AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00826

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00826.t1 MTR_2g023340 85.271 258 21 5 1 255 1 244 9.71e-146 407
MS.gene00826.t1 MTR_7g113680 49.730 185 85 6 66 249 133 310 5.19e-52 171
MS.gene00826.t1 MTR_1g082660 52.096 167 64 6 66 228 82 236 3.27e-49 162
MS.gene00826.t1 MTR_3g099180 56.250 128 52 1 67 194 37 160 6.82e-44 148
MS.gene00826.t1 MTR_3g099180 56.250 128 52 1 67 194 37 160 7.23e-44 147
MS.gene00826.t1 MTR_2g081600 59.740 77 30 1 86 161 23 99 1.08e-23 92.8
MS.gene00826.t1 MTR_2g081630 59.740 77 30 1 86 161 23 99 1.20e-23 92.4
MS.gene00826.t1 MTR_3g012030 44.872 78 43 0 86 163 9 86 2.76e-13 68.6
MS.gene00826.t1 MTR_8g041420 42.308 78 45 0 86 163 9 86 1.18e-12 66.6
MS.gene00826.t1 MTR_5g088760 38.462 78 48 0 86 163 9 86 5.67e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00826.t1 AT1G54830 54.037 161 67 4 66 222 51 208 8.51e-51 166
MS.gene00826.t1 AT1G54830 54.037 161 67 4 66 222 51 208 8.51e-51 166
MS.gene00826.t1 AT1G54830 54.037 161 67 4 66 222 51 208 8.51e-51 166
MS.gene00826.t1 AT1G08970 53.448 174 57 7 67 235 62 216 7.32e-50 164
MS.gene00826.t1 AT1G08970 53.448 174 57 7 67 235 62 216 7.32e-50 164
MS.gene00826.t1 AT1G08970 53.448 174 57 7 67 235 62 216 7.32e-50 164
MS.gene00826.t1 AT1G08970 53.448 174 57 7 67 235 62 216 7.32e-50 164
MS.gene00826.t1 AT1G56170 61.240 129 44 3 64 190 55 179 8.48e-49 160
MS.gene00826.t1 AT1G56170 61.240 129 44 3 64 190 55 179 8.48e-49 160
MS.gene00826.t1 AT3G48590 52.597 154 55 3 67 216 47 186 3.40e-47 157
MS.gene00826.t1 AT5G63470 57.812 128 52 1 67 192 60 187 5.81e-45 152
MS.gene00826.t1 AT5G63470 57.812 128 52 1 67 192 60 187 5.81e-45 152
MS.gene00826.t1 AT5G50480 47.500 160 68 5 63 221 35 179 4.29e-38 132
MS.gene00826.t1 AT5G27910 41.765 170 77 6 62 229 16 165 1.49e-31 115
MS.gene00826.t1 AT5G50490 46.154 104 53 1 62 165 16 116 3.45e-26 101
MS.gene00826.t1 AT5G50470 41.818 110 55 2 67 170 48 154 5.21e-23 93.6
MS.gene00826.t1 AT5G38140 40.777 103 59 1 60 162 44 144 2.95e-22 91.3

Find 57 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGCTTAATCTTCTGAATT+TGG 0.149271 2.3:-64864673 None:intergenic
ATTGGGACACTTTCTCTTCT+TGG 0.187927 2.3:-64864451 None:intergenic
AATGGAGCGTGACATATTTA+TGG 0.236296 2.3:+64864420 MS.gene00826:CDS
GGCGAGGCACTGATACTATT+TGG 0.252757 2.3:-64863982 None:intergenic
TGGTCCTCCAAGAATGCTTA+TGG 0.263320 2.3:+64864543 MS.gene00826:CDS
GGCATGTGAAATGTTTATTA+TGG 0.268895 2.3:+64864264 MS.gene00826:CDS
TGTCTTCCCATAAGCATTCT+TGG 0.296015 2.3:-64864550 None:intergenic
GTTGTCGGTGAGAGATTTCT+TGG 0.314048 2.3:-64864063 None:intergenic
GAATTTGGCAAATCAGTAGA+AGG 0.372595 2.3:-64864658 None:intergenic
ATCTTCTTAATCCTTGCTAA+TGG 0.378288 2.3:-64864181 None:intergenic
GTGCCACCTCAGTATGTTGC+AGG 0.380885 2.3:+64864511 MS.gene00826:CDS
TAATAAGGAACATTCCCTAT+TGG 0.390711 2.3:-64864469 None:intergenic
ACAGACATAGGCAGATAATA+AGG 0.391390 2.3:-64864484 None:intergenic
AATAAGGAACATTCCCTATT+GGG 0.400669 2.3:-64864468 None:intergenic
CCCGTTGTAAGGAGGTTGAT+TGG 0.412220 2.3:-64864578 None:intergenic
AGAAGAGAAAGTGTCCCAAT+AGG 0.412571 2.3:+64864454 MS.gene00826:CDS
GGAAACATTTGATTTGCAAA+AGG 0.414669 2.3:-64864613 None:intergenic
ATGGAGCGTGACATATTTAT+GGG 0.417294 2.3:+64864421 MS.gene00826:CDS
GAAACATTTGATTTGCAAAA+GGG 0.434507 2.3:-64864612 None:intergenic
ACTGTTGATTTCAAAAGTAA+TGG 0.437192 2.3:+64864154 MS.gene00826:CDS
GAAGAGAAAGTGTCCCAATA+GGG 0.454022 2.3:+64864455 MS.gene00826:CDS
TCTACTCAGGTATGATGAAA+AGG 0.465576 2.3:-64864032 None:intergenic
GGTCCTCCAAGAATGCTTAT+GGG 0.469493 2.3:+64864544 MS.gene00826:CDS
CCGTTGTAAGGAGGTTGATT+GGG 0.477387 2.3:-64864577 None:intergenic
CCAATCAACCTCCTTACAAC+GGG 0.477395 2.3:+64864578 MS.gene00826:CDS
CATGCCTTAGCAAACAGAAT+AGG 0.486382 2.3:-64864247 None:intergenic
CCTAGTTGATATTGTCCCTA+GGG 0.487741 2.3:+64864390 MS.gene00826:CDS
TGGAGCTAGCAACAAGGTCA+TGG 0.501489 2.3:+64864284 MS.gene00826:CDS
CCCTAGGGACAATATCAACT+AGG 0.511793 2.3:-64864390 None:intergenic
TGTGATGGATGCCCGTTGTA+AGG 0.514096 2.3:-64864589 None:intergenic
TATGTTGCAGGTCCATCATA+TGG 0.515120 2.3:+64864523 MS.gene00826:CDS
CTTGGAGTTGAACTCTACTC+AGG 0.515545 2.3:-64864045 None:intergenic
GGCACCTATTCTGTTTGCTA+AGG 0.530640 2.3:+64864243 MS.gene00826:CDS
AAGATCATGAAAGCTGATGA+AGG 0.545148 2.3:+64864199 MS.gene00826:CDS
TGATTTGCAAAAGGGTGTGA+TGG 0.553637 2.3:-64864604 None:intergenic
GCACTTGCAGTGTGAAACAA+AGG 0.556863 2.3:-64864004 None:intergenic
TCCTAGTTGATATTGTCCCT+AGG 0.558927 2.3:+64864389 MS.gene00826:CDS
CTTCCCATAAGCATTCTTGG+AGG 0.580142 2.3:-64864547 None:intergenic
GGAGCTAGCAACAAGGTCAT+GGG 0.582315 2.3:+64864285 MS.gene00826:CDS
CACTTGCAGTGTGAAACAAA+GGG 0.597437 2.3:-64864003 None:intergenic
GTAATGGCTTGCCATTAGCA+AGG 0.597965 2.3:+64864170 MS.gene00826:CDS
CCCAATCAACCTCCTTACAA+CGG 0.599569 2.3:+64864577 MS.gene00826:CDS
ATTCTTGGAGGACCATATGA+TGG 0.609961 2.3:-64864535 None:intergenic
GGTGGCACATGAACAGACAT+AGG 0.629233 2.3:-64864496 None:intergenic
AAAAGACACAAGAGGAACGA+AGG 0.630879 2.3:+64863930 MS.gene00826:CDS
AAGGTCATGGGCTAATACAG+AGG 0.637560 2.3:+64864297 MS.gene00826:CDS
TGGAGCGTGACATATTTATG+GGG 0.644468 2.3:+64864422 MS.gene00826:CDS
GCAGTGTGAAACAAAGGGCG+AGG 0.647228 2.3:-64863998 None:intergenic
TATGGATCAAAAGACACAAG+AGG 0.647854 2.3:+64863922 None:intergenic
AATTTGGCAAATCAGTAGAA+GGG 0.648246 2.3:-64864657 None:intergenic
GATGGATGCCCGTTGTAAGG+AGG 0.657482 2.3:-64864586 None:intergenic
GGAGCGTGACATATTTATGG+GGG 0.659242 2.3:+64864423 MS.gene00826:CDS
AGTGAGTATGATATCAGCTG+AGG 0.690629 2.3:+64864222 MS.gene00826:CDS
TTATTATGGAGCTAGCAACA+AGG 0.697305 2.3:+64864278 MS.gene00826:CDS
GAGCGTGACATATTTATGGG+GGG 0.703925 2.3:+64864424 MS.gene00826:CDS
GGACCTGCAACATACTGAGG+TGG 0.712994 2.3:-64864514 None:intergenic
GATGGACCTGCAACATACTG+AGG 0.735823 2.3:-64864517 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTGTTGATTTCAAAAGTAA+TGG + chr2.3:64864154-64864173 MS.gene00826:CDS 25.0%
!!! ATTCTTGTTGTTTTTGTTGT+CGG - chr2.3:64864081-64864100 None:intergenic 25.0%
!!! GAAACATTTGATTTGCAAAA+GGG - chr2.3:64864615-64864634 None:intergenic 25.0%
AATAAGGAACATTCCCTATT+GGG - chr2.3:64864471-64864490 None:intergenic 30.0%
AATTTGGCAAATCAGTAGAA+GGG - chr2.3:64864660-64864679 None:intergenic 30.0%
ATCTTCTTAATCCTTGCTAA+TGG - chr2.3:64864184-64864203 None:intergenic 30.0%
CAAGAATTGCAGAAAAAACT+TGG + chr2.3:64864094-64864113 MS.gene00826:CDS 30.0%
GGCATGTGAAATGTTTATTA+TGG + chr2.3:64864264-64864283 MS.gene00826:CDS 30.0%
TAATAAGGAACATTCCCTAT+TGG - chr2.3:64864472-64864491 None:intergenic 30.0%
!! GGAAACATTTGATTTGCAAA+AGG - chr2.3:64864616-64864635 None:intergenic 30.0%
!! TGGTTTGATTGATTTTGTGT+TGG - chr2.3:64863965-64863984 None:intergenic 30.0%
AAGATCATGAAAGCTGATGA+AGG + chr2.3:64864199-64864218 MS.gene00826:CDS 35.0%
AATGGAGCGTGACATATTTA+TGG + chr2.3:64864420-64864439 MS.gene00826:CDS 35.0%
ACAGACATAGGCAGATAATA+AGG - chr2.3:64864487-64864506 None:intergenic 35.0%
ATGGAGCGTGACATATTTAT+GGG + chr2.3:64864421-64864440 MS.gene00826:CDS 35.0%
GAATTTGGCAAATCAGTAGA+AGG - chr2.3:64864661-64864680 None:intergenic 35.0%
TCTACTCAGGTATGATGAAA+AGG - chr2.3:64864035-64864054 None:intergenic 35.0%
TTATTATGGAGCTAGCAACA+AGG + chr2.3:64864278-64864297 MS.gene00826:CDS 35.0%
!! AAGGGTCGTTTTCTTTCTTT+GGG - chr2.3:64864642-64864661 None:intergenic 35.0%
!!! TTCATTTTGTTTTGCCCAGA+AGG - chr2.3:64864122-64864141 None:intergenic 35.0%
AAAAGACACAAGAGGAACGA+AGG + chr2.3:64863930-64863949 MS.gene00826:CDS 40.0%
AGAAAAAACTTGGCACCTTC+TGG + chr2.3:64864104-64864123 MS.gene00826:CDS 40.0%
AGTGAGTATGATATCAGCTG+AGG + chr2.3:64864222-64864241 MS.gene00826:CDS 40.0%
ATTCTTGGAGGACCATATGA+TGG - chr2.3:64864538-64864557 None:intergenic 40.0%
ATTGGGACACTTTCTCTTCT+TGG - chr2.3:64864454-64864473 None:intergenic 40.0%
CACTTGCAGTGTGAAACAAA+GGG - chr2.3:64864006-64864025 None:intergenic 40.0%
CATGCCTTAGCAAACAGAAT+AGG - chr2.3:64864250-64864269 None:intergenic 40.0%
GAAAAAACTTGGCACCTTCT+GGG + chr2.3:64864105-64864124 MS.gene00826:CDS 40.0%
TATGTTGCAGGTCCATCATA+TGG + chr2.3:64864523-64864542 MS.gene00826:CDS 40.0%
TGGAGCGTGACATATTTATG+GGG + chr2.3:64864422-64864441 MS.gene00826:CDS 40.0%
TGTCCCTAGGGAAAAAACAA+TGG + chr2.3:64864402-64864421 MS.gene00826:CDS 40.0%
TGTCTTCCCATAAGCATTCT+TGG - chr2.3:64864553-64864572 None:intergenic 40.0%
! CCTAGTTGATATTGTCCCTA+GGG + chr2.3:64864390-64864409 MS.gene00826:CDS 40.0%
! TCCTAGTTGATATTGTCCCT+AGG + chr2.3:64864389-64864408 MS.gene00826:CDS 40.0%
! TGATTTGCAAAAGGGTGTGA+TGG - chr2.3:64864607-64864626 None:intergenic 40.0%
!! AGAAGAGAAAGTGTCCCAAT+AGG + chr2.3:64864454-64864473 MS.gene00826:CDS 40.0%
!! AGGGTCGTTTTCTTTCTTTG+GGG - chr2.3:64864641-64864660 None:intergenic 40.0%
!! GAAGAGAAAGTGTCCCAATA+GGG + chr2.3:64864455-64864474 MS.gene00826:CDS 40.0%
!! GAAGGGTCGTTTTCTTTCTT+TGG - chr2.3:64864643-64864662 None:intergenic 40.0%
!!! GCTCCATTGTTTTTTCCCTA+GGG - chr2.3:64864408-64864427 None:intergenic 40.0%
!!! TCGTTTTCTTTCTTTGGGGT+TGG - chr2.3:64864637-64864656 None:intergenic 40.0%
CCAATCAACCTCCTTACAAC+GGG + chr2.3:64864578-64864597 MS.gene00826:CDS 45.0%
CCCAATCAACCTCCTTACAA+CGG + chr2.3:64864577-64864596 MS.gene00826:CDS 45.0%
CCCTAGGGACAATATCAACT+AGG - chr2.3:64864393-64864412 None:intergenic 45.0%
CTTCCCATAAGCATTCTTGG+AGG - chr2.3:64864550-64864569 None:intergenic 45.0%
CTTGGAGTTGAACTCTACTC+AGG - chr2.3:64864048-64864067 None:intergenic 45.0%
GAGCGTGACATATTTATGGG+GGG + chr2.3:64864424-64864443 MS.gene00826:CDS 45.0%
GCACTTGCAGTGTGAAACAA+AGG - chr2.3:64864007-64864026 None:intergenic 45.0%
GGAGCGTGACATATTTATGG+GGG + chr2.3:64864423-64864442 MS.gene00826:CDS 45.0%
GGTCCTCCAAGAATGCTTAT+GGG + chr2.3:64864544-64864563 MS.gene00826:CDS 45.0%
GTTGTCGGTGAGAGATTTCT+TGG - chr2.3:64864066-64864085 None:intergenic 45.0%
TGGTCCTCCAAGAATGCTTA+TGG + chr2.3:64864543-64864562 MS.gene00826:CDS 45.0%
! AAGGTCATGGGCTAATACAG+AGG + chr2.3:64864297-64864316 MS.gene00826:CDS 45.0%
! CCGTTGTAAGGAGGTTGATT+GGG - chr2.3:64864580-64864599 None:intergenic 45.0%
! GGCACCTATTCTGTTTGCTA+AGG + chr2.3:64864243-64864262 MS.gene00826:CDS 45.0%
! GTAATGGCTTGCCATTAGCA+AGG + chr2.3:64864170-64864189 MS.gene00826:CDS 45.0%
!!! CGCTCCATTGTTTTTTCCCT+AGG - chr2.3:64864409-64864428 None:intergenic 45.0%
GATGGACCTGCAACATACTG+AGG - chr2.3:64864520-64864539 None:intergenic 50.0%
GGAGCTAGCAACAAGGTCAT+GGG + chr2.3:64864285-64864304 MS.gene00826:CDS 50.0%
GGTGGCACATGAACAGACAT+AGG - chr2.3:64864499-64864518 None:intergenic 50.0%
TGGAGCTAGCAACAAGGTCA+TGG + chr2.3:64864284-64864303 MS.gene00826:CDS 50.0%
! CCCGTTGTAAGGAGGTTGAT+TGG - chr2.3:64864581-64864600 None:intergenic 50.0%
!! GGCGAGGCACTGATACTATT+TGG - chr2.3:64863985-64864004 None:intergenic 50.0%
!! TGTGATGGATGCCCGTTGTA+AGG - chr2.3:64864592-64864611 None:intergenic 50.0%
GATGGATGCCCGTTGTAAGG+AGG - chr2.3:64864589-64864608 None:intergenic 55.0%
GCAGTGTGAAACAAAGGGCG+AGG - chr2.3:64864001-64864020 None:intergenic 55.0%
GGACCTGCAACATACTGAGG+TGG - chr2.3:64864517-64864536 None:intergenic 55.0%
GTGCCACCTCAGTATGTTGC+AGG + chr2.3:64864511-64864530 MS.gene00826:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 64863923 64864690 64863923 ID=MS.gene00826
chr2.3 mRNA 64863923 64864690 64863923 ID=MS.gene00826.t1;Parent=MS.gene00826
chr2.3 exon 64863923 64864690 64863923 ID=MS.gene00826.t1.exon1;Parent=MS.gene00826.t1
chr2.3 CDS 64863923 64864690 64863923 ID=cds.MS.gene00826.t1;Parent=MS.gene00826.t1
Gene Sequence

>MS.gene00826

ATGGATCAAAAGACACAAGAGGAACGAAGGAATGATACACCAACACAAAATCAATCAAACCAAATAGTATCAGTGCCTCGCCCTTTGTTTCACACTGCAAGTGCTTCTGCCTTTTCATCATACCTGAGTAGAGTTCAACTCCAAGAAATCTCTCACCGACAACAAAAACAACAAGAATTGCAGAAAAAACTTGGCACCTTCTGGGCAAAACAAAATGAAGAAGTTCAGAAGACTGTTGATTTCAAAAGTAATGGCTTGCCATTAGCAAGGATTAAGAAGATCATGAAAGCTGATGAAGGAGTGAGTATGATATCAGCTGAGGCACCTATTCTGTTTGCTAAGGCATGTGAAATGTTTATTATGGAGCTAGCAACAAGGTCATGGGCTAATACAGAGGTGAACAAAAGAAAGACACTTCAAAAGAGTGACATTGCATCTGCTGTCTCAAGTAATGAAGTGTTTGATTTCCTAGTTGATATTGTCCCTAGGGAAAAAACAATGGAGCGTGACATATTTATGGGGGGTATACCAAGAAGAGAAAGTGTCCCAATAGGGAATGTTCCTTATTATCTGCCTATGTCTGTTCATGTGCCACCTCAGTATGTTGCAGGTCCATCATATGGTCCTCCAAGAATGCTTATGGGAAGACATCTTCCCAATCAACCTCCTTACAACGGGCATCCATCACACCCTTTTGCAAATCAAATGTTTCCAACCCCAAAGAAAGAAAACGACCCTTCTACTGATTTGCCAAATTCAGAAGATTAA
Protein sequence

>MS.gene00826.t1

MDQKTQEERRNDTPTQNQSNQIVSVPRPLFHTASASAFSSYLSRVQLQEISHRQQKQQELQKKLGTFWAKQNEEVQKTVDFKSNGLPLARIKKIMKADEGVSMISAEAPILFAKACEMFIMELATRSWANTEVNKRKTLQKSDIASAVSSNEVFDFLVDIVPREKTMERDIFMGGIPRRESVPIGNVPYYLPMSVHVPPQYVAGPSYGPPRMLMGRHLPNQPPYNGHPSHPFANQMFPTPKKENDPSTDLPNSED