AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014036.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014036.01.T01 MTR_4g051097 100.000 81 0 0 1 81 1 81 1.59e-50 153
MsG0380014036.01.T01 MTR_0002s0540 95.745 47 2 0 1 47 1 47 1.71e-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
MsG0380014036.01.T01 ATCG00140 96.296 81 3 0 1 81 1 81 1.56e-48 148

Find 26 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGAAGCTTTAACTATTTA+TGG 0.037973 3:-48712415 MsG0380014036.01.T01:CDS
CGGAAGCAGAGGACAAAATA+AGG 0.270738 3:-48712465 MsG0380014036.01.T01:CDS
GCCGTCGGGCTTGCTTCTAT+TGG 0.311843 3:-48712547 MsG0380014036.01.T01:CDS
GCTGCTTCTGTTATCGCTGC+TGG 0.315135 3:-48712574 MsG0380014036.01.T01:CDS
TGGAAGCTTTAACTATTTAT+GGG 0.316470 3:-48712414 MsG0380014036.01.T01:CDS
GCTGCAGGGCAAGCTGTAGA+AGG 0.363265 3:-48712502 MsG0380014036.01.T01:CDS
GGGTACTTTATTACTTAGTC+TGG 0.366228 3:-48712443 MsG0380014036.01.T01:CDS
GCTTCTATTGGACCTGGAGT+TGG 0.416315 3:-48712535 MsG0380014036.01.T01:CDS
TCGCTGCTGGGTTGGCCGTC+GGG 0.427770 3:-48712561 MsG0380014036.01.T01:CDS
ATCGCTGCTGGGTTGGCCGT+CGG 0.428270 3:-48712562 MsG0380014036.01.T01:CDS
AAAAGATTAAACAAAAGGAT+TGG 0.459809 3:+48712363 None:intergenic
AGCTTTAACTATTTATGGGC+TGG 0.460263 3:-48712410 MsG0380014036.01.T01:CDS
CTGCTTCTGTTATCGCTGCT+GGG 0.461552 3:-48712573 MsG0380014036.01.T01:CDS
GGAAGCAGAGGACAAAATAA+GGG 0.473459 3:-48712464 MsG0380014036.01.T01:CDS
AGAAGGGATTGCGCGACAAC+CGG 0.475077 3:-48712485 MsG0380014036.01.T01:CDS
GGGCTTGCTTCTATTGGACC+TGG 0.481695 3:-48712541 MsG0380014036.01.T01:CDS
GTTGGTCAAGGTACAGCTGC+AGG 0.497139 3:-48712517 MsG0380014036.01.T01:CDS
TTCTGTTATCGCTGCTGGGT+TGG 0.514112 3:-48712569 MsG0380014036.01.T01:CDS
ATTGGACCTGGAGTTGGTCA+AGG 0.543278 3:-48712529 MsG0380014036.01.T01:CDS
TGCGCGACAACCGGAAGCAG+AGG 0.554171 3:-48712476 MsG0380014036.01.T01:CDS
CTGCAGGGCAAGCTGTAGAA+GGG 0.582070 3:-48712501 MsG0380014036.01.T01:CDS
GCTGTACCTTGACCAACTCC+AGG 0.593501 3:+48712523 None:intergenic
TCCAATAGAAGCAAGCCCGA+CGG 0.638086 3:+48712546 None:intergenic
ACAGAAGCAGCAGAAATCAG+TGG 0.640161 3:+48712586 None:intergenic
TTGGTCAAGGTACAGCTGCA+GGG 0.643472 3:-48712516 MsG0380014036.01.T01:CDS
GAAGCAGAGGACAAAATAAG+GGG 0.658398 3:-48712463 MsG0380014036.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGGAAGCTTTAACTATTTA+TGG - Chr3:48712546-48712565 MsG0380014036.01.T01:CDS 25.0%
!! TGGAAGCTTTAACTATTTAT+GGG - Chr3:48712547-48712566 MsG0380014036.01.T01:CDS 25.0%
!!! ATTACTTAGTCTGGCTTTTA+TGG - Chr3:48712527-48712546 MsG0380014036.01.T01:CDS 30.0%
GGGTACTTTATTACTTAGTC+TGG - Chr3:48712518-48712537 MsG0380014036.01.T01:CDS 35.0%
! AGCTTTAACTATTTATGGGC+TGG - Chr3:48712551-48712570 MsG0380014036.01.T01:CDS 35.0%
GAAGCAGAGGACAAAATAAG+GGG - Chr3:48712498-48712517 MsG0380014036.01.T01:CDS 40.0%
GGAAGCAGAGGACAAAATAA+GGG - Chr3:48712497-48712516 MsG0380014036.01.T01:CDS 40.0%
!!! CTTATTTTGTCCTCTGCTTC+CGG + Chr3:48712498-48712517 None:intergenic 40.0%
ACAGAAGCAGCAGAAATCAG+TGG + Chr3:48712378-48712397 None:intergenic 45.0%
CGGAAGCAGAGGACAAAATA+AGG - Chr3:48712496-48712515 MsG0380014036.01.T01:CDS 45.0%
CTGCTTCTGTTATCGCTGCT+GGG - Chr3:48712388-48712407 MsG0380014036.01.T01:CDS 50.0%
GCTTCTATTGGACCTGGAGT+TGG - Chr3:48712426-48712445 MsG0380014036.01.T01:CDS 50.0%
TCCAATAGAAGCAAGCCCGA+CGG + Chr3:48712418-48712437 None:intergenic 50.0%
TTCTGTTATCGCTGCTGGGT+TGG - Chr3:48712392-48712411 MsG0380014036.01.T01:CDS 50.0%
TTGGTCAAGGTACAGCTGCA+GGG - Chr3:48712445-48712464 MsG0380014036.01.T01:CDS 50.0%
! ATTGGACCTGGAGTTGGTCA+AGG - Chr3:48712432-48712451 MsG0380014036.01.T01:CDS 50.0%
AGAAGGGATTGCGCGACAAC+CGG - Chr3:48712476-48712495 MsG0380014036.01.T01:CDS 55.0%
CTGCAGGGCAAGCTGTAGAA+GGG - Chr3:48712460-48712479 MsG0380014036.01.T01:CDS 55.0%
GCTGCTTCTGTTATCGCTGC+TGG - Chr3:48712387-48712406 MsG0380014036.01.T01:CDS 55.0%
GCTGTACCTTGACCAACTCC+AGG + Chr3:48712441-48712460 None:intergenic 55.0%
GTTGGTCAAGGTACAGCTGC+AGG - Chr3:48712444-48712463 MsG0380014036.01.T01:CDS 55.0%
! GGGCTTGCTTCTATTGGACC+TGG - Chr3:48712420-48712439 MsG0380014036.01.T01:CDS 55.0%
GCTGCAGGGCAAGCTGTAGA+AGG - Chr3:48712459-48712478 MsG0380014036.01.T01:CDS 60.0%
! GCCGTCGGGCTTGCTTCTAT+TGG - Chr3:48712414-48712433 MsG0380014036.01.T01:CDS 60.0%
TGCGCGACAACCGGAAGCAG+AGG - Chr3:48712485-48712504 MsG0380014036.01.T01:CDS 65.0%
!! ATCGCTGCTGGGTTGGCCGT+CGG - Chr3:48712399-48712418 MsG0380014036.01.T01:CDS 65.0%
!! TCGCTGCTGGGTTGGCCGTC+GGG - Chr3:48712400-48712419 MsG0380014036.01.T01:CDS 70.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48712369 48712614 48712369 ID=MsG0380014036.01;Name=MsG0380014036.01
Chr3 mRNA 48712369 48712614 48712369 ID=MsG0380014036.01.T01;Parent=MsG0380014036.01;Name=MsG0380014036.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|81
Chr3 exon 48712369 48712614 48712369 ID=MsG0380014036.01.T01:exon:9424;Parent=MsG0380014036.01.T01
Chr3 CDS 48712369 48712614 48712369 ID=MsG0380014036.01.T01:cds;Parent=MsG0380014036.01.T01
Chr3 mRNA 48712369 48712437 48712369 ID=MsG0380014036.01.T02;Parent=MsG0380014036.01;Name=MsG0380014036.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|22
Chr3 exon 48712369 48712437 48712369 ID=MsG0380014036.01.T02:exon:9425;Parent=MsG0380014036.01.T02
Chr3 CDS 48712369 48712437 48712369 ID=MsG0380014036.01.T02:cds;Parent=MsG0380014036.01.T02
Gene Sequence

>MsG0380014036.01.T01

ATGGATCCACTGATTTCTGCTGCTTCTGTTATCGCTGCTGGGTTGGCCGTCGGGCTTGCTTCTATTGGACCTGGAGTTGGTCAAGGTACAGCTGCAGGGCAAGCTGTAGAAGGGATTGCGCGACAACCGGAAGCAGAGGACAAAATAAGGGGTACTTTATTACTTAGTCTGGCTTTTATGGAAGCTTTAACTATTTATGGGCTGGTTGTAGCATTAGCACTTTTATTTGCCAATCCTTTTGTTTAA

>MsG0380014036.01.T02

ATGGAAGCTTTAACTATTTATGGGCTGGTTGTAGCATTAGCACTTTTATTTGCCAATCCTTTTGTTTAA

Protein sequence

>MsG0380014036.01.T01

MDPLISAASVIAAGLAVGLASIGPGVGQGTAAGQAVEGIARQPEAEDKIRGTLLLSLAFMEALTIYGLVVALALLFANPFV*

>MsG0380014036.01.T02

MEALTIYGLVVALALLFANPFV*