AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014247.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014247.01.T01 MTR_3g053510 95.146 103 4 1 1 102 1 103 2.65e-67 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATGAATTTGTGAGTTTAA+TGG 0.250143 3:+51847906 MsG0380014247.01.T01:three_prime_UTR
AACATGCTTTGATAGAATTA+TGG 0.258618 3:+51847525 MsG0380014247.01.T01:intron
GTGAAATAATAAGAATTTCT+TGG 0.259819 3:+51847938 MsG0380014247.01.T01:three_prime_UTR
AGTGAAGAAGAGTGAGGAAT+TGG 0.296391 3:-51846802 None:intergenic
TAAAATCAAAAGGACATTCT+TGG 0.301367 3:+51848058 MsG0380014247.01.T01:three_prime_UTR
GTGTGCAAAGTTGTCCGTTT+AGG 0.345761 3:+51846626 MsG0380014247.01.T01:five_prime_UTR
TGGAGACTTCATGAATCATT+AGG 0.353959 3:+51848001 MsG0380014247.01.T01:three_prime_UTR
AATATTGAAGTTGGGAGAAT+GGG 0.360100 3:-51846715 None:intergenic
GTACAAGGAGCATTGATCTT+AGG 0.360884 3:+51847740 MsG0380014247.01.T01:exon
AAAGGAAAGTCATTTGATAA+AGG 0.376794 3:+51847563 MsG0380014247.01.T01:CDS
AAAATTAAATGGTACCTTGA+TGG 0.391314 3:-51846876 None:intergenic
GTCTACACATATATATCTAT+TGG 0.392894 3:-51846580 None:intergenic
TGAAATTCTTCAGCTGTAGA+TGG 0.429413 3:-51847594 None:intergenic
AACACTTCATGCAACCTAAA+CGG 0.458091 3:-51846640 None:intergenic
GAGAATGGGGATGTGTCTAT+AGG 0.462776 3:-51846701 None:intergenic
AAATATTGAAGTTGGGAGAA+TGG 0.473143 3:-51846716 None:intergenic
GTGAAGAAGAGTGAGGAATT+GGG 0.473632 3:-51846801 None:intergenic
TTGTAGAAGAATGGTCTAGA+GGG 0.502419 3:-51846851 None:intergenic
TGCTGCTGAAGAAGCTGCTA+AGG 0.518120 3:+51847686 MsG0380014247.01.T01:CDS
AAGCTGCTAAGGGTAATTCA+AGG 0.521770 3:+51847697 MsG0380014247.01.T01:CDS
TGGACAAGAAGTGAAGGAAA+AGG 0.524067 3:+51847545 MsG0380014247.01.T01:CDS
TTGATGGAGTTGTAGAAGAA+TGG 0.525498 3:-51846860 None:intergenic
AATCAAAAGGACATTCTTGG+TGG 0.525713 3:+51848061 MsG0380014247.01.T01:three_prime_UTR
GTTGTAGAAGAATGGTCTAG+AGG 0.544303 3:-51846852 None:intergenic
GAGAGTAACCATACCATGGC+TGG 0.545967 3:+51846776 MsG0380014247.01.T01:exon
ATTGGGCACCAGCCATGGTA+TGG 0.547369 3:-51846784 None:intergenic
GAGGAATTGGGCACCAGCCA+TGG 0.552723 3:-51846789 None:intergenic
CACACTCTGCACCCTCACAT+AGG 0.569289 3:-51846608 None:intergenic
ACACTCTGCACCCTCACATA+GGG 0.570563 3:-51846607 None:intergenic
AATGGGGATGTGTCTATAGG+TGG 0.571409 3:-51846698 None:intergenic
TACACGTGGTGTTGTTGAAG+TGG 0.573045 3:-51846663 None:intergenic
AGCTGAAGAATTTCAGAGAG+TGG 0.590235 3:+51847602 MsG0380014247.01.T01:CDS
GTGGCAGAAGAGAAAACCAA+TGG 0.605337 3:+51847621 MsG0380014247.01.T01:CDS
ATTCTTCTACAACTCCATCA+AGG 0.606836 3:+51846862 MsG0380014247.01.T01:CDS
GAATTATGGACAAGAAGTGA+AGG 0.611950 3:+51847539 MsG0380014247.01.T01:intron
ATATTGAAGTTGGGAGAATG+GGG 0.618895 3:-51846714 None:intergenic
AAATGTTAAGAACAAGTACA+AGG 0.627029 3:+51847725 MsG0380014247.01.T01:CDS
CTCTGCACCCTCACATAGGG+TGG 0.636479 3:-51846604 None:intergenic
GAGAGAGAGTAACCATACCA+TGG 0.643543 3:+51846772 MsG0380014247.01.T01:exon
AAGATGAGTGAAGAAGAGTG+AGG 0.651606 3:-51846808 None:intergenic
GCTGCTGAAGAAGCTGCTAA+GGG 0.655312 3:+51847687 MsG0380014247.01.T01:CDS
TGTAGACACCACCCTATGTG+AGG 0.695960 3:+51846596 MsG0380014247.01.T01:five_prime_UTR
GGAAGCTAGTGATGTACACG+TGG 0.764840 3:-51846677 None:intergenic
GTAGACACCACCCTATGTGA+GGG 0.775960 3:+51846597 MsG0380014247.01.T01:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTAATTAAAAACATCAA+GGG - Chr3:51846905-51846924 None:intergenic 10.0%
!!! ATTTTTTTCTTTCAATTAAT+TGG + Chr3:51846932-51846951 MsG0380014247.01.T01:intron 10.0%
!!! TTTTAAAAAATCACATAATT+AGG - Chr3:51847437-51847456 None:intergenic 10.0%
!! CAATTTAATTAAAAACATCA+AGG - Chr3:51846906-51846925 None:intergenic 15.0%
!!! TTAAATTTTAGTTTGTACTT+TGG + Chr3:51847062-51847081 MsG0380014247.01.T01:intron 15.0%
!! AAAAATCTTTACTTTCTTGA+TGG - Chr3:51847242-51847261 None:intergenic 20.0%
!! AAAATCTTTACTTTCTTGAT+GGG - Chr3:51847241-51847260 None:intergenic 20.0%
!! AGAGTAAAAATATTGAAGTT+GGG - Chr3:51846726-51846745 None:intergenic 20.0%
!! ATCAAGGGATAAAAATTAAA+TGG - Chr3:51846890-51846909 None:intergenic 20.0%
!! CAATAATTAATAGACAACTA+CGG - Chr3:51847497-51847516 None:intergenic 20.0%
!! CTCCATCTAAATAAAAAAAA+TGG - Chr3:51847986-51848005 None:intergenic 20.0%
!! GTGAAATAATAAGAATTTCT+TGG + Chr3:51847938-51847957 MsG0380014247.01.T01:three_prime_UTR 20.0%
!! TTATGAATTTGTGAGTTTAA+TGG + Chr3:51847906-51847925 MsG0380014247.01.T01:three_prime_UTR 20.0%
!!! CTCCATTTTTTTTATTTAGA+TGG + Chr3:51847981-51848000 MsG0380014247.01.T01:three_prime_UTR 20.0%
!!! TTGTTTTGTAAGTTAGAATA+AGG + Chr3:51847795-51847814 MsG0380014247.01.T01:three_prime_UTR 20.0%
! AAAATTAAATGGTACCTTGA+TGG - Chr3:51846879-51846898 None:intergenic 25.0%
! AAAGGAAAGTCATTTGATAA+AGG + Chr3:51847563-51847582 MsG0380014247.01.T01:CDS 25.0%
! AAATGTTAAGAACAAGTACA+AGG + Chr3:51847725-51847744 MsG0380014247.01.T01:CDS 25.0%
! AACATGCTTTGATAGAATTA+TGG + Chr3:51847525-51847544 MsG0380014247.01.T01:intron 25.0%
! AACTCTACATGCAATAATTA+AGG - Chr3:51847133-51847152 None:intergenic 25.0%
! ATTTGACATCTTTACTCAAA+TGG + Chr3:51847277-51847296 MsG0380014247.01.T01:intron 25.0%
! GAAAATTAAAGGTTGAAAAG+TGG + Chr3:51847192-51847211 MsG0380014247.01.T01:intron 25.0%
! GAGAGTAAAAATATTGAAGT+TGG - Chr3:51846727-51846746 None:intergenic 25.0%
! GTCTACACATATATATCTAT+TGG - Chr3:51846583-51846602 None:intergenic 25.0%
! TAAAATCAAAAGGACATTCT+TGG + Chr3:51848058-51848077 MsG0380014247.01.T01:three_prime_UTR 25.0%
! TTGAGTAAAGATGTCAAATT+TGG - Chr3:51847276-51847295 None:intergenic 25.0%
! TTTGACATCTTTACTCAAAT+GGG + Chr3:51847278-51847297 MsG0380014247.01.T01:intron 25.0%
!! TAGCAATTACACAAACTTTT+TGG - Chr3:51847836-51847855 None:intergenic 25.0%
AAAGTAAGAATGATCCTAGT+AGG + Chr3:51847008-51847027 MsG0380014247.01.T01:intron 30.0%
AAATATTGAAGTTGGGAGAA+TGG - Chr3:51846719-51846738 None:intergenic 30.0%
AATATTGAAGTTGGGAGAAT+GGG - Chr3:51846718-51846737 None:intergenic 30.0%
AATTACAAGTGTCTATGTGT+CGG - Chr3:51847411-51847430 None:intergenic 30.0%
TTAATAGACAACTACGGATA+CGG - Chr3:51847491-51847510 None:intergenic 30.0%
TTTGTGAGGTGGAAAATTAA+AGG + Chr3:51847181-51847200 MsG0380014247.01.T01:intron 30.0%
!! AGATTTGTTAGTTGTGTTTG+AGG + Chr3:51847101-51847120 MsG0380014247.01.T01:intron 30.0%
!!! TTTCACTTTTTGTGTTCCAT+TGG - Chr3:51847640-51847659 None:intergenic 30.0%
AACACTTCATGCAACCTAAA+CGG - Chr3:51846643-51846662 None:intergenic 35.0%
ATATTGAAGTTGGGAGAATG+GGG - Chr3:51846717-51846736 None:intergenic 35.0%
ATTCTTCTACAACTCCATCA+AGG + Chr3:51846862-51846881 MsG0380014247.01.T01:CDS 35.0%
GAATTATGGACAAGAAGTGA+AGG + Chr3:51847539-51847558 MsG0380014247.01.T01:intron 35.0%
TGAAATTCTTCAGCTGTAGA+TGG - Chr3:51847597-51847616 None:intergenic 35.0%
TGGAGACTTCATGAATCATT+AGG + Chr3:51848001-51848020 MsG0380014247.01.T01:three_prime_UTR 35.0%
TTGATGGAGTTGTAGAAGAA+TGG - Chr3:51846863-51846882 None:intergenic 35.0%
TTGTAGAAGAATGGTCTAGA+GGG - Chr3:51846854-51846873 None:intergenic 35.0%
! AATTTTCCACCTCACAAAAC+AGG - Chr3:51847179-51847198 None:intergenic 35.0%
AAGATGAGTGAAGAAGAGTG+AGG - Chr3:51846811-51846830 None:intergenic 40.0%
AAGCTGCTAAGGGTAATTCA+AGG + Chr3:51847697-51847716 MsG0380014247.01.T01:CDS 40.0%
AGCTGAAGAATTTCAGAGAG+TGG + Chr3:51847602-51847621 MsG0380014247.01.T01:CDS 40.0%
AGTGAAGAAGAGTGAGGAAT+TGG - Chr3:51846805-51846824 None:intergenic 40.0%
CTTCAACTCAATCTCCTACT+AGG - Chr3:51847025-51847044 None:intergenic 40.0%
GTGAAGAAGAGTGAGGAATT+GGG - Chr3:51846804-51846823 None:intergenic 40.0%
GTTGTAGAAGAATGGTCTAG+AGG - Chr3:51846855-51846874 None:intergenic 40.0%
TGGACAAGAAGTGAAGGAAA+AGG + Chr3:51847545-51847564 MsG0380014247.01.T01:CDS 40.0%
!! GTACAAGGAGCATTGATCTT+AGG + Chr3:51847740-51847759 MsG0380014247.01.T01:exon 40.0%
AATGGGGATGTGTCTATAGG+TGG - Chr3:51846701-51846720 None:intergenic 45.0%
GAGAATGGGGATGTGTCTAT+AGG - Chr3:51846704-51846723 None:intergenic 45.0%
GAGAGAGAGTAACCATACCA+TGG + Chr3:51846772-51846791 MsG0380014247.01.T01:exon 45.0%
GTGGCAGAAGAGAAAACCAA+TGG + Chr3:51847621-51847640 MsG0380014247.01.T01:CDS 45.0%
GTGTGCAAAGTTGTCCGTTT+AGG + Chr3:51846626-51846645 MsG0380014247.01.T01:five_prime_UTR 45.0%
! CATGATCCTGTTTTGTGAGG+TGG + Chr3:51847170-51847189 MsG0380014247.01.T01:intron 45.0%
! CTGCATGATCCTGTTTTGTG+AGG + Chr3:51847167-51847186 MsG0380014247.01.T01:intron 45.0%
!! TACACGTGGTGTTGTTGAAG+TGG - Chr3:51846666-51846685 None:intergenic 45.0%
!!! TATTAATTTTTAAAATCAAA+AGG + Chr3:51848048-51848067 MsG0380014247.01.T01:three_prime_UTR 5.0%
ACACTCTGCACCCTCACATA+GGG - Chr3:51846610-51846629 None:intergenic 50.0%
GAGAGTAACCATACCATGGC+TGG + Chr3:51846776-51846795 MsG0380014247.01.T01:exon 50.0%
GCTGCTGAAGAAGCTGCTAA+GGG + Chr3:51847687-51847706 MsG0380014247.01.T01:CDS 50.0%
GGAAGCTAGTGATGTACACG+TGG - Chr3:51846680-51846699 None:intergenic 50.0%
GGTTACTCTCTCTCTCTCTG+AGG - Chr3:51846766-51846785 None:intergenic 50.0%
GTAGACACCACCCTATGTGA+GGG + Chr3:51846597-51846616 MsG0380014247.01.T01:five_prime_UTR 50.0%
TGCTGCTGAAGAAGCTGCTA+AGG + Chr3:51847686-51847705 MsG0380014247.01.T01:CDS 50.0%
TGTAGACACCACCCTATGTG+AGG + Chr3:51846596-51846615 MsG0380014247.01.T01:five_prime_UTR 50.0%
! TACTCTCTCTCTCTCTGAGG+AGG - Chr3:51846763-51846782 None:intergenic 50.0%
ATTGGGCACCAGCCATGGTA+TGG - Chr3:51846787-51846806 None:intergenic 55.0%
CACACTCTGCACCCTCACAT+AGG - Chr3:51846611-51846630 None:intergenic 55.0%
ACGGACACGAGACACGACAC+TGG - Chr3:51847472-51847491 None:intergenic 60.0%
CTCTGCACCCTCACATAGGG+TGG - Chr3:51846607-51846626 None:intergenic 60.0%
GAGGAATTGGGCACCAGCCA+TGG - Chr3:51846792-51846811 None:intergenic 60.0%
!! GTCTATGTGTCGGTGTCGCG+TGG - Chr3:51847401-51847420 None:intergenic 60.0%
!! GTGTCGGTGTCGCGTGGTGT+CGG - Chr3:51847395-51847414 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 51846573 51848082 51846573 ID=MsG0380014247.01;Name=MsG0380014247.01
Chr3 mRNA 51846573 51848082 51846573 ID=MsG0380014247.01.T01;Parent=MsG0380014247.01;Name=MsG0380014247.01.T01;_AED=0.50;_eAED=0.50;_QI=218|1|1|1|0|0.5|2|327|102
Chr3 exon 51846573 51846883 51846573 ID=MsG0380014247.01.T01:exon:10129;Parent=MsG0380014247.01.T01
Chr3 exon 51847540 51848082 51847540 ID=MsG0380014247.01.T01:exon:10130;Parent=MsG0380014247.01.T01
Chr3 five_prime_UTR 51846573 51846790 51846573 ID=MsG0380014247.01.T01:five_prime_utr;Parent=MsG0380014247.01.T01
Chr3 CDS 51846791 51846883 51846791 ID=MsG0380014247.01.T01:cds;Parent=MsG0380014247.01.T01
Chr3 CDS 51847540 51847755 51847540 ID=MsG0380014247.01.T01:cds;Parent=MsG0380014247.01.T01
Chr3 three_prime_UTR 51847756 51848082 51847756 ID=MsG0380014247.01.T01:three_prime_utr;Parent=MsG0380014247.01.T01
Gene Sequence

>MsG0380014247.01.T01

ATGGCTGGTGCCCAATTCCTCACTCTTCTTCACTCATCTTCAAGATCTTCTTTGCTCAAACCCTCTAGACCATTCTTCTACAACTCCATCAAGAATTATGGACAAGAAGTGAAGGAAAAGGAAAGTCATTTGATAAAGGAGAGAGCACCATCTACAGCTGAAGAATTTCAGAGAGTGGCAGAAGAGAAAACCAATGGAACACAAAAAGTGAAAAGTCAAACAGTTGATAAAGCAATTGATGCTGCTGAAGAAGCTGCTAAGGGTAATTCAAGGATTGAAAATGTTAAGAACAAGTACAAGGAGCATTGA
Protein sequence

>MsG0380014247.01.T01

MAGAQFLTLLHSSSRSSLLKPSRPFFYNSIKNYGQEVKEKESHLIKERAPSTAEEFQRVAEEKTNGTQKVKSQTVDKAIDAAEEAAKGNSRIENVKNKYKEH*