AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84934

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84934.t1 MTR_1g053530 56.279 215 76 6 52 262 36 236 1.11e-65 207
MS.gene84934.t1 MTR_1g046810 32.424 330 128 13 30 315 37 315 3.07e-28 111
MS.gene84934.t1 MTR_1g052185 30.137 292 152 13 31 313 30 278 1.01e-20 90.5
MS.gene84934.t1 MTR_4g073310 26.159 302 132 8 14 314 16 227 5.31e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 65 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGAAAGTTGTTGCCTCTA+TGG 0.288255 1.3:+37576445 None:intergenic
ACTCTCATCACAAAACAAAA+AGG 0.340650 1.3:-37576560 MS.gene84934:CDS
TCATCTTCACCAGGGTTGTT+TGG 0.341135 1.3:+37575784 None:intergenic
TCATCTTCACCAGGGTTGTT+TGG 0.341135 1.3:+37575823 None:intergenic
TGAGGAACCAACTCATGAAT+TGG 0.350528 1.3:-37575752 MS.gene84934:CDS
ATAATTCCAGCTCCGTTTCA+TGG 0.360348 1.3:+37576197 None:intergenic
GTTCTCTTCATTATCATCAT+TGG 0.362989 1.3:+37575882 None:intergenic
TCTTCGAAGTCGAACCATAT+TGG 0.367921 1.3:+37576298 None:intergenic
ATGAAATCGCACAGCCAATA+TGG 0.368027 1.3:-37576312 MS.gene84934:CDS
ATCATTGGAAGCAGATTGAT+TGG 0.381296 1.3:+37575897 None:intergenic
GAGGAACCAACTCATGAATT+GGG 0.382420 1.3:-37575751 MS.gene84934:CDS
AAATACTTTCTCAAATCAAT+TGG 0.400225 1.3:+37576240 None:intergenic
TGATTCCCAACAAGGTTGTT+AGG 0.405927 1.3:+37576117 None:intergenic
CGATCACCTAACAACCTTGT+TGG 0.409603 1.3:-37576123 MS.gene84934:CDS
TGCAGAAATGTGGGTGGGAA+TGG 0.425504 1.3:-37576069 MS.gene84934:CDS
TGCCTCTATGGAATGCTTTG+TGG 0.438332 1.3:+37576457 None:intergenic
GATCACCTAACAACCTTGTT+GGG 0.442776 1.3:-37576122 MS.gene84934:CDS
TCATCTGTCAATGCACTGAA+TGG 0.463276 1.3:-37576339 MS.gene84934:CDS
TGTGACAGAGAATTCTCAAC+TGG 0.474765 1.3:-37576495 MS.gene84934:CDS
TACTTTCTCAAATCAATTGG+TGG 0.486384 1.3:+37576243 None:intergenic
TCTGCTTCATCATCTTCACC+AGG 0.486883 1.3:+37575814 None:intergenic
GCAGAAATGTGGGTGGGAAT+GGG 0.488317 1.3:-37576068 MS.gene84934:CDS
TTTGCTTCATCATCTTCACC+AGG 0.497903 1.3:+37575775 None:intergenic
TTCATGGTCACATACCTCAT+TGG 0.503644 1.3:+37576213 None:intergenic
TTTAACCCCAATTCATGAGT+TGG 0.505846 1.3:+37575745 None:intergenic
CAATTGGTGGAAATTGATCC+AGG 0.509751 1.3:+37576256 None:intergenic
GGAATCACCGTGTCACGAAA+AGG 0.512728 1.3:-37576101 MS.gene84934:CDS
TTCTCAACTGGTAATGCTCT+CGG 0.517217 1.3:-37576483 MS.gene84934:CDS
GATCAAACTTTGCAGAAATG+TGG 0.524856 1.3:-37576079 MS.gene84934:CDS
ATATGGTTCGACTTCGAAGA+AGG 0.528018 1.3:-37576295 MS.gene84934:CDS
CAACAAGGTTGTTAGGTGAT+CGG 0.537111 1.3:+37576124 None:intergenic
ATGTGACCATGAAACGGAGC+TGG 0.548343 1.3:-37576203 MS.gene84934:CDS
ATCAAACTTTGCAGAAATGT+GGG 0.554714 1.3:-37576078 MS.gene84934:CDS
AAAAGGAGTGTTGTTGATCA+TGG 0.555395 1.3:-37576543 MS.gene84934:CDS
ATGGTCACATACCTCATTGG+TGG 0.556780 1.3:+37576216 None:intergenic
GGGTAGTAAGATTTATGACC+TGG 0.563188 1.3:-37576274 MS.gene84934:CDS
TGAGGTATGTGACCATGAAA+CGG 0.563267 1.3:-37576209 MS.gene84934:CDS
GAAGATCAGAGAGCAAGGTA+TGG 0.572806 1.3:-37576040 MS.gene84934:CDS
TTATGTTGCAGAAACAATGT+TGG 0.573586 1.3:-37576157 MS.gene84934:CDS
TCATCTGCATCATCATCCAC+TGG 0.575486 1.3:+37575691 None:intergenic
AATCAATGAGAAGAACAAGT+TGG 0.575910 1.3:-37575971 MS.gene84934:CDS
AGAAGAACAAGTTGGTGGTG+AGG 0.577583 1.3:-37575963 MS.gene84934:CDS
AACTTTGCAGAAATGTGGGT+GGG 0.585412 1.3:-37576074 MS.gene84934:CDS
GCAACGAACACATGAATGGT+TGG 0.590907 1.3:+37576374 None:intergenic
CAATGAGAAGAACAAGTTGG+TGG 0.592690 1.3:-37575968 MS.gene84934:CDS
TGAAGATGATGAAGCAAATG+AGG 0.593094 1.3:-37575770 MS.gene84934:CDS
CGATTTGAATGAGCTGCCAG+TGG 0.597243 1.3:-37575707 MS.gene84934:CDS
GATCAGAGAGCAAGGTATGG+TGG 0.597334 1.3:-37576037 MS.gene84934:CDS
AAGATGAAGATCAGAGAGCA+AGG 0.598147 1.3:-37576045 MS.gene84934:CDS
TATGGTTCGACTTCGAAGAA+GGG 0.600043 1.3:-37576294 MS.gene84934:CDS
TTGCTTCATCATCTTCACCA+GGG 0.604583 1.3:+37575776 None:intergenic
CTGCTTCATCATCTTCACCA+GGG 0.614062 1.3:+37575815 None:intergenic
TGACACGGTGATTCCCAACA+AGG 0.616814 1.3:+37576109 None:intergenic
AAACTTTGCAGAAATGTGGG+TGG 0.628923 1.3:-37576075 MS.gene84934:CDS
AGGAACCAACTCATGAATTG+GGG 0.629510 1.3:-37575750 MS.gene84934:CDS
GAAAGTATTTGCCACCAATG+AGG 0.638748 1.3:-37576227 MS.gene84934:CDS
GGCCACAAAGCATTCCATAG+AGG 0.645608 1.3:-37576459 MS.gene84934:CDS
TGCTGCAACGAACACATGAA+TGG 0.655011 1.3:+37576370 None:intergenic
TGAAGATGATGAAGCAGATG+AGG 0.659995 1.3:-37575809 MS.gene84934:CDS
TGAAGATGATGAAGCAGATG+AGG 0.659995 1.3:-37575848 MS.gene84934:CDS
AATGAAGAGAACAACAACAC+TGG 0.663304 1.3:-37575871 MS.gene84934:CDS
GTGAGGTTAAAGATTCCGAA+TGG 0.667579 1.3:-37575946 MS.gene84934:CDS
GATGAGGAACCAAACAACCC+TGG 0.684317 1.3:-37575793 MS.gene84934:CDS
GATGAGGAACCAAACAACCC+TGG 0.684317 1.3:-37575832 MS.gene84934:CDS
TCAACTGGTAATGCTCTCGG+CGG 0.775161 1.3:-37576480 MS.gene84934:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACTTTCTCAAATCAAT+TGG + chr1.3:37576050-37576069 None:intergenic 20.0%
AACAAAGAAAAACATGCTGA+TGG - chr1.3:37575876-37575895 MS.gene84934:CDS 30.0%
AATCAATGAGAAGAACAAGT+TGG - chr1.3:37576316-37576335 MS.gene84934:CDS 30.0%
ACTCTCATCACAAAACAAAA+AGG - chr1.3:37575727-37575746 MS.gene84934:CDS 30.0%
ATCAAACTTTGCAGAAATGT+GGG - chr1.3:37576209-37576228 MS.gene84934:CDS 30.0%
GTTCTCTTCATTATCATCAT+TGG + chr1.3:37576408-37576427 None:intergenic 30.0%
TACTTTCTCAAATCAATTGG+TGG + chr1.3:37576047-37576066 None:intergenic 30.0%
TTATGTTGCAGAAACAATGT+TGG - chr1.3:37576130-37576149 MS.gene84934:CDS 30.0%
! CTTGTGATTTTTGAATGACA+AGG + chr1.3:37576367-37576386 None:intergenic 30.0%
AAAGAAAGTTGTTGCCTCTA+TGG + chr1.3:37575845-37575864 None:intergenic 35.0%
AATGAAGAGAACAACAACAC+TGG - chr1.3:37576416-37576435 MS.gene84934:CDS 35.0%
ATCATTGGAAGCAGATTGAT+TGG + chr1.3:37576393-37576412 None:intergenic 35.0%
GATCAAACTTTGCAGAAATG+TGG - chr1.3:37576208-37576227 MS.gene84934:CDS 35.0%
TGAAGATGATGAAGCAAATG+AGG - chr1.3:37576517-37576536 MS.gene84934:CDS 35.0%
TTTAACCCCAATTCATGAGT+TGG + chr1.3:37576545-37576564 None:intergenic 35.0%
! AGAGGCAACAACTTTCTTTT+AGG - chr1.3:37575846-37575865 MS.gene84934:CDS 35.0%
! TTTTGAATGACAAGGCCATT+CGG + chr1.3:37576359-37576378 None:intergenic 35.0%
!! AAAAGGAGTGTTGTTGATCA+TGG - chr1.3:37575744-37575763 MS.gene84934:CDS 35.0%
AAACTTTGCAGAAATGTGGG+TGG - chr1.3:37576212-37576231 MS.gene84934:CDS 40.0%
AACTTTGCAGAAATGTGGGT+GGG - chr1.3:37576213-37576232 MS.gene84934:CDS 40.0%
AAGATGAAGATCAGAGAGCA+AGG - chr1.3:37576242-37576261 MS.gene84934:CDS 40.0%
AGGAACCAACTCATGAATTG+GGG - chr1.3:37576537-37576556 MS.gene84934:CDS 40.0%
ATAATTCCAGCTCCGTTTCA+TGG + chr1.3:37576093-37576112 None:intergenic 40.0%
ATATGGTTCGACTTCGAAGA+AGG - chr1.3:37575992-37576011 MS.gene84934:CDS 40.0%
ATGAAATCGCACAGCCAATA+TGG - chr1.3:37575975-37575994 MS.gene84934:CDS 40.0%
CAACAAGGTTGTTAGGTGAT+CGG + chr1.3:37576166-37576185 None:intergenic 40.0%
CAATTGGTGGAAATTGATCC+AGG + chr1.3:37576034-37576053 None:intergenic 40.0%
GAGGAACCAACTCATGAATT+GGG - chr1.3:37576536-37576555 MS.gene84934:CDS 40.0%
GATCACCTAACAACCTTGTT+GGG - chr1.3:37576165-37576184 MS.gene84934:CDS 40.0%
GGGTAGTAAGATTTATGACC+TGG - chr1.3:37576013-37576032 MS.gene84934:CDS 40.0%
GTGAGGTTAAAGATTCCGAA+TGG - chr1.3:37576341-37576360 MS.gene84934:CDS 40.0%
TATGGTTCGACTTCGAAGAA+GGG - chr1.3:37575993-37576012 MS.gene84934:CDS 40.0%
TCATCTGTCAATGCACTGAA+TGG - chr1.3:37575948-37575967 MS.gene84934:CDS 40.0%
TCTTCGAAGTCGAACCATAT+TGG + chr1.3:37575992-37576011 None:intergenic 40.0%
TGAAGATGATGAAGCAGATG+AGG - chr1.3:37576439-37576458 MS.gene84934:CDS 40.0%
TGAGGAACCAACTCATGAAT+TGG - chr1.3:37576535-37576554 MS.gene84934:CDS 40.0%
TGAGGTATGTGACCATGAAA+CGG - chr1.3:37576078-37576097 MS.gene84934:CDS 40.0%
TGATTCCCAACAAGGTTGTT+AGG + chr1.3:37576173-37576192 None:intergenic 40.0%
TGTGACAGAGAATTCTCAAC+TGG - chr1.3:37575792-37575811 MS.gene84934:CDS 40.0%
TTCATGGTCACATACCTCAT+TGG + chr1.3:37576077-37576096 None:intergenic 40.0%
TTGCTTCATCATCTTCACCA+GGG + chr1.3:37576514-37576533 None:intergenic 40.0%
TTTGCTTCATCATCTTCACC+AGG + chr1.3:37576515-37576534 None:intergenic 40.0%
! CAATGAGAAGAACAAGTTGG+TGG - chr1.3:37576319-37576338 MS.gene84934:CDS 40.0%
! GTTTGATCCTTTTCGTGACA+CGG + chr1.3:37576196-37576215 None:intergenic 40.0%
! TTCTCAACTGGTAATGCTCT+CGG - chr1.3:37575804-37575823 MS.gene84934:CDS 40.0%
!! GAAAGTATTTGCCACCAATG+AGG - chr1.3:37576060-37576079 MS.gene84934:CDS 40.0%
ATGGTCACATACCTCATTGG+TGG + chr1.3:37576074-37576093 None:intergenic 45.0%
CGATCACCTAACAACCTTGT+TGG - chr1.3:37576164-37576183 MS.gene84934:CDS 45.0%
CTGCTTCATCATCTTCACCA+GGG + chr1.3:37576436-37576455 None:intergenic 45.0%
GAAGATCAGAGAGCAAGGTA+TGG - chr1.3:37576247-37576266 MS.gene84934:CDS 45.0%
GCAACGAACACATGAATGGT+TGG + chr1.3:37575916-37575935 None:intergenic 45.0%
TCATCTGCATCATCATCCAC+TGG + chr1.3:37576599-37576618 None:intergenic 45.0%
TCATCTTCACCAGGGTTGTT+TGG + chr1.3:37576467-37576486 None:intergenic 45.0%
TCTGCTTCATCATCTTCACC+AGG + chr1.3:37576437-37576456 None:intergenic 45.0%
TGCCTCTATGGAATGCTTTG+TGG + chr1.3:37575833-37575852 None:intergenic 45.0%
TGCTGCAACGAACACATGAA+TGG + chr1.3:37575920-37575939 None:intergenic 45.0%
!! AGAAGAACAAGTTGGTGGTG+AGG - chr1.3:37576324-37576343 MS.gene84934:CDS 45.0%
ATGTGACCATGAAACGGAGC+TGG - chr1.3:37576084-37576103 MS.gene84934:CDS 50.0%
CGATTTGAATGAGCTGCCAG+TGG - chr1.3:37576580-37576599 MS.gene84934:CDS 50.0%
GATCAGAGAGCAAGGTATGG+TGG - chr1.3:37576250-37576269 MS.gene84934:CDS 50.0%
GATGAGGAACCAAACAACCC+TGG - chr1.3:37576455-37576474 MS.gene84934:CDS 50.0%
GCAGAAATGTGGGTGGGAAT+GGG - chr1.3:37576219-37576238 MS.gene84934:CDS 50.0%
GGAATCACCGTGTCACGAAA+AGG - chr1.3:37576186-37576205 MS.gene84934:CDS 50.0%
TGACACGGTGATTCCCAACA+AGG + chr1.3:37576181-37576200 None:intergenic 50.0%
TGCAGAAATGTGGGTGGGAA+TGG - chr1.3:37576218-37576237 MS.gene84934:CDS 50.0%
! GGCCACAAAGCATTCCATAG+AGG - chr1.3:37575828-37575847 MS.gene84934:CDS 50.0%
! TCAACTGGTAATGCTCTCGG+CGG - chr1.3:37575807-37575826 MS.gene84934:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 37575678 37576631 37575678 ID=MS.gene84934
chr1.3 mRNA 37575678 37576631 37575678 ID=MS.gene84934.t1;Parent=MS.gene84934
chr1.3 exon 37575678 37576631 37575678 ID=MS.gene84934.t1.exon1;Parent=MS.gene84934.t1
chr1.3 CDS 37575678 37576631 37575678 ID=cds.MS.gene84934.t1;Parent=MS.gene84934.t1
Gene Sequence

>MS.gene84934

ATGAAGCATTTTTTTTCTTCTGCTTCTTCTTCTTCTTCTTCTTCATCTCACTCTCATCACAAAACAAAAAGGAGTGTTGTTGATCATGGTGCAAAACTTCACAAATGTGATTTGTGTGACAGAGAATTCTCAACTGGTAATGCTCTCGGCGGCCACAAAGCATTCCATAGAGGCAACAACTTTCTTTTAGGAAAAATCAACAAAGAAAAACATGCTGATGGTATTAAGATCGAAACCAACCATTCATGTGTTCGTTGCAGCAAGACTTTTTCATCTGTCAATGCACTGAATGGACACATGAAATCGCACAGCCAATATGGTTCGACTTCGAAGAAGGGTAGTAAGATTTATGACCTGGATCAATTTCCACCAATTGATTTGAGAAAGTATTTGCCACCAATGAGGTATGTGACCATGAAACGGAGCTGGAATTATGTTATTAATGTTGAAGCTTATGTTGCAGAAACAATGTTGGATCTGTCACACCGATCACCTAACAACCTTGTTGGGAATCACCGTGTCACGAAAAGGATCAAACTTTGCAGAAATGTGGGTGGGAATGGGAAGATGAAGATCAGAGAGCAAGGTATGGTGGTAAAACATTGTGTTGATGAAACAATTGTGAGAGAGACTGATCAAATCAATGAGAAGAACAAGTTGGTGGTGAGGTTAAAGATTCCGAATGGCCTTGTCATTCAAAAATCACAAGCTTCCAATCAATCTGCTTCCAATGATGATAATGAAGAGAACAACAACACTGGTGAAGATGATGAAGCAGATGAGGAACCAAACAACCCTGGTGAAGATGATGAAGCAGATGAGGAACCAAACAACCCTGGTGAAGATGATGAAGCAAATGAGGAACCAACTCATGAATTGGGGTTAAATGTTGTTCGAGATTTCGATTTGAATGAGCTGCCAGTGGATGATGATGCAGATGAAACCGCCCATTAG
Protein sequence

>MS.gene84934.t1

MKHFFSSASSSSSSSSHSHHKTKRSVVDHGAKLHKCDLCDREFSTGNALGGHKAFHRGNNFLLGKINKEKHADGIKIETNHSCVRCSKTFSSVNALNGHMKSHSQYGSTSKKGSKIYDLDQFPPIDLRKYLPPMRYVTMKRSWNYVINVEAYVAETMLDLSHRSPNNLVGNHRVTKRIKLCRNVGGNGKMKIREQGMVVKHCVDETIVRETDQINEKNKLVVRLKIPNGLVIQKSQASNQSASNDDNEENNNTGEDDEADEEPNNPGEDDEADEEPNNPGEDDEANEEPTHELGLNVVRDFDLNELPVDDDADETAH