AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54033


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54033.t1 MTR_2g095080 91.892 222 18 0 1 222 1 222 3.39e-135 379
MS.gene54033.t1 MTR_2g095130 82.883 222 36 2 1 222 1 220 2.02e-123 348
MS.gene54033.t1 MTR_2g095060 73.874 222 55 2 1 222 1 219 1.24e-107 308
MS.gene54033.t1 MTR_2g095170 76.623 154 31 2 1 154 1 149 3.36e-80 237
MS.gene54033.t1 MTR_7g077110 52.121 165 66 5 61 222 34 188 1.41e-45 150
MS.gene54033.t1 MTR_7g077050 52.121 165 66 5 61 222 32 186 1.44e-45 150
MS.gene54033.t1 MTR_4g036290 55.479 146 60 4 80 222 45 188 1.89e-45 150
MS.gene54033.t1 MTR_7g076960 54.422 147 63 4 78 222 41 185 3.06e-44 146
MS.gene54033.t1 MTR_8g031170 57.576 132 53 3 90 220 61 190 3.76e-44 146
MS.gene54033.t1 MTR_7g077010 54.054 148 63 4 78 222 44 189 5.61e-44 146
MS.gene54033.t1 MTR_7g076990 54.054 148 63 4 78 222 43 188 6.64e-43 143
MS.gene54033.t1 MTR_4g036300 54.054 148 63 4 78 222 43 188 6.64e-43 143
MS.gene54033.t1 MTR_7g077000 56.489 131 54 3 93 222 2 130 7.04e-43 141
MS.gene54033.t1 MTR_7g076770 53.378 148 64 4 78 222 44 189 1.47e-42 142
MS.gene54033.t1 MTR_7g012350 53.378 148 64 4 78 222 43 188 1.82e-42 142
MS.gene54033.t1 MTR_7g076920 53.378 148 64 4 78 222 43 188 2.36e-42 142
MS.gene54033.t1 MTR_7g077090 53.378 148 64 4 78 222 44 189 3.78e-42 141
MS.gene54033.t1 MTR_7g012340 49.697 165 70 5 61 222 34 188 5.13e-42 141
MS.gene54033.t1 MTR_4g036410 52.027 148 66 4 78 222 25 170 3.85e-41 138
MS.gene54033.t1 MTR_7g076970 52.027 148 66 4 78 222 44 189 5.06e-41 138
MS.gene54033.t1 MTR_8g031150 43.571 140 64 4 84 222 21 146 5.83e-28 103
MS.gene54033.t1 MTR_8g031120 48.276 116 48 3 108 222 34 138 8.02e-27 100
MS.gene54033.t1 MTR_8g031160 45.968 124 50 3 98 219 12 120 7.80e-26 97.4
MS.gene54033.t1 MTR_7g077040 41.985 131 46 4 78 206 22 124 1.80e-20 84.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 70 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGAAAATTTATTAGAATT+AGG 0.191553 2.3:-6823933 MS.gene54033:CDS
GACTGTTTATGATGTTAAAA+AGG 0.240792 2.3:+6824452 None:intergenic
TGGAAAATTTATTAGAATTA+GGG 0.287537 2.3:-6823932 MS.gene54033:CDS
GTAGCTGTGTGGAATGCATT+AGG 0.386867 2.3:-6823793 MS.gene54033:CDS
GTGGTGGTGAAGGTGATGGT+TGG 0.387064 2.3:+6824302 None:intergenic
CAGATGCGGCTCCCAACATT+GGG 0.392199 2.3:+6824328 None:intergenic
GAAAATCATACCCTCAATAT+AGG 0.396741 2.3:-6824225 MS.gene54033:CDS
TCCGTCGCACTGTAAGTTGC+TGG 0.406235 2.3:+6824246 None:intergenic
GGTCAACTCATTTGCATCAA+TGG 0.423201 2.3:-6824367 MS.gene54033:CDS
CAAGCCATAGTCCATGTAAC+TGG 0.428721 2.3:+6823745 None:intergenic
TGGTGGTGAAGGTGATGGTT+GGG 0.431597 2.3:+6824303 None:intergenic
GGTGGTGGTGGTGAAGGTGA+TGG 0.438170 2.3:+6824298 None:intergenic
GCAGATGCGGCTCCCAACAT+TGG 0.452933 2.3:+6824327 None:intergenic
CCACTCTTTCTGAGTTGCTA+TGG 0.462618 2.3:+6823995 None:intergenic
ATTAGAATTAGGGCGTCAAA+TGG 0.462946 2.3:-6823922 MS.gene54033:CDS
TAGCTGTGTGGAATGCATTA+GGG 0.471319 2.3:-6823792 MS.gene54033:CDS
AGAGTGGTGGCGTTGTCGAC+TGG 0.476191 2.3:-6823979 MS.gene54033:CDS
TTGTGTGCCGGAGGATACAT+AGG 0.484081 2.3:+6824192 None:intergenic
GTGGAGAACACCTATATTGA+GGG 0.484892 2.3:+6824215 None:intergenic
GATGGTACAGCGGAGGTTCA+AGG 0.490470 2.3:-6823957 MS.gene54033:CDS
CTTCACCACCACCACCAAGC+GGG 0.522294 2.3:-6824291 MS.gene54033:CDS
CCGCTTGGTGGTGGTGGTGA+AGG 0.523573 2.3:+6824292 None:intergenic
TGCAATGATGACCCCAATGT+TGG 0.526465 2.3:-6824340 MS.gene54033:CDS
AGTACCAGTTACATGGACTA+TGG 0.528194 2.3:-6823749 MS.gene54033:CDS
GGTGGAGAACACCTATATTG+AGG 0.533675 2.3:+6824214 None:intergenic
AGTGAGTAACGCTTGTGTGC+CGG 0.546015 2.3:+6824180 None:intergenic
GCAATGATGACCCCAATGTT+GGG 0.547076 2.3:-6824339 MS.gene54033:CDS
GACCAGTGTGATTCAGTGAA+TGG 0.548137 2.3:-6823874 MS.gene54033:CDS
ACTGTAAGTTGCTGGTGGAT+CGG 0.560131 2.3:+6824254 None:intergenic
TTCACCACCACCACCAAGCG+GGG 0.560779 2.3:-6824290 MS.gene54033:CDS
TTAGAATTAGGGCGTCAAAT+GGG 0.564756 2.3:-6823921 MS.gene54033:CDS
TGTCGTAACAATATTGTGGA+TGG 0.577139 2.3:-6823820 MS.gene54033:CDS
ATGGTGTAGTACCAGTTACA+TGG 0.578391 2.3:-6823756 MS.gene54033:CDS
AATGCTATTTCCTCATGCAA+TGG 0.584516 2.3:-6824418 MS.gene54033:CDS
GTGATGGTTGGGAGCAGATG+CGG 0.586266 2.3:+6824314 None:intergenic
TCTCCACCCTATGTATCCTC+CGG 0.587429 2.3:-6824199 MS.gene54033:CDS
AGAACTCTCAACGACTGCGC+TGG 0.593695 2.3:-6824388 MS.gene54033:CDS
GTCGCACTGTAAGTTGCTGG+TGG 0.593908 2.3:+6824249 None:intergenic
CCATAGCAACTCAGAAAGAG+TGG 0.600849 2.3:-6823995 MS.gene54033:CDS
GGATGTGATGCGGAGCATGC+AGG 0.601600 2.3:-6823853 MS.gene54033:CDS
TTAGGGTTGAATACAAATGA+TGG 0.607340 2.3:-6823775 MS.gene54033:CDS
CTATCTTTAACAGGAGGAGA+CGG 0.608488 2.3:-6824048 MS.gene54033:intron
GTCAAATGGGAGGACTGTGA+CGG 0.609042 2.3:-6823908 MS.gene54033:CDS
TTAACAGGAGGAGACGGAGG+AGG 0.612561 2.3:-6824042 MS.gene54033:intron
GAGGACTGTGACGGCGAAAG+TGG 0.613441 2.3:-6823899 MS.gene54033:CDS
ACCAGCAACTTACAGTGCGA+CGG 0.617204 2.3:-6824247 MS.gene54033:CDS
GAGTAACGCTTGTGTGCCGG+AGG 0.623702 2.3:+6824183 None:intergenic
ACCTTGTCGTAACAATATTG+TGG 0.624388 2.3:-6823824 MS.gene54033:CDS
TGGTGGCGTTGTCGACTGGA+TGG 0.626878 2.3:-6823975 MS.gene54033:CDS
TACAGCGGAGGTTCAAGGTG+TGG 0.632283 2.3:-6823952 MS.gene54033:CDS
GAAATAGCATTTGTGAGGAA+CGG 0.636932 2.3:+6824430 None:intergenic
TGTGTGCCGGAGGATACATA+GGG 0.638124 2.3:+6824193 None:intergenic
CAGTCGTTGAGAGTTCTACA+AGG 0.643040 2.3:+6824394 None:intergenic
ATGAGGAAATAGCATTTGTG+AGG 0.643440 2.3:+6824425 None:intergenic
GAATTAGGGCGTCAAATGGG+AGG 0.651543 2.3:-6823918 MS.gene54033:CDS
TCACCACCACCACCAAGCGG+GGG 0.652883 2.3:-6824289 MS.gene54033:CDS
ATCCATTCACTGAATCACAC+TGG 0.661311 2.3:+6823872 None:intergenic
TCGACTGGATGGTACAGCGG+AGG 0.671589 2.3:-6823964 MS.gene54033:CDS
TCTACAAGGTCCATTGCATG+AGG 0.672658 2.3:+6824408 None:intergenic
CCTTCACCACCACCACCAAG+CGG 0.675680 2.3:-6824292 MS.gene54033:CDS
GTGCCGGAGGATACATAGGG+TGG 0.681653 2.3:+6824196 None:intergenic
ACAATATTGTTACGACAAGG+TGG 0.682938 2.3:+6823826 None:intergenic
AGGTGCTTCTCAGTGCGATG+AGG 0.686218 2.3:-6824022 MS.gene54033:CDS
TTGTCGACTGGATGGTACAG+CGG 0.686803 2.3:-6823967 MS.gene54033:CDS
TCTTTAACAGGAGGAGACGG+AGG 0.687923 2.3:-6824045 MS.gene54033:intron
TTCAGTGAATGGATGTGATG+CGG 0.689445 2.3:-6823863 MS.gene54033:CDS
AGATGCGGCTCCCAACATTG+GGG 0.690440 2.3:+6824329 None:intergenic
TCCACAATATTGTTACGACA+AGG 0.694171 2.3:+6823823 None:intergenic
TAGCAACTCAGAAAGAGTGG+TGG 0.700359 2.3:-6823992 MS.gene54033:CDS
TGGATGGATCTGTAGCTGTG+TGG 0.738134 2.3:-6823804 MS.gene54033:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAGTTGAATATTATTTA+AGG + chr2.3:6824150-6824169 None:intergenic 10.0%
!! TGGAAAATTTATTAGAATTA+GGG - chr2.3:6824305-6824324 MS.gene54033:CDS 15.0%
!! GTGGAAAATTTATTAGAATT+AGG - chr2.3:6824304-6824323 MS.gene54033:CDS 20.0%
!! TATGATGTTAAAAAGGAAAA+TGG + chr2.3:6823781-6823800 None:intergenic 20.0%
! AATCTCAAACTATCTTTAAC+AGG - chr2.3:6824180-6824199 MS.gene54033:CDS 25.0%
! GACTGTTTATGATGTTAAAA+AGG + chr2.3:6823788-6823807 None:intergenic 25.0%
!! AGTTATGATTACTTGATAGT+TGG + chr2.3:6824115-6824134 None:intergenic 25.0%
GAAAATCATACCCTCAATAT+AGG - chr2.3:6824012-6824031 MS.gene54033:CDS 30.0%
TTAGGGTTGAATACAAATGA+TGG - chr2.3:6824462-6824481 MS.gene54033:CDS 30.0%
ACAATATTGTTACGACAAGG+TGG + chr2.3:6824414-6824433 None:intergenic 35.0%
ACCTTGTCGTAACAATATTG+TGG - chr2.3:6824413-6824432 MS.gene54033:CDS 35.0%
ATGAGGAAATAGCATTTGTG+AGG + chr2.3:6823815-6823834 None:intergenic 35.0%
CTCAAACTATCTTTAACAGG+AGG - chr2.3:6824183-6824202 MS.gene54033:CDS 35.0%
GAAATAGCATTTGTGAGGAA+CGG + chr2.3:6823810-6823829 None:intergenic 35.0%
TCCACAATATTGTTACGACA+AGG + chr2.3:6824417-6824436 None:intergenic 35.0%
TGTCGTAACAATATTGTGGA+TGG - chr2.3:6824417-6824436 MS.gene54033:CDS 35.0%
! ATTAGAATTAGGGCGTCAAA+TGG - chr2.3:6824315-6824334 MS.gene54033:CDS 35.0%
! TTAGAATTAGGGCGTCAAAT+GGG - chr2.3:6824316-6824335 MS.gene54033:CDS 35.0%
!! AATGCTATTTCCTCATGCAA+TGG - chr2.3:6823819-6823838 MS.gene54033:CDS 35.0%
!! ACTTTGAACGATTTTAGCGA+AGG - chr2.3:6824077-6824096 MS.gene54033:intron 35.0%
ATCCATTCACTGAATCACAC+TGG + chr2.3:6824368-6824387 None:intergenic 40.0%
ATGGTGTAGTACCAGTTACA+TGG - chr2.3:6824481-6824500 MS.gene54033:CDS 40.0%
CTATCTTTAACAGGAGGAGA+CGG - chr2.3:6824189-6824208 MS.gene54033:CDS 40.0%
GGTCAACTCATTTGCATCAA+TGG - chr2.3:6823870-6823889 MS.gene54033:CDS 40.0%
GTGGAGAACACCTATATTGA+GGG + chr2.3:6824025-6824044 None:intergenic 40.0%
TAGCTGTGTGGAATGCATTA+GGG - chr2.3:6824445-6824464 MS.gene54033:CDS 40.0%
TTCAGTGAATGGATGTGATG+CGG - chr2.3:6824374-6824393 MS.gene54033:CDS 40.0%
! AGTACCAGTTACATGGACTA+TGG - chr2.3:6824488-6824507 MS.gene54033:CDS 40.0%
CAAGCCATAGTCCATGTAAC+TGG + chr2.3:6824495-6824514 None:intergenic 45.0%
CAGTCGTTGAGAGTTCTACA+AGG + chr2.3:6823846-6823865 None:intergenic 45.0%
CCACTCTTTCTGAGTTGCTA+TGG + chr2.3:6824245-6824264 None:intergenic 45.0%
CCATAGCAACTCAGAAAGAG+TGG - chr2.3:6824242-6824261 MS.gene54033:CDS 45.0%
GACCAGTGTGATTCAGTGAA+TGG - chr2.3:6824363-6824382 MS.gene54033:CDS 45.0%
GCAATGATGACCCCAATGTT+GGG - chr2.3:6823898-6823917 MS.gene54033:CDS 45.0%
GGTGGAGAACACCTATATTG+AGG + chr2.3:6824026-6824045 None:intergenic 45.0%
GTAGCTGTGTGGAATGCATT+AGG - chr2.3:6824444-6824463 MS.gene54033:CDS 45.0%
TAGCAACTCAGAAAGAGTGG+TGG - chr2.3:6824245-6824264 MS.gene54033:CDS 45.0%
TCTACAAGGTCCATTGCATG+AGG + chr2.3:6823832-6823851 None:intergenic 45.0%
TGCAATGATGACCCCAATGT+TGG - chr2.3:6823897-6823916 MS.gene54033:CDS 45.0%
! ACTGTAAGTTGCTGGTGGAT+CGG + chr2.3:6823986-6824005 None:intergenic 45.0%
ACCAGCAACTTACAGTGCGA+CGG - chr2.3:6823990-6824009 MS.gene54033:CDS 50.0%
AGTGAGTAACGCTTGTGTGC+CGG + chr2.3:6824060-6824079 None:intergenic 50.0%
GTCAAATGGGAGGACTGTGA+CGG - chr2.3:6824329-6824348 MS.gene54033:CDS 50.0%
TCTCCACCCTATGTATCCTC+CGG - chr2.3:6824038-6824057 MS.gene54033:CDS 50.0%
TCTTTAACAGGAGGAGACGG+AGG - chr2.3:6824192-6824211 MS.gene54033:CDS 50.0%
TGGATGGATCTGTAGCTGTG+TGG - chr2.3:6824433-6824452 MS.gene54033:CDS 50.0%
TGTGTGCCGGAGGATACATA+GGG + chr2.3:6824047-6824066 None:intergenic 50.0%
TTGTGTGCCGGAGGATACAT+AGG + chr2.3:6824048-6824067 None:intergenic 50.0%
! GAATTAGGGCGTCAAATGGG+AGG - chr2.3:6824319-6824338 MS.gene54033:CDS 50.0%
! TGGTGGTGAAGGTGATGGTT+GGG + chr2.3:6823937-6823956 None:intergenic 50.0%
! TTGTCGACTGGATGGTACAG+CGG - chr2.3:6824270-6824289 MS.gene54033:CDS 50.0%
AGAACTCTCAACGACTGCGC+TGG - chr2.3:6823849-6823868 MS.gene54033:CDS 55.0%
AGATGCGGCTCCCAACATTG+GGG + chr2.3:6823911-6823930 None:intergenic 55.0%
AGGTGCTTCTCAGTGCGATG+AGG - chr2.3:6824215-6824234 MS.gene54033:CDS 55.0%
CAGATGCGGCTCCCAACATT+GGG + chr2.3:6823912-6823931 None:intergenic 55.0%
GATGGTACAGCGGAGGTTCA+AGG - chr2.3:6824280-6824299 MS.gene54033:CDS 55.0%
GTCGCACTGTAAGTTGCTGG+TGG + chr2.3:6823991-6824010 None:intergenic 55.0%
GTGATGGTTGGGAGCAGATG+CGG + chr2.3:6823926-6823945 None:intergenic 55.0%
TACAGCGGAGGTTCAAGGTG+TGG - chr2.3:6824285-6824304 MS.gene54033:CDS 55.0%
TCCGTCGCACTGTAAGTTGC+TGG + chr2.3:6823994-6824013 None:intergenic 55.0%
TTAACAGGAGGAGACGGAGG+AGG - chr2.3:6824195-6824214 MS.gene54033:CDS 55.0%
! GTGGTGGTGAAGGTGATGGT+TGG + chr2.3:6823938-6823957 None:intergenic 55.0%
CCTTCACCACCACCACCAAG+CGG - chr2.3:6823945-6823964 MS.gene54033:CDS 60.0%
CTTCACCACCACCACCAAGC+GGG - chr2.3:6823946-6823965 MS.gene54033:CDS 60.0%
GAGGACTGTGACGGCGAAAG+TGG - chr2.3:6824338-6824357 MS.gene54033:CDS 60.0%
GAGTAACGCTTGTGTGCCGG+AGG + chr2.3:6824057-6824076 None:intergenic 60.0%
GCAGATGCGGCTCCCAACAT+TGG + chr2.3:6823913-6823932 None:intergenic 60.0%
GGATGTGATGCGGAGCATGC+AGG - chr2.3:6824384-6824403 MS.gene54033:CDS 60.0%
GTGCCGGAGGATACATAGGG+TGG + chr2.3:6824044-6824063 None:intergenic 60.0%
TCGACTGGATGGTACAGCGG+AGG - chr2.3:6824273-6824292 MS.gene54033:CDS 60.0%
TTCACCACCACCACCAAGCG+GGG - chr2.3:6823947-6823966 MS.gene54033:CDS 60.0%
! AGAGTGGTGGCGTTGTCGAC+TGG - chr2.3:6824258-6824277 MS.gene54033:CDS 60.0%
! TGGTGGCGTTGTCGACTGGA+TGG - chr2.3:6824262-6824281 MS.gene54033:CDS 60.0%
!! GGTGGTGGTGGTGAAGGTGA+TGG + chr2.3:6823942-6823961 None:intergenic 60.0%
TCACCACCACCACCAAGCGG+GGG - chr2.3:6823948-6823967 MS.gene54033:CDS 65.0%
!! CCGCTTGGTGGTGGTGGTGA+AGG + chr2.3:6823948-6823967 None:intergenic 65.0%
CAAGTCCCACCACCCCCGCT+TGG + chr2.3:6823963-6823982 None:intergenic 70.0%
CACCACCAAGCGGGGGTGGT+GGG - chr2.3:6823955-6823974 MS.gene54033:CDS 70.0%
CCACCACCAAGCGGGGGTGG+TGG - chr2.3:6823954-6823973 MS.gene54033:CDS 75.0%
CCACCACCACCAAGCGGGGG+TGG - chr2.3:6823951-6823970 MS.gene54033:CDS 75.0%
GTCCCACCACCCCCGCTTGG+TGG + chr2.3:6823960-6823979 None:intergenic 75.0%
! CCACCACCCCCGCTTGGTGG+TGG + chr2.3:6823957-6823976 None:intergenic 75.0%
!! CCACCCCCGCTTGGTGGTGG+TGG + chr2.3:6823954-6823973 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 6823744 6824515 6823744 ID=MS.gene54033
chr2.3 mRNA 6823744 6824515 6823744 ID=MS.gene54033.t1;Parent=MS.gene54033
chr2.3 exon 6824161 6824515 6824161 ID=MS.gene54033.t1.exon1;Parent=MS.gene54033.t1
chr2.3 CDS 6824161 6824515 6824161 ID=cds.MS.gene54033.t1;Parent=MS.gene54033.t1
chr2.3 exon 6823744 6824057 6823744 ID=MS.gene54033.t1.exon2;Parent=MS.gene54033.t1
chr2.3 CDS 6823744 6824057 6823744 ID=cds.MS.gene54033.t1;Parent=MS.gene54033.t1
Gene Sequence

>MS.gene54033

ATGGCTCAGATATCAAATCTTGTTTTTTTAGCTTCCATTTTCCTTTTTAACATCATAAACAGTCCGTTCCTCACAAATGCTATTTCCTCATGCAATGGACCTTGTAGAACTCTCAACGACTGCGCTGGTCAACTCATTTGCATCAATGGCAAATGCAATGATGACCCCAATGTTGGGAGCCGCATCTGCTCCCAACCATCACCTTCACCACCACCACCAAGCGGGGGTGGTGGGACTTGCCGATCCACCAGCAACTTACAGTGCGACGGAAAATCATACCCTCAATATAGGTGTTCTCCACCCTATGTATCCTCCGGCACACAAGCGTTACTCACTTTGAACGATTTTAGCGAAGGTAACATGTATAACCAACTATCAAGTAATCATAACTAACTTGTAACTACCTTAAATAATATTCAACTAATTAATTTTAATAAATCTCAAACTATCTTTAACAGGAGGAGACGGAGGAGGTGCTTCTCAGTGCGATGAGGTATTCCATAGCAACTCAGAAAGAGTGGTGGCGTTGTCGACTGGATGGTACAGCGGAGGTTCAAGGTGTGGAAAATTTATTAGAATTAGGGCGTCAAATGGGAGGACTGTGACGGCGAAAGTGGTTGACCAGTGTGATTCAGTGAATGGATGTGATGCGGAGCATGCAGGTCAGCCACCTTGTCGTAACAATATTGTGGATGGATCTGTAGCTGTGTGGAATGCATTAGGGTTGAATACAAATGATGGTGTAGTACCAGTTACATGGACTATGGCTTGA

Protein sequence

>MS.gene54033.t1

MAQISNLVFLASIFLFNIINSPFLTNAISSCNGPCRTLNDCAGQLICINGKCNDDPNVGSRICSQPSPSPPPPSGGGGTCRSTSNLQCDGKSYPQYRCSPPYVSSGTQALLTLNDFSEGGDGGGASQCDEVFHSNSERVVALSTGWYSGGSRCGKFIRIRASNGRTVTAKVVDQCDSVNGCDAEHAGQPPCRNNIVDGSVAVWNALGLNTNDGVVPVTWTMA