AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene51424

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGTGGTGGAGACTCGTTTA+TGG 0.268230 2.2:-54223078 None:intergenic
TTTCCCTTGATTAATTGCTT+TGG 0.314214 2.2:-54223120 None:intergenic
TCATCATCTAGCCATTTATA+TGG 0.328544 2.2:-54223362 None:intergenic
ATGAAATTGTTTGGTTGTAT+AGG 0.333031 2.2:+54222955 MS.gene51424:CDS
CTATTGTCTTCTTCTATGCT+TGG 0.334263 2.2:-54223152 None:intergenic
AAAGATGCATGTGGAGATAA+TGG 0.348455 2.2:+54223451 MS.gene51424:CDS
TAATTAATTATGAAATTGTT+TGG 0.354883 2.2:+54222946 MS.gene51424:CDS
GTCTCCACCACCCCTTGATA+TGG 0.365900 2.2:+54223088 MS.gene51424:CDS
ATTGAATATTGATGAGGGTT+TGG 0.371754 2.2:+54223337 MS.gene51424:CDS
GGAGATAATGGAAACAAATA+AGG 0.374313 2.2:+54223463 MS.gene51424:CDS
TTGAATATTGATGAGGGTTT+GGG 0.380724 2.2:+54223338 MS.gene51424:CDS
ATTTGTGGCTCATCATATAA+TGG 0.388625 2.2:+54223500 MS.gene51424:CDS
CCCACAAGCAAGTCTTCATT+TGG 0.393338 2.2:-54223613 None:intergenic
ATAATGAGATAAAGAACTAT+TGG 0.401279 2.2:+54223015 MS.gene51424:CDS
ATTATGATCAGTTGTCTGAT+TGG 0.412238 2.2:+54223573 MS.gene51424:CDS
AGGGTTTGGGACCATATAAA+TGG 0.422279 2.2:+54223351 MS.gene51424:CDS
TTTCTTTAGGCATTGGTTCA+AGG 0.441266 2.2:-54223196 None:intergenic
TTATGATCAGTTGTCTGATT+GGG 0.447767 2.2:+54223574 MS.gene51424:CDS
TGCTTGTGGGGTCCAGGCAT+TGG 0.457725 2.2:+54223626 MS.gene51424:CDS
TTCTTTAGGCATTGGTTCAA+GGG 0.459777 2.2:-54223195 None:intergenic
AATGAATTGAATATTGATGA+GGG 0.462618 2.2:+54223332 MS.gene51424:CDS
AAGACTTGCTTGTGGGGTCC+AGG 0.468518 2.2:+54223620 MS.gene51424:CDS
GAATAATATTTATGAAATGA+AGG 0.480192 2.2:+54223271 MS.gene51424:CDS
CCAAATGAAGACTTGCTTGT+GGG 0.483699 2.2:+54223613 MS.gene51424:CDS
ACATCCAAAGCAATTAATCA+AGG 0.485763 2.2:+54223116 MS.gene51424:CDS
ATCTCATTATCTGTTCGTCC+TGG 0.494018 2.2:-54223002 None:intergenic
TTCATGATTTCACCAATGCC+TGG 0.500438 2.2:-54223638 None:intergenic
GGCATTGGTGAAATCATGAA+TGG 0.500573 2.2:+54223641 MS.gene51424:CDS
TGGATGTAGATGCCATATCA+AGG 0.504399 2.2:-54223100 None:intergenic
TATAATGGAGAGAGTGGAGA+AGG 0.506418 2.2:+54223515 MS.gene51424:CDS
AAATGAATTGAATATTGATG+AGG 0.544069 2.2:+54223331 MS.gene51424:CDS
AATAATATTTATGAAATGAA+GGG 0.558223 2.2:+54223272 MS.gene51424:CDS
ATTGGAACTCTCATTTGAGA+AGG 0.563317 2.2:+54223033 MS.gene51424:CDS
AAATTGTTTGGTTGTATAGG+TGG 0.577527 2.2:+54222958 MS.gene51424:CDS
GATGCCATATCAAGGGGTGG+TGG 0.580470 2.2:-54223092 None:intergenic
GGATGTAGATGCCATATCAA+GGG 0.582178 2.2:-54223099 None:intergenic
CAAATGAAGACTTGCTTGTG+GGG 0.583434 2.2:+54223614 MS.gene51424:CDS
CATCCAAAGCAATTAATCAA+GGG 0.597288 2.2:+54223117 MS.gene51424:CDS
GAAATGAAAAGTGAAATTTG+TGG 0.604467 2.2:+54223485 MS.gene51424:CDS
GTGATAGCATCACATTTACC+AGG 0.608146 2.2:+54222984 MS.gene51424:CDS
TCACAATACTATAATGTACA+AGG 0.616095 2.2:+54223227 MS.gene51424:CDS
TCATCATATAATGGAGAGAG+TGG 0.620420 2.2:+54223509 MS.gene51424:CDS
CATAGAAGAAGACAATAGCA+TGG 0.634357 2.2:+54223157 MS.gene51424:CDS
ACCAAATGAAGACTTGCTTG+TGG 0.648427 2.2:+54223612 MS.gene51424:CDS
GATGTAGATGCCATATCAAG+GGG 0.659513 2.2:-54223098 None:intergenic
AGACAACTGATCATAATCTG+TGG 0.681864 2.2:-54223567 None:intergenic
ATAATGGAGAGAGTGGAGAA+GGG 0.683863 2.2:+54223516 MS.gene51424:CDS
GTAGATGCCATATCAAGGGG+TGG 0.684370 2.2:-54223095 None:intergenic
TGACTCTAGAAAGATGCATG+TGG 0.707312 2.2:+54223442 MS.gene51424:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATATTTATGAAATGAA+GGG + chr2.2:54223272-54223291 MS.gene51424:CDS 10.0%
!! TAATTAATTATGAAATTGTT+TGG + chr2.2:54222946-54222965 MS.gene51424:CDS 10.0%
!! GAATAATATTTATGAAATGA+AGG + chr2.2:54223271-54223290 MS.gene51424:CDS 15.0%
!!! ATATTCAATTCATTTTTACT+AGG - chr2.2:54223326-54223345 None:intergenic 15.0%
!!! TATTCAATTCATTTTTACTA+GGG - chr2.2:54223325-54223344 None:intergenic 15.0%
!! AAATGAATTGAATATTGATG+AGG + chr2.2:54223331-54223350 MS.gene51424:CDS 20.0%
!! AATGAATTGAATATTGATGA+GGG + chr2.2:54223332-54223351 MS.gene51424:CDS 20.0%
!! ATAATGAGATAAAGAACTAT+TGG + chr2.2:54223015-54223034 MS.gene51424:CDS 20.0%
!!! TTCGTAACATGTTTTTAAAT+GGG + chr2.2:54223396-54223415 MS.gene51424:CDS 20.0%
! ATGAAATTGTTTGGTTGTAT+AGG + chr2.2:54222955-54222974 MS.gene51424:CDS 25.0%
! GAAATGAAAAGTGAAATTTG+TGG + chr2.2:54223485-54223504 MS.gene51424:CDS 25.0%
! TCACAATACTATAATGTACA+AGG + chr2.2:54223227-54223246 MS.gene51424:CDS 25.0%
!!! AACATGTTTTTAAATGGGAT+AGG + chr2.2:54223401-54223420 MS.gene51424:CDS 25.0%
!!! CTTCGTAACATGTTTTTAAA+TGG + chr2.2:54223395-54223414 MS.gene51424:CDS 25.0%
!!! TGTGAAGTTGTTTTTTCTTT+AGG - chr2.2:54223212-54223231 None:intergenic 25.0%
AAATTGTTTGGTTGTATAGG+TGG + chr2.2:54222958-54222977 MS.gene51424:CDS 30.0%
ACATCCAAAGCAATTAATCA+AGG + chr2.2:54223116-54223135 MS.gene51424:CDS 30.0%
ATTATGATCAGTTGTCTGAT+TGG + chr2.2:54223573-54223592 MS.gene51424:CDS 30.0%
ATTGAATATTGATGAGGGTT+TGG + chr2.2:54223337-54223356 MS.gene51424:CDS 30.0%
ATTTGTGGCTCATCATATAA+TGG + chr2.2:54223500-54223519 MS.gene51424:CDS 30.0%
CATCCAAAGCAATTAATCAA+GGG + chr2.2:54223117-54223136 MS.gene51424:CDS 30.0%
TCATCATCTAGCCATTTATA+TGG - chr2.2:54223365-54223384 None:intergenic 30.0%
TTATGATCAGTTGTCTGATT+GGG + chr2.2:54223574-54223593 MS.gene51424:CDS 30.0%
TTGAATATTGATGAGGGTTT+GGG + chr2.2:54223338-54223357 MS.gene51424:CDS 30.0%
TTTCCCTTGATTAATTGCTT+TGG - chr2.2:54223123-54223142 None:intergenic 30.0%
!! GGAGATAATGGAAACAAATA+AGG + chr2.2:54223463-54223482 MS.gene51424:CDS 30.0%
!!! GTTGTTTTTTCTTTAGGCAT+TGG - chr2.2:54223206-54223225 None:intergenic 30.0%
AAAGATGCATGTGGAGATAA+TGG + chr2.2:54223451-54223470 MS.gene51424:CDS 35.0%
AGACAACTGATCATAATCTG+TGG - chr2.2:54223570-54223589 None:intergenic 35.0%
ATTGGAACTCTCATTTGAGA+AGG + chr2.2:54223033-54223052 MS.gene51424:CDS 35.0%
CATAGAAGAAGACAATAGCA+TGG + chr2.2:54223157-54223176 MS.gene51424:CDS 35.0%
CTATTGTCTTCTTCTATGCT+TGG - chr2.2:54223155-54223174 None:intergenic 35.0%
! TCATCATATAATGGAGAGAG+TGG + chr2.2:54223509-54223528 MS.gene51424:CDS 35.0%
!! TTCTTTAGGCATTGGTTCAA+GGG - chr2.2:54223198-54223217 None:intergenic 35.0%
!! TTTCTTTAGGCATTGGTTCA+AGG - chr2.2:54223199-54223218 None:intergenic 35.0%
ATCTCATTATCTGTTCGTCC+TGG - chr2.2:54223005-54223024 None:intergenic 40.0%
GATGTAGATGCCATATCAAG+GGG - chr2.2:54223101-54223120 None:intergenic 40.0%
GGATGTAGATGCCATATCAA+GGG - chr2.2:54223102-54223121 None:intergenic 40.0%
GTGATAGCATCACATTTACC+AGG + chr2.2:54222984-54223003 MS.gene51424:CDS 40.0%
TGGATGTAGATGCCATATCA+AGG - chr2.2:54223103-54223122 None:intergenic 40.0%
TTCATGATTTCACCAATGCC+TGG - chr2.2:54223641-54223660 None:intergenic 40.0%
! ACCAAATGAAGACTTGCTTG+TGG + chr2.2:54223612-54223631 MS.gene51424:CDS 40.0%
! AGGGTTTGGGACCATATAAA+TGG + chr2.2:54223351-54223370 MS.gene51424:CDS 40.0%
! ATAATGGAGAGAGTGGAGAA+GGG + chr2.2:54223516-54223535 MS.gene51424:CDS 40.0%
! CAAATGAAGACTTGCTTGTG+GGG + chr2.2:54223614-54223633 MS.gene51424:CDS 40.0%
! CCAAATGAAGACTTGCTTGT+GGG + chr2.2:54223613-54223632 MS.gene51424:CDS 40.0%
! TATAATGGAGAGAGTGGAGA+AGG + chr2.2:54223515-54223534 MS.gene51424:CDS 40.0%
! TGACTCTAGAAAGATGCATG+TGG + chr2.2:54223442-54223461 MS.gene51424:CDS 40.0%
!! GGCATTGGTGAAATCATGAA+TGG + chr2.2:54223641-54223660 MS.gene51424:CDS 40.0%
CCCACAAGCAAGTCTTCATT+TGG - chr2.2:54223616-54223635 None:intergenic 45.0%
GTAGATGCCATATCAAGGGG+TGG - chr2.2:54223098-54223117 None:intergenic 50.0%
GATGCCATATCAAGGGGTGG+TGG - chr2.2:54223095-54223114 None:intergenic 55.0%
GTCTCCACCACCCCTTGATA+TGG + chr2.2:54223088-54223107 MS.gene51424:CDS 55.0%
! AAGACTTGCTTGTGGGGTCC+AGG + chr2.2:54223620-54223639 MS.gene51424:CDS 55.0%
!! GGGTGGTGGAGACTCGTTTA+TGG - chr2.2:54223081-54223100 None:intergenic 55.0%
TGCTTGTGGGGTCCAGGCAT+TGG + chr2.2:54223626-54223645 MS.gene51424:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 54222938 54223676 54222938 ID=MS.gene51424
chr2.2 mRNA 54222938 54223676 54222938 ID=MS.gene51424.t1;Parent=MS.gene51424
chr2.2 exon 54222938 54223676 54222938 ID=MS.gene51424.t1.exon1;Parent=MS.gene51424.t1
chr2.2 CDS 54222938 54223676 54222938 ID=cds.MS.gene51424.t1;Parent=MS.gene51424.t1
Gene Sequence

>MS.gene51424

TGTGAACTTAATTAATTATGAAATTGTTTGGTTGTATAGGTGGTCAGTGATAGCATCACATTTACCAGGACGAACAGATAATGAGATAAAGAACTATTGGAACTCTCATTTGAGAAGGAAAATTTACTGCTTCATGAGATCCATAAACGAGTCTCCACCACCCCTTGATATGGCATCTACATCCAAAGCAATTAATCAAGGGAAAATAAATAATCCAAGCATAGAAGAAGACAATAGCATGGCTTTGATTCAAAATTCCCTTGAACCAATGCCTAAAGAAAAAACAACTTCACAATACTATAATGTACAAGGAGTTGAAGATATTTCGTGTGAGAATAATATTTATGAAATGAAGGGTAACATAAATAATACAGTTGCATCATACCCTAGTAAAAATGAATTGAATATTGATGAGGGTTTGGGACCATATAAATGGCTAGATGATGAAATTATGAAACTTCGTAACATGTTTTTAAATGGGATAGGAAATTATAATTATGATTGTGACTCTAGAAAGATGCATGTGGAGATAATGGAAACAAATAAGGAAATGAAAAGTGAAATTTGTGGCTCATCATATAATGGAGAGAGTGGAGAAGGGTACATTTCTAATGCATCAGTAAATTCTGCCACAGATTATGATCAGTTGTCTGATTGGGACTTTTGTCAAGAAGACCAAATGAAGACTTGCTTGTGGGGTCCAGGCATTGGTGAAATCATGAATGGTTTTTATCAGTAA
Protein sequence

>MS.gene51424.t1

CELNULUNCLVVUVVSDSITFTRTNRUUDKELLELSFEKENLLLHEIHKRVSTTPUYGIYIQSNUSRENKUSKHRRRQUHGFDSKFPUTNAURKNNFTILUCTRSURYFVUEUYLUNEGUHKUYSCIIPUUKUIEYUUGFGTIUMARUUNYETSUHVFKWDRKLULULULUKDACGDNGNKUGNEKUNLWLIIUWREWRRVHFUCISKFCHRLUSVVULGLLSRRPNEDLLVGSRHWUNHEWFLSV