AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0880047344.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880047344.01.T01 MTR_4g125480 71.667 60 2 1 11 70 979 1023 7.01e-20 81.6
MsG0880047344.01.T01 MTR_2g041470 61.667 60 8 1 11 70 760 804 1.41e-15 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880047344.01.T01 AT5G35560 62.295 61 8 1 9 69 719 764 7.30e-15 67.4
MsG0880047344.01.T01 AT5G35560 62.295 61 8 1 9 69 693 738 8.04e-15 67.4

Find 11 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTAATCCCTGTTATGGAT+TGG 0.373186 8:+85023589 None:intergenic
GTTAATCCCTGTTATGGATT+GGG 0.379614 8:+85023590 None:intergenic
CTCTTCTGTACAAAAGGAAT+AGG 0.398245 8:+85025320 MsG0880047344.01.T01:CDS
CGTCCTCTCTTCTGTACAAA+AGG 0.426094 8:+85025314 MsG0880047344.01.T01:CDS
TCTTCTGTACAAAAGGAATA+GGG 0.440816 8:+85025321 MsG0880047344.01.T01:CDS
TGAAAGGCCGATCGCGATGC+GGG 0.506734 8:-85024562 None:intergenic
GCTCATTCCCGCATCGCGAT+CGG 0.510279 8:+85024555 MsG0880047344.01.T01:CDS
TCGCGATCGGCCTTTCATGA+AGG 0.527167 8:+85024568 MsG0880047344.01.T01:CDS
AAGAAATAAACCTTCATGAA+AGG 0.534930 8:-85024578 None:intergenic
ACGAAAAGCTGTTTAGCACA+AGG 0.648990 8:-85025258 None:intergenic
ATGAAAGGCCGATCGCGATG+CGG 0.666016 8:-85024563 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAACTAATAAATATAAA+AGG - Chr8:85024181-85024200 None:intergenic 10.0%
!!! TAATGTTTTTAAATTTCAAA+CGG + Chr8:85024638-85024657 MsG0880047344.01.T01:intron 10.0%
!!! TTTTTAAATTATACACAATA+AGG - Chr8:85024375-85024394 None:intergenic 10.0%
!! CACTAAAAAATTACAATTAA+TGG - Chr8:85024242-85024261 None:intergenic 15.0%
!! TAAAAATTTATCAGCAAATT+AGG - Chr8:85023716-85023735 None:intergenic 15.0%
!!! ATTTGCTGATAAATTTTTAT+TGG + Chr8:85023717-85023736 MsG0880047344.01.T01:intron 15.0%
!! AATTTGTAAATGAAAAGAGT+TGG + Chr8:85024393-85024412 MsG0880047344.01.T01:intron 20.0%
!!! ATATAGTAATTTGTACCTTT+AGG + Chr8:85024502-85024521 MsG0880047344.01.T01:intron 20.0%
!!! TGATTTATATCCTTATTTCT+AGG - Chr8:85024204-85024223 None:intergenic 20.0%
! AAGAAATAAACCTTCATGAA+AGG - Chr8:85024581-85024600 None:intergenic 25.0%
! ACAGTAAGATATAATAGAGT+AGG + Chr8:85023984-85024003 MsG0880047344.01.T01:intron 25.0%
! ACATATTACGAGTTTATTGT+AGG - Chr8:85024109-85024128 None:intergenic 25.0%
! ACTGTATTGAAATAATGTAG+AGG - Chr8:85023777-85023796 None:intergenic 25.0%
! AGTAAGATATAATAGAGTAG+GGG + Chr8:85023986-85024005 MsG0880047344.01.T01:intron 25.0%
! CAATAAGGTTTAAATCAGAA+AGG - Chr8:85024360-85024379 None:intergenic 25.0%
! CAGTAAGATATAATAGAGTA+GGG + Chr8:85023985-85024004 MsG0880047344.01.T01:intron 25.0%
! CATTTATTAACGAATAACGA+TGG - Chr8:85024430-85024449 None:intergenic 25.0%
! CTACATTATTTCAATACAGT+TGG + Chr8:85023777-85023796 MsG0880047344.01.T01:intron 25.0%
! GTAAAGAATTTCACTCAAAA+AGG - Chr8:85023684-85023703 None:intergenic 25.0%
! TATTCCTTGTGTATATATAG+AGG - Chr8:85024288-85024307 None:intergenic 25.0%
!! AATTTAGCGAGACAAATTTT+TGG - Chr8:85024810-85024829 None:intergenic 25.0%
!! TAATTTTTCCTAATGACCAT+TGG - Chr8:85023952-85023971 None:intergenic 25.0%
!! TTCTCTGATTTTTATCTTCT+TGG + Chr8:85024750-85024769 MsG0880047344.01.T01:intron 25.0%
!!! TTAGTTTGTTCCTAGAAATA+AGG + Chr8:85024191-85024210 MsG0880047344.01.T01:intron 25.0%
!!! TTTCTTTTTCAACTTTGAAC+CGG + Chr8:85024920-85024939 MsG0880047344.01.T01:intron 25.0%
AAAAATGATGTTAACACGCA+CGG + Chr8:85023886-85023905 MsG0880047344.01.T01:intron 30.0%
ACAAGGAATAACAATGAGAA+AGG + Chr8:85024298-85024317 MsG0880047344.01.T01:intron 30.0%
ACTAAAAGCGACAGTAATAT+AGG - Chr8:85023857-85023876 None:intergenic 30.0%
ATGGTTGTAACTTTGTATTG+TGG + Chr8:85024889-85024908 MsG0880047344.01.T01:intron 30.0%
GCTTGAAAAATGAAAACCAT+TGG + Chr8:85024987-85025006 MsG0880047344.01.T01:intron 30.0%
GTAACCTCTATATATACACA+AGG + Chr8:85024281-85024300 MsG0880047344.01.T01:intron 30.0%
GTGTATATATAGAGGTTACA+AGG - Chr8:85024280-85024299 None:intergenic 30.0%
TCAAAAGCAAAGATACCTAA+AGG - Chr8:85024520-85024539 None:intergenic 30.0%
TGGTTGTAACTTTGTATTGT+GGG + Chr8:85024890-85024909 MsG0880047344.01.T01:intron 30.0%
! AGAAATATTGACTGATAAGC+CGG - Chr8:85024942-85024961 None:intergenic 30.0%
! CACATACAGAATGCATATTT+TGG - Chr8:85024714-85024733 None:intergenic 30.0%
! TTCAAGTTCAGTGATATGAA+TGG + Chr8:85023747-85023766 MsG0880047344.01.T01:intron 30.0%
!! ATACAGAATGCATATTTTGG+AGG - Chr8:85024711-85024730 None:intergenic 30.0%
!! CAGCTTAATTTTGTTTGTCT+TGG + Chr8:85025136-85025155 MsG0880047344.01.T01:intron 30.0%
!! TTAGGTATCTTTGCTTTTGA+AGG + Chr8:85024520-85024539 MsG0880047344.01.T01:intron 30.0%
AAGTCAACTCCTTATTCACA+CGG - Chr8:85024153-85024172 None:intergenic 35.0%
GGTTGTAACTTTGTATTGTG+GGG + Chr8:85024891-85024910 MsG0880047344.01.T01:intron 35.0%
GTTTAAATCAGAAAGGCAAG+TGG - Chr8:85024353-85024372 None:intergenic 35.0%
TAGATGATCCAATGGTCATT+AGG + Chr8:85023941-85023960 MsG0880047344.01.T01:intron 35.0%
TGAGCTTGAGTGTAAACTTT+AGG + Chr8:85023801-85023820 MsG0880047344.01.T01:intron 35.0%
! AAGCTTCATTTTGCACTAGA+AGG + Chr8:85025018-85025037 MsG0880047344.01.T01:intron 35.0%
! ATTCCTTTTGTACAGAAGAG+AGG - Chr8:85025320-85025339 None:intergenic 35.0%
! GAACATGCGCATAATCTTTT+TGG + Chr8:85025095-85025114 MsG0880047344.01.T01:intron 35.0%
!! CTTTTGAAGGAGAGTTTCAT+CGG + Chr8:85024533-85024552 MsG0880047344.01.T01:CDS 35.0%
AACTGCAACTACTCCAACTA+TGG - Chr8:85024022-85024041 None:intergenic 40.0%
ACGAAAAGCTGTTTAGCACA+AGG - Chr8:85025261-85025280 None:intergenic 40.0%
CACTATCTTTCAGACAAGCT+TGG + Chr8:85024837-85024856 MsG0880047344.01.T01:intron 40.0%
CAGCCTTACTTTGCATTTCT+AGG - Chr8:85024086-85024105 None:intergenic 40.0%
CCTCCTAGAAATGCAAAGTA+AGG + Chr8:85024080-85024099 MsG0880047344.01.T01:intron 40.0%
TCAACGAGTAGATGATCCAA+TGG + Chr8:85023933-85023952 MsG0880047344.01.T01:intron 40.0%
! CCTTACTTTGCATTTCTAGG+AGG - Chr8:85024083-85024102 None:intergenic 40.0%
! TTGTGCTAAACAGCTTTTCG+TGG + Chr8:85025260-85025279 MsG0880047344.01.T01:CDS 40.0%
!! AGTAGTTGCAGTTTGACTTG+CGG + Chr8:85024029-85024048 MsG0880047344.01.T01:intron 40.0%
!! CAGAATGCATATTTTGGAGG+TGG - Chr8:85024708-85024727 None:intergenic 40.0%
!! TGCAAAATGAAGCTTGCTAG+AGG - Chr8:85025013-85025032 None:intergenic 40.0%
AATCAGAAAGGCAAGTGGCA+CGG - Chr8:85024348-85024367 None:intergenic 45.0%
CGTCCTCTCTTCTGTACAAA+AGG + Chr8:85025314-85025333 MsG0880047344.01.T01:CDS 45.0%
GGCTTTGCTTTACGCTATAG+TGG + Chr8:85023907-85023926 MsG0880047344.01.T01:intron 45.0%
TATTCACACGGCAGACTTCA+GGG - Chr8:85024141-85024160 None:intergenic 45.0%
TGAAGTCTGCCGTGTGAATA+AGG + Chr8:85024141-85024160 MsG0880047344.01.T01:intron 45.0%
TGCACTAGAAGGCTACTTCA+AGG + Chr8:85025029-85025048 MsG0880047344.01.T01:intron 45.0%
TTATTCACACGGCAGACTTC+AGG - Chr8:85024142-85024161 None:intergenic 45.0%
! ACTTTGCATTTCTAGGAGGC+TGG - Chr8:85024079-85024098 None:intergenic 45.0%
!! TAAGCTTGTTGCAGAGGCTT+GGG + Chr8:85024865-85024884 MsG0880047344.01.T01:intron 45.0%
CAAGCCTCTGCAACAAGCTT+AGG - Chr8:85024866-85024885 None:intergenic 50.0%
GCACGGCATGTCACGAATAA+TGG - Chr8:85024331-85024350 None:intergenic 50.0%
GGGAGTCTAGTTGCCATAGT+TGG + Chr8:85024006-85024025 MsG0880047344.01.T01:intron 50.0%
TTGTTGCAGAGGCTTGGGAA+TGG + Chr8:85024870-85024889 MsG0880047344.01.T01:intron 50.0%
!! CTAAGCTTGTTGCAGAGGCT+TGG + Chr8:85024864-85024883 MsG0880047344.01.T01:intron 50.0%
!! GTCTCCTAAGCTTGTTGCAG+AGG + Chr8:85024859-85024878 MsG0880047344.01.T01:intron 50.0%
!! TGAAGCTTGCTAGAGGCCAA+TGG - Chr8:85025006-85025025 None:intergenic 50.0%
ATGAAAGGCCGATCGCGATG+CGG - Chr8:85024566-85024585 None:intergenic 55.0%
TCGCGATCGGCCTTTCATGA+AGG + Chr8:85024568-85024587 MsG0880047344.01.T01:CDS 55.0%
! TGCATTTCTAGGAGGCTGGC+TGG - Chr8:85024075-85024094 None:intergenic 55.0%
GCTCATTCCCGCATCGCGAT+CGG + Chr8:85024555-85024574 MsG0880047344.01.T01:CDS 60.0%
TGAAAGGCCGATCGCGATGC+GGG - Chr8:85024565-85024584 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr8 gene 85023603 85025341 85023603 ID=MsG0880047344.01;Name=MsG0880047344.01
Chr8 mRNA 85023603 85025341 85023603 ID=MsG0880047344.01.T01;Parent=MsG0880047344.01;Name=MsG0880047344.01.T01;_AED=0.49;_eAED=0.69;_QI=0|0|0.33|1|0|0|3|0|70
Chr8 exon 85023603 85023635 85023603 ID=MsG0880047344.01.T01:exon:6458;Parent=MsG0880047344.01.T01
Chr8 exon 85024524 85024589 85024524 ID=MsG0880047344.01.T01:exon:6459;Parent=MsG0880047344.01.T01
Chr8 exon 85025228 85025341 85025228 ID=MsG0880047344.01.T01:exon:6460;Parent=MsG0880047344.01.T01
Chr8 CDS 85023603 85023635 85023603 ID=MsG0880047344.01.T01:cds;Parent=MsG0880047344.01.T01
Chr8 CDS 85024524 85024589 85024524 ID=MsG0880047344.01.T01:cds;Parent=MsG0880047344.01.T01
Chr8 CDS 85025228 85025341 85025228 ID=MsG0880047344.01.T01:cds;Parent=MsG0880047344.01.T01
Gene Sequence

>MsG0880047344.01.T01

ATGGATTGGGTAATTTGTAAATGTAATATTCAAGTATCTTTGCTTTTGAAGGAGAGTTTCATCGGCTCATTCCCGCATCGCGATCGGCCTTTCATGAAGATCACTAATGCAGATTTATATACTTTGTTGCCTTGTGCTAAACAGCTTTTCGTGGATACACAGCTTTTTTCTGTACACACAGACATCGTCCTCTCTTCTGTACAAAAGGAATAG
Protein sequence

>MsG0880047344.01.T01

MDWVICKCNIQVSLLLKESFIGSFPHRDRPFMKITNADLYTLLPCAKQLFVDTQLFSVHTDIVLSSVQKE*