AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380017021.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017021.01.T01 MTR_3g099500 58.594 128 12 3 4 123 42 136 2.06e-33 122
MsG0380017021.01.T01 MTR_3g099500 58.594 128 12 3 4 123 42 136 2.59e-33 122
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATCTAAATTTACCTTTC+AGG 0.162754 3:-90796670 None:intergenic
CTTCTTCCTAAAATTGTAAA+AGG 0.244968 3:-90796505 None:intergenic
CTTGAATCGATCTTATGATT+AGG 0.335450 3:+90795677 None:intergenic
AATGCTAATGCTAATGCTTA+TGG 0.348338 3:+90795879 MsG0380017021.01.T01:CDS
CTCCAGGCCAAGCTTTCCGT+TGG 0.375032 3:+90796567 MsG0380017021.01.T01:CDS
CAAGAGAAGGTTTCAAGCTT+AGG 0.393866 3:+90795838 MsG0380017021.01.T01:CDS
AAGTTTAGTAAGCAAACATC+TGG 0.417882 3:+90795703 MsG0380017021.01.T01:CDS
TCCAGGCCAAGCTTTCCGTT+GGG 0.476321 3:+90796568 MsG0380017021.01.T01:CDS
CCATCATGGGAGACTTCTCC+AGG 0.497759 3:+90796551 MsG0380017021.01.T01:CDS
GGCATAGGTTAGACAAGAGA+AGG 0.508231 3:+90795825 MsG0380017021.01.T01:intron
TGCTCAAGAAGAGGTCCTTA+AGG 0.512559 3:+90795905 MsG0380017021.01.T01:CDS
GTGTATCACAAGTCGACAAT+GGG 0.523496 3:+90796590 MsG0380017021.01.T01:CDS
CCTGGAGAAGTCTCCCATGA+TGG 0.533738 3:-90796551 None:intergenic
GGAAGAAGCCATCGAAGTGA+TGG 0.535096 3:+90796520 MsG0380017021.01.T01:CDS
TCTAAATTTACCTTTCAGGA+AGG 0.539587 3:-90796666 None:intergenic
TGATGGAGAACAGACCATCA+TGG 0.540649 3:+90796537 MsG0380017021.01.T01:CDS
GATACACCCAACGGAAAGCT+TGG 0.542357 3:-90796574 None:intergenic
TCTGTTCTCCATCACTTCGA+TGG 0.545443 3:-90796528 None:intergenic
TTTGTTTGCTCCTTCCTGAA+AGG 0.546372 3:+90796656 MsG0380017021.01.T01:CDS
ACCCAACGGAAAGCTTGGCC+TGG 0.549175 3:-90796569 None:intergenic
ATTCTCACAGTTAACGATGC+TGG 0.554059 3:-90796234 None:intergenic
GATGGAGAACAGACCATCAT+GGG 0.563202 3:+90796538 MsG0380017021.01.T01:CDS
GGTGTATCACAAGTCGACAA+TGG 0.589086 3:+90796589 MsG0380017021.01.T01:CDS
TTATGGTCGTGCTCAAGAAG+AGG 0.634354 3:+90795896 MsG0380017021.01.T01:CDS
TCGACTTGTGATACACCCAA+CGG 0.689996 3:-90796583 None:intergenic
AAGCAAATCGAACTATAGTG+AGG 0.714422 3:+90795726 MsG0380017021.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAATATAAATGAGTAAAT+AGG - Chr3:90796370-90796389 None:intergenic 15.0%
!!! TCGAAAATTTGAATTTTTTT+TGG - Chr3:90796149-90796168 None:intergenic 15.0%
!!! TGAATTTTGATTGAAAATTT+TGG + Chr3:90795804-90795823 MsG0380017021.01.T01:intron 15.0%
!! GTTAAACGTTGTAAAATTTA+GGG + Chr3:90796276-90796295 MsG0380017021.01.T01:intron 20.0%
!!! GATTTTTAACGAATAATTCA+GGG + Chr3:90796071-90796090 MsG0380017021.01.T01:intron 20.0%
!!! TGATTTTTAACGAATAATTC+AGG + Chr3:90796070-90796089 MsG0380017021.01.T01:intron 20.0%
! AGAATAAAAAAAGCCTAGAA+TGG - Chr3:90795949-90795968 None:intergenic 25.0%
! CTTCTTCCTAAAATTGTAAA+AGG - Chr3:90796508-90796527 None:intergenic 25.0%
! GGTTAAACGTTGTAAAATTT+AGG + Chr3:90796275-90796294 MsG0380017021.01.T01:intron 25.0%
!! GTCTTACCTTTTACAATTTT+AGG + Chr3:90796499-90796518 MsG0380017021.01.T01:CDS 25.0%
!!! TTGATTGAAAATTTTGGCAT+AGG + Chr3:90795810-90795829 MsG0380017021.01.T01:intron 25.0%
AAGTTTAGTAAGCAAACATC+TGG + Chr3:90795703-90795722 MsG0380017021.01.T01:CDS 30.0%
AATGCTAATGCTAATGCTTA+TGG + Chr3:90795879-90795898 MsG0380017021.01.T01:CDS 30.0%
GATAGTAAGTGACATAATTC+AGG + Chr3:90796039-90796058 MsG0380017021.01.T01:intron 30.0%
TCGTTGACATAAATACCTTA+AGG - Chr3:90795923-90795942 None:intergenic 30.0%
TTTAACCGTTAAGTAACTCA+GGG + Chr3:90796007-90796026 MsG0380017021.01.T01:intron 30.0%
! CTAGCTATTTCGATTAATCT+GGG + Chr3:90796304-90796323 MsG0380017021.01.T01:intron 30.0%
! TAGCTATTTCGATTAATCTG+GGG + Chr3:90796305-90796324 MsG0380017021.01.T01:intron 30.0%
! TCTAGCTATTTCGATTAATC+TGG + Chr3:90796303-90796322 MsG0380017021.01.T01:intron 30.0%
!! GATCGACTTGTATAAATTCA+AGG + Chr3:90796336-90796355 MsG0380017021.01.T01:intron 30.0%
!!! GCTTTTGACTGCTATTTTAA+CGG + Chr3:90796442-90796461 MsG0380017021.01.T01:intron 30.0%
AAGCAAATCGAACTATAGTG+AGG + Chr3:90795726-90795745 MsG0380017021.01.T01:CDS 35.0%
AATTGACGAAGGGACTAAAT+GGG + Chr3:90796254-90796273 MsG0380017021.01.T01:intron 35.0%
CCTGATAAAAAAGTCTAACG+CGG - Chr3:90795982-90796001 None:intergenic 35.0%
GTTTAACCGTTAAGTAACTC+AGG + Chr3:90796006-90796025 MsG0380017021.01.T01:intron 35.0%
TAACTGTGAGAATTGACGAA+GGG + Chr3:90796244-90796263 MsG0380017021.01.T01:intron 35.0%
TTAACTGTGAGAATTGACGA+AGG + Chr3:90796243-90796262 MsG0380017021.01.T01:intron 35.0%
!!! CGCGTTAGACTTTTTTATCA+GGG + Chr3:90795980-90795999 MsG0380017021.01.T01:intron 35.0%
AAAGTCTAACGCGGAGATAT+CGG - Chr3:90795973-90795992 None:intergenic 40.0%
AGTCAACTTCCACATGTACA+AGG - Chr3:90796182-90796201 None:intergenic 40.0%
ATGTCAACGAACACCATTCT+AGG + Chr3:90795933-90795952 MsG0380017021.01.T01:intron 40.0%
ATTCTCACAGTTAACGATGC+TGG - Chr3:90796237-90796256 None:intergenic 40.0%
CAAGAGAAGGTTTCAAGCTT+AGG + Chr3:90795838-90795857 MsG0380017021.01.T01:CDS 40.0%
GAAATTCGTCCTTGTACATG+TGG + Chr3:90796170-90796189 MsG0380017021.01.T01:intron 40.0%
GAATTGACGAAGGGACTAAA+TGG + Chr3:90796253-90796272 MsG0380017021.01.T01:intron 40.0%
GTGTATCACAAGTCGACAAT+GGG + Chr3:90796590-90796609 MsG0380017021.01.T01:CDS 40.0%
TCGATCCCTGAGTTACTTAA+CGG - Chr3:90796015-90796034 None:intergenic 40.0%
TGTACATGTGGAAGTTGACT+TGG + Chr3:90796182-90796201 MsG0380017021.01.T01:intron 40.0%
TTTGTTTGCTCCTTCCTGAA+AGG + Chr3:90796656-90796675 MsG0380017021.01.T01:CDS 40.0%
!!! CCGCGTTAGACTTTTTTATC+AGG + Chr3:90795979-90795998 MsG0380017021.01.T01:intron 40.0%
CATTGCAACAGACTCACAAC+AGG - Chr3:90796480-90796499 None:intergenic 45.0%
GATGGAGAACAGACCATCAT+GGG + Chr3:90796538-90796557 MsG0380017021.01.T01:CDS 45.0%
GGCATAGGTTAGACAAGAGA+AGG + Chr3:90795825-90795844 MsG0380017021.01.T01:intron 45.0%
GGTGTATCACAAGTCGACAA+TGG + Chr3:90796589-90796608 MsG0380017021.01.T01:CDS 45.0%
TCTGTTCTCCATCACTTCGA+TGG - Chr3:90796531-90796550 None:intergenic 45.0%
TGATGGAGAACAGACCATCA+TGG + Chr3:90796537-90796556 MsG0380017021.01.T01:CDS 45.0%
TGCTCAAGAAGAGGTCCTTA+AGG + Chr3:90795905-90795924 MsG0380017021.01.T01:CDS 45.0%
TTATGGTCGTGCTCAAGAAG+AGG + Chr3:90795896-90795915 MsG0380017021.01.T01:CDS 45.0%
! TCGACTTGTGATACACCCAA+CGG - Chr3:90796586-90796605 None:intergenic 45.0%
GATACACCCAACGGAAAGCT+TGG - Chr3:90796577-90796596 None:intergenic 50.0%
GGAAGAAGCCATCGAAGTGA+TGG + Chr3:90796520-90796539 MsG0380017021.01.T01:CDS 50.0%
!! TGTCGCATTAAGCGCTGACA+TGG - Chr3:90796212-90796231 None:intergenic 50.0%
CCATCATGGGAGACTTCTCC+AGG + Chr3:90796551-90796570 MsG0380017021.01.T01:CDS 55.0%
CCTGGAGAAGTCTCCCATGA+TGG - Chr3:90796554-90796573 None:intergenic 55.0%
TCCAGGCCAAGCTTTCCGTT+GGG + Chr3:90796568-90796587 MsG0380017021.01.T01:CDS 55.0%
ACCCAACGGAAAGCTTGGCC+TGG - Chr3:90796572-90796591 None:intergenic 60.0%
CTCCAGGCCAAGCTTTCCGT+TGG + Chr3:90796567-90796586 MsG0380017021.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 90795691 90796681 90795691 ID=MsG0380017021.01;Name=MsG0380017021.01
Chr3 mRNA 90795691 90796681 90795691 ID=MsG0380017021.01.T01;Parent=MsG0380017021.01;Name=MsG0380017021.01.T01;_AED=0.50;_eAED=0.65;_QI=0|0.33|0.25|1|0.33|0.5|4|0|123
Chr3 exon 90795691 90795747 90795691 ID=MsG0380017021.01.T01:exon:15646;Parent=MsG0380017021.01.T01
Chr3 exon 90795837 90795926 90795837 ID=MsG0380017021.01.T01:exon:15647;Parent=MsG0380017021.01.T01
Chr3 exon 90796218 90796248 90796218 ID=MsG0380017021.01.T01:exon:15648;Parent=MsG0380017021.01.T01
Chr3 exon 90796488 90796681 90796488 ID=MsG0380017021.01.T01:exon:15649;Parent=MsG0380017021.01.T01
Chr3 CDS 90795691 90795747 90795691 ID=MsG0380017021.01.T01:cds;Parent=MsG0380017021.01.T01
Chr3 CDS 90795837 90795926 90795837 ID=MsG0380017021.01.T01:cds;Parent=MsG0380017021.01.T01
Chr3 CDS 90796218 90796248 90796218 ID=MsG0380017021.01.T01:cds;Parent=MsG0380017021.01.T01
Chr3 CDS 90796488 90796681 90796488 ID=MsG0380017021.01.T01:cds;Parent=MsG0380017021.01.T01
Gene Sequence

>MsG0380017021.01.T01

ATGATTAGGTTGAAGTTTAGTAAGCAAACATCTGGAAGCAAATCGAACTATAGTGAGACAAGAGAAGGTTTCAAGCTTAGGACAACTAATGCTAATGCTAATGCTAATGCTAATGCTTATGGTCGTGCTCAAGAAGAGGTCCTTAAGCGCTTAATGCGACACGCCAGCATCGTTAACTTCTGTTGCAATGTCTTACCTTTTACAATTTTAGGAAGAAGCCATCGAAGTGATGGAGAACAGACCATCATGGGAGACTTCTCCAGGCCAAGCTTTCCGTTGGGTGTATCACAAGTCGACAATGGGATCAATTTTGCTATATTTTCACAGCATGCAAATGCTGTCACACTTTGTTTGCTCCTTCCTGAAAGGTAA
Protein sequence

>MsG0380017021.01.T01

MIRLKFSKQTSGSKSNYSETREGFKLRTTNANANANANAYGRAQEEVLKRLMRHASIVNFCCNVLPFTILGRSHRSDGEQTIMGDFSRPSFPLGVSQVDNGINFAIFSQHANAVTLCLLLPER*