AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0350440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0350440 MtrunA17_Chr3g0085011 75.510 98 17 1 1 91 1 98 3.78e-47 145
Msa0350440 MtrunA17_Chr3g0084961 75.824 91 12 2 1 91 1 81 1.39e-41 130
Msa0350440 MtrunA17_Chr3g0084991 88.060 67 8 0 25 91 28 94 2.78e-39 125
Msa0350440 MtrunA17_Chr3g0084931 65.217 69 24 0 23 91 13 81 4.98e-24 86.7
Msa0350440 MtrunA17_Chr5g0442291 47.619 63 33 0 29 91 8 70 3.34e-14 61.6
Msa0350440 MtrunA17_Chr1g0184411 44.444 63 35 0 29 91 8 70 7.20e-12 55.5
Msa0350440 MtrunA17_Chr5g0419531 41.270 63 37 0 29 91 7 69 2.21e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATTGTTCAAATGAGATT+TGG 0.239176 3_1:+15493761 Msa0350440:three_prime_UTR
TTAGAATAAACAAGGGGATT+TGG 0.267661 3_1:+15493833 Msa0350440:three_prime_UTR
TCAGACCAACTTCTTCTTGT+AGG 0.296174 3_1:-15493552 None:intergenic
TAGAATAAACAAGGGGATTT+GGG 0.320830 3_1:+15493834 Msa0350440:three_prime_UTR
CAACATACAATCGAACTCTT+TGG 0.322647 3_1:-15493686 None:intergenic
TCACTTGGCAAGGGTTCATT+TGG 0.330216 3_1:-15493085 None:intergenic
ATATTGTTCAAATGAGATTT+GGG 0.371910 3_1:+15493762 Msa0350440:three_prime_UTR
TTGATGAATCAACCAATTGT+TGG 0.386467 3_1:-15493735 None:intergenic
AGAAGCAGAGAGGAAAATAA+AGG 0.396970 3_1:+15493596 Msa0350440:CDS
GTATGTTGATGAATCTAATA+AGG 0.406117 3_1:+15493701 Msa0350440:CDS
AACATACAATCGAACTCTTT+GGG 0.421595 3_1:-15493685 None:intergenic
GTCACCAGGGCTCCAACAAT+TGG 0.468531 3_1:+15493723 Msa0350440:CDS
GGTTCATTTGGCTGCTCCTG+AGG 0.488032 3_1:-15493073 None:intergenic
AAAATAAAGGAAGAGATGCC+TGG 0.497171 3_1:+15493609 Msa0350440:CDS
GAAATTCGAGTGGTGCCTCC+TGG 0.516148 3_1:+15493636 Msa0350440:CDS
TCATTTGGCTGCTCCTGAGG+AGG 0.525124 3_1:-15493070 None:intergenic
ACCACTCGAATTTCAACTCC+AGG 0.541025 3_1:-15493627 None:intergenic
ACAAGGAACAAATCCTCCTC+AGG 0.544834 3_1:+15493057 Msa0350440:CDS
TCAACCAATTGTTGGAGCCC+TGG 0.547441 3_1:-15493727 None:intergenic
ACATTAGAACTCACTTGGCA+AGG 0.548421 3_1:-15493095 None:intergenic
ATAATCCTACAAGAAGAAGT+TGG 0.549258 3_1:+15493547 Msa0350440:CDS
TAGTTTGGTATTCATGGCAG+AGG 0.551246 3_1:+15493024 None:intergenic
ATGAATCTAATAAGGTCACC+AGG 0.557287 3_1:+15493709 Msa0350440:CDS
CATTAGAACTCACTTGGCAA+GGG 0.564463 3_1:-15493094 None:intergenic
AGAAGTTGGTCTGAGCTAGT+TGG 0.565121 3_1:+15493561 Msa0350440:CDS
TCAGCAGTAACAAAATAGCC+AGG 0.584623 3_1:-15493654 None:intergenic
TGTAATTTGAAGAATAAACA+AGG 0.595208 3_1:+15493870 Msa0350440:three_prime_UTR
AGATTTGGGTATAATGCTAG+AGG 0.635650 3_1:+15493776 Msa0350440:three_prime_UTR
GTAATTTGAAGAATAAACAA+GGG 0.646457 3_1:+15493871 Msa0350440:three_prime_UTR
TGAATCTAATAAGGTCACCA+GGG 0.698547 3_1:+15493710 Msa0350440:CDS
GCCTGGAGTTGAAATTCGAG+TGG 0.708630 3_1:+15493626 Msa0350440:CDS
TCACTGCAGAAGAAGCAGAG+AGG 0.716587 3_1:+15493586 Msa0350440:CDS
GCAGTAACAAAATAGCCAGG+AGG 0.750368 3_1:-15493651 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGATATTGAATATATATTT+TGG + chr3_1:15493465-15493484 Msa0350440:intron 10.0%
!!! ATGATATTGAATATATATTT+TGG + chr3_1:15493465-15493484 Msa0350440:intron 10.0%
!! CTAAATCTTATTGAATAATT+TGG - chr3_1:15493149-15493168 None:intergenic 15.0%
!! AAAGAAATATTATGTTACTA+TGG - chr3_1:15493403-15493422 None:intergenic 15.0%
!!! TTTTTACTTAGAATAAACAA+GGG + chr3_1:15493826-15493845 Msa0350440:three_prime_UTR 15.0%
!! CTAAATCTTATTGAATAATT+TGG - chr3_1:15493149-15493168 None:intergenic 15.0%
!! AAAGAAATATTATGTTACTA+TGG - chr3_1:15493403-15493422 None:intergenic 15.0%
!!! TTTTTACTTAGAATAAACAA+GGG + chr3_1:15493826-15493845 Msa0350440:three_prime_UTR 15.0%
!! AATATTGTTCAAATGAGATT+TGG + chr3_1:15493761-15493780 Msa0350440:three_prime_UTR 20.0%
!! ATATTGTTCAAATGAGATTT+GGG + chr3_1:15493762-15493781 Msa0350440:three_prime_UTR 20.0%
!!! GTTTTTACTTAGAATAAACA+AGG + chr3_1:15493825-15493844 Msa0350440:three_prime_UTR 20.0%
!!! TTTTACTTAGAATAAACAAG+GGG + chr3_1:15493827-15493846 Msa0350440:three_prime_UTR 20.0%
!! TGTAATTTGAAGAATAAACA+AGG + chr3_1:15493870-15493889 Msa0350440:three_prime_UTR 20.0%
!! GTAATTTGAAGAATAAACAA+GGG + chr3_1:15493871-15493890 Msa0350440:three_prime_UTR 20.0%
!! AATATTGTTCAAATGAGATT+TGG + chr3_1:15493761-15493780 Msa0350440:three_prime_UTR 20.0%
!! ATATTGTTCAAATGAGATTT+GGG + chr3_1:15493762-15493781 Msa0350440:three_prime_UTR 20.0%
!!! GTTTTTACTTAGAATAAACA+AGG + chr3_1:15493825-15493844 Msa0350440:three_prime_UTR 20.0%
!!! TTTTACTTAGAATAAACAAG+GGG + chr3_1:15493827-15493846 Msa0350440:three_prime_UTR 20.0%
!! TGTAATTTGAAGAATAAACA+AGG + chr3_1:15493870-15493889 Msa0350440:three_prime_UTR 20.0%
!! GTAATTTGAAGAATAAACAA+GGG + chr3_1:15493871-15493890 Msa0350440:three_prime_UTR 20.0%
! TAAAAATTCACGTGAATAAG+TGG + chr3_1:15493229-15493248 Msa0350440:intron 25.0%
! AAAAATTCACGTGAATAAGT+GGG + chr3_1:15493230-15493249 Msa0350440:intron 25.0%
!!! TCTAACTTTTATTTGACACA+CGG + chr3_1:15493373-15493392 Msa0350440:intron 25.0%
!! GTATGTTGATGAATCTAATA+AGG + chr3_1:15493701-15493720 Msa0350440:CDS 25.0%
! TAAAAATTCACGTGAATAAG+TGG + chr3_1:15493229-15493248 Msa0350440:intron 25.0%
! AAAAATTCACGTGAATAAGT+GGG + chr3_1:15493230-15493249 Msa0350440:intron 25.0%
!!! TCTAACTTTTATTTGACACA+CGG + chr3_1:15493373-15493392 Msa0350440:intron 25.0%
!! GTATGTTGATGAATCTAATA+AGG + chr3_1:15493701-15493720 Msa0350440:CDS 25.0%
ATAATCCTACAAGAAGAAGT+TGG + chr3_1:15493547-15493566 Msa0350440:CDS 30.0%
AACATACAATCGAACTCTTT+GGG - chr3_1:15493688-15493707 None:intergenic 30.0%
TTGATGAATCAACCAATTGT+TGG - chr3_1:15493738-15493757 None:intergenic 30.0%
TTAGAATAAACAAGGGGATT+TGG + chr3_1:15493833-15493852 Msa0350440:three_prime_UTR 30.0%
TAGAATAAACAAGGGGATTT+GGG + chr3_1:15493834-15493853 Msa0350440:three_prime_UTR 30.0%
ATAATCCTACAAGAAGAAGT+TGG + chr3_1:15493547-15493566 Msa0350440:CDS 30.0%
AACATACAATCGAACTCTTT+GGG - chr3_1:15493688-15493707 None:intergenic 30.0%
TTGATGAATCAACCAATTGT+TGG - chr3_1:15493738-15493757 None:intergenic 30.0%
TTAGAATAAACAAGGGGATT+TGG + chr3_1:15493833-15493852 Msa0350440:three_prime_UTR 30.0%
TAGAATAAACAAGGGGATTT+GGG + chr3_1:15493834-15493853 Msa0350440:three_prime_UTR 30.0%
GAGAAACATTAGAACTCACT+TGG - chr3_1:15493103-15493122 None:intergenic 35.0%
!! CAAACACAAGACTGTCATTT+TGG - chr3_1:15493182-15493201 None:intergenic 35.0%
ACAACTCATTGCATGATCTA+GGG - chr3_1:15493271-15493290 None:intergenic 35.0%
TACAACTCATTGCATGATCT+AGG - chr3_1:15493272-15493291 None:intergenic 35.0%
GTCACTGTGTTATGATAAGT+TGG - chr3_1:15493427-15493446 None:intergenic 35.0%
AGAAGCAGAGAGGAAAATAA+AGG + chr3_1:15493596-15493615 Msa0350440:CDS 35.0%
AAAATAAAGGAAGAGATGCC+TGG + chr3_1:15493609-15493628 Msa0350440:CDS 35.0%
CAACATACAATCGAACTCTT+TGG - chr3_1:15493689-15493708 None:intergenic 35.0%
ATGAATCTAATAAGGTCACC+AGG + chr3_1:15493709-15493728 Msa0350440:CDS 35.0%
TGAATCTAATAAGGTCACCA+GGG + chr3_1:15493710-15493729 Msa0350440:CDS 35.0%
AGATTTGGGTATAATGCTAG+AGG + chr3_1:15493776-15493795 Msa0350440:three_prime_UTR 35.0%
!!! GGGTTTTGTTGTGACATTTT+CGG + chr3_1:15493891-15493910 Msa0350440:three_prime_UTR 35.0%
!!! GGTTTTGTTGTGACATTTTC+GGG + chr3_1:15493892-15493911 Msa0350440:three_prime_UTR 35.0%
GAGAAACATTAGAACTCACT+TGG - chr3_1:15493103-15493122 None:intergenic 35.0%
!! CAAACACAAGACTGTCATTT+TGG - chr3_1:15493182-15493201 None:intergenic 35.0%
ACAACTCATTGCATGATCTA+GGG - chr3_1:15493271-15493290 None:intergenic 35.0%
TACAACTCATTGCATGATCT+AGG - chr3_1:15493272-15493291 None:intergenic 35.0%
GTCACTGTGTTATGATAAGT+TGG - chr3_1:15493427-15493446 None:intergenic 35.0%
AGAAGCAGAGAGGAAAATAA+AGG + chr3_1:15493596-15493615 Msa0350440:CDS 35.0%
AAAATAAAGGAAGAGATGCC+TGG + chr3_1:15493609-15493628 Msa0350440:CDS 35.0%
CAACATACAATCGAACTCTT+TGG - chr3_1:15493689-15493708 None:intergenic 35.0%
ATGAATCTAATAAGGTCACC+AGG + chr3_1:15493709-15493728 Msa0350440:CDS 35.0%
TGAATCTAATAAGGTCACCA+GGG + chr3_1:15493710-15493729 Msa0350440:CDS 35.0%
AGATTTGGGTATAATGCTAG+AGG + chr3_1:15493776-15493795 Msa0350440:three_prime_UTR 35.0%
!!! GGGTTTTGTTGTGACATTTT+CGG + chr3_1:15493891-15493910 Msa0350440:three_prime_UTR 35.0%
!!! GGTTTTGTTGTGACATTTTC+GGG + chr3_1:15493892-15493911 Msa0350440:three_prime_UTR 35.0%
CATTAGAACTCACTTGGCAA+GGG - chr3_1:15493097-15493116 None:intergenic 40.0%
ACATTAGAACTCACTTGGCA+AGG - chr3_1:15493098-15493117 None:intergenic 40.0%
TCAGACCAACTTCTTCTTGT+AGG - chr3_1:15493555-15493574 None:intergenic 40.0%
TCAGCAGTAACAAAATAGCC+AGG - chr3_1:15493657-15493676 None:intergenic 40.0%
CATTAGAACTCACTTGGCAA+GGG - chr3_1:15493097-15493116 None:intergenic 40.0%
ACATTAGAACTCACTTGGCA+AGG - chr3_1:15493098-15493117 None:intergenic 40.0%
TCAGACCAACTTCTTCTTGT+AGG - chr3_1:15493555-15493574 None:intergenic 40.0%
TCAGCAGTAACAAAATAGCC+AGG - chr3_1:15493657-15493676 None:intergenic 40.0%
GCAGAGGAAAAACAAGGACA+AGG + chr3_1:15493040-15493059 Msa0350440:CDS 45.0%
ACAAGGAACAAATCCTCCTC+AGG + chr3_1:15493057-15493076 Msa0350440:CDS 45.0%
TCACTTGGCAAGGGTTCATT+TGG - chr3_1:15493088-15493107 None:intergenic 45.0%
! AGAAGTTGGTCTGAGCTAGT+TGG + chr3_1:15493561-15493580 Msa0350440:CDS 45.0%
ACCACTCGAATTTCAACTCC+AGG - chr3_1:15493630-15493649 None:intergenic 45.0%
GCAGTAACAAAATAGCCAGG+AGG - chr3_1:15493654-15493673 None:intergenic 45.0%
GCAGAGGAAAAACAAGGACA+AGG + chr3_1:15493040-15493059 Msa0350440:CDS 45.0%
ACAAGGAACAAATCCTCCTC+AGG + chr3_1:15493057-15493076 Msa0350440:CDS 45.0%
TCACTTGGCAAGGGTTCATT+TGG - chr3_1:15493088-15493107 None:intergenic 45.0%
! AGAAGTTGGTCTGAGCTAGT+TGG + chr3_1:15493561-15493580 Msa0350440:CDS 45.0%
ACCACTCGAATTTCAACTCC+AGG - chr3_1:15493630-15493649 None:intergenic 45.0%
GCAGTAACAAAATAGCCAGG+AGG - chr3_1:15493654-15493673 None:intergenic 45.0%
!! AAAATTAAATAATTTATTTC+AGG + chr3_1:15493519-15493538 Msa0350440:intron 5.0%
!! AAATTAAATAATTTATTTCA+GGG + chr3_1:15493520-15493539 Msa0350440:intron 5.0%
!! AAAATTAAATAATTTATTTC+AGG + chr3_1:15493519-15493538 Msa0350440:intron 5.0%
!! AAATTAAATAATTTATTTCA+GGG + chr3_1:15493520-15493539 Msa0350440:intron 5.0%
TCACTGCAGAAGAAGCAGAG+AGG + chr3_1:15493586-15493605 Msa0350440:CDS 50.0%
GCCTGGAGTTGAAATTCGAG+TGG + chr3_1:15493626-15493645 Msa0350440:CDS 50.0%
TCAACCAATTGTTGGAGCCC+TGG - chr3_1:15493730-15493749 None:intergenic 50.0%
TCACTGCAGAAGAAGCAGAG+AGG + chr3_1:15493586-15493605 Msa0350440:CDS 50.0%
GCCTGGAGTTGAAATTCGAG+TGG + chr3_1:15493626-15493645 Msa0350440:CDS 50.0%
TCAACCAATTGTTGGAGCCC+TGG - chr3_1:15493730-15493749 None:intergenic 50.0%
TCATTTGGCTGCTCCTGAGG+AGG - chr3_1:15493073-15493092 None:intergenic 55.0%
GGTTCATTTGGCTGCTCCTG+AGG - chr3_1:15493076-15493095 None:intergenic 55.0%
GAAATTCGAGTGGTGCCTCC+TGG + chr3_1:15493636-15493655 Msa0350440:CDS 55.0%
GTCACCAGGGCTCCAACAAT+TGG + chr3_1:15493723-15493742 Msa0350440:CDS 55.0%
TCATTTGGCTGCTCCTGAGG+AGG - chr3_1:15493073-15493092 None:intergenic 55.0%
GGTTCATTTGGCTGCTCCTG+AGG - chr3_1:15493076-15493095 None:intergenic 55.0%
GAAATTCGAGTGGTGCCTCC+TGG + chr3_1:15493636-15493655 Msa0350440:CDS 55.0%
GTCACCAGGGCTCCAACAAT+TGG + chr3_1:15493723-15493742 Msa0350440:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 15493037 15493919 15493037 ID=Msa0350440;Name=Msa0350440
chr3_1 mRNA 15493037 15493919 15493037 ID=Msa0350440-mRNA-1;Parent=Msa0350440;Name=Msa0350440-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|1|0.5|1|1|1|2|170|91
chr3_1 exon 15493037 15493103 15493037 ID=Msa0350440-mRNA-1:exon:3783;Parent=Msa0350440-mRNA-1
chr3_1 exon 15493541 15493919 15493541 ID=Msa0350440-mRNA-1:exon:3784;Parent=Msa0350440-mRNA-1
chr3_1 CDS 15493037 15493103 15493037 ID=Msa0350440-mRNA-1:cds;Parent=Msa0350440-mRNA-1
chr3_1 CDS 15493541 15493749 15493541 ID=Msa0350440-mRNA-1:cds;Parent=Msa0350440-mRNA-1
chr3_1 three_prime_UTR 15493750 15493919 15493750 ID=Msa0350440-mRNA-1:three_prime_utr;Parent=Msa0350440-mRNA-1
Gene Sequence

>Msa0350440

ATGGCAGAGGAAAAACAAGGACAAGGAACAAATCCTCCTCAGGAGCAGCCAAATGAACCCTTGCCAAGGACAAATAATCCTACAAGAAGAAGTTGGTCTGAGCTAGTTGGTGTCACTGCAGAAGAAGCAGAGAGGAAAATAAAGGAAGAGATGCCTGGAGTTGAAATTCGAGTGGTGCCTCCTGGCTATTTTGTTACTGCTGATTATAAGACCCAAAGAGTTCGATTGTATGTTGATGAATCTAATAAGGTCACCAGGGCTCCAACAATTGGTTGA
Protein sequence

>Msa0350440

MAEEKQGQGTNPPQEQPNEPLPRTNNPTRRSWSELVGVTAEEAERKIKEEMPGVEIRVVPPGYFVTADYKTQRVRLYVDESNKVTRAPTIG*