AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059891

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059891.t1 MTR_2g080260 96.935 261 8 0 5 265 81 341 0.0 534
MS.gene059891.t1 MTR_2g080230 94.253 261 15 0 5 265 81 341 0.0 520
MS.gene059891.t1 MTR_8g464300 74.615 260 66 0 6 265 82 341 6.54e-147 415
MS.gene059891.t1 MTR_4g059670 50.000 244 118 2 5 246 154 395 7.93e-87 264
MS.gene059891.t1 MTR_4g059630 47.951 244 123 2 5 246 145 386 4.70e-85 259
MS.gene059891.t1 MTR_2g021580 43.590 273 136 5 3 265 67 331 1.44e-77 238
MS.gene059891.t1 MTR_2g030835 43.223 273 137 5 3 265 66 330 8.79e-76 233
MS.gene059891.t1 MTR_2g030825 43.077 260 142 3 9 265 339 595 8.50e-73 233
MS.gene059891.t1 MTR_2g030845 42.692 260 143 3 9 265 340 596 1.24e-71 230
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059891.t1 AT5G54370 65.909 264 85 2 5 265 76 337 1.01e-132 379
MS.gene059891.t1 AT1G54890 62.782 266 94 3 5 265 82 347 3.56e-124 357
MS.gene059891.t1 AT4G27400 61.217 263 98 2 6 265 80 341 7.47e-122 351
MS.gene059891.t1 AT5G60520 52.402 229 107 1 5 231 99 327 2.52e-87 263
MS.gene059891.t1 AT5G60530 50.633 237 114 1 5 238 199 435 2.28e-85 261
MS.gene059891.t1 AT3G19430 43.130 262 144 3 8 265 322 582 9.01e-73 233
MS.gene059891.t1 AT3G19430 43.130 262 144 3 8 265 299 559 9.11e-73 233

Find 77 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGCCACACCATCATCAATT+TGG 0.212135 2.2:+15127638 MS.gene059891:CDS
ACAGATATTTCAGCAACTTC+TGG 0.256973 2.2:-15127805 None:intergenic
CATCAGGAATCTGATAATTA+TGG 0.264771 2.2:-15127864 None:intergenic
ATTGCCACGCCTGGCTTTGC+CGG 0.284921 2.2:-15127988 None:intergenic
GATCCACGACCATTACAATT+TGG 0.298259 2.2:-15127409 None:intergenic
TCCAAGAACTCCTTCAACTT+TGG 0.319801 2.2:-15127938 None:intergenic
GATGTGCAGTTCAAATTCTA+TGG 0.321248 2.2:+15127907 MS.gene059891:CDS
CATGTAGAGAGGTGACCTTC+AGG 0.334170 2.2:-15127715 None:intergenic
TCCAAAGTTGAAGGAGTTCT+TGG 0.337116 2.2:+15127937 MS.gene059891:CDS
TAAAACGAGCATTGATTTGA+AGG 0.368629 2.2:-15127528 None:intergenic
CAGATATTTCAGCAACTTCT+GGG 0.400574 2.2:-15127804 None:intergenic
AGCCACACCATCATCAATTT+GGG 0.401698 2.2:+15127639 MS.gene059891:CDS
GAAGGCTTGGAGATTGAATA+TGG 0.405534 2.2:+15128108 MS.gene059891:CDS
GATCTGCATGCTTGGACCCT+CGG 0.411633 2.2:+15127428 MS.gene059891:CDS
GGCGTGGCAATGCCGGTCAT+TGG 0.420807 2.2:+15128000 MS.gene059891:CDS
TATACTTGGATTCAAGCATT+GGG 0.425530 2.2:+15127583 MS.gene059891:CDS
AGATTCAGTGCAGGAAGGCT+TGG 0.436915 2.2:+15128095 MS.gene059891:CDS
AACTATACCATTACCACTGC+TGG 0.442336 2.2:-15128154 None:intergenic
CCTCGGTTCGTTGGTGCGGA+TGG 0.452228 2.2:+15127445 MS.gene059891:CDS
AAAGCCAGGCGTGGCAATGC+CGG 0.457703 2.2:+15127993 MS.gene059891:CDS
TTGGTCTCCCTTGCGGCCTA+AGG 0.460474 2.2:-15127555 None:intergenic
GGAGACCAAGGGATTATACT+TGG 0.461637 2.2:+15127569 MS.gene059891:CDS
ATGACCGGCATTGCCACGCC+TGG 0.467891 2.2:-15127997 None:intergenic
ATGGATTCTACTGTCCTCCT+TGG 0.475359 2.2:-15127845 None:intergenic
GTGGCAATGCCGGTCATTGG+AGG 0.478744 2.2:+15128003 MS.gene059891:CDS
TTATACTTGGATTCAAGCAT+TGG 0.481860 2.2:+15127582 MS.gene059891:CDS
TGAGCAAAACAATCATCATC+AGG 0.483129 2.2:-15127880 None:intergenic
TTTCAAAATCCGGCAAAGCC+AGG 0.488564 2.2:+15127979 MS.gene059891:CDS
CTACTGTCCTCCTTGGTGAC+AGG 0.494181 2.2:-15127838 None:intergenic
CTGAAGGTCACCTCTCTACA+TGG 0.503524 2.2:+15127716 MS.gene059891:CDS
GGAGATTGAATATGGTATGA+TGG 0.508182 2.2:+15128116 MS.gene059891:CDS
TGCTTGGACCCTCGGTTCGT+TGG 0.509275 2.2:+15127436 MS.gene059891:CDS
TTCTGTTAAAGATTCAGTGC+AGG 0.514763 2.2:+15128086 MS.gene059891:CDS
AAACCAAATTGTAATGGTCG+TGG 0.516808 2.2:+15127406 MS.gene059891:CDS
TGGCAATGCCGGTCATTGGA+GGG 0.520893 2.2:+15128004 MS.gene059891:CDS
TGGTCGTGGATCTGCATGCT+TGG 0.528868 2.2:+15127420 MS.gene059891:CDS
ATGTAGAGAGGTGACCTTCA+GGG 0.531349 2.2:-15127714 None:intergenic
GGACCCTCGGTTCGTTGGTG+CGG 0.532291 2.2:+15127441 MS.gene059891:CDS
TTGTCTTCCCCTCCAATGAC+CGG 0.533192 2.2:-15128012 None:intergenic
GGTGGTGCCAGCAGTGGTAA+TGG 0.535725 2.2:+15128147 MS.gene059891:CDS
CAAGACAATCTGAAGAAACA+AGG 0.537212 2.2:-15128050 None:intergenic
TTTATCGGCCTTAGGCCGCA+AGG 0.538998 2.2:+15127547 MS.gene059891:CDS
GGTTTATCGTCCAAAGTTGA+AGG 0.540641 2.2:+15127928 MS.gene059891:CDS
TGAATCCAAGTATAATCCCT+TGG 0.542313 2.2:-15127574 None:intergenic
CGTCATAAGAGAGCTTCAAA+TGG 0.545184 2.2:-15127675 None:intergenic
AGTGCTCATTCCTCCTTCCA+TGG 0.545876 2.2:-15127483 None:intergenic
ATCTGAAGAAACAAGGGATG+TGG 0.547311 2.2:-15128043 None:intergenic
GGCAATGCCGGTCATTGGAG+GGG 0.549475 2.2:+15128005 MS.gene059891:CDS
CCTCGGATTGCCATGTAGAG+AGG 0.553637 2.2:-15127726 None:intergenic
GGTCGTAAACCAAATTGTAA+TGG 0.554034 2.2:+15127400 MS.gene059891:CDS
TCGTCATCCCAAATTGATGA+TGG 0.560527 2.2:-15127646 None:intergenic
TATATAGTGGATATGAGAGC+AGG 0.573507 2.2:+15127379 None:intergenic
AAAAGTTGTGTGAATCAAAG+AGG 0.574407 2.2:-15127609 None:intergenic
CATTTGAAGCTCTCTTATGA+CGG 0.574479 2.2:+15127676 MS.gene059891:CDS
TTAGGCCGCAAGGGAGACCA+AGG 0.575605 2.2:+15127557 MS.gene059891:CDS
GAAGCTCTCTTATGACGGAA+AGG 0.577165 2.2:+15127681 MS.gene059891:CDS
ATCGAATGAGAACGGTGTCA+TGG 0.591031 2.2:+15127774 MS.gene059891:CDS
TGCACTGGTGGTGCCAGCAG+TGG 0.591546 2.2:+15128141 MS.gene059891:CDS
TAATCCCTTGGTCTCCCTTG+CGG 0.596610 2.2:-15127562 None:intergenic
TTATCGGCCTTAGGCCGCAA+GGG 0.605783 2.2:+15127548 MS.gene059891:CDS
GTTAAAGATTCAGTGCAGGA+AGG 0.612449 2.2:+15128090 MS.gene059891:CDS
GGTATGATGGATTGCACTGG+TGG 0.616779 2.2:+15128129 MS.gene059891:CDS
CAATGTGGTGCCTGTCACCA+AGG 0.622527 2.2:+15127828 MS.gene059891:CDS
ATACTTGGATTCAAGCATTG+GGG 0.623520 2.2:+15127584 MS.gene059891:CDS
CATCCGCACCAACGAACCGA+GGG 0.629982 2.2:-15127444 None:intergenic
AAGGATCTCGTAATCCCTGA+AGG 0.634498 2.2:+15127700 MS.gene059891:CDS
CCATCCGCACCAACGAACCG+AGG 0.635702 2.2:-15127445 None:intergenic
ATCCCAAATTGATGATGGTG+TGG 0.638854 2.2:-15127641 None:intergenic
AAGACAATCTGAAGAAACAA+GGG 0.640149 2.2:-15128049 None:intergenic
CCTCTCTACATGGCAATCCG+AGG 0.646287 2.2:+15127726 MS.gene059891:CDS
AAATCCGGCAAAGCCAGGCG+TGG 0.649193 2.2:+15127984 MS.gene059891:CDS
GAGAGAACATCGAATGAGAA+CGG 0.650582 2.2:+15127766 MS.gene059891:CDS
TACTTGGATTCAAGCATTGG+GGG 0.654990 2.2:+15127585 MS.gene059891:CDS
TATGGTATGATGGATTGCAC+TGG 0.671149 2.2:+15128126 MS.gene059891:CDS
TAGGCCGCAAGGGAGACCAA+GGG 0.706685 2.2:+15127558 MS.gene059891:CDS
TGCTGAAATATCTGTCAATG+TGG 0.712131 2.2:+15127813 MS.gene059891:CDS
TGTGGTGCCTGTCACCAAGG+AGG 0.732407 2.2:+15127831 MS.gene059891:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAAAGTTGTGTGAATCAAAG+AGG - chr2.2:15127612-15127631 None:intergenic 30.0%
AAGACAATCTGAAGAAACAA+GGG - chr2.2:15128052-15128071 None:intergenic 30.0%
CATCAGGAATCTGATAATTA+TGG - chr2.2:15127867-15127886 None:intergenic 30.0%
TATACTTGGATTCAAGCATT+GGG + chr2.2:15127583-15127602 MS.gene059891:CDS 30.0%
TTATACTTGGATTCAAGCAT+TGG + chr2.2:15127582-15127601 MS.gene059891:CDS 30.0%
! CAAATCAATGCTCGTTTTAT+CGG + chr2.2:15127532-15127551 MS.gene059891:CDS 30.0%
!! TAAAACGAGCATTGATTTGA+AGG - chr2.2:15127531-15127550 None:intergenic 30.0%
!! TGATGATTGTTTTGCTCATT+TGG + chr2.2:15127885-15127904 MS.gene059891:CDS 30.0%
AAACCAAATTGTAATGGTCG+TGG + chr2.2:15127406-15127425 MS.gene059891:CDS 35.0%
ACAGATATTTCAGCAACTTC+TGG - chr2.2:15127808-15127827 None:intergenic 35.0%
CAAGACAATCTGAAGAAACA+AGG - chr2.2:15128053-15128072 None:intergenic 35.0%
CAGATATTTCAGCAACTTCT+GGG - chr2.2:15127807-15127826 None:intergenic 35.0%
GATGTGCAGTTCAAATTCTA+TGG + chr2.2:15127907-15127926 MS.gene059891:CDS 35.0%
GGAGATTGAATATGGTATGA+TGG + chr2.2:15128116-15128135 MS.gene059891:CDS 35.0%
GGTCGTAAACCAAATTGTAA+TGG + chr2.2:15127400-15127419 MS.gene059891:CDS 35.0%
TGAATCCAAGTATAATCCCT+TGG - chr2.2:15127577-15127596 None:intergenic 35.0%
TGAGCAAAACAATCATCATC+AGG - chr2.2:15127883-15127902 None:intergenic 35.0%
TGCTGAAATATCTGTCAATG+TGG + chr2.2:15127813-15127832 MS.gene059891:CDS 35.0%
TTCTGTTAAAGATTCAGTGC+AGG + chr2.2:15128086-15128105 MS.gene059891:CDS 35.0%
! ATACTTGGATTCAAGCATTG+GGG + chr2.2:15127584-15127603 MS.gene059891:CDS 35.0%
! CATTTGAAGCTCTCTTATGA+CGG + chr2.2:15127676-15127695 MS.gene059891:CDS 35.0%
! TCAGCCAGATTTTCAAAATC+CGG + chr2.2:15127969-15127988 MS.gene059891:CDS 35.0%
! TTGTTTTCTACTTCCATGGA+AGG + chr2.2:15127470-15127489 MS.gene059891:CDS 35.0%
!! TTTGCCGGATTTTGAAAATC+TGG - chr2.2:15127976-15127995 None:intergenic 35.0%
!!! GACTCTAAGTTGATTTTCCT+CGG - chr2.2:15127746-15127765 None:intergenic 35.0%
AACTATACCATTACCACTGC+TGG - chr2.2:15128157-15128176 None:intergenic 40.0%
AAGCCACACCATCATCAATT+TGG + chr2.2:15127638-15127657 MS.gene059891:CDS 40.0%
AGCCACACCATCATCAATTT+GGG + chr2.2:15127639-15127658 MS.gene059891:CDS 40.0%
ATCTGAAGAAACAAGGGATG+TGG - chr2.2:15128046-15128065 None:intergenic 40.0%
CGTCATAAGAGAGCTTCAAA+TGG - chr2.2:15127678-15127697 None:intergenic 40.0%
GAAGGCTTGGAGATTGAATA+TGG + chr2.2:15128108-15128127 MS.gene059891:CDS 40.0%
GAGAGAACATCGAATGAGAA+CGG + chr2.2:15127766-15127785 MS.gene059891:CDS 40.0%
GATCCACGACCATTACAATT+TGG - chr2.2:15127412-15127431 None:intergenic 40.0%
GGTTTATCGTCCAAAGTTGA+AGG + chr2.2:15127928-15127947 MS.gene059891:CDS 40.0%
GTTAAAGATTCAGTGCAGGA+AGG + chr2.2:15128090-15128109 MS.gene059891:CDS 40.0%
TCCAAAGTTGAAGGAGTTCT+TGG + chr2.2:15127937-15127956 MS.gene059891:CDS 40.0%
TCCAAGAACTCCTTCAACTT+TGG - chr2.2:15127941-15127960 None:intergenic 40.0%
TCGTCATCCCAAATTGATGA+TGG - chr2.2:15127649-15127668 None:intergenic 40.0%
! GGCATTGTTTTCTACTTCCA+TGG + chr2.2:15127466-15127485 MS.gene059891:CDS 40.0%
! TTTTCTACTTCCATGGAAGG+AGG + chr2.2:15127473-15127492 MS.gene059891:CDS 40.0%
!! ATCCCAAATTGATGATGGTG+TGG - chr2.2:15127644-15127663 None:intergenic 40.0%
!! TACTTGGATTCAAGCATTGG+GGG + chr2.2:15127585-15127604 MS.gene059891:CDS 40.0%
!! TATGGTATGATGGATTGCAC+TGG + chr2.2:15128126-15128145 MS.gene059891:CDS 40.0%
AAGGATCTCGTAATCCCTGA+AGG + chr2.2:15127700-15127719 MS.gene059891:CDS 45.0%
ATGGATTCTACTGTCCTCCT+TGG - chr2.2:15127848-15127867 None:intergenic 45.0%
ATGTAGAGAGGTGACCTTCA+GGG - chr2.2:15127717-15127736 None:intergenic 45.0%
GGAGACCAAGGGATTATACT+TGG + chr2.2:15127569-15127588 MS.gene059891:CDS 45.0%
TTTCAAAATCCGGCAAAGCC+AGG + chr2.2:15127979-15127998 MS.gene059891:CDS 45.0%
! ATCGAATGAGAACGGTGTCA+TGG + chr2.2:15127774-15127793 MS.gene059891:CDS 45.0%
! ATGCTCGTTTTATCGGCCTT+AGG + chr2.2:15127539-15127558 MS.gene059891:CDS 45.0%
! GAAGCTCTCTTATGACGGAA+AGG + chr2.2:15127681-15127700 MS.gene059891:CDS 45.0%
AGATTCAGTGCAGGAAGGCT+TGG + chr2.2:15128095-15128114 MS.gene059891:CDS 50.0%
AGTGCTCATTCCTCCTTCCA+TGG - chr2.2:15127486-15127505 None:intergenic 50.0%
CATGTAGAGAGGTGACCTTC+AGG - chr2.2:15127718-15127737 None:intergenic 50.0%
CTGAAGGTCACCTCTCTACA+TGG + chr2.2:15127716-15127735 MS.gene059891:CDS 50.0%
TAATCCCTTGGTCTCCCTTG+CGG - chr2.2:15127565-15127584 None:intergenic 50.0%
TTGTCTTCCCCTCCAATGAC+CGG - chr2.2:15128015-15128034 None:intergenic 50.0%
!! GGTATGATGGATTGCACTGG+TGG + chr2.2:15128129-15128148 MS.gene059891:CDS 50.0%
CAATGTGGTGCCTGTCACCA+AGG + chr2.2:15127828-15127847 MS.gene059891:CDS 55.0%
CCTCGGATTGCCATGTAGAG+AGG - chr2.2:15127729-15127748 None:intergenic 55.0%
CCTCTCTACATGGCAATCCG+AGG + chr2.2:15127726-15127745 MS.gene059891:CDS 55.0%
GATCTGCATGCTTGGACCCT+CGG + chr2.2:15127428-15127447 MS.gene059891:CDS 55.0%
TGGCAATGCCGGTCATTGGA+GGG + chr2.2:15128004-15128023 MS.gene059891:CDS 55.0%
TGGTCGTGGATCTGCATGCT+TGG + chr2.2:15127420-15127439 MS.gene059891:CDS 55.0%
TTATCGGCCTTAGGCCGCAA+GGG + chr2.2:15127548-15127567 MS.gene059891:CDS 55.0%
TTTATCGGCCTTAGGCCGCA+AGG + chr2.2:15127547-15127566 MS.gene059891:CDS 55.0%
! CTACTGTCCTCCTTGGTGAC+AGG - chr2.2:15127841-15127860 None:intergenic 55.0%
AAAGCCAGGCGTGGCAATGC+CGG + chr2.2:15127993-15128012 MS.gene059891:CDS 60.0%
AAATCCGGCAAAGCCAGGCG+TGG + chr2.2:15127984-15128003 MS.gene059891:CDS 60.0%
CATCCGCACCAACGAACCGA+GGG - chr2.2:15127447-15127466 None:intergenic 60.0%
GGCAATGCCGGTCATTGGAG+GGG + chr2.2:15128005-15128024 MS.gene059891:CDS 60.0%
GTGGCAATGCCGGTCATTGG+AGG + chr2.2:15128003-15128022 MS.gene059891:CDS 60.0%
TAGGCCGCAAGGGAGACCAA+GGG + chr2.2:15127558-15127577 MS.gene059891:CDS 60.0%
TGTGGTGCCTGTCACCAAGG+AGG + chr2.2:15127831-15127850 MS.gene059891:CDS 60.0%
TTAGGCCGCAAGGGAGACCA+AGG + chr2.2:15127557-15127576 MS.gene059891:CDS 60.0%
TTGGTCTCCCTTGCGGCCTA+AGG - chr2.2:15127558-15127577 None:intergenic 60.0%
! GGTGGTGCCAGCAGTGGTAA+TGG + chr2.2:15128147-15128166 MS.gene059891:CDS 60.0%
! TGCTTGGACCCTCGGTTCGT+TGG + chr2.2:15127436-15127455 MS.gene059891:CDS 60.0%
!! ATTGCCACGCCTGGCTTTGC+CGG - chr2.2:15127991-15128010 None:intergenic 60.0%
ATGACCGGCATTGCCACGCC+TGG - chr2.2:15128000-15128019 None:intergenic 65.0%
CCATCCGCACCAACGAACCG+AGG - chr2.2:15127448-15127467 None:intergenic 65.0%
GGCGTGGCAATGCCGGTCAT+TGG + chr2.2:15128000-15128019 MS.gene059891:CDS 65.0%
! CCTCGGTTCGTTGGTGCGGA+TGG + chr2.2:15127445-15127464 MS.gene059891:CDS 65.0%
! GGACCCTCGGTTCGTTGGTG+CGG + chr2.2:15127441-15127460 MS.gene059891:CDS 65.0%
! TGCACTGGTGGTGCCAGCAG+TGG + chr2.2:15128141-15128160 MS.gene059891:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 15127391 15128188 15127391 ID=MS.gene059891
chr2.2 mRNA 15127391 15128188 15127391 ID=MS.gene059891.t1;Parent=MS.gene059891
chr2.2 exon 15127391 15128188 15127391 ID=MS.gene059891.t1.exon1;Parent=MS.gene059891.t1
chr2.2 CDS 15127391 15128188 15127391 ID=cds.MS.gene059891.t1;Parent=MS.gene059891.t1
Gene Sequence

>MS.gene059891

ATGAGAGCAGGTCGTAAACCAAATTGTAATGGTCGTGGATCTGCATGCTTGGACCCTCGGTTCGTTGGTGCGGATGGCATTGTTTTCTACTTCCATGGAAGGAGGAATGAGCACTTCAGCTTGATATCTGACGTGAACCTTCAAATCAATGCTCGTTTTATCGGCCTTAGGCCGCAAGGGAGACCAAGGGATTATACTTGGATTCAAGCATTGGGGGTCCTCTTTGATTCACACAACTTTTCTATTGAAGCCACACCATCATCAATTTGGGATGACGAAGTTGACCATTTGAAGCTCTCTTATGACGGAAAGGATCTCGTAATCCCTGAAGGTCACCTCTCTACATGGCAATCCGAGGAAAATCAACTTAGAGTCGAGAGAACATCGAATGAGAACGGTGTCATGGTTACAATCCCAGAAGTTGCTGAAATATCTGTCAATGTGGTGCCTGTCACCAAGGAGGACAGTAGAATCCATAATTATCAGATTCCTGATGATGATTGTTTTGCTCATTTGGATGTGCAGTTCAAATTCTATGGTTTATCGTCCAAAGTTGAAGGAGTTCTTGGAAGAACTTATCAGCCAGATTTTCAAAATCCGGCAAAGCCAGGCGTGGCAATGCCGGTCATTGGAGGGGAAGACAAGTATAGAACCACATCCCTTGTTTCTTCAGATTGTCTTGCTTGTATATTCTCTTCTGTTAAAGATTCAGTGCAGGAAGGCTTGGAGATTGAATATGGTATGATGGATTGCACTGGTGGTGCCAGCAGTGGTAATGGTATAGTTTGCAGAAGATAA
Protein sequence

>MS.gene059891.t1

MRAGRKPNCNGRGSACLDPRFVGADGIVFYFHGRRNEHFSLISDVNLQINARFIGLRPQGRPRDYTWIQALGVLFDSHNFSIEATPSSIWDDEVDHLKLSYDGKDLVIPEGHLSTWQSEENQLRVERTSNENGVMVTIPEVAEISVNVVPVTKEDSRIHNYQIPDDDCFAHLDVQFKFYGLSSKVEGVLGRTYQPDFQNPAKPGVAMPVIGGEDKYRTTSLVSSDCLACIFSSVKDSVQEGLEIEYGMMDCTGGASSGNGIVCRR