AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52962

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52962.t1 MTR_1g075780 76.224 143 16 1 12 136 3 145 3.16e-75 220
MS.gene52962.t1 MTR_4g063510 31.977 172 63 4 17 136 13 182 1.42e-16 72.4
MS.gene52962.t1 MTR_1g075840 41.935 124 42 6 36 136 1 117 1.48e-14 65.5
MS.gene52962.t1 MTR_1g041455 31.646 158 70 7 14 136 13 167 2.24e-13 63.5
MS.gene52962.t1 MTR_5g056450 32.215 149 66 6 1 124 1 139 5.33e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGACACATCAGTGAATT+TGG 0.236191 1.1:-56730805 MS.gene52962:CDS
TTATCCAACATGTTGATATA+TGG 0.260832 1.1:+56730861 None:intergenic
ATGGGAAAATTGGGTGGTAA+AGG 0.416030 1.1:+56730993 None:intergenic
TAAAGGGTTGGCCATTGATT+CGG 0.428827 1.1:+56731010 None:intergenic
TGGGAAAATTGGGTGGTAAA+GGG 0.468596 1.1:+56730994 None:intergenic
CAATCCTCAGGCCGAATCAA+TGG 0.469990 1.1:-56731021 MS.gene52962:CDS
CATTGATTCGGCCTGAGGAT+TGG 0.472364 1.1:+56731022 None:intergenic
CCACCAGTCCCTTGTTGTTG+TGG 0.476108 1.1:+56730915 None:intergenic
AAGCCACCTTGAGTCTCATA+TGG 0.484456 1.1:-56731081 MS.gene52962:CDS
CAAAATTATTGATATTGCTA+CGG 0.495293 1.1:+56731150 None:intergenic
ACAACAAGGGACTGGTGGTA+TGG 0.510630 1.1:-56730910 MS.gene52962:CDS
ATTCGGCCTGAGGATTGGTA+TGG 0.511741 1.1:+56731027 None:intergenic
TTGGCCATTGATTCGGCCTG+AGG 0.541375 1.1:+56731017 None:intergenic
CTTGAGCCATATGAGACTCA+AGG 0.558137 1.1:+56731075 None:intergenic
ATTAAACCATACCAATCCTC+AGG 0.560036 1.1:-56731033 MS.gene52962:CDS
ATGGAAGTCTCTCCGATCGA+TGG 0.567201 1.1:-56730891 MS.gene52962:CDS
TAAGCCATATATCAACATGT+TGG 0.587500 1.1:-56730865 MS.gene52962:CDS
TTTGGCATGGGAAAATTGGG+TGG 0.600647 1.1:+56730987 None:intergenic
AAAATTGGGTGGTAAAGGGT+TGG 0.611916 1.1:+56730998 None:intergenic
TTTCAGCAACCACAACAACA+AGG 0.614643 1.1:-56730924 MS.gene52962:CDS
CAACCACAACAACAAGGGAC+TGG 0.623235 1.1:-56730918 MS.gene52962:CDS
CCACAACAACAAGGGACTGG+TGG 0.623856 1.1:-56730915 MS.gene52962:CDS
TATGGCTTAGTTCCATCGAT+CGG 0.625287 1.1:+56730879 None:intergenic
TTCAGCAACCACAACAACAA+GGG 0.626204 1.1:-56730923 MS.gene52962:CDS
GAGCCATATGAGACTCAAGG+TGG 0.728487 1.1:+56731078 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATCAATAATTTTGTATG+TGG - chr1.1:56730827-56730846 MS.gene52962:CDS 15.0%
!! CAAAATTATTGATATTGCTA+CGG + chr1.1:56730823-56730842 None:intergenic 20.0%
!!! TTGTTTTCATGTAATGATTT+TGG + chr1.1:56731004-56731023 None:intergenic 20.0%
! TTATCCAACATGTTGATATA+TGG + chr1.1:56731112-56731131 None:intergenic 25.0%
!!! AAATAACTTGCTTTTAACGA+AGG + chr1.1:56731029-56731048 None:intergenic 25.0%
TAAGCCATATATCAACATGT+TGG - chr1.1:56731105-56731124 MS.gene52962:CDS 30.0%
! AATGAAGACATTTTTCTCGA+TGG + chr1.1:56731137-56731156 None:intergenic 30.0%
! ATGAAGACATTTTTCTCGAT+GGG + chr1.1:56731136-56731155 None:intergenic 30.0%
!! TCATGTAATGATTTTGGCAT+GGG + chr1.1:56730998-56731017 None:intergenic 30.0%
!! TTCATGTAATGATTTTGGCA+TGG + chr1.1:56730999-56731018 None:intergenic 30.0%
ATTAAACCATACCAATCCTC+AGG - chr1.1:56730937-56730956 MS.gene52962:CDS 35.0%
CAATGACACATCAGTGAATT+TGG - chr1.1:56731165-56731184 MS.gene52962:CDS 35.0%
!! GATTTTGGCATGGGAAAATT+GGG + chr1.1:56730989-56731008 None:intergenic 35.0%
!! TGATTTTGGCATGGGAAAAT+TGG + chr1.1:56730990-56731009 None:intergenic 35.0%
AAAATTGGGTGGTAAAGGGT+TGG + chr1.1:56730975-56730994 None:intergenic 40.0%
ATGGGAAAATTGGGTGGTAA+AGG + chr1.1:56730980-56730999 None:intergenic 40.0%
TATGGCTTAGTTCCATCGAT+CGG + chr1.1:56731094-56731113 None:intergenic 40.0%
TGGGAAAATTGGGTGGTAAA+GGG + chr1.1:56730979-56730998 None:intergenic 40.0%
TTCAGCAACCACAACAACAA+GGG - chr1.1:56731047-56731066 MS.gene52962:CDS 40.0%
TTTCAGCAACCACAACAACA+AGG - chr1.1:56731046-56731065 MS.gene52962:CDS 40.0%
!! TAAAGGGTTGGCCATTGATT+CGG + chr1.1:56730963-56730982 None:intergenic 40.0%
AAGCCACCTTGAGTCTCATA+TGG - chr1.1:56730889-56730908 MS.gene52962:CDS 45.0%
CTTGAGCCATATGAGACTCA+AGG + chr1.1:56730898-56730917 None:intergenic 45.0%
TTTGGCATGGGAAAATTGGG+TGG + chr1.1:56730986-56731005 None:intergenic 45.0%
ATGGAAGTCTCTCCGATCGA+TGG - chr1.1:56731079-56731098 MS.gene52962:CDS 50.0%
CAACCACAACAACAAGGGAC+TGG - chr1.1:56731052-56731071 MS.gene52962:CDS 50.0%
CAATCCTCAGGCCGAATCAA+TGG - chr1.1:56730949-56730968 MS.gene52962:CDS 50.0%
GAGCCATATGAGACTCAAGG+TGG + chr1.1:56730895-56730914 None:intergenic 50.0%
! ACAACAAGGGACTGGTGGTA+TGG - chr1.1:56731060-56731079 MS.gene52962:CDS 50.0%
! ATTCGGCCTGAGGATTGGTA+TGG + chr1.1:56730946-56730965 None:intergenic 50.0%
!! CATTGATTCGGCCTGAGGAT+TGG + chr1.1:56730951-56730970 None:intergenic 50.0%
CCACAACAACAAGGGACTGG+TGG - chr1.1:56731055-56731074 MS.gene52962:CDS 55.0%
!! CCACCAGTCCCTTGTTGTTG+TGG + chr1.1:56731058-56731077 None:intergenic 55.0%
!! TTGGCCATTGATTCGGCCTG+AGG + chr1.1:56730956-56730975 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 56730791 56731201 56730791 ID=MS.gene52962
chr1.1 mRNA 56730791 56731201 56730791 ID=MS.gene52962.t1;Parent=MS.gene52962
chr1.1 exon 56730791 56731201 56730791 ID=MS.gene52962.t1.exon1;Parent=MS.gene52962.t1
chr1.1 CDS 56730791 56731201 56730791 ID=cds.MS.gene52962.t1;Parent=MS.gene52962.t1
Gene Sequence

>MS.gene52962

ATGGGTGACGATTTCACTCAAGAGAACAACCGTAGCAATATCAATAATTTTGTATGTGGATTGTGCAATCATGATTGTACAAACTTCGAATCACTCATAAGCCACCTTGAGTCTCATATGGCTCAAGAAAATCTTGCTATTGCAAGATTAAACCATACCAATCCTCAGGCCGAATCAATGGCCAACCCTTTACCACCCAATTTTCCCATGCCAAAATCATTACATGAAAACAAAACCTTCGTTAAAAGCAAGTTATTTCAGCAACCACAACAACAAGGGACTGGTGGTATGGAAGTCTCTCCGATCGATGGAACTAAGCCATATATCAACATGTTGGATAAACCCATCGAGAAAAATGTCTTCATTAACATCATCAATGACACATCAGTGAATTTGGAGTTAAAGCTCTAG
Protein sequence

>MS.gene52962.t1

MGDDFTQENNRSNINNFVCGLCNHDCTNFESLISHLESHMAQENLAIARLNHTNPQAESMANPLPPNFPMPKSLHENKTFVKSKLFQQPQQQGTGGMEVSPIDGTKPYINMLDKPIEKNVFINIINDTSVNLELKL