AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52933

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52933.t1 MTR_1g075780 76.224 143 16 1 12 136 3 145 3.27e-75 220
MS.gene52933.t1 MTR_4g063510 31.977 172 63 4 17 136 13 182 1.48e-16 72.4
MS.gene52933.t1 MTR_1g075840 41.935 124 42 6 36 136 1 117 1.29e-14 65.9
MS.gene52933.t1 MTR_1g041455 31.646 158 70 7 14 136 13 167 2.29e-13 63.5
MS.gene52933.t1 MTR_5g056450 32.215 149 66 6 1 124 1 139 5.56e-12 59.7
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:+56773601 MS.gene52933:CDS
TTATCCAACATGTTGATATA+TGG 0.260832 1.1:-56773545 None:intergenic
ATGGGAAAATTGGGTGGTAA+AGG 0.416030 1.1:-56773413 None:intergenic
TAAAGGGTTGGCCATTGATT+CGG 0.428827 1.1:-56773396 None:intergenic
TGGGAAAATTGGGTGGTAAA+GGG 0.468596 1.1:-56773412 None:intergenic
CAATCCTCAGGCCGAATCAA+TGG 0.469990 1.1:+56773385 MS.gene52933:CDS
CATTGATTCGGCCTGAGGAT+TGG 0.472364 1.1:-56773384 None:intergenic
CCACCAGTCCCTTGTTGTTG+TGG 0.476108 1.1:-56773491 None:intergenic
AAGCCACCTTGAGTCTCATA+TGG 0.484456 1.1:+56773325 MS.gene52933:CDS
CAAAATTATTGATATTGCTA+CGG 0.495293 1.1:-56773256 None:intergenic
ACAACAAGGGACTGGTGGTA+TGG 0.510630 1.1:+56773496 MS.gene52933:CDS
ATTCGGCCTGAGGATTGGTA+TGG 0.511741 1.1:-56773379 None:intergenic
TTGGCCATTGATTCGGCCTG+AGG 0.541375 1.1:-56773389 None:intergenic
CTTGAGCCATATGAGACTCA+AGG 0.558137 1.1:-56773331 None:intergenic
ATTAAACCATACCAATCCTC+AGG 0.560036 1.1:+56773373 MS.gene52933:CDS
ATGGAAGTCTCTCCGATCGA+TGG 0.567201 1.1:+56773515 MS.gene52933:CDS
TAAGCCATATATCAACATGT+TGG 0.587500 1.1:+56773541 MS.gene52933:CDS
TTTGGCATGGGAAAATTGGG+TGG 0.600647 1.1:-56773419 None:intergenic
AAAATTGGGTGGTAAAGGGT+TGG 0.611916 1.1:-56773408 None:intergenic
TTTCAGCAACCACAACAACA+AGG 0.614643 1.1:+56773482 MS.gene52933:CDS
CAACCACAACAACAAGGGAC+TGG 0.623235 1.1:+56773488 MS.gene52933:CDS
CCACAACAACAAGGGACTGG+TGG 0.623856 1.1:+56773491 MS.gene52933:CDS
TATGGCTTAGTTCCATCGAT+CGG 0.625287 1.1:-56773527 None:intergenic
TTCAGCAACCACAACAACAA+GGG 0.626204 1.1:+56773483 MS.gene52933:CDS
GAGCCATATGAGACTCAAGG+TGG 0.728487 1.1:-56773328 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATCAATAATTTTGTATG+TGG + chr1.1:56773263-56773282 MS.gene52933:CDS 15.0%
!! CAAAATTATTGATATTGCTA+CGG - chr1.1:56773259-56773278 None:intergenic 20.0%
!!! TTGTTTTCATGTAATGATTT+TGG - chr1.1:56773440-56773459 None:intergenic 20.0%
! TTATCCAACATGTTGATATA+TGG - chr1.1:56773548-56773567 None:intergenic 25.0%
!!! AAATAACTTGCTTTTAACGA+AGG - chr1.1:56773465-56773484 None:intergenic 25.0%
TAAGCCATATATCAACATGT+TGG + chr1.1:56773541-56773560 MS.gene52933:CDS 30.0%
! AATGAAGACATTTTTCTCGA+TGG - chr1.1:56773573-56773592 None:intergenic 30.0%
! ATGAAGACATTTTTCTCGAT+GGG - chr1.1:56773572-56773591 None:intergenic 30.0%
!! TCATGTAATGATTTTGGCAT+GGG - chr1.1:56773434-56773453 None:intergenic 30.0%
!! TTCATGTAATGATTTTGGCA+TGG - chr1.1:56773435-56773454 None:intergenic 30.0%
ATTAAACCATACCAATCCTC+AGG + chr1.1:56773373-56773392 MS.gene52933:CDS 35.0%
CAATGACACATCAGTGAATT+TGG + chr1.1:56773601-56773620 MS.gene52933:CDS 35.0%
!! GATTTTGGCATGGGAAAATT+GGG - chr1.1:56773425-56773444 None:intergenic 35.0%
!! TGATTTTGGCATGGGAAAAT+TGG - chr1.1:56773426-56773445 None:intergenic 35.0%
AAAATTGGGTGGTAAAGGGT+TGG - chr1.1:56773411-56773430 None:intergenic 40.0%
ATGGGAAAATTGGGTGGTAA+AGG - chr1.1:56773416-56773435 None:intergenic 40.0%
TATGGCTTAGTTCCATCGAT+CGG - chr1.1:56773530-56773549 None:intergenic 40.0%
TGGGAAAATTGGGTGGTAAA+GGG - chr1.1:56773415-56773434 None:intergenic 40.0%
TTCAGCAACCACAACAACAA+GGG + chr1.1:56773483-56773502 MS.gene52933:CDS 40.0%
TTTCAGCAACCACAACAACA+AGG + chr1.1:56773482-56773501 MS.gene52933:CDS 40.0%
!! TAAAGGGTTGGCCATTGATT+CGG - chr1.1:56773399-56773418 None:intergenic 40.0%
AAGCCACCTTGAGTCTCATA+TGG + chr1.1:56773325-56773344 MS.gene52933:CDS 45.0%
CTTGAGCCATATGAGACTCA+AGG - chr1.1:56773334-56773353 None:intergenic 45.0%
TTTGGCATGGGAAAATTGGG+TGG - chr1.1:56773422-56773441 None:intergenic 45.0%
ATGGAAGTCTCTCCGATCGA+TGG + chr1.1:56773515-56773534 MS.gene52933:CDS 50.0%
CAACCACAACAACAAGGGAC+TGG + chr1.1:56773488-56773507 MS.gene52933:CDS 50.0%
CAATCCTCAGGCCGAATCAA+TGG + chr1.1:56773385-56773404 MS.gene52933:CDS 50.0%
GAGCCATATGAGACTCAAGG+TGG - chr1.1:56773331-56773350 None:intergenic 50.0%
! ACAACAAGGGACTGGTGGTA+TGG + chr1.1:56773496-56773515 MS.gene52933:CDS 50.0%
! ATTCGGCCTGAGGATTGGTA+TGG - chr1.1:56773382-56773401 None:intergenic 50.0%
!! CATTGATTCGGCCTGAGGAT+TGG - chr1.1:56773387-56773406 None:intergenic 50.0%
CCACAACAACAAGGGACTGG+TGG + chr1.1:56773491-56773510 MS.gene52933:CDS 55.0%
!! CCACCAGTCCCTTGTTGTTG+TGG - chr1.1:56773494-56773513 None:intergenic 55.0%
!! TTGGCCATTGATTCGGCCTG+AGG - chr1.1:56773392-56773411 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 56773227 56773637 56773227 ID=MS.gene52933
chr1.1 mRNA 56773227 56773637 56773227 ID=MS.gene52933.t1;Parent=MS.gene52933
chr1.1 exon 56773227 56773637 56773227 ID=MS.gene52933.t1.exon1;Parent=MS.gene52933.t1
chr1.1 CDS 56773227 56773637 56773227 ID=cds.MS.gene52933.t1;Parent=MS.gene52933.t1
Gene Sequence

>MS.gene52933

ATGGGTGACGATTTCGCTCAAGAGAACAACCGTAGCAATATCAATAATTTTGTATGTGGATTGTGCAATCATGATTGCACAAACTTCGAATCACTCATAAGCCACCTTGAGTCTCATATGGCTCAAGAAAATCTTGCTATTGCAAGATTAAACCATACCAATCCTCAGGCCGAATCAATGGCCAACCCTTTACCACCCAATTTTCCCATGCCAAAATCATTACATGAAAACAAAACCTTCGTTAAAAGCAAGTTATTTCAGCAACCACAACAACAAGGGACTGGTGGTATGGAAGTCTCTCCGATCGATGGAACTAAGCCATATATCAACATGTTGGATAAACCCATCGAGAAAAATGTCTTCATTAACATCATCAATGACACATCAGTGAATTTGGAGTTAAAGCTCTAG
Protein sequence

>MS.gene52933.t1

MGDDFAQENNRSNINNFVCGLCNHDCTNFESLISHLESHMAQENLAIARLNHTNPQAESMANPLPPNFPMPKSLHENKTFVKSKLFQQPQQQGTGGMEVSPIDGTKPYINMLDKPIEKNVFINIINDTSVNLELKL