AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000446.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000446.01.T01 MTR_1g015750 96.591 88 3 0 4 91 305 392 2.45e-56 178
MsG0180000446.01.T01 MTR_1g015750 96.591 88 3 0 4 91 297 384 2.65e-56 178
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000446.01.T01 AT2G26300 87.500 88 11 0 4 91 296 383 7.24e-52 166
MsG0180000446.01.T01 AT2G26300 87.500 88 11 0 4 91 296 383 7.24e-52 166

Find 34 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCCACATTCATCTTTAA+AGG 0.198789 1:+6174945 MsG0180000446.01.T01:three_prime_UTR
GAAGAGGTGAGATCAGATTT+TGG 0.248220 1:+6174815 MsG0180000446.01.T01:three_prime_UTR
CGCTATCCGGAGCAGTGTTC+TGG 0.283333 1:-6174618 None:intergenic
TCCCTCTTATATAACATATA+TGG 0.321851 1:-6174775 None:intergenic
ATGTCTTCTTCACAACCTTC+TGG 0.325401 1:-6174681 None:intergenic
ATGTTCAATCTCTTGTTTCC+CGG 0.350590 1:-6173777 None:intergenic
ATTTCTTGTAAAATCTTTGT+TGG 0.379713 1:+6174887 MsG0180000446.01.T01:three_prime_UTR
TCTCCACATTCATCTTTAAA+GGG 0.398409 1:+6174946 MsG0180000446.01.T01:three_prime_UTR
GACTACCAGCCACTTTCAAC+CGG 0.403399 1:+6173758 MsG0180000446.01.T01:CDS
GACCATATATGTTATATAAG+AGG 0.427557 1:+6174773 MsG0180000446.01.T01:three_prime_UTR
AACATATATGGTCCACTCAT+TGG 0.452839 1:-6174763 None:intergenic
GAGACGGAGGAATCTCTTTG+AGG 0.457860 1:+6174726 MsG0180000446.01.T01:CDS
CGGAGGAATCTCTTTGAGGC+TGG 0.474033 1:+6174730 MsG0180000446.01.T01:CDS
AACACGCGGTCTACGCTATC+CGG 0.486792 1:-6174631 None:intergenic
GTTTCCCGGTTGAAAGTGGC+TGG 0.493695 1:-6173763 None:intergenic
ACCGCGTGTTTAAGATATAT+AGG 0.512353 1:+6174644 MsG0180000446.01.T01:CDS
TCTTGTTTCCCGGTTGAAAG+TGG 0.524400 1:-6173767 None:intergenic
AAAATCTTTGTTGGAGTGAG+TGG 0.531296 1:+6174896 MsG0180000446.01.T01:three_prime_UTR
AACCACTCACATACATTAAG+CGG 0.544573 1:-6173731 None:intergenic
TCTTTGTTGGAGTGAGTGGA+TGG 0.546756 1:+6174900 MsG0180000446.01.T01:three_prime_UTR
ACCATATATGTTATATAAGA+GGG 0.562322 1:+6174774 MsG0180000446.01.T01:three_prime_UTR
ATATTTCCAGAACACTGCTC+CGG 0.563292 1:+6174612 MsG0180000446.01.T01:CDS
GACCACTGCACTTGACCAGA+AGG 0.565096 1:+6174666 MsG0180000446.01.T01:CDS
TTCCCCTTTAAAGATGAATG+TGG 0.570351 1:-6174949 None:intergenic
CTCCACATTCATCTTTAAAG+GGG 0.572440 1:+6174947 MsG0180000446.01.T01:three_prime_UTR
TGGAGTGAGTGGATGGAGAA+AGG 0.573704 1:+6174907 MsG0180000446.01.T01:three_prime_UTR
AACCTTCTGGTCAAGTGCAG+TGG 0.574510 1:-6174668 None:intergenic
ACCACTCACATACATTAAGC+GGG 0.592242 1:-6173730 None:intergenic
TTGATGAGACTTTGAGACGG+AGG 0.624845 1:+6174713 MsG0180000446.01.T01:CDS
TTGTTGATGAGACTTTGAGA+CGG 0.630412 1:+6174710 MsG0180000446.01.T01:CDS
ACTACCAGCCACTTTCAACC+GGG 0.630833 1:+6173759 MsG0180000446.01.T01:CDS
TCCCGCTTAATGTATGTGAG+TGG 0.652970 1:+6173729 MsG0180000446.01.T01:CDS
TCCTATATATCTTAAACACG+CGG 0.695502 1:-6174645 None:intergenic
GGCTTGTTATGACCAATGAG+TGG 0.702624 1:+6174751 MsG0180000446.01.T01:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATATTTTTACAATGAAG+AGG + Chr1:6174799-6174818 MsG0180000446.01.T01:three_prime_UTR 15.0%
!! ACCATATATGTTATATAAGA+GGG + Chr1:6174774-6174793 MsG0180000446.01.T01:three_prime_UTR 20.0%
!! ATTTCTTGTAAAATCTTTGT+TGG + Chr1:6174887-6174906 MsG0180000446.01.T01:three_prime_UTR 20.0%
!! TCTCAGTTAAAATAAGTTAT+TGG - Chr1:6174368-6174387 None:intergenic 20.0%
!! TTTGGATAAACAACTTAATT+TGG + Chr1:6173874-6173893 MsG0180000446.01.T01:intron 20.0%
!!! TAATATAACATAGTCAGTTT+TGG + Chr1:6174167-6174186 MsG0180000446.01.T01:intron 20.0%
! AAGCTATTCTGAATAGTTTA+TGG + Chr1:6174002-6174021 MsG0180000446.01.T01:intron 25.0%
! AATCATGACGTAATTTATCA+TGG - Chr1:6174460-6174479 None:intergenic 25.0%
! AGTAACTTATTTATAGCCTT+AGG + Chr1:6173811-6173830 MsG0180000446.01.T01:intron 25.0%
! GACCATATATGTTATATAAG+AGG + Chr1:6174773-6174792 MsG0180000446.01.T01:three_prime_UTR 25.0%
! GTTTGTGAAGAAAAAATTTG+AGG + Chr1:6174585-6174604 MsG0180000446.01.T01:CDS 25.0%
! TCCCTCTTATATAACATATA+TGG - Chr1:6174778-6174797 None:intergenic 25.0%
!! ATTAAGTTGTTTATCCAAAC+AGG - Chr1:6173873-6173892 None:intergenic 25.0%
!! TTAAGTTGTTTATCCAAACA+GGG - Chr1:6173872-6173891 None:intergenic 25.0%
ATCTCCACATTCATCTTTAA+AGG + Chr1:6174945-6174964 MsG0180000446.01.T01:three_prime_UTR 30.0%
TAATTCCTATGAACTTGTAG+TGG - Chr1:6174506-6174525 None:intergenic 30.0%
TCCTATATATCTTAAACACG+CGG - Chr1:6174648-6174667 None:intergenic 30.0%
TCTCCACATTCATCTTTAAA+GGG + Chr1:6174946-6174965 MsG0180000446.01.T01:three_prime_UTR 30.0%
! ATGGACAAACTCTTTATTTC+AGG + Chr1:6174563-6174582 MsG0180000446.01.T01:intron 30.0%
! GCATTAGTTTACAAATGCTT+AGG - Chr1:6174323-6174342 None:intergenic 30.0%
!! TTTTGGGTATACTAGAAGTA+AGG + Chr1:6174832-6174851 MsG0180000446.01.T01:three_prime_UTR 30.0%
AAAATCTTTGTTGGAGTGAG+TGG + Chr1:6174896-6174915 MsG0180000446.01.T01:three_prime_UTR 35.0%
AACATATATGGTCCACTCAT+TGG - Chr1:6174766-6174785 None:intergenic 35.0%
AACCACTCACATACATTAAG+CGG - Chr1:6173734-6173753 None:intergenic 35.0%
ACAAGCTTCAACATGAGTAT+GGG - Chr1:6174136-6174155 None:intergenic 35.0%
TACAAGCTTCAACATGAGTA+TGG - Chr1:6174137-6174156 None:intergenic 35.0%
TTTCTTACCTACGTTGAAAG+TGG + Chr1:6174478-6174497 MsG0180000446.01.T01:intron 35.0%
! AAGAGGTGAGATCAGATTTT+GGG + Chr1:6174816-6174835 MsG0180000446.01.T01:three_prime_UTR 35.0%
! ACCGCGTGTTTAAGATATAT+AGG + Chr1:6174644-6174663 MsG0180000446.01.T01:CDS 35.0%
! ATGTTCAATCTCTTGTTTCC+CGG - Chr1:6173780-6173799 None:intergenic 35.0%
! CTCCACATTCATCTTTAAAG+GGG + Chr1:6174947-6174966 MsG0180000446.01.T01:three_prime_UTR 35.0%
! GATGAAAATAGCTTGTGACA+TGG - Chr1:6174052-6174071 None:intergenic 35.0%
! TTCCCCTTTAAAGATGAATG+TGG - Chr1:6174952-6174971 None:intergenic 35.0%
! TTGTTGATGAGACTTTGAGA+CGG + Chr1:6174710-6174729 MsG0180000446.01.T01:CDS 35.0%
AATTTGGCGCTTATAGCACA+AGG + Chr1:6173890-6173909 MsG0180000446.01.T01:intron 40.0%
ACCACTCACATACATTAAGC+GGG - Chr1:6173733-6173752 None:intergenic 40.0%
AGGCTATAATTCAACGCCTA+AGG - Chr1:6173830-6173849 None:intergenic 40.0%
ATATTTCCAGAACACTGCTC+CGG + Chr1:6174612-6174631 MsG0180000446.01.T01:CDS 40.0%
ATGTCTTCTTCACAACCTTC+TGG - Chr1:6174684-6174703 None:intergenic 40.0%
ATTTGGCGCTTATAGCACAA+GGG + Chr1:6173891-6173910 MsG0180000446.01.T01:intron 40.0%
CAAGCTTCAACATGAGTATG+GGG - Chr1:6174135-6174154 None:intergenic 40.0%
TGGTACCACTACAAGTTCAT+AGG + Chr1:6174498-6174517 MsG0180000446.01.T01:intron 40.0%
! GAAGAGGTGAGATCAGATTT+TGG + Chr1:6174815-6174834 MsG0180000446.01.T01:three_prime_UTR 40.0%
!! AAGCACTTCTGAGACTGTTT+CGG - Chr1:6174074-6174093 None:intergenic 40.0%
AACATGAGTATGGGGAAGCT+TGG - Chr1:6174127-6174146 None:intergenic 45.0%
AGTGGTACCACTTTCAACGT+AGG - Chr1:6174488-6174507 None:intergenic 45.0%
TCCAGCGCAACGAATTAACA+TGG + Chr1:6174544-6174563 MsG0180000446.01.T01:intron 45.0%
TCCATGTTAATTCGTTGCGC+TGG - Chr1:6174548-6174567 None:intergenic 45.0%
TCCCGCTTAATGTATGTGAG+TGG + Chr1:6173729-6173748 MsG0180000446.01.T01:CDS 45.0%
TCTTTGTTGGAGTGAGTGGA+TGG + Chr1:6174900-6174919 MsG0180000446.01.T01:three_prime_UTR 45.0%
! TCTTGTTTCCCGGTTGAAAG+TGG - Chr1:6173770-6173789 None:intergenic 45.0%
!! AGCCTTGAGCATTGAAGACT+TGG + Chr1:6173845-6173864 MsG0180000446.01.T01:intron 45.0%
!! GCCTTGAGCATTGAAGACTT+GGG + Chr1:6173846-6173865 MsG0180000446.01.T01:intron 45.0%
!! GGCTTGTTATGACCAATGAG+TGG + Chr1:6174751-6174770 MsG0180000446.01.T01:exon 45.0%
!! TTGATGAGACTTTGAGACGG+AGG + Chr1:6174713-6174732 MsG0180000446.01.T01:CDS 45.0%
AACCTTCTGGTCAAGTGCAG+TGG - Chr1:6174671-6174690 None:intergenic 50.0%
GAGACGGAGGAATCTCTTTG+AGG + Chr1:6174726-6174745 MsG0180000446.01.T01:CDS 50.0%
GCCCAAGTCTTCAATGCTCA+AGG - Chr1:6173850-6173869 None:intergenic 50.0%
TGAGTATGGGGAAGCTTGGA+TGG - Chr1:6174123-6174142 None:intergenic 50.0%
TGGAGTGAGTGGATGGAGAA+AGG + Chr1:6174907-6174926 MsG0180000446.01.T01:three_prime_UTR 50.0%
TTGAAGACTTGGGCCCTGTT+TGG + Chr1:6173856-6173875 MsG0180000446.01.T01:intron 50.0%
! ACTACCAGCCACTTTCAACC+GGG + Chr1:6173759-6173778 MsG0180000446.01.T01:CDS 50.0%
! GACTACCAGCCACTTTCAAC+CGG + Chr1:6173758-6173777 MsG0180000446.01.T01:CDS 50.0%
AACACGCGGTCTACGCTATC+CGG - Chr1:6174634-6174653 None:intergenic 55.0%
AATTCGTTGCGCTGGACTGC+TGG - Chr1:6174540-6174559 None:intergenic 55.0%
GACCACTGCACTTGACCAGA+AGG + Chr1:6174666-6174685 MsG0180000446.01.T01:CDS 55.0%
GTTTCCCGGTTGAAAGTGGC+TGG - Chr1:6173766-6173785 None:intergenic 55.0%
!! CGGAGGAATCTCTTTGAGGC+TGG + Chr1:6174730-6174749 MsG0180000446.01.T01:CDS 55.0%
CGCTATCCGGAGCAGTGTTC+TGG - Chr1:6174621-6174640 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 6173710 6175058 6173710 ID=MsG0180000446.01;Name=MsG0180000446.01
Chr1 mRNA 6173710 6175058 6173710 ID=MsG0180000446.01.T01;Parent=MsG0180000446.01;Name=MsG0180000446.01.T01;_AED=0.50;_eAED=0.50;_QI=0|1|0.5|1|1|1|2|296|91
Chr1 exon 6174585 6175058 6174585 ID=MsG0180000446.01.T01:exon:27977;Parent=MsG0180000446.01.T01
Chr1 exon 6173710 6173807 6173710 ID=MsG0180000446.01.T01:exon:27976;Parent=MsG0180000446.01.T01
Chr1 CDS 6173710 6173807 6173710 ID=MsG0180000446.01.T01:cds;Parent=MsG0180000446.01.T01
Chr1 CDS 6174585 6174762 6174585 ID=MsG0180000446.01.T01:cds;Parent=MsG0180000446.01.T01
Chr1 three_prime_UTR 6174763 6175058 6174763 ID=MsG0180000446.01.T01:three_prime_utr;Parent=MsG0180000446.01.T01
Gene Sequence

>MsG0180000446.01.T01

ATGTTTTGTATTGTGCAGGTCCCGCTTAATGTATGTGAGTGGTTCAAAGACTACCAGCCACTTTCAACCGGGAAACAAGAGATTGAACATGCATACGAGTTTGTGAAGAAAAAATTTGAGGAATCATATTTCCAGAACACTGCTCCGGATAGCGTAGACCGCGTGTTTAAGATATATAGGACCACTGCACTTGACCAGAAGGTTGTGAAGAAGACATTCAAGCTTGTTGATGAGACTTTGAGACGGAGGAATCTCTTTGAGGCTGGCTTGTTATGA

Protein sequence

>MsG0180000446.01.T01

MFCIVQVPLNVCEWFKDYQPLSTGKQEIEHAYEFVKKKFEESYFQNTAPDSVDRVFKIYRTTALDQKVVKKTFKLVDETLRRRNLFEAGLL*