AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000295.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000295.01.T01 MTR_1g018760 100.000 89 0 0 1 89 1 89 5.63e-58 181
MsG0180000295.01.T01 MTR_3g102370 87.640 89 11 0 1 89 1 89 2.15e-49 159
MsG0180000295.01.T01 MTR_1g094030 87.640 89 11 0 1 89 1 89 2.15e-48 156
MsG0180000295.01.T01 MTR_4g109920 63.953 86 30 1 3 87 2 87 5.44e-31 111
MsG0180000295.01.T01 MTR_4g109900 62.353 85 32 0 3 87 2 86 1.84e-30 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000295.01.T01 AT3G16150 91.011 89 8 0 1 89 1 89 6.89e-53 168
MsG0180000295.01.T01 AT5G08100 61.364 88 33 1 1 87 1 88 4.31e-27 101

Find 33 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGACGATGCGGTGCCGTTTC+AGG 0.158496 1:+4096634 MsG0180000295.01.T01:CDS
GGATCTGCCCTGACGGAAAA+AGG 0.260928 1:+4096572 MsG0180000295.01.T01:CDS
AACGGCACCGCATCGTCTTT+TGG 0.318929 1:-4096629 None:intergenic
AACGGATCCATTATTCAATT+CGG 0.328084 1:+4096544 MsG0180000295.01.T01:CDS
GTTATTGAAGGTGAGGGAAT+TGG 0.347604 1:+4096520 MsG0180000295.01.T01:intron
CTTACTCGTGTTCTCAATCT+TGG 0.354252 1:+4096147 MsG0180000295.01.T01:CDS
TGACGTTGAAGAGGGAGATT+AGG 0.362167 1:-4096105 None:intergenic
AACACGAGTAAGAAGTTGTT+TGG 0.379765 1:-4096136 None:intergenic
AACATCGATGGCAGAAAGAT+TGG 0.396249 1:-4096187 None:intergenic
ATTGCTGTGCATGGTGGTGC+TGG 0.397163 1:+4096075 MsG0180000295.01.T01:CDS
ACGGATCCATTATTCAATTC+GGG 0.402987 1:+4096545 MsG0180000295.01.T01:CDS
CCACGACCCGAATTGAATAA+TGG 0.409899 1:-4096551 None:intergenic
TACTGTGGTTAAACCTGAAA+CGG 0.417200 1:-4096647 None:intergenic
AGAGAGAAACATGGGTGGTT+GGG 0.423456 1:+4096050 MsG0180000295.01.T01:exon
CCATTATTCAATTCGGGTCG+TGG 0.423817 1:+4096551 MsG0180000295.01.T01:CDS
GGTTGGGCAATTGCTGTGCA+TGG 0.428468 1:+4096066 MsG0180000295.01.T01:CDS
CTCTCTGAACTTTACCCTTA+CGG 0.430981 1:-4096019 None:intergenic
GGAAATGGAGGCTAGCATAA+TGG 0.434511 1:+4096601 MsG0180000295.01.T01:CDS
GACGTTGAAGAGGGAGATTA+GGG 0.438575 1:-4096104 None:intergenic
CTTCTTCTTGACGTTGAAGA+GGG 0.497744 1:-4096113 None:intergenic
GAGTTTGAGAGAGAGAAACA+TGG 0.504074 1:+4096041 MsG0180000295.01.T01:exon
GAGAGAGAAACATGGGTGGT+TGG 0.505927 1:+4096049 MsG0180000295.01.T01:exon
GCTTCTTCTTGACGTTGAAG+AGG 0.520285 1:-4096114 None:intergenic
AGTTTGAGAGAGAGAAACAT+GGG 0.545658 1:+4096042 MsG0180000295.01.T01:exon
GAAGGTGAGGGAATTGGAAA+CGG 0.565330 1:+4096526 MsG0180000295.01.T01:intron
GGGTCGTGGATCTGCCCTGA+CGG 0.570628 1:+4096565 MsG0180000295.01.T01:CDS
CATCGATGTTGTTGAACTTG+TGG 0.587378 1:+4096200 MsG0180000295.01.T01:CDS
ATGGAGGCTAGCATAATGGA+TGG 0.598729 1:+4096605 MsG0180000295.01.T01:CDS
CACAAGTTCAACAACATCGA+TGG 0.615685 1:-4096199 None:intergenic
TTGAGAGAGAGAAACATGGG+TGG 0.619739 1:+4096045 MsG0180000295.01.T01:exon
AAAAGGAACGGTGGAAATGG+AGG 0.622339 1:+4096589 MsG0180000295.01.T01:CDS
TGGGCAATTGCTGTGCATGG+TGG 0.661106 1:+4096069 MsG0180000295.01.T01:CDS
GGATGGACCAAAAGACGATG+CGG 0.704321 1:+4096622 MsG0180000295.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTATTTTTGTTATTGA+AGG + Chr1:4096508-4096527 MsG0180000295.01.T01:intron 10.0%
!!! AGAATATTTTAACTATTCCA+AGG + Chr1:4096459-4096478 MsG0180000295.01.T01:intron 20.0%
!!! TATAGTTTTATTTGATGTCA+CGG - Chr1:4096360-4096379 None:intergenic 20.0%
! TTCTTGTTAATCATGTAGTT+TGG - Chr1:4096443-4096462 None:intergenic 25.0%
! TTTAACTATTCCAAGGAATT+TGG + Chr1:4096466-4096485 MsG0180000295.01.T01:intron 25.0%
!!! ATTTTTGTTATTGAAGGTGA+GGG + Chr1:4096514-4096533 MsG0180000295.01.T01:intron 25.0%
!!! GTGTTTTTGTTATTGATGTT+TGG - Chr1:4096000-4096019 None:intergenic 25.0%
!!! TATTTTTGTTATTGAAGGTG+AGG + Chr1:4096513-4096532 MsG0180000295.01.T01:intron 25.0%
AACGGATCCATTATTCAATT+CGG + Chr1:4096544-4096563 MsG0180000295.01.T01:CDS 30.0%
CAATAACAAAAACACCGTAA+GGG + Chr1:4096005-4096024 MsG0180000295.01.T01:five_prime_UTR 30.0%
CCATGAAGTAATAATGGTAA+CGG - Chr1:4096334-4096353 None:intergenic 30.0%
TCAATAACAAAAACACCGTA+AGG + Chr1:4096004-4096023 MsG0180000295.01.T01:five_prime_UTR 30.0%
AAAAAAGGGACATGACAAGA+TGG - Chr1:4096299-4096318 None:intergenic 35.0%
AACACGAGTAAGAAGTTGTT+TGG - Chr1:4096139-4096158 None:intergenic 35.0%
AACTATTCCAAGGAATTTGG+AGG + Chr1:4096469-4096488 MsG0180000295.01.T01:intron 35.0%
AAGATGGAAACATGTGTATG+TGG - Chr1:4096283-4096302 None:intergenic 35.0%
ACGGATCCATTATTCAATTC+GGG + Chr1:4096545-4096564 MsG0180000295.01.T01:CDS 35.0%
ACTATTCCAAGGAATTTGGA+GGG + Chr1:4096470-4096489 MsG0180000295.01.T01:intron 35.0%
AGATGGAAACATGTGTATGT+GGG - Chr1:4096282-4096301 None:intergenic 35.0%
AGTTTGAGAGAGAGAAACAT+GGG + Chr1:4096042-4096061 MsG0180000295.01.T01:exon 35.0%
CCGTTACCATTATTACTTCA+TGG + Chr1:4096331-4096350 MsG0180000295.01.T01:intron 35.0%
GGTGGAAAAGGAACAAAAAA+GGG - Chr1:4096313-4096332 None:intergenic 35.0%
! AGGAAGTGTGGACAATATTA+TGG - Chr1:4096255-4096274 None:intergenic 35.0%
!! AATAATGGTAACGGTGGAAA+AGG - Chr1:4096325-4096344 None:intergenic 35.0%
!! TGAAGTAATAATGGTAACGG+TGG - Chr1:4096331-4096350 None:intergenic 35.0%
AACATCGATGGCAGAAAGAT+TGG - Chr1:4096190-4096209 None:intergenic 40.0%
ATAATCCCCTCCAAATTCCT+TGG - Chr1:4096479-4096498 None:intergenic 40.0%
CACAAGTTCAACAACATCGA+TGG - Chr1:4096202-4096221 None:intergenic 40.0%
CATCGATGTTGTTGAACTTG+TGG + Chr1:4096200-4096219 MsG0180000295.01.T01:CDS 40.0%
CGGTAGCCATGAAGTAATAA+TGG - Chr1:4096340-4096359 None:intergenic 40.0%
CGGTGGAAAAGGAACAAAAA+AGG - Chr1:4096314-4096333 None:intergenic 40.0%
CTATTCCAAGGAATTTGGAG+GGG + Chr1:4096471-4096490 MsG0180000295.01.T01:intron 40.0%
CTCTCTGAACTTTACCCTTA+CGG - Chr1:4096022-4096041 None:intergenic 40.0%
CTTACTCGTGTTCTCAATCT+TGG + Chr1:4096147-4096166 MsG0180000295.01.T01:CDS 40.0%
CTTCTTCTTGACGTTGAAGA+GGG - Chr1:4096116-4096135 None:intergenic 40.0%
GAGTTTGAGAGAGAGAAACA+TGG + Chr1:4096041-4096060 MsG0180000295.01.T01:exon 40.0%
GTTATTGAAGGTGAGGGAAT+TGG + Chr1:4096520-4096539 MsG0180000295.01.T01:intron 40.0%
AAAAGGAACGGTGGAAATGG+AGG + Chr1:4096589-4096608 MsG0180000295.01.T01:CDS 45.0%
AACATGTGTATGTGGGTACG+AGG - Chr1:4096275-4096294 None:intergenic 45.0%
ACAAACGAATCGTAGCGTCA+AGG + Chr1:4096380-4096399 MsG0180000295.01.T01:intron 45.0%
AGAGAGAAACATGGGTGGTT+GGG + Chr1:4096050-4096069 MsG0180000295.01.T01:exon 45.0%
CAAACGAATCGTAGCGTCAA+GGG + Chr1:4096381-4096400 MsG0180000295.01.T01:intron 45.0%
CCACGACCCGAATTGAATAA+TGG - Chr1:4096554-4096573 None:intergenic 45.0%
CCATTATTCAATTCGGGTCG+TGG + Chr1:4096551-4096570 MsG0180000295.01.T01:CDS 45.0%
GAAGGTGAGGGAATTGGAAA+CGG + Chr1:4096526-4096545 MsG0180000295.01.T01:intron 45.0%
GACGTTGAAGAGGGAGATTA+GGG - Chr1:4096107-4096126 None:intergenic 45.0%
GCTTCTTCTTGACGTTGAAG+AGG - Chr1:4096117-4096136 None:intergenic 45.0%
GGAAAAAGGAACGGTGGAAA+TGG + Chr1:4096586-4096605 MsG0180000295.01.T01:CDS 45.0%
GGAAATGGAGGCTAGCATAA+TGG + Chr1:4096601-4096620 MsG0180000295.01.T01:CDS 45.0%
TGACGTTGAAGAGGGAGATT+AGG - Chr1:4096108-4096127 None:intergenic 45.0%
TTGAGAGAGAGAAACATGGG+TGG + Chr1:4096045-4096064 MsG0180000295.01.T01:exon 45.0%
! ATGGAGGCTAGCATAATGGA+TGG + Chr1:4096605-4096624 MsG0180000295.01.T01:CDS 45.0%
GAGAGAGAAACATGGGTGGT+TGG + Chr1:4096049-4096068 MsG0180000295.01.T01:exon 50.0%
GGATGGACCAAAAGACGATG+CGG + Chr1:4096622-4096641 MsG0180000295.01.T01:CDS 50.0%
TATGTGGGTACGAGGAAGTG+TGG - Chr1:4096267-4096286 None:intergenic 50.0%
TGCCCTGACGGAAAAAGGAA+CGG + Chr1:4096577-4096596 MsG0180000295.01.T01:CDS 50.0%
! CACCGTTCCTTTTTCCGTCA+GGG - Chr1:4096582-4096601 None:intergenic 50.0%
!! CGGTGCCGTTTCAGGTTTAA+GGG + Chr1:4096642-4096661 MsG0180000295.01.T01:CDS 50.0%
CCTGACGGAAAAAGGAACGG+TGG + Chr1:4096580-4096599 MsG0180000295.01.T01:CDS 55.0%
GGATCTGCCCTGACGGAAAA+AGG + Chr1:4096572-4096591 MsG0180000295.01.T01:CDS 55.0%
GGTTGGGCAATTGCTGTGCA+TGG + Chr1:4096066-4096085 MsG0180000295.01.T01:CDS 55.0%
TGGGCAATTGCTGTGCATGG+TGG + Chr1:4096069-4096088 MsG0180000295.01.T01:CDS 55.0%
! AACGGCACCGCATCGTCTTT+TGG - Chr1:4096632-4096651 None:intergenic 55.0%
! ATTGCTGTGCATGGTGGTGC+TGG + Chr1:4096075-4096094 MsG0180000295.01.T01:CDS 55.0%
! CCACCGTTCCTTTTTCCGTC+AGG - Chr1:4096583-4096602 None:intergenic 55.0%
!! GCGGTGCCGTTTCAGGTTTA+AGG + Chr1:4096641-4096660 MsG0180000295.01.T01:CDS 55.0%
!! AGACGATGCGGTGCCGTTTC+AGG + Chr1:4096634-4096653 MsG0180000295.01.T01:CDS 60.0%
GGGTCGTGGATCTGCCCTGA+CGG + Chr1:4096565-4096584 MsG0180000295.01.T01:CDS 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 4095973 4096661 4095973 ID=MsG0180000295.01;Name=MsG0180000295.01
Chr1 mRNA 4095973 4096661 4095973 ID=MsG0180000295.01.T01;Parent=MsG0180000295.01;Name=MsG0180000295.01.T01;_AED=0.49;_eAED=0.49;_QI=87|1|1|1|0.33|0.25|4|0|97
Chr1 exon 4096530 4096661 4096530 ID=MsG0180000295.01.T01:exon:5728;Parent=MsG0180000295.01.T01
Chr1 exon 4095973 4096221 4095973 ID=MsG0180000295.01.T01:exon:5727;Parent=MsG0180000295.01.T01
Chr1 five_prime_UTR 4095973 4096059 4095973 ID=MsG0180000295.01.T01:five_prime_utr;Parent=MsG0180000295.01.T01
Chr1 CDS 4096060 4096221 4096060 ID=MsG0180000295.01.T01:cds;Parent=MsG0180000295.01.T01
Chr1 CDS 4096530 4096661 4096530 ID=MsG0180000295.01.T01:cds;Parent=MsG0180000295.01.T01
Gene Sequence

>MsG0180000295.01.T01

ATGGGTGGTTGGGCAATTGCTGTGCATGGTGGTGCTGGTGTTGACCCTAATCTCCCTCTTCAACGTCAAGAAGAAGCCAAACAACTTCTTACTCGTGTTCTCAATCTTGGCATCTCTGCTCTTCGTTCCAATCTTTCTGCCATCGATGTTGTTGAACTTGTGGTGAGGGAATTGGAAACGGATCCATTATTCAATTCGGGTCGTGGATCTGCCCTGACGGAAAAAGGAACGGTGGAAATGGAGGCTAGCATAATGGATGGACCAAAAGACGATGCGGTGCCGTTTCAGGTTTAA

Protein sequence

>MsG0180000295.01.T01

MGGWAIAVHGGAGVDPNLPLQRQEEAKQLLTRVLNLGISALRSNLSAIDVVELVVRELETDPLFNSGRGSALTEKGTVEMEASIMDGPKDDAVPFQV*