AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene069965


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene069965.t1 MTR_3g013635 73.103 145 36 2 1 144 1 143 1.67e-66 198
MS.gene069965.t1 MTR_3g013635 73.103 145 36 2 1 144 1 143 1.67e-66 198
MS.gene069965.t1 MTR_8g040740 62.759 145 51 2 1 144 1 143 2.20e-58 178
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene069965.t1 AT5G61170 59.722 144 55 2 1 143 1 142 7.81e-54 166
MS.gene069965.t1 AT3G02080 57.931 145 58 2 1 144 1 143 9.62e-54 166
MS.gene069965.t1 AT5G15520 58.451 142 56 2 1 141 1 140 1.43e-51 160

Find 48 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGAAGACTGCAAGGTTTA+AGG 0.181111 3.3:+79452047 MS.gene069965:CDS
GGAGCATTCCAGAGGATTTA+TGG 0.204853 3.3:+79452286 MS.gene069965:CDS
TTCCAGTGGCTGGAGGGATT+TGG 0.292563 3.3:+79452721 MS.gene069965:CDS
TTCACAATATCTGTCCATTC+TGG 0.341460 3.3:-79452030 None:intergenic
AGGGATTTGGACCAAGTTGC+TGG 0.348464 3.3:+79452734 MS.gene069965:CDS
CCTTGGTGTCCATCTCAATA+AGG 0.385015 3.3:-79452403 None:intergenic
GACTGCAAGGTTTAAGGAGT+TGG 0.416477 3.3:+79452053 MS.gene069965:CDS
ACCCCTCAAGTAGATCTTCC+TGG 0.431786 3.3:-79452250 None:intergenic
GACTTCCACCATAAATCCTC+TGG 0.453242 3.3:-79452294 None:intergenic
GTCCAAATCCCTCCAGCCAC+TGG 0.453555 3.3:-79452723 None:intergenic
CTCTGACGTAGTAACCAGTC+TGG 0.460039 3.3:-79452087 None:intergenic
CACTGCTACTTGCAGATATG+AGG 0.478292 3.3:-79452337 None:intergenic
TCTGCTCATCTCAAAAGATC+TGG 0.481965 3.3:+79451107 MS.gene069965:CDS
GGAAGATCACTTCCAGTGGC+TGG 0.482355 3.3:+79452711 MS.gene069965:CDS
GTGCCGCAGCTTCCATGGCC+AGG 0.485644 3.3:+79452232 MS.gene069965:intron
AGTAACCAGTCTGGGTCATA+AGG 0.485903 3.3:-79452078 None:intergenic
CCTCTGGAATGCTCCAACAC+CGG 0.495845 3.3:-79452278 None:intergenic
TATGGTGGAAGTCAGAGAAA+TGG 0.514768 3.3:+79452304 MS.gene069965:CDS
CAAGTAGATCTTCCTGGCCA+TGG 0.517027 3.3:-79452244 None:intergenic
GGCCAGGAAGATCTACTTGA+GGG 0.518439 3.3:+79452248 MS.gene069965:CDS
TGAGGGGTGGACTCCGGTGT+TGG 0.525924 3.3:+79452265 MS.gene069965:CDS
TAACAATACGTCCAGCAACT+TGG 0.533492 3.3:-79452745 None:intergenic
TGGCTCCTTATGACCCAGAC+TGG 0.538624 3.3:+79452073 MS.gene069965:CDS
AACAGTCCTTGCGGTAGCCA+TGG 0.543735 3.3:-79451048 None:intergenic
AACAGATGGAGCTTCCAGAA+TGG 0.551656 3.3:+79452016 MS.gene069965:intron
TTGAAGAATGTGGCGAGCAA+TGG 0.555153 3.3:-79452363 None:intergenic
TCTACTTGAGGGGTGGACTC+CGG 0.558575 3.3:+79452259 MS.gene069965:CDS
GAACATGAACCTTATTGAGA+TGG 0.561257 3.3:+79452394 MS.gene069965:CDS
ACTGGTTACTACGTCAGAGC+TGG 0.580139 3.3:+79452091 MS.gene069965:CDS
CTCATATCTGCAAGTAGCAG+TGG 0.586534 3.3:+79452338 MS.gene069965:CDS
GATCACTTCCAGTGGCTGGA+GGG 0.602221 3.3:+79452715 MS.gene069965:CDS
TGCTACTTGCAGATATGAGG+TGG 0.608459 3.3:-79452334 None:intergenic
CAGATATTGTGAAGACTGCA+AGG 0.617924 3.3:+79452040 MS.gene069965:CDS
TCTGACGTAGTAACCAGTCT+GGG 0.619497 3.3:-79452086 None:intergenic
AGGAAGATCTACTTGAGGGG+TGG 0.621735 3.3:+79452252 MS.gene069965:CDS
GGCACACCATGGCTACCGCA+AGG 0.623985 3.3:+79451042 None:intergenic
TCATCTCAAAAGATCTGGCA+AGG 0.635281 3.3:+79451112 MS.gene069965:CDS
AGATCACTTCCAGTGGCTGG+AGG 0.640848 3.3:+79452714 MS.gene069965:CDS
CCGGTGTTGGAGCATTCCAG+AGG 0.649356 3.3:+79452278 MS.gene069965:CDS
CTTATTGAGATGGACACCAA+GGG 0.649426 3.3:+79452404 MS.gene069965:CDS
GGCAGGAAGATCACTTCCAG+TGG 0.649610 3.3:+79452707 MS.gene069965:CDS
TGGCCAGGAAGATCTACTTG+AGG 0.650322 3.3:+79452247 MS.gene069965:CDS
CCTTATTGAGATGGACACCA+AGG 0.671459 3.3:+79452403 MS.gene069965:CDS
GCATTCCAGAGGATTTATGG+TGG 0.673361 3.3:+79452289 MS.gene069965:CDS
AACATCTTGAACAGTCCTTG+CGG 0.675305 3.3:-79451057 None:intergenic
TCTGCAACTGTTGAAGAATG+TGG 0.679137 3.3:-79452373 None:intergenic
GCCAGGAAGATCTACTTGAG+GGG 0.686642 3.3:+79452249 MS.gene069965:CDS
TTATTGAGATGGACACCAAG+GGG 0.704884 3.3:+79452405 MS.gene069965:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTGTTAATTTAAACAA+GGG - chr3.3:79452152-79452171 None:intergenic 10.0%
!!! TTTTTTTGTTAATTTAAACA+AGG - chr3.3:79452153-79452172 None:intergenic 10.0%
!!! TTTTTTTTTTTTATTTGAAG+AGG + chr3.3:79451199-79451218 MS.gene069965:intron 10.0%
!! TATATCTATGTAATTAGATA+AGG - chr3.3:79451781-79451800 None:intergenic 15.0%
!!! AAAACCAAAATGAAATTTTT+CGG - chr3.3:79451150-79451169 None:intergenic 15.0%
!!! ATCAAAAACATTTTTTTGTT+AGG - chr3.3:79451453-79451472 None:intergenic 15.0%
!!! TTAATGTTATGTTTTATGTT+AGG + chr3.3:79451358-79451377 MS.gene069965:intron 15.0%
!!! TTGTTTTTGTTAATCAAATT+AGG + chr3.3:79451657-79451676 MS.gene069965:intron 15.0%
!! AACAAAAAAATAACTTTCGA+GGG + chr3.3:79452163-79452182 MS.gene069965:intron 20.0%
!! ATATGAACTATACAATTACA+CGG - chr3.3:79451942-79451961 None:intergenic 20.0%
!! ATGTTAAAAACATGATATGA+AGG - chr3.3:79452667-79452686 None:intergenic 20.0%
!! CTAATTACATAGATATACTT+GGG + chr3.3:79451784-79451803 MS.gene069965:intron 20.0%
!! TAACAAAAAAATAACTTTCG+AGG + chr3.3:79452162-79452181 MS.gene069965:intron 20.0%
!! TCTAATTACATAGATATACT+TGG + chr3.3:79451783-79451802 MS.gene069965:intron 20.0%
!! TGTTAAAAACATGATATGAA+GGG - chr3.3:79452666-79452685 None:intergenic 20.0%
!! TTATAATTGATACGAATGAT+TGG + chr3.3:79451916-79451935 MS.gene069965:intron 20.0%
!! TTGTATAGTTCATATTTAGT+TGG + chr3.3:79451947-79451966 MS.gene069965:intron 20.0%
!!! ACAAATTTTGAAAGTTCAAA+AGG - chr3.3:79451750-79451769 None:intergenic 20.0%
!!! CAAATTTTGAAAGTTCAAAA+GGG - chr3.3:79451749-79451768 None:intergenic 20.0%
!!! TGTTTTTGATTTGATTTGAT+TGG + chr3.3:79451463-79451482 MS.gene069965:intron 20.0%
! CATCTGTTCATAACAAAATA+AGG - chr3.3:79452004-79452023 None:intergenic 25.0%
!! GTTATGTTTTATGTTAGGTT+TGG + chr3.3:79451363-79451382 MS.gene069965:intron 25.0%
!! TTCACCGAAAAATTTCATTT+TGG + chr3.3:79451143-79451162 MS.gene069965:intron 25.0%
!! TTGATTTTTCTTTATCACAG+TGG + chr3.3:79452686-79452705 MS.gene069965:intron 25.0%
!!! ATTTGTTTTGATTTGCTTCA+TGG + chr3.3:79451223-79451242 MS.gene069965:intron 25.0%
!!! CTTATTTTGTTATGAACAGA+TGG + chr3.3:79452002-79452021 MS.gene069965:intron 25.0%
!!! GAACTTTCAAAATTTGTTGT+TGG + chr3.3:79451753-79451772 MS.gene069965:intron 25.0%
!!! GTGCTTTTATTTATAGTGAT+TGG + chr3.3:79452603-79452622 MS.gene069965:intron 25.0%
!!! TTTGTTTTGATTTGCTTCAT+GGG + chr3.3:79451224-79451243 MS.gene069965:intron 25.0%
! ACATTGCAATTTTCAACAAC+AGG - chr3.3:79452205-79452224 None:intergenic 30.0%
AACTACTGCTCAACAAATGT+TGG - chr3.3:79452567-79452586 None:intergenic 35.0%
CTACGGTTTACAATAGGAAT+AGG + chr3.3:79452455-79452474 MS.gene069965:intron 35.0%
GAACATGAACCTTATTGAGA+TGG + chr3.3:79452394-79452413 MS.gene069965:CDS 35.0%
GTTAATTTAAACAAGGGACC+AGG - chr3.3:79452146-79452165 None:intergenic 35.0%
TACATAGATATACTTGGGCA+TGG + chr3.3:79451789-79451808 MS.gene069965:intron 35.0%
TATTCAAGCTCTACTTCAAC+TGG + chr3.3:79451881-79451900 MS.gene069965:intron 35.0%
TTCACAATATCTGTCCATTC+TGG - chr3.3:79452033-79452052 None:intergenic 35.0%
TTGATTCAGAGTTACGCATT+TGG + chr3.3:79451544-79451563 MS.gene069965:intron 35.0%
! TTATCTTTGTTAGCCTGCTA+CGG + chr3.3:79452438-79452457 MS.gene069965:intron 35.0%
! TTTTTCTTTATCACAGTGGC+AGG + chr3.3:79452690-79452709 MS.gene069965:intron 35.0%
!! GTTTGATTTTGTGCATTTCC+TGG + chr3.3:79452125-79452144 MS.gene069965:intron 35.0%
AACATCTTGAACAGTCCTTG+CGG - chr3.3:79451060-79451079 None:intergenic 40.0%
CAGATATTGTGAAGACTGCA+AGG + chr3.3:79452040-79452059 MS.gene069965:CDS 40.0%
CTTATTGAGATGGACACCAA+GGG + chr3.3:79452404-79452423 MS.gene069965:CDS 40.0%
GATAATGAGTTCTTACCCCT+TGG - chr3.3:79452423-79452442 None:intergenic 40.0%
GCTCAACAAATGTTGGTATC+AGG - chr3.3:79452560-79452579 None:intergenic 40.0%
TAACAATACGTCCAGCAACT+TGG - chr3.3:79452748-79452767 None:intergenic 40.0%
TCATCTCAAAAGATCTGGCA+AGG + chr3.3:79451112-79451131 MS.gene069965:CDS 40.0%
TCTGCAACTGTTGAAGAATG+TGG - chr3.3:79452376-79452395 None:intergenic 40.0%
TCTGCTCATCTCAAAAGATC+TGG + chr3.3:79451107-79451126 MS.gene069965:CDS 40.0%
TGTGAAGACTGCAAGGTTTA+AGG + chr3.3:79452047-79452066 MS.gene069965:CDS 40.0%
TTATTGAGATGGACACCAAG+GGG + chr3.3:79452405-79452424 MS.gene069965:CDS 40.0%
TTCCTATTGTAAACCGTAGC+AGG - chr3.3:79452454-79452473 None:intergenic 40.0%
! TATGGTGGAAGTCAGAGAAA+TGG + chr3.3:79452304-79452323 MS.gene069965:CDS 40.0%
AACAGATGGAGCTTCCAGAA+TGG + chr3.3:79452016-79452035 MS.gene069965:intron 45.0%
AAGCTCTACTTCAACTGGTG+TGG + chr3.3:79451886-79451905 MS.gene069965:intron 45.0%
AGCCTGCTACGGTTTACAAT+AGG + chr3.3:79452449-79452468 MS.gene069965:intron 45.0%
AGTAACCAGTCTGGGTCATA+AGG - chr3.3:79452081-79452100 None:intergenic 45.0%
CATGGTTTCATCTCACGTGT+TGG + chr3.3:79451807-79451826 MS.gene069965:intron 45.0%
CCTTATTGAGATGGACACCA+AGG + chr3.3:79452403-79452422 MS.gene069965:CDS 45.0%
CTCATATCTGCAAGTAGCAG+TGG + chr3.3:79452338-79452357 MS.gene069965:CDS 45.0%
GACTGCAAGGTTTAAGGAGT+TGG + chr3.3:79452053-79452072 MS.gene069965:CDS 45.0%
GACTTCCACCATAAATCCTC+TGG - chr3.3:79452297-79452316 None:intergenic 45.0%
GCATTCCAGAGGATTTATGG+TGG + chr3.3:79452289-79452308 MS.gene069965:CDS 45.0%
TCTGACGTAGTAACCAGTCT+GGG - chr3.3:79452089-79452108 None:intergenic 45.0%
TTGAAGAATGTGGCGAGCAA+TGG - chr3.3:79452366-79452385 None:intergenic 45.0%
! CACTGCTACTTGCAGATATG+AGG - chr3.3:79452340-79452359 None:intergenic 45.0%
! GGAGCATTCCAGAGGATTTA+TGG + chr3.3:79452286-79452305 MS.gene069965:CDS 45.0%
! TGCTACTTGCAGATATGAGG+TGG - chr3.3:79452337-79452356 None:intergenic 45.0%
!! CCTTGGTGTCCATCTCAATA+AGG - chr3.3:79452406-79452425 None:intergenic 45.0%
ACCCCTCAAGTAGATCTTCC+TGG - chr3.3:79452253-79452272 None:intergenic 50.0%
ACTGGTTACTACGTCAGAGC+TGG + chr3.3:79452091-79452110 MS.gene069965:CDS 50.0%
AGGAAGATCTACTTGAGGGG+TGG + chr3.3:79452252-79452271 MS.gene069965:CDS 50.0%
AGGGATTTGGACCAAGTTGC+TGG + chr3.3:79452734-79452753 MS.gene069965:CDS 50.0%
CAAGTAGATCTTCCTGGCCA+TGG - chr3.3:79452247-79452266 None:intergenic 50.0%
CTCTGACGTAGTAACCAGTC+TGG - chr3.3:79452090-79452109 None:intergenic 50.0%
GCCAGGAAGATCTACTTGAG+GGG + chr3.3:79452249-79452268 MS.gene069965:CDS 50.0%
GGCCAGGAAGATCTACTTGA+GGG + chr3.3:79452248-79452267 MS.gene069965:CDS 50.0%
TGGCCAGGAAGATCTACTTG+AGG + chr3.3:79452247-79452266 MS.gene069965:CDS 50.0%
! TTTTTGTGCCGCAGCTTCCA+TGG + chr3.3:79452227-79452246 MS.gene069965:intron 50.0%
AGATCACTTCCAGTGGCTGG+AGG + chr3.3:79452714-79452733 MS.gene069965:CDS 55.0%
GATCACTTCCAGTGGCTGGA+GGG + chr3.3:79452715-79452734 MS.gene069965:CDS 55.0%
GGAAGATCACTTCCAGTGGC+TGG + chr3.3:79452711-79452730 MS.gene069965:CDS 55.0%
GGCAGGAAGATCACTTCCAG+TGG + chr3.3:79452707-79452726 MS.gene069965:CDS 55.0%
TGGCTCCTTATGACCCAGAC+TGG + chr3.3:79452073-79452092 MS.gene069965:CDS 55.0%
TTCCAGTGGCTGGAGGGATT+TGG + chr3.3:79452721-79452740 MS.gene069965:CDS 55.0%
! TCTACTTGAGGGGTGGACTC+CGG + chr3.3:79452259-79452278 MS.gene069965:CDS 55.0%
!! CCTCTGGAATGCTCCAACAC+CGG - chr3.3:79452281-79452300 None:intergenic 55.0%
CTTCCTGGCCATGGAAGCTG+CGG - chr3.3:79452238-79452257 None:intergenic 60.0%
GTCCAAATCCCTCCAGCCAC+TGG - chr3.3:79452726-79452745 None:intergenic 60.0%
! CCGGTGTTGGAGCATTCCAG+AGG + chr3.3:79452278-79452297 MS.gene069965:CDS 60.0%
! TGAGGGGTGGACTCCGGTGT+TGG + chr3.3:79452265-79452284 MS.gene069965:CDS 65.0%
GTGCCGCAGCTTCCATGGCC+AGG + chr3.3:79452232-79452251 MS.gene069965:intron 70.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 79451050 79452778 79451050 ID=MS.gene069965
chr3.3 mRNA 79451050 79452778 79451050 ID=MS.gene069965.t1;Parent=MS.gene069965
chr3.3 exon 79451050 79451133 79451050 ID=MS.gene069965.t1.exon1;Parent=MS.gene069965.t1
chr3.3 CDS 79451050 79451133 79451050 ID=cds.MS.gene069965.t1;Parent=MS.gene069965.t1
chr3.3 exon 79452021 79452112 79452021 ID=MS.gene069965.t1.exon2;Parent=MS.gene069965.t1
chr3.3 CDS 79452021 79452112 79452021 ID=cds.MS.gene069965.t1;Parent=MS.gene069965.t1
chr3.3 exon 79452241 79452426 79452241 ID=MS.gene069965.t1.exon3;Parent=MS.gene069965.t1
chr3.3 CDS 79452241 79452426 79452241 ID=cds.MS.gene069965.t1;Parent=MS.gene069965.t1
chr3.3 exon 79452706 79452778 79452706 ID=MS.gene069965.t1.exon4;Parent=MS.gene069965.t1
chr3.3 CDS 79452706 79452778 79452706 ID=cds.MS.gene069965.t1;Parent=MS.gene069965.t1
Gene Sequence

>MS.gene069965

ATGGCTACCGCAAGGACTGTTCAAGATGTTTCTTCACACGAGTTTGTCAAAGCTTACTCTGCTCATCTCAAAAGATCTGGCAAGGTTAATCAATTCACCGAAAAATTTCATTTTGGTTTTTCTAATTGATTGTGTATGATTCGATTGTTTTTTTTTTTTTTATTTGAAGAGGAATTTGTTTTGATTTGCTTCATGGGTTCATGAATATTTGTTGAATTATTCTGTTTTAGTAGCTTTTTTGTTTTTGTTATTTTTATTTATTTATAAATTGTCATGCTTTATTGTTTAGATTTGTGTTTTTTGTGTTTTTAATGTTATGTTTTATGTTAGGTTTGGTAAAGTTTATAACTTGATCTACTTCGTTGCTGTGTCTTGTTGAATGTAGTTTTGTTTGTCTAATCCTAACAAAAAAATGTTTTTGATTTGATTTGATTGGATTAATAAATAGAAAAATGTTCGTTGTGATGTTAATATGCTGTAATTTTTATAAGTGATTGATTCAGAGTTACGCATTTGGTTCAGAAAACTAGTGACATGATAGATTTGTGATTTTTCTCTTACACTTGTTTTTGATTAGTTTTAGTGAATACATTCAAGTTGATTATGATTGTTTTTGTTAATCAAATTAGGAATGATTTTCTGTATTATATGATGTTGATGACAGTTTTTATTTTTTTATGCTATGAATTGTAATGTCCCTTTTGAACTTTCAAAATTTGTTGTTGGATCCTTATCTAATTACATAGATATACTTGGGCATGGTTTCATCTCACGTGTTGGCTTAGTTTTAGATATAACTTTCATTATGCTTTTGATTTTTTATGTATTATGTATTCAAGCTCTACTTCAACTGGTGTGGATCTAGTTTATAATTGATACGAATGATTGGCCGTGTAATTGTATAGTTCATATTTAGTTGGATTATTATTTCTAATTATAGTTTTTTGTTTTCCTTATTTTGTTATGAACAGATGGAGCTTCCAGAATGGACAGATATTGTGAAGACTGCAAGGTTTAAGGAGTTGGCTCCTTATGACCCAGACTGGTTACTACGTCAGAGCTGGTGAGTTTCTGTGTTTGATTTTGTGCATTTCCTGGTCCCTTGTTTAAATTAACAAAAAAATAACTTTCGAGGGTACATTTTTTGATCAACCTGTTGTTGAAAATTGCAATGTGTTTTTTGTGCCGCAGCTTCCATGGCCAGGAAGATCTACTTGAGGGGTGGACTCCGGTGTTGGAGCATTCCAGAGGATTTATGGTGGAAGTCAGAGAAATGGCAGTCGTCCACCTCATATCTGCAAGTAGCAGTGGTTCCATTGCTCGCCACATTCTTCAACAGTTGCAGAACATGAACCTTATTGAGATGGACACCAAGGGGTAAGAACTCATTATCTTTGTTAGCCTGCTACGGTTTACAATAGGAATAGGACGATTAAGAGAATAGTAACAAAGATTAGTCAAAGCTCAGCAATGTAAATCAAATAGTTTATTTAATGTTCACTTGTATCCTGATACCAACATTTGTTGAGCAGTAGTTGATGCTTTCTGCATCTGTGCTTTTATTTATAGTGATTGGCATTTGCTCAAAAATAGTTTATGCTATTCTGCATCAGCCCTTCATATCATGTTTTTAACATTGATTTTTCTTTATCACAGTGGCAGGAAGATCACTTCCAGTGGCTGGAGGGATTTGGACCAAGTTGCTGGACGTATTGTTATTGCACCTTGA

Protein sequence

>MS.gene069965.t1

MATARTVQDVSSHEFVKAYSAHLKRSGKMELPEWTDIVKTARFKELAPYDPDWLLRQSCFHGQEDLLEGWTPVLEHSRGFMVEVREMAVVHLISASSSGSIARHILQQLQNMNLIEMDTKGGRKITSSGWRDLDQVAGRIVIAP