACTGA+TGG + chr1_2:73082888-73082907 Msa0090950:CDS 30.0%
AGAGAAAAATTCTGCTTTGT+TGG + chr1_2:73082945-73082964 Msa0090950:intron 30.0%
! CGATGCAAAAAATAAGTTGA+AGG + chr1_2:73083014-73083033 Msa0090950:intron 30.0%
AATTCAAATTTGTAAGAGGG+AGG + chr1_2:73083045-73083064 Msa0090950:intron 30.0%
ATTCAAATTTGTAAGAGGGA+GGG + chr1_2:73083046-73083065 Msa0090950:intron 30.0%
TAACCCTAACCCTAAAAATT+TGG - chr1_2:73083074-73083093 None:intergenic 30.0%
AAACTAAAAGACAATTGGGA+GGG - chr1_2:73083132-73083151 None:intergenic 30.0%
ACTCATTGAAGAAGATACTT+GGG - chr1_2:73083297-73083316 None:intergenic 30.0%
AACTCATTGAAGAAGATACT+TGG - chr1_2:73083298-73083317 None:intergenic 30.0%
!! TTTTTACCTTGCTTCTGAAA+TGG - chr1_2:73083328-73083347 None:intergenic 30.0%
!! AAATTTTTCGAACGTTGAGT+CGG + chr1_2:73083487-73083506 Msa0090950:intron 30.0%
TTAGGCTTCTTTCAAAATCA+AGG + chr1_2:73083697-73083716 Msa0090950:intron 30.0%
TAATGGAAAAATACATGCGT+GGG - chr1_2:73083811-73083830 None:intergenic 30.0%
CAAACAGAATATGAAACTGA+AGG - chr1_2:73083873-73083892 None:intergenic 30.0%
CTTCAGTTTCATATTCTGTT+TGG + chr1_2:73083871-73083890 Msa0090950:intron 30.0%
TTATACTAACCTGATTTCTC+TGG + chr1_2:73083902-73083921 Msa0090950:intron 30.0%
GTTTAATGCATATGATTGGT+AGG + chr1_2:73083979-73083998 Msa0090950:intron 30.0%
!! GTTTGTTTTCCTCTTCTTTT+TGG + chr1_2:73084001-73084020 Msa0090950:intron 30.0%
!!! GACTTTTTTGTCGTTTGTTT+TGG + chr1_2:73084061-73084080 Msa0090950:intron 30.0%
CAATGGAGGAAATTAATTTC+AGG - chr1_2:73084534-73084553 None:intergenic 30.0%
ATCACATACACATCAAACAA+TGG - chr1_2:73084551-73084570 None:intergenic 30.0%
CATTCATTCTCAAGATATGT+TGG + chr1_2:73084649-73084668 Msa0090950:intron 30.0%
CAAATGGTAAGTGTTTCTTA+TGG + chr1_2:73084687-73084706 Msa0090950:intron 30.0%
GTTTCAGATCTGATAAGAAA+TGG + chr1_2:73084719-73084738 Msa0090950:intron 30.0%
GTAAAGGAATCATTGAAGTT+AGG - chr1_2:73084808-73084827 None:intergenic 30.0%
AACATGCCATCTATACAATT+AGG - chr1_2:73084889-73084908 None:intergenic 30.0%
!! ACAAACAAACGTTTAAGTTG+AGG - chr1_2:73085030-73085049 None:intergenic 30.0%
TCAACTTAAACGTTTGTTTG+TGG + chr1_2:73085029-73085048 Msa0090950:intron 30.0%
!!! GGAAATGGAATCTTATTTTG+TGG - chr1_2:73085079-73085098 None:intergenic 30.0%
TGGAAAGTAAAGAAAATGCT+AGG - chr1_2:73085205-73085224 None:intergenic 30.0%
CATGGAGGAAATAGTAAAAA+TGG - chr1_2:73085306-73085325 None:intergenic 30.0%
!!! TTTTGACTTTTGATGTGGTT+TGG + chr1_2:73085360-73085379 Msa0090950:intron 30.0%
AAATAAAGTAAGGTAAGCCA+TGG - chr1_2:73085449-73085468 None:intergenic 30.0%
ATTCCAGCTACAATATGATT+TGG + chr1_2:73085499-73085518 Msa0090950:CDS 30.0%
AAACCAAATCATATTGTAGC+TGG - chr1_2:73085505-73085524 None:intergenic 30.0%
!!! GCTACAATATGATTTGGTTT+TGG + chr1_2:73085505-73085524 Msa0090950:CDS 30.0%
AAAATGAAGAGAAAGCAACG+TGG + chr1_2:73082968-73082987 Msa0090950:intron 35.0%
AAATGAAGAGAAAGCAACGT+GGG + chr1_2:73082969-73082988 Msa0090950:intron 35.0%
CAAACTAAAAGACAATTGGG+AGG - chr1_2:73083133-73083152 None:intergenic 35.0%
TGCAGTGATGCCTAAAAATT+TGG + chr1_2:73083171-73083190 Msa0090950:intron 35.0%
GCAGTGATGCCTAAAAATTT+GGG + chr1_2:73083172-73083191 Msa0090950:intron 35.0%
ATAACTCCATTTCAGAAGCA+AGG + chr1_2:73083319-73083338 Msa0090950:intron 35.0%
! AACCTTTTGTCACAAAGAAG+AGG - chr1_2:73083600-73083619 None:intergenic 35.0%
CTAATGGAAAAATACATGCG+TGG - chr1_2:73083812-73083831 None:intergenic 35.0%
CAAACAAAACCAGAGAAATC+AGG - chr1_2:73083914-73083933 None:intergenic 35.0%
!!! CTGATTTCTCTGGTTTTGTT+TGG + chr1_2:73083912-73083931 Msa0090950:intron 35.0%
TAAGAACTCCCAAAAAGAAG+AGG - chr1_2:73084013-73084032 None:intergenic 35.0%
!! CTTCTTTTTGGGAGTTCTTA+AGG + chr1_2:73084013-73084032 Msa0090950:intron 35.0%
TTATGATCATGAGACGTTTG+AGG + chr1_2:73084111-73084130 Msa0090950:intron 35.0%
GTCTCAATCTGAAAAACTGA+TGG + chr1_2:73084138-73084157 Msa0090950:intron 35.0%
GTTTCTCTCTATCACTTTGT+AGG + chr1_2:73084377-73084396 Msa0090950:intron 35.0%
GTGTTCTCAAAACCTAATTC+AGG - chr1_2:73084429-73084448 None:intergenic 35.0%
!! TTTTGAGAACACACATGTAG+AGG + chr1_2:73084437-73084456 Msa0090950:CDS 35.0%
ACATACACATCAAACAATGG+AGG - chr1_2:73084548-73084567 None:intergenic 35.0%
GCAGCAAAAGCAATAACAAA+TGG + chr1_2:73084671-73084690 Msa0090950:intron 35.0%
!! GTGGTATCTAGAGTTTTATG+TGG + chr1_2:73085048-73085067 Msa0090950:intron 35.0%
ATAATCAGCTACACAGGAAA+TGG - chr1_2:73085094-73085113 None:intergenic 35.0%
CCTTTAATAATCAGCTACAC+AGG - chr1_2:73085100-73085119 None:intergenic 35.0%
CCTGTGTAGCTGATTATTAA+AGG + chr1_2:73085097-73085116 Msa0090950:intron 35.0%
GAATCTTCAAGAAATCATGG+AGG - chr1_2:73085321-73085340 None:intergenic 35.0%
!! TTTTGATGTGGTTTGGATGT+TGG + chr1_2:73085367-73085386 Msa0090950:intron 35.0%
CATCACAAATTAGACGGTTA+TGG - chr1_2:73085396-73085415 None:intergenic 35.0%
TCAGAGAAAGACTGATGGAA+TGG + chr1_2:73082893-73082912 Msa0090950:CDS 40.0%
!!! GCGCCAAATTTTTAGGGTTA+GGG + chr1_2:73083068-73083087 Msa0090950:intron 40.0%
GGTTATGCATAGTGAACCTT+TGG + chr1_2:73083089-73083108 Msa0090950:intron 40.0%
GTGATGCCTAAAAATTTGGG+TGG + chr1_2:73083175-73083194 Msa0090950:intron 40.0%
! GCAATGCCACCCAAATTTTT+AGG - chr1_2:73083184-73083203 None:intergenic 40.0%
! AACCTGATTGGTCAATTGTG+TGG - chr1_2:73083226-73083245 None:intergenic 40.0%
TGTGTGTCTCAAAACCTGAT+TGG - chr1_2:73083238-73083257 None:intergenic 40.0%
! CGTCATCATCTCAGAGTTTT+CGG - chr1_2:73083422-73083441 None:intergenic 40.0%
GATAACGATGCGAAAGCTAA+CGG + chr1_2:73083446-73083465 Msa0090950:intron 40.0%
ATAACGATGCGAAAGCTAAC+GGG + chr1_2:73083447-73083466 Msa0090950:intron 40.0%
CTCCTCTTCTTTGTGACAAA+AGG + chr1_2:73083595-73083614 Msa0090950:intron 40.0%
CTGCCCTTATAGAACACTAA+TGG - chr1_2:73083828-73083847 None:intergenic 40.0%
TCTATAAGGGCAGTGATAGA+TGG + chr1_2:73083835-73083854 Msa0090950:intron 40.0%
!! GAGCTTGCTAAACCTGAATT+AGG + chr1_2:73084414-73084433 Msa0090950:CDS 40.0%
! CAACTGCATTTTGCAATTGC+AGG + chr1_2:73084610-73084629 Msa0090950:intron 40.0%
! TTTTGCAATTGCAGGAGCTA+TGG + chr1_2:73084618-73084637 Msa0090950:intron 40.0%
TTTGCAATTGCAGGAGCTAT+GGG + chr1_2:73084619-73084638 Msa0090950:intron 40.0%
TATTGAAGAAACTCCGTGAG+TGG - chr1_2:73085236-73085255 None:intergenic 40.0%
CACAAATTAGACGGTTATGG+AGG - chr1_2:73085393-73085412 None:intergenic 40.0%
! TCTAAAACCATGTTCAGCCA+TGG + chr1_2:73085429-73085448 Msa0090950:intron 40.0%
! TAGCTGGAATTTTGCTTCGA+TGG - chr1_2:73085489-73085508 None:intergenic 40.0%
!!! GGTTTTGGAATAATAGGGGT+AGG + chr1_2:73085520-73085539 Msa0090950:CDS 40.0%
GGTAGGCATATTGATCTTGA+AGG + chr1_2:73085537-73085556 Msa0090950:CDS 40.0%
!!! GGCGCCAAATTTTTAGGGTT+AGG + chr1_2:73083067-73083086 Msa0090950:intron 45.0%
! CTGATTGGTCAATTGTGTGG+TGG - chr1_2:73083223-73083242 None:intergenic 45.0%
CACCACACAATTGACCAATC+AGG + chr1_2:73083221-73083240 Msa0090950:intron 45.0%
AGAGAGAGAGAGAGATGGAA+TGG - chr1_2:73083363-73083382 None:intergenic 45.0%
AAAGCTAACGGGATCGAATG+TGG + chr1_2:73083458-73083477 Msa0090950:intron 45.0%
!! TTTTTCGAACGTTGAGTCGG+AGG + chr1_2:73083490-73083509 Msa0090950:intron 45.0%
GTCACATTCACACAGAGAAG+AGG - chr1_2:73083536-73083555 None:intergenic 45.0%
!!! GGTTTTGTTTGGTGACAGAC+TGG + chr1_2:73083923-73083942 Msa0090950:intron 45.0%
! GTGCTCTGTTTGAAGTGTAG+TGG + chr1_2:73084282-73084301 Msa0090950:intron 45.0%
TTCCATCTGTTTGCCACTCA+CGG + chr1_2:73085220-73085239 Msa0090950:intron 45.0%
!!! AGGGAGGGCGCCAAATTTTT+AGG + chr1_2:73083061-73083080 Msa0090950:intron 50.0%
!!! GGGAGGGCGCCAAATTTTTA+GGG + chr1_2:73083062-73083081 Msa0090950:intron 50.0%
GAGAGAGAGAGAGAGAGAGA+TGG - chr1_2:73083368-73083387 None:intergenic 50.0%
TGAGTCGGAGGAAGCGAATA+CGG + chr1_2:73083502-73083521 Msa0090950:intron 50.0%
AGGTAAGCCATGGCTGAACA+TGG - chr1_2:73085439-73085458 None:intergenic 50.0%
CTCCGTGAGTGGCAAACAGA+TGG - chr1_2:73085225-73085244 None:intergenic 55.0%
CGGCGATGCACATCGCAAAG+AGG - chr1_2:73083402-73083421 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 73082882 73085572 73082882 ID=Msa0090950;Name=Msa0090950
chr1_2 mRNA 73082882 73085572 73082882 ID=Msa0090950-mRNA-1;Parent=Msa0090950;Name=Msa0090950-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0|0.33|0.66|1|0.66|3|0|62
chr1_2 exon 73082882 73082914 73082882 ID=Msa0090950-mRNA-1:exon:25460;Parent=Msa0090950-mRNA-1
chr1_2 exon 73084399 73084458 73084399 ID=Msa0090950-mRNA-1:exon:25461;Parent=Msa0090950-mRNA-1
chr1_2 exon 73085477 73085572 73085477 ID=Msa0090950-mRNA-1:exon:25462;Parent=Msa0090950-mRNA-1
chr1_2 CDS 73082882 73082914 73082882 ID=Msa0090950-mRNA-1:cds;Parent=Msa0090950-mRNA-1
chr1_2 CDS 73084399 73084458 73084399 ID=Msa0090950-mRNA-1:cds;Parent=Msa0090950-mRNA-1
chr1_2 CDS 73085477 73085572 73085477 ID=Msa0090950-mRNA-1:cds;Parent=Msa0090950-mRNA-1
Gene Sequence

>Msa0090950

ATGAAGAAAAATCAGAGAAAGACTGATGGAATGGTTCATAAAGTTGTTGAGCTTGCTAAACCTGAATTAGGTTTTGAGAACACACATGTAGAGAAAATGTCTCCATCGAAGCAAAATTCCAGCTACAATATGATTTGGTTTTGGAATAATAGGGGTAGGCATATTGATCTTGAAGGATTTTGGAATTAG

Protein sequence

>Msa0090950

MKKNQRKTDGMVHKVVELAKPELGFENTHVEKMSPSKQNSSYNMIWFWNNRGRHIDLEGFWN*