AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0271820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0271820 MtrunA17_Chr2g0315291 66.154 130 25 2 1 126 1 115 8.94e-37 122
Msa0271820 MtrunA17_Chr2g0315331 50.000 146 51 2 1 126 1 144 4.15e-32 111
Msa0271820 MtrunA17_Chr2g0315301 53.147 143 45 5 1 124 1 140 2.41e-31 108
Msa0271820 MtrunA17_Chr2g0315321 60.000 130 31 3 1 126 1 113 4.05e-31 107
Msa0271820 MtrunA17_Chr2g0315311 56.557 122 40 3 1 113 1 118 1.68e-24 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGGATTCTTTCGATTACT+TGG 0.383958 2_3:+3338265 None:intergenic
AGCACAGGCGGAGGAGGATT+GGG 0.392310 2_3:-3338238 Msa0271820:CDS
AGCACAGGAAGCGGAGGATT+GGG 0.405594 2_3:-3338355 Msa0271820:CDS
TAGCACAGGCGGAGGAGGAT+TGG 0.413090 2_3:-3338239 Msa0271820:CDS
CTCCGCTTCCTGTGCTACCC+GGG 0.415668 2_3:+3338362 None:intergenic
CCTCCTCCGCCTGTGCTACC+TGG 0.415974 2_3:+3338244 None:intergenic
TAGCACAGGAAGCGGAGGAT+TGG 0.426443 2_3:-3338356 Msa0271820:CDS
CCTCCGCTTCCTGTGCTACC+CGG 0.427212 2_3:+3338361 None:intergenic
GGCGGAGGAGGATTGGGAAC+TGG 0.445749 2_3:-3338232 Msa0271820:CDS
TTTCAAATGGCTCTTGCTGC+AGG 0.461051 2_3:-3338889 None:intergenic
GGGTTGGCAGAACTGGTATG+TGG 0.480519 2_3:+3338857 None:intergenic
CCAGGTAGCACAGGCGGAGG+AGG 0.487226 2_3:-3338244 Msa0271820:CDS
GGTTGGCAGAACTGGTATGT+GGG 0.514276 2_3:+3338858 None:intergenic
TCCGCTTCCTGTGCTACCCG+GGG 0.514938 2_3:+3338363 None:intergenic
GGAAGCGGAGGATTGGGAAC+TGG 0.515122 2_3:-3338349 Msa0271820:CDS
ATTGGGAACTGGTCCGAAAA+CGG 0.529672 2_3:-3338338 Msa0271820:CDS
TGCACAAACAACTAGTACTC+AGG 0.551675 2_3:-3338209 Msa0271820:CDS
AAGAATCCACCAGGTAGCAC+AGG 0.570025 2_3:-3338253 Msa0271820:CDS
TCAATCTTACTGCCAATGAG+TGG 0.586404 2_3:-3338147 Msa0271820:CDS
AACAACTAGTACTCAGGTGG+AGG 0.594211 2_3:-3338203 Msa0271820:CDS
CCTCCGCCTGTGCTACCTGG+TGG 0.595864 2_3:+3338247 None:intergenic
CCACCAGGTAGCACAGGCGG+AGG 0.597247 2_3:-3338247 Msa0271820:CDS
CCGGGTAGCACAGGAAGCGG+AGG 0.602411 2_3:-3338361 Msa0271820:CDS
AGTTGATCGAAAGAAACCCC+CGG 0.606931 2_3:-3338380 Msa0271820:CDS
CAATCTTACTGCCAATGAGT+GGG 0.616463 2_3:-3338146 Msa0271820:CDS
GAGAATACTCAGCGACGTGG+AGG 0.622518 2_3:-3338316 Msa0271820:CDS
AATCCACCAGGTAGCACAGG+CGG 0.634430 2_3:-3338250 Msa0271820:CDS
AGTAATCGAAAGAATCCACC+AGG 0.647364 2_3:-3338262 Msa0271820:CDS
CCGCTTCCTGTGCTACCCGG+GGG 0.651421 2_3:+3338364 None:intergenic
TCTTACTGCCAATGAGTGGG+TGG 0.702286 2_3:-3338143 None:intergenic
ACGGAGAATACTCAGCGACG+TGG 0.705185 2_3:-3338319 Msa0271820:CDS
ACAAACAACTAGTACTCAGG+TGG 0.706249 2_3:-3338206 Msa0271820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATTTTTAACTTGTTCA+GGG + chr2_3:3338445-3338464 None:intergenic 15.0%
!!! AATAAATTTTTAACTTGTTC+AGG + chr2_3:3338446-3338465 None:intergenic 15.0%
!!! TACTGATTTATAAAATCTAA+AGG + chr2_3:3338499-3338518 None:intergenic 15.0%
!!! TAGATTTTATAAATCAGTAT+AGG - chr2_3:3338500-3338519 Msa0271820:intron 15.0%
!!! AGATTTTATAAATCAGTATA+GGG - chr2_3:3338501-3338520 Msa0271820:intron 15.0%
!! AACTTATAATAAACTATCAT+TGG - chr2_3:3338542-3338561 Msa0271820:intron 15.0%
!!! ATAAATTTTTAACTTGTTCA+GGG + chr2_3:3338445-3338464 None:intergenic 15.0%
!!! AATAAATTTTTAACTTGTTC+AGG + chr2_3:3338446-3338465 None:intergenic 15.0%
!!! TACTGATTTATAAAATCTAA+AGG + chr2_3:3338499-3338518 None:intergenic 15.0%
!!! TAGATTTTATAAATCAGTAT+AGG - chr2_3:3338500-3338519 Msa0271820:intron 15.0%
!!! AGATTTTATAAATCAGTATA+GGG - chr2_3:3338501-3338520 Msa0271820:intron 15.0%
!! AACTTATAATAAACTATCAT+TGG - chr2_3:3338542-3338561 Msa0271820:intron 15.0%
!!! GTAATTGTCATAGATTTTTT+AGG + chr2_3:3338207-3338226 None:intergenic 20.0%
!! TAATTATATACGTATGCTTA+AGG - chr2_3:3338281-3338300 Msa0271820:CDS 20.0%
!!! GTAATTGTCATAGATTTTTT+AGG + chr2_3:3338207-3338226 None:intergenic 20.0%
!! TAATTATATACGTATGCTTA+AGG - chr2_3:3338281-3338300 Msa0271820:CDS 20.0%
! TTTAAATTAGCCATGATTCA+TGG - chr2_3:3338396-3338415 Msa0271820:CDS 25.0%
!!! AGTATAGGGAATTTTTTGTA+TGG - chr2_3:3338515-3338534 Msa0271820:intron 25.0%
!!! TGTTTTGTTTTTCTTGTTGT+TGG + chr2_3:3338625-3338644 None:intergenic 25.0%
! TTTAAATTAGCCATGATTCA+TGG - chr2_3:3338396-3338415 Msa0271820:CDS 25.0%
!!! AGTATAGGGAATTTTTTGTA+TGG - chr2_3:3338515-3338534 Msa0271820:intron 25.0%
!!! TGTTTTGTTTTTCTTGTTGT+TGG + chr2_3:3338625-3338644 None:intergenic 25.0%
!!! ATTTTTTAGGCACATAGTTG+GGG + chr2_3:3338194-3338213 None:intergenic 30.0%
!!! GATTTTTTAGGCACATAGTT+GGG + chr2_3:3338195-3338214 None:intergenic 30.0%
!!! AGATTTTTTAGGCACATAGT+TGG + chr2_3:3338196-3338215 None:intergenic 30.0%
GTTAATCAAACCATGAATCA+TGG + chr2_3:3338409-3338428 None:intergenic 30.0%
AAAACCACCAAAAAATTCTG+AGG - chr2_3:3338737-3338756 Msa0271820:intron 30.0%
!!! ATTTTTTAGGCACATAGTTG+GGG + chr2_3:3338194-3338213 None:intergenic 30.0%
!!! GATTTTTTAGGCACATAGTT+GGG + chr2_3:3338195-3338214 None:intergenic 30.0%
!!! AGATTTTTTAGGCACATAGT+TGG + chr2_3:3338196-3338215 None:intergenic 30.0%
GTTAATCAAACCATGAATCA+TGG + chr2_3:3338409-3338428 None:intergenic 30.0%
AAAACCACCAAAAAATTCTG+AGG - chr2_3:3338737-3338756 Msa0271820:intron 30.0%
!!! TTTTTTAGGCACATAGTTGG+GGG + chr2_3:3338193-3338212 None:intergenic 35.0%
!!! TTTTTTAGGCACATAGTTGG+GGG + chr2_3:3338193-3338212 None:intergenic 35.0%
!!! CTTGGTGCCTCAGAATTTTT+TGG + chr2_3:3338747-3338766 None:intergenic 40.0%
! GGTGGATTCTTTCGATTACT+TGG + chr2_3:3338765-3338784 None:intergenic 40.0%
AGTAATCGAAAGAATCCACC+AGG - chr2_3:3338765-3338784 Msa0271820:intron 40.0%
TGCACAAACAACTAGTACTC+AGG - chr2_3:3338818-3338837 Msa0271820:intron 40.0%
ACAAACAACTAGTACTCAGG+TGG - chr2_3:3338821-3338840 Msa0271820:CDS 40.0%
TCAATCTTACTGCCAATGAG+TGG - chr2_3:3338880-3338899 Msa0271820:CDS 40.0%
CAATCTTACTGCCAATGAGT+GGG - chr2_3:3338881-3338900 Msa0271820:CDS 40.0%
!!! CTTGGTGCCTCAGAATTTTT+TGG + chr2_3:3338747-3338766 None:intergenic 40.0%
! GGTGGATTCTTTCGATTACT+TGG + chr2_3:3338765-3338784 None:intergenic 40.0%
AGTAATCGAAAGAATCCACC+AGG - chr2_3:3338765-3338784 Msa0271820:intron 40.0%
TGCACAAACAACTAGTACTC+AGG - chr2_3:3338818-3338837 Msa0271820:intron 40.0%
ACAAACAACTAGTACTCAGG+TGG - chr2_3:3338821-3338840 Msa0271820:CDS 40.0%
TCAATCTTACTGCCAATGAG+TGG - chr2_3:3338880-3338899 Msa0271820:CDS 40.0%
CAATCTTACTGCCAATGAGT+GGG - chr2_3:3338881-3338900 Msa0271820:CDS 40.0%
AGTTGATCGAAAGAAACCCC+CGG - chr2_3:3338647-3338666 Msa0271820:intron 45.0%
ATTGGGAACTGGTCCGAAAA+CGG - chr2_3:3338689-3338708 Msa0271820:intron 45.0%
! CGCTGAGTATTCTCCGTTTT+CGG + chr2_3:3338705-3338724 None:intergenic 45.0%
!!! GGTGCCTCAGAATTTTTTGG+TGG + chr2_3:3338744-3338763 None:intergenic 45.0%
AACAACTAGTACTCAGGTGG+AGG - chr2_3:3338824-3338843 Msa0271820:CDS 45.0%
AGTTGATCGAAAGAAACCCC+CGG - chr2_3:3338647-3338666 Msa0271820:intron 45.0%
ATTGGGAACTGGTCCGAAAA+CGG - chr2_3:3338689-3338708 Msa0271820:intron 45.0%
! CGCTGAGTATTCTCCGTTTT+CGG + chr2_3:3338705-3338724 None:intergenic 45.0%
!!! GGTGCCTCAGAATTTTTTGG+TGG + chr2_3:3338744-3338763 None:intergenic 45.0%
AACAACTAGTACTCAGGTGG+AGG - chr2_3:3338824-3338843 Msa0271820:CDS 45.0%
GGTTGGCAGAACTGGTATGT+GGG + chr2_3:3338172-3338191 None:intergenic 50.0%
TTAGGCACATAGTTGGGGGT+TGG + chr2_3:3338189-3338208 None:intergenic 50.0%
GTTGATCGAAAGAAACCCCC+GGG - chr2_3:3338648-3338667 Msa0271820:intron 50.0%
AAGAATCCACCAGGTAGCAC+AGG - chr2_3:3338774-3338793 Msa0271820:intron 50.0%
GGTTGGCAGAACTGGTATGT+GGG + chr2_3:3338172-3338191 None:intergenic 50.0%
TTAGGCACATAGTTGGGGGT+TGG + chr2_3:3338189-3338208 None:intergenic 50.0%
GTTGATCGAAAGAAACCCCC+GGG - chr2_3:3338648-3338667 Msa0271820:intron 50.0%
AAGAATCCACCAGGTAGCAC+AGG - chr2_3:3338774-3338793 Msa0271820:intron 50.0%
! GGGTTGGCAGAACTGGTATG+TGG + chr2_3:3338173-3338192 None:intergenic 55.0%
! TAGTTGGGGGTTGGCAGAAC+TGG + chr2_3:3338180-3338199 None:intergenic 55.0%
TAGCACAGGAAGCGGAGGAT+TGG - chr2_3:3338671-3338690 Msa0271820:intron 55.0%
AGCACAGGAAGCGGAGGATT+GGG - chr2_3:3338672-3338691 Msa0271820:intron 55.0%
ACGGAGAATACTCAGCGACG+TGG - chr2_3:3338708-3338727 Msa0271820:intron 55.0%
GAGAATACTCAGCGACGTGG+AGG - chr2_3:3338711-3338730 Msa0271820:intron 55.0%
AATCCACCAGGTAGCACAGG+CGG - chr2_3:3338777-3338796 Msa0271820:intron 55.0%
! GGGTTGGCAGAACTGGTATG+TGG + chr2_3:3338173-3338192 None:intergenic 55.0%
! TAGTTGGGGGTTGGCAGAAC+TGG + chr2_3:3338180-3338199 None:intergenic 55.0%
TAGCACAGGAAGCGGAGGAT+TGG - chr2_3:3338671-3338690 Msa0271820:intron 55.0%
AGCACAGGAAGCGGAGGATT+GGG - chr2_3:3338672-3338691 Msa0271820:intron 55.0%
ACGGAGAATACTCAGCGACG+TGG - chr2_3:3338708-3338727 Msa0271820:intron 55.0%
GAGAATACTCAGCGACGTGG+AGG - chr2_3:3338711-3338730 Msa0271820:intron 55.0%
AATCCACCAGGTAGCACAGG+CGG - chr2_3:3338777-3338796 Msa0271820:intron 55.0%
AAGAAACCCCCGGGTAGCAC+AGG - chr2_3:3338657-3338676 Msa0271820:intron 60.0%
GGAAGCGGAGGATTGGGAAC+TGG - chr2_3:3338678-3338697 Msa0271820:intron 60.0%
TAGCACAGGCGGAGGAGGAT+TGG - chr2_3:3338788-3338807 Msa0271820:intron 60.0%
AGCACAGGCGGAGGAGGATT+GGG - chr2_3:3338789-3338808 Msa0271820:intron 60.0%
AAGAAACCCCCGGGTAGCAC+AGG - chr2_3:3338657-3338676 Msa0271820:intron 60.0%
GGAAGCGGAGGATTGGGAAC+TGG - chr2_3:3338678-3338697 Msa0271820:intron 60.0%
TAGCACAGGCGGAGGAGGAT+TGG - chr2_3:3338788-3338807 Msa0271820:intron 60.0%
AGCACAGGCGGAGGAGGATT+GGG - chr2_3:3338789-3338808 Msa0271820:intron 60.0%
TCCGCTTCCTGTGCTACCCG+GGG + chr2_3:3338667-3338686 None:intergenic 65.0%
CTCCGCTTCCTGTGCTACCC+GGG + chr2_3:3338668-3338687 None:intergenic 65.0%
CCTCCGCTTCCTGTGCTACC+CGG + chr2_3:3338669-3338688 None:intergenic 65.0%
GGCGGAGGAGGATTGGGAAC+TGG - chr2_3:3338795-3338814 Msa0271820:intron 65.0%
TCCGCTTCCTGTGCTACCCG+GGG + chr2_3:3338667-3338686 None:intergenic 65.0%
CTCCGCTTCCTGTGCTACCC+GGG + chr2_3:3338668-3338687 None:intergenic 65.0%
CCTCCGCTTCCTGTGCTACC+CGG + chr2_3:3338669-3338688 None:intergenic 65.0%
GGCGGAGGAGGATTGGGAAC+TGG - chr2_3:3338795-3338814 Msa0271820:intron 65.0%
CCGCTTCCTGTGCTACCCGG+GGG + chr2_3:3338666-3338685 None:intergenic 70.0%
CCCCCGGGTAGCACAGGAAG+CGG - chr2_3:3338663-3338682 Msa0271820:intron 70.0%
CCGGGTAGCACAGGAAGCGG+AGG - chr2_3:3338666-3338685 Msa0271820:intron 70.0%
CCTCCGCCTGTGCTACCTGG+TGG + chr2_3:3338783-3338802 None:intergenic 70.0%
CCACCAGGTAGCACAGGCGG+AGG - chr2_3:3338780-3338799 Msa0271820:intron 70.0%
CCTCCTCCGCCTGTGCTACC+TGG + chr2_3:3338786-3338805 None:intergenic 70.0%
CCAGGTAGCACAGGCGGAGG+AGG - chr2_3:3338783-3338802 Msa0271820:intron 70.0%
CCGCTTCCTGTGCTACCCGG+GGG + chr2_3:3338666-3338685 None:intergenic 70.0%
CCCCCGGGTAGCACAGGAAG+CGG - chr2_3:3338663-3338682 Msa0271820:intron 70.0%
CCGGGTAGCACAGGAAGCGG+AGG - chr2_3:3338666-3338685 Msa0271820:intron 70.0%
CCTCCGCCTGTGCTACCTGG+TGG + chr2_3:3338783-3338802 None:intergenic 70.0%
CCACCAGGTAGCACAGGCGG+AGG - chr2_3:3338780-3338799 Msa0271820:intron 70.0%
CCTCCTCCGCCTGTGCTACC+TGG + chr2_3:3338786-3338805 None:intergenic 70.0%
CCAGGTAGCACAGGCGGAGG+AGG - chr2_3:3338783-3338802 Msa0271820:intron 70.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 3338144 3338905 3338144 ID=Msa0271820;Name=Msa0271820
chr2_3 mRNA 3338144 3338905 3338144 ID=Msa0271820-mRNA-1;Parent=Msa0271820;Name=Msa0271820-mRNA-1;_AED=0.38;_eAED=0.38;_QI=0|0|0|1|1|1|2|0|126
chr2_3 exon 3338820 3338905 3338820 ID=Msa0271820-mRNA-1:exon:1689;Parent=Msa0271820-mRNA-1
chr2_3 exon 3338144 3338435 3338144 ID=Msa0271820-mRNA-1:exon:1688;Parent=Msa0271820-mRNA-1
chr2_3 CDS 3338820 3338905 3338820 ID=Msa0271820-mRNA-1:cds;Parent=Msa0271820-mRNA-1
chr2_3 CDS 3338144 3338435 3338144 ID=Msa0271820-mRNA-1:cds;Parent=Msa0271820-mRNA-1
Gene Sequence

>Msa0271820

ATGGCTCTTGCTGCAGGTAGCTTCACCCACATACCAGTTCTGCCAACCCCCAACTATGTGCCTAAAAAATCTATGACAATTACTATAAAATGTGCCAACAACAAGAAAAACAAAACAAAAGTTGATCGAAAGAAACCCCCGGGTAGCACAGGAAGCGGAGGATTGGGAACTGGTCCGAAAACGGAGAATACTCAGCGACGTGGAGGAAAAAAACCACCAAAAAATTCTGAGGCACCAAGTAATCGAAAGAATCCACCAGGTAGCACAGGCGGAGGAGGATTGGGAACTGGTGCACAAACAACTAGTACTCAGGTGGAGGATGATGAAGATCAACTTGACAACACTTTTGCATTCAATCTTACTGCCAATGAGTGGGTG

Protein sequence

>Msa0271820

MALAAGSFTHIPVLPTPNYVPKKSMTITIKCANNKKNKTKVDRKKPPGSTGSGGLGTGPKTENTQRRGGKKPPKNSEAPSNRKNPPGSTGGGGLGTGAQTTSTQVEDDEDQLDNTFAFNLTANEWV