AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene80306

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80306.t1 MTR_2g049610 80.309 259 30 2 4 262 2 239 7.25e-154 428
MS.gene80306.t1 MTR_2g049630 61.660 253 63 5 1 245 1 227 2.97e-97 290
MS.gene80306.t1 MTR_2g049530 70.115 174 50 1 1 172 1 174 5.54e-84 249
MS.gene80306.t1 MTR_4g107170 46.606 221 103 5 1 214 1 213 2.15e-60 191
MS.gene80306.t1 MTR_4g045977 44.681 235 101 6 4 222 2 223 2.21e-56 186
MS.gene80306.t1 MTR_1g115290 49.689 161 57 4 40 195 2 143 9.84e-42 140
MS.gene80306.t1 MTR_6g018920 39.355 155 87 2 4 152 2 155 4.84e-32 120
MS.gene80306.t1 MTR_1g114730 40.385 156 86 2 4 153 2 156 1.11e-31 119
MS.gene80306.t1 MTR_6g005440 34.158 202 119 6 4 192 2 202 1.45e-30 116
MS.gene80306.t1 MTR_6g005450 38.065 155 89 3 4 152 2 155 3.50e-26 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 46 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAAATCCATCTATTGTTTC+TGG 0.124929 2.4:+42025208 None:intergenic
ACTTGGTAATGTTGCATATT+TGG 0.170747 2.4:-42025293 MS.gene80306:CDS
GGAATGGGAAACTCAATTTA+TGG 0.183833 2.4:-42025245 MS.gene80306:CDS
TCTTTCACATCAAAGATCTT+TGG 0.287719 2.4:+42025727 None:intergenic
ATGCAACAAAGTACTGAAAA+TGG 0.300561 2.4:-42025514 MS.gene80306:CDS
CACAATCTCTTTGTGCACTT+TGG 0.338528 2.4:+42025663 None:intergenic
ATGATTACAAGCTTGAATCT+TGG 0.383659 2.4:+42025558 None:intergenic
TCCTGACCAGGTTTAGCAAC+TGG 0.388453 2.4:+42025265 None:intergenic
TCATGGATATGTTGCATTTG+AGG 0.410645 2.4:+42025400 None:intergenic
GCTTTGCCAGAAACAATAGA+TGG 0.415718 2.4:-42025214 MS.gene80306:CDS
ACTTGGTGAAGTTGAAGAAT+TGG 0.421405 2.4:-42025344 MS.gene80306:CDS
CTATTAAACACATTCAAGAT+TGG 0.421571 2.4:-42025948 MS.gene80306:CDS
TGCTAAACCTGGTCAGGAAT+GGG 0.447809 2.4:-42025260 MS.gene80306:CDS
TGTGAGGAGACAACATTATT+CGG 0.449930 2.4:+42025454 None:intergenic
ATGTTGTCTCCTCACATTCA+AGG 0.456551 2.4:-42025447 MS.gene80306:CDS
TCCAGTTGCTAAACCTGGTC+AGG 0.458685 2.4:-42025266 MS.gene80306:CDS
TGAGTTTCCCATTCCTGACC+AGG 0.483105 2.4:+42025253 None:intergenic
GAATCTTGTGGCATAGTCAT+TGG 0.501448 2.4:+42025808 None:intergenic
ATGAAGCATGGATGCCAAGT+TGG 0.507763 2.4:+42025628 None:intergenic
CAATCAAAGAAGCAATGGAT+TGG 0.512118 2.4:-42025905 MS.gene80306:CDS
TTGCTAAACCTGGTCAGGAA+TGG 0.512431 2.4:-42025261 MS.gene80306:CDS
CCTTCCATGTTCATGAAGCA+TGG 0.519687 2.4:+42025616 None:intergenic
GCATCCATGCTTCATGAACA+TGG 0.521603 2.4:-42025620 MS.gene80306:CDS
ATACAAGCAACAAAAGATTG+AGG 0.523829 2.4:-42025758 MS.gene80306:CDS
GTGGCTTCAAATGATCATCA+TGG 0.534306 2.4:+42025383 None:intergenic
GCTTGCTTAATTGTGTATGA+TGG 0.534651 2.4:-42025841 MS.gene80306:CDS
GTTTAATAGTTAATTTCCCA+CGG 0.538383 2.4:+42025962 None:intergenic
TACAAGCAACAAAAGATTGA+GGG 0.545039 2.4:-42025757 MS.gene80306:CDS
ACATTCAAGATTGGAGAGCT+CGG 0.553672 2.4:-42025939 MS.gene80306:CDS
CCATGCTTCATGAACATGGA+AGG 0.554983 2.4:-42025616 MS.gene80306:CDS
ACTTTCAATCAAAGAAGCAA+TGG 0.559273 2.4:-42025910 MS.gene80306:CDS
GATTGGGCTAGTCAAGTACT+TGG 0.562422 2.4:-42025310 MS.gene80306:CDS
GTAGAAATGGGTCGTGCCCG+TGG 0.563669 2.4:-42025979 None:intergenic
CATGCTTCATGAACATGGAA+GGG 0.576308 2.4:-42025615 MS.gene80306:CDS
ATGCTTCATGAACATGGAAG+GGG 0.583471 2.4:-42025614 MS.gene80306:CDS
TTTAATAGTTAATTTCCCAC+GGG 0.586000 2.4:+42025963 None:intergenic
GATGATCCAGTTGCTAAACC+TGG 0.589750 2.4:-42025271 MS.gene80306:CDS
ATCAAGCTTCCTTGAATGTG+AGG 0.590592 2.4:+42025438 None:intergenic
CTTAGTGATACTAATCGACT+TGG 0.592888 2.4:-42025361 MS.gene80306:CDS
TGATGAAAATGTATCCAACT+TGG 0.601327 2.4:-42025642 MS.gene80306:CDS
CACAAGATTCGACAATTGTA+CGG 0.605972 2.4:-42025795 MS.gene80306:CDS
TTAATTGTGTATGATGGTGA+TGG 0.608708 2.4:-42025835 MS.gene80306:CDS
CGTACAATTGTCGAATCTTG+TGG 0.612214 2.4:+42025796 None:intergenic
TAGAAATGGGTCGTGCCCGT+GGG 0.613629 2.4:-42025978 None:intergenic
CACTACTCAGACGCAAAATG+TGG 0.617631 2.4:-42025479 MS.gene80306:CDS
AGTCGATTAGTATCACTAAG+TGG 0.621773 2.4:+42025364 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CTATTAAACACATTCAAGAT+TGG - chr2.4:42025232-42025251 MS.gene80306:CDS 25.0%
! GTTTAATAGTTAATTTCCCA+CGG + chr2.4:42025221-42025240 None:intergenic 25.0%
! TAAAATCCATCTATTGTTTC+TGG + chr2.4:42025975-42025994 None:intergenic 25.0%
! TTTAATAGTTAATTTCCCAC+GGG + chr2.4:42025220-42025239 None:intergenic 25.0%
!! AATTGGATGATTTTATGGAT+TGG - chr2.4:42025853-42025872 MS.gene80306:CDS 25.0%
!! ATTGGATGATTTTATGGATT+GGG - chr2.4:42025854-42025873 MS.gene80306:CDS 25.0%
!! TGAAGAATTGGATGATTTTA+TGG - chr2.4:42025848-42025867 MS.gene80306:CDS 25.0%
ACTTTCAATCAAAGAAGCAA+TGG - chr2.4:42025270-42025289 MS.gene80306:CDS 30.0%
ATACAAGCAACAAAAGATTG+AGG - chr2.4:42025422-42025441 MS.gene80306:CDS 30.0%
ATGATTACAAGCTTGAATCT+TGG + chr2.4:42025625-42025644 None:intergenic 30.0%
TACAAGCAACAAAAGATTGA+GGG - chr2.4:42025423-42025442 MS.gene80306:CDS 30.0%
TCTTTCACATCAAAGATCTT+TGG + chr2.4:42025456-42025475 None:intergenic 30.0%
TGATGAAAATGTATCCAACT+TGG - chr2.4:42025538-42025557 MS.gene80306:CDS 30.0%
! TTAATTGTGTATGATGGTGA+TGG - chr2.4:42025345-42025364 MS.gene80306:CDS 30.0%
!! ACTTGGTAATGTTGCATATT+TGG - chr2.4:42025887-42025906 MS.gene80306:CDS 30.0%
!! ATGCAACAAAGTACTGAAAA+TGG - chr2.4:42025666-42025685 MS.gene80306:CDS 30.0%
!! TCTGAATTTTCTAGCAAGTT+TGG - chr2.4:42025309-42025328 MS.gene80306:CDS 30.0%
!!! TTGCTTGTATTTTTCAAGCA+TGG + chr2.4:42025412-42025431 None:intergenic 30.0%
AGTCGATTAGTATCACTAAG+TGG + chr2.4:42025819-42025838 None:intergenic 35.0%
CAATCAAAGAAGCAATGGAT+TGG - chr2.4:42025275-42025294 MS.gene80306:CDS 35.0%
CACAAGATTCGACAATTGTA+CGG - chr2.4:42025385-42025404 MS.gene80306:CDS 35.0%
CTTAGTGATACTAATCGACT+TGG - chr2.4:42025819-42025838 MS.gene80306:CDS 35.0%
GCTTGCTTAATTGTGTATGA+TGG - chr2.4:42025339-42025358 MS.gene80306:CDS 35.0%
GGAATGGGAAACTCAATTTA+TGG - chr2.4:42025935-42025954 MS.gene80306:CDS 35.0%
TCATGGATATGTTGCATTTG+AGG + chr2.4:42025783-42025802 None:intergenic 35.0%
TGTGAGGAGACAACATTATT+CGG + chr2.4:42025729-42025748 None:intergenic 35.0%
! ACTTGGTGAAGTTGAAGAAT+TGG - chr2.4:42025836-42025855 MS.gene80306:CDS 35.0%
ACATTCAAGATTGGAGAGCT+CGG - chr2.4:42025241-42025260 MS.gene80306:CDS 40.0%
ATCAAGCTTCCTTGAATGTG+AGG + chr2.4:42025745-42025764 None:intergenic 40.0%
ATGCTTCATGAACATGGAAG+GGG - chr2.4:42025566-42025585 MS.gene80306:CDS 40.0%
ATGTTGTCTCCTCACATTCA+AGG - chr2.4:42025733-42025752 MS.gene80306:CDS 40.0%
CACAATCTCTTTGTGCACTT+TGG + chr2.4:42025520-42025539 None:intergenic 40.0%
CATGCTTCATGAACATGGAA+GGG - chr2.4:42025565-42025584 MS.gene80306:CDS 40.0%
CGTACAATTGTCGAATCTTG+TGG + chr2.4:42025387-42025406 None:intergenic 40.0%
GAATCTTGTGGCATAGTCAT+TGG + chr2.4:42025375-42025394 None:intergenic 40.0%
GCTTTGCCAGAAACAATAGA+TGG - chr2.4:42025966-42025985 MS.gene80306:CDS 40.0%
GTGGCTTCAAATGATCATCA+TGG + chr2.4:42025800-42025819 None:intergenic 40.0%
ATGAAGCATGGATGCCAAGT+TGG + chr2.4:42025555-42025574 None:intergenic 45.0%
CACTACTCAGACGCAAAATG+TGG - chr2.4:42025701-42025720 MS.gene80306:CDS 45.0%
CCATGCTTCATGAACATGGA+AGG - chr2.4:42025564-42025583 MS.gene80306:CDS 45.0%
CCTTCCATGTTCATGAAGCA+TGG + chr2.4:42025567-42025586 None:intergenic 45.0%
GATGATCCAGTTGCTAAACC+TGG - chr2.4:42025909-42025928 MS.gene80306:CDS 45.0%
GCATCCATGCTTCATGAACA+TGG - chr2.4:42025560-42025579 MS.gene80306:CDS 45.0%
TGCTAAACCTGGTCAGGAAT+GGG - chr2.4:42025920-42025939 MS.gene80306:CDS 45.0%
TTGCTAAACCTGGTCAGGAA+TGG - chr2.4:42025919-42025938 MS.gene80306:CDS 45.0%
!! GATTGGGCTAGTCAAGTACT+TGG - chr2.4:42025870-42025889 MS.gene80306:CDS 45.0%
TCCAGTTGCTAAACCTGGTC+AGG - chr2.4:42025914-42025933 MS.gene80306:CDS 50.0%
TCCTGACCAGGTTTAGCAAC+TGG + chr2.4:42025918-42025937 None:intergenic 50.0%
TGAGTTTCCCATTCCTGACC+AGG + chr2.4:42025930-42025949 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 42025207 42025995 42025207 ID=MS.gene80306
chr2.4 mRNA 42025207 42025995 42025207 ID=MS.gene80306.t1;Parent=MS.gene80306
chr2.4 exon 42025207 42025995 42025207 ID=MS.gene80306.t1.exon1;Parent=MS.gene80306.t1
chr2.4 CDS 42025207 42025995 42025207 ID=cds.MS.gene80306.t1;Parent=MS.gene80306.t1
Gene Sequence

>MS.gene80306

ATGGGTCGTGCCCGTGGGAAATTAACTATTAAACACATTCAAGATTGGAGAGCTCGGAAATCAACTTTCAATCAAAGAAGCAATGGATTGGCAAAAAAAGTTTCTGAATTTTCTAGCAAGTTTGGAGTTGAAGCTTGCTTAATTGTGTATGATGGTGATGGTAGACCAATGACTATGCCACAAGATTCGACAATTGTACGGTCCATGCTTGAAAAATACAAGCAACAAAAGATTGAGGGTACAACTCCAAAGATCTTTGATGTGAAAGACTATTTTGCAAATAAGAAGAATAAGATTGAAGCTGATATTTCCAAAGTGCACAAAGAGATTGTGATGAAAATGTATCCAACTTGGCATCCATGCTTCATGAACATGGAAGGGGAACAGCTCAAAACTTTCATTGCTATTGTAGATGCCAAGATTCAAGCTTGTAATCATAAAATTAACATGCTAAAGAAAATGCAACAAAGTACTGAAAATGGTTTCATGCTAAACACTACTCAGACGCAAAATGTGGCTCCGAATAATGTTGTCTCCTCACATTCAAGGAAGCTTGATGTCACTGATAGATTTCCTCAAATGCAACATATCCATGATGATCATTTGAAGCCACTTAGTGATACTAATCGACTTGGTGAAGTTGAAGAATTGGATGATTTTATGGATTGGGCTAGTCAAGTACTTGGTAATGTTGCATATTTGGATGATCCAGTTGCTAAACCTGGTCAGGAATGGGAAACTCAATTTATGGATTTTGATGCTTTGCCAGAAACAATAGATGGATTTTAA
Protein sequence

>MS.gene80306.t1

MGRARGKLTIKHIQDWRARKSTFNQRSNGLAKKVSEFSSKFGVEACLIVYDGDGRPMTMPQDSTIVRSMLEKYKQQKIEGTTPKIFDVKDYFANKKNKIEADISKVHKEIVMKMYPTWHPCFMNMEGEQLKTFIAIVDAKIQACNHKINMLKKMQQSTENGFMLNTTQTQNVAPNNVVSSHSRKLDVTDRFPQMQHIHDDHLKPLSDTNRLGEVEELDDFMDWASQVLGNVAYLDDPVAKPGQEWETQFMDFDALPETIDGF