AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52254

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52254.t1 MTR_7g077620 55.639 266 64 5 5 217 105 369 3.71e-86 260
MS.gene52254.t1 MTR_7g077650 54.513 277 57 6 5 220 104 372 2.66e-82 249
MS.gene52254.t1 MTR_7g077660 55.019 269 65 6 5 220 103 368 3.86e-82 249
MS.gene52254.t1 MTR_7g076110 47.101 276 86 6 5 220 38 313 1.90e-71 220
MS.gene52254.t1 MTR_7g076100 51.477 237 59 4 38 220 66 300 4.82e-65 203
MS.gene52254.t1 MTR_5g038260 35.862 290 110 10 5 220 96 383 9.68e-36 130
MS.gene52254.t1 MTR_1g108740 37.828 267 98 11 3 218 95 344 3.81e-34 125
MS.gene52254.t1 MTR_5g038230 35.714 266 113 11 5 218 94 353 3.59e-32 120
MS.gene52254.t1 MTR_1g016150 43.636 165 59 6 3 166 104 235 3.16e-28 107
MS.gene52254.t1 MTR_1g064570 32.907 313 111 15 3 220 92 400 2.04e-27 107
MS.gene52254.t1 MTR_7g076130 43.269 104 35 1 58 137 45 148 3.35e-19 81.3
MS.gene52254.t1 MTR_5g082770 37.624 202 69 10 5 152 90 288 1.01e-15 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGGTTATAAGAAGCATTT+AGG 0.173622 7.4:-28567917 MS.gene52254:CDS
CAAACTCCACATTCACAAAT+TGG 0.228464 7.4:-28568092 MS.gene52254:CDS
TTCTCGTAGTAAGTAAAATT+AGG 0.242633 7.4:+28568245 None:intergenic
AATGAACAAACTTGAGAGTT+TGG 0.291432 7.4:-28568038 MS.gene52254:CDS
CCATGGTTGGCTTGCATTAA+CGG 0.321484 7.4:-28568591 MS.gene52254:CDS
TTCTAGAGGTGGCAGAATAA+TGG 0.328071 7.4:+28568517 None:intergenic
GGAGCTACACTGTACTTAAA+AGG 0.330559 7.4:+28568539 None:intergenic
TAATCACTTGGGCTTGTAAT+GGG 0.338599 7.4:+28568464 None:intergenic
CTCCATATACATATTGTATT+AGG 0.366385 7.4:-28568211 MS.gene52254:intron
CACCTAATACAATATGTATA+TGG 0.372006 7.4:+28568209 None:intergenic
CTCCAAGTTGGAAAAGGATT+CGG 0.375437 7.4:-28567954 MS.gene52254:CDS
AAGGTTATAAGAAGCATTTA+GGG 0.384574 7.4:-28567916 MS.gene52254:CDS
AAAAGGATTCACTAGAGTTA+TGG 0.384998 7.4:+28568556 None:intergenic
TCTCGTAGTAAGTAAAATTA+GGG 0.391917 7.4:+28568246 None:intergenic
AGCCTCTTGTTTCTCCAAGT+TGG 0.404761 7.4:-28567966 MS.gene52254:CDS
TCTAGAGGTGGCAGAATAAT+GGG 0.416332 7.4:+28568518 None:intergenic
TTGTTTCTCCAAGTTGGAAA+AGG 0.437802 7.4:-28567960 MS.gene52254:CDS
AAGCCAACCATGGCTACAAC+CGG 0.461155 7.4:+28568601 None:intergenic
ATAATCACTTGGGCTTGTAA+TGG 0.476686 7.4:+28568463 None:intergenic
ACCTCTAGAAGCTGTTTACA+AGG 0.481405 7.4:-28568504 MS.gene52254:CDS
TGGCCGGTTGTAGCCATGGT+TGG 0.485159 7.4:-28568604 MS.gene52254:CDS
ACGAGGATTATTGAGCTTGA+AGG 0.494091 7.4:+28568286 None:intergenic
TACAAGCCCAAGTGATTATG+TGG 0.499442 7.4:-28568459 MS.gene52254:CDS
GAGATCTATAATGTGAAGGA+TGG 0.509549 7.4:-28567890 MS.gene52254:CDS
CGCGTCTATCAGCAAATACC+AGG 0.511958 7.4:+28568324 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.549128 7.4:+28568452 None:intergenic
CTAGTTCCAATTTGTGAATG+TGG 0.551800 7.4:+28568086 None:intergenic
GGTCAATCCCATTGAAATTG+TGG 0.557740 7.4:+28567806 None:intergenic
ATGTGAAGGATGGAAGCTTA+CGG 0.560055 7.4:-28567880 MS.gene52254:CDS
TGCATTCGCTCGAAGGAAAG+TGG 0.562548 7.4:+28567845 None:intergenic
TGTAATGGGGTCAGCAGACA+AGG 0.568289 7.4:+28568478 None:intergenic
CCGTTAATGCAAGCCAACCA+TGG 0.592476 7.4:+28568591 None:intergenic
TTCCAACTTGGAGAAACAAG+AGG 0.597328 7.4:+28567964 None:intergenic
GTTGCAGCGATTTACAATTG+TGG 0.603650 7.4:-28568437 MS.gene52254:intron
GTTAGAGATCTATAATGTGA+AGG 0.603732 7.4:-28567894 MS.gene52254:CDS
AATCACTTGGGCTTGTAATG+GGG 0.606028 7.4:+28568465 None:intergenic
AACTTGGAGAAACAAGAGGC+TGG 0.606698 7.4:+28567968 None:intergenic
ATTGAGCTTGAAGGATACAA+TGG 0.615993 7.4:+28568295 None:intergenic
CTGGTATTTGCTGATAGACG+CGG 0.630780 7.4:-28568323 MS.gene52254:CDS
CTGCAACCACATAATCACTT+GGG 0.636696 7.4:+28568453 None:intergenic
ACCTTGTAAACAGCTTCTAG+AGG 0.643596 7.4:+28568503 None:intergenic
TTGTAAACAGCTTCTAGAGG+TGG 0.647947 7.4:+28568506 None:intergenic
GCATAGAAGTTGAATCACCA+CGG 0.688735 7.4:+28567990 None:intergenic
TTGGAACTAGACGTCCAGAG+TGG 0.702846 7.4:-28568073 MS.gene52254:CDS
TCATTTGAGTCATCACAACG+AGG 0.749759 7.4:+28568269 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTAATGTTGTATTTTATAA+AGG - chr7.4:28568072-28568091 MS.gene52254:CDS 15.0%
! ATGATTTCACGAAATAAACA+TGG + chr7.4:28568255-28568274 None:intergenic 25.0%
! CACCTAATACAATATGTATA+TGG + chr7.4:28568213-28568232 None:intergenic 25.0%
! CTCCATATACATATTGTATT+AGG - chr7.4:28568208-28568227 MS.gene52254:intron 25.0%
! TCTCGTAGTAAGTAAAATTA+GGG + chr7.4:28568176-28568195 None:intergenic 25.0%
! TTACACAAATCCAAAATGAT+TGG + chr7.4:28568032-28568051 None:intergenic 25.0%
! TTCTCGTAGTAAGTAAAATT+AGG + chr7.4:28568177-28568196 None:intergenic 25.0%
!!! AAGGTTATAAGAAGCATTTA+GGG - chr7.4:28568503-28568522 MS.gene52254:CDS 25.0%
!!! GAAGACAACATTTTATTTGT+CGG - chr7.4:28568403-28568422 MS.gene52254:intron 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.4:28567866-28567885 None:intergenic 30.0%
AATGAACAAACTTGAGAGTT+TGG - chr7.4:28568381-28568400 MS.gene52254:intron 30.0%
GTTAGAGATCTATAATGTGA+AGG - chr7.4:28568525-28568544 MS.gene52254:CDS 30.0%
TATTTCGTGAAATCATTGAC+CGG - chr7.4:28568259-28568278 MS.gene52254:CDS 30.0%
! GGTTTTACCACAATTTCAAT+GGG - chr7.4:28568606-28568625 MS.gene52254:CDS 30.0%
! TGTTGTATTTTATAAAGGCC+TGG - chr7.4:28568077-28568096 MS.gene52254:CDS 30.0%
!! GAAGGTTATAAGAAGCATTT+AGG - chr7.4:28568502-28568521 MS.gene52254:CDS 30.0%
!!! TCGGTTTATTTTGTTTGTGA+AGG - chr7.4:28568484-28568503 MS.gene52254:CDS 30.0%
ATAATCACTTGGGCTTGTAA+TGG + chr7.4:28567959-28567978 None:intergenic 35.0%
ATTGAGCTTGAAGGATACAA+TGG + chr7.4:28568127-28568146 None:intergenic 35.0%
CAAACTCCACATTCACAAAT+TGG - chr7.4:28568327-28568346 MS.gene52254:CDS 35.0%
CTAGTTCCAATTTGTGAATG+TGG + chr7.4:28568336-28568355 None:intergenic 35.0%
GAGATCTATAATGTGAAGGA+TGG - chr7.4:28568529-28568548 MS.gene52254:CDS 35.0%
TAATCACTTGGGCTTGTAAT+GGG + chr7.4:28567958-28567977 None:intergenic 35.0%
! AAAGAGCAAGCCAATCATTT+TGG - chr7.4:28568019-28568038 MS.gene52254:CDS 35.0%
! GGGTTTTACCACAATTTCAA+TGG - chr7.4:28568605-28568624 MS.gene52254:CDS 35.0%
! TTGTTTCTCCAAGTTGGAAA+AGG - chr7.4:28568459-28568478 MS.gene52254:CDS 35.0%
!! ATTTTATTTGTCGGAAACCG+TGG - chr7.4:28568412-28568431 MS.gene52254:intron 35.0%
!! TTTGTTCAAGTTTTCCACTC+TGG + chr7.4:28568363-28568382 None:intergenic 35.0%
AAAAAGTTGCATTCGCTCGA+AGG + chr7.4:28568584-28568603 None:intergenic 40.0%
AATCACTTGGGCTTGTAATG+GGG + chr7.4:28567957-28567976 None:intergenic 40.0%
AATCATTGACCGGAGACATA+TGG - chr7.4:28568269-28568288 MS.gene52254:CDS 40.0%
ACCTTGTAAACAGCTTCTAG+AGG + chr7.4:28567919-28567938 None:intergenic 40.0%
ACGAGGATTATTGAGCTTGA+AGG + chr7.4:28568136-28568155 None:intergenic 40.0%
ATGTGAAGGATGGAAGCTTA+CGG - chr7.4:28568539-28568558 MS.gene52254:CDS 40.0%
CTGCAACCACATAATCACTT+GGG + chr7.4:28567969-28567988 None:intergenic 40.0%
GCATAGAAGTTGAATCACCA+CGG + chr7.4:28568432-28568451 None:intergenic 40.0%
GGAGCTACACTGTACTTAAA+AGG + chr7.4:28567883-28567902 None:intergenic 40.0%
GTTGCAGCGATTTACAATTG+TGG - chr7.4:28567982-28568001 MS.gene52254:CDS 40.0%
TACAAGCCCAAGTGATTATG+TGG - chr7.4:28567960-28567979 MS.gene52254:CDS 40.0%
TCATTTGAGTCATCACAACG+AGG + chr7.4:28568153-28568172 None:intergenic 40.0%
TCTAGAGGTGGCAGAATAAT+GGG + chr7.4:28567904-28567923 None:intergenic 40.0%
TTCCAACTTGGAGAAACAAG+AGG + chr7.4:28568458-28568477 None:intergenic 40.0%
! AACCGAATCCTTTTCCAACT+TGG + chr7.4:28568470-28568489 None:intergenic 40.0%
! ACCTCTAGAAGCTGTTTACA+AGG - chr7.4:28567915-28567934 MS.gene52254:CDS 40.0%
! CTCCAAGTTGGAAAAGGATT+CGG - chr7.4:28568465-28568484 MS.gene52254:CDS 40.0%
! TTCTAGAGGTGGCAGAATAA+TGG + chr7.4:28567905-28567924 None:intergenic 40.0%
! TTGTAAACAGCTTCTAGAGG+TGG + chr7.4:28567916-28567935 None:intergenic 40.0%
!!! CGAGCGAATGCAACTTTTTT+GGG - chr7.4:28568585-28568604 MS.gene52254:CDS 40.0%
!!! TCGAGCGAATGCAACTTTTT+TGG - chr7.4:28568584-28568603 MS.gene52254:CDS 40.0%
AACTTGGAGAAACAAGAGGC+TGG + chr7.4:28568454-28568473 None:intergenic 45.0%
ATTGACCGGAGACATATGGA+TGG - chr7.4:28568273-28568292 MS.gene52254:CDS 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.4:28567970-28567989 None:intergenic 45.0%
TCTCACCATCCATATGTCTC+CGG + chr7.4:28568281-28568300 None:intergenic 45.0%
! AGCCTCTTGTTTCTCCAAGT+TGG - chr7.4:28568453-28568472 MS.gene52254:CDS 45.0%
! CTGGTATTTGCTGATAGACG+CGG - chr7.4:28568096-28568115 MS.gene52254:CDS 45.0%
!! CCATGGTTGGCTTGCATTAA+CGG - chr7.4:28567828-28567847 MS.gene52254:CDS 45.0%
AAGCCAACCATGGCTACAAC+CGG + chr7.4:28567821-28567840 None:intergenic 50.0%
CCGTTAATGCAAGCCAACCA+TGG + chr7.4:28567831-28567850 None:intergenic 50.0%
CGCGTCTATCAGCAAATACC+AGG + chr7.4:28568098-28568117 None:intergenic 50.0%
TGCATTCGCTCGAAGGAAAG+TGG + chr7.4:28568577-28568596 None:intergenic 50.0%
TTGGAACTAGACGTCCAGAG+TGG - chr7.4:28568346-28568365 MS.gene52254:intron 50.0%
! TGTAATGGGGTCAGCAGACA+AGG + chr7.4:28567944-28567963 None:intergenic 50.0%
!! TTTTTGGCCGGTTGTAGCCA+TGG - chr7.4:28567811-28567830 MS.gene52254:CDS 50.0%
TGGCCGGTTGTAGCCATGGT+TGG - chr7.4:28567815-28567834 MS.gene52254:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 28567808 28568633 28567808 ID=MS.gene52254
chr7.4 mRNA 28567808 28568633 28567808 ID=MS.gene52254.t1;Parent=MS.gene52254
chr7.4 exon 28568438 28568633 28568438 ID=MS.gene52254.t1.exon1;Parent=MS.gene52254.t1
chr7.4 CDS 28568438 28568633 28568438 ID=cds.MS.gene52254.t1;Parent=MS.gene52254.t1
chr7.4 exon 28568212 28568347 28568212 ID=MS.gene52254.t1.exon2;Parent=MS.gene52254.t1
chr7.4 CDS 28568212 28568347 28568212 ID=cds.MS.gene52254.t1;Parent=MS.gene52254.t1
chr7.4 exon 28567808 28568138 28567808 ID=MS.gene52254.t1.exon3;Parent=MS.gene52254.t1
chr7.4 CDS 28567808 28568138 28567808 ID=cds.MS.gene52254.t1;Parent=MS.gene52254.t1
Gene Sequence

>MS.gene52254

ATGTTTTTGGCCGGTTGTAGCCATGGTTGGCTTGCATTAACGGATGATAACAAAGCCATAACTCTAGTGAATCCTTTTAAGTACAGTGTAGCTCCCATTATTCTGCCACCTCTAGAAGCTGTTTACAAGGTTACCTTGTCTGCTGACCCCATTACAAGCCCAAGTGATTATGTGGTTGCAGCGATTTACAATTGTGGTTTTCTCGCTTTCAAAAGAGCAAGCCAATCATTTTGGATTTGTGTAAACAGAAATGAATTTCATTTCACTAATGTTGTATTTTATAAAGGCCTGGTATTTGCTGATAGACGCGGAAATACCATTGTATCCTTCAAGCTCAATAATCCTCGTTGTGATGACTCAAATGACCCTAATTTTACTTACTACGAGAAGATAGCTAGTACTCCATATACATATTGTATTAGGTGAACAGTATTATTATAGCTGCCATGTTTATTTCGTGAAATCATTGACCGGAGACATATGGATGGTGAGAAGATGTAATGTCGACAATCATTCGTTCAAACTCCACATTCACAAATTGGAACTAGACGTCCAGAGTGGAAAACTTGAACAAATGAACAAACTTGAGAGTTTGGAAGACAACATTTTATTTGTCGGAAACCGTGGTGATTCAACTTCTATGCCAGCCTCTTGTTTCTCCAAGTTGGAAAAGGATTCGGTTTATTTTGTTTGTGAAGGTTATAAGAAGCATTTAGGGTTAGAGATCTATAATGTGAAGGATGGAAGCTTACGGAGACAATCTTTACCACTTTCCTTCGAGCGAATGCAACTTTTTTGGGTTTTACCACAATTTCAATGGGATTGA
Protein sequence

>MS.gene52254.t1

MFLAGCSHGWLALTDDNKAITLVNPFKYSVAPIILPPLEAVYKVTLSADPITSPSDYVVAAIYNCGLVFADRRGNTIVSFKLNNPRCDDSNDPNFTYYEKIASTPYTYCIRCNVDNHSFKLHIHKLELDVQSGKLEQMNKLESLEDNILFVGNRGDSTSMPASCFSKLEKDSVYFVCEGYKKHLGLEIYNVKDGSLRRQSLPLSFERMQLFWVLPQFQWD