AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24222

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24222.t1 MTR_1g023230 99.174 121 0 1 1 120 108 228 6.02e-83 248
MS.gene24222.t1 MTR_3g112510 59.910 222 69 7 11 225 82 290 7.56e-73 223
MS.gene24222.t1 MTR_8g076620 54.357 241 78 7 1 228 110 331 2.45e-68 213
MS.gene24222.t1 MTR_5g021130 54.661 236 89 6 7 228 92 323 4.15e-68 212
MS.gene24222.t1 MTR_5g089750 45.062 162 81 3 15 168 249 410 1.21e-38 139
MS.gene24222.t1 MTR_3g014660 40.113 177 95 4 1 167 119 294 2.14e-35 128
MS.gene24222.t1 MTR_4g071110 41.892 148 62 2 12 159 14 137 5.98e-33 120
MS.gene24222.t1 MTR_8g039110 39.779 181 95 3 15 181 124 304 4.80e-32 119
MS.gene24222.t1 MTR_0363s0040 75.556 45 11 0 15 59 124 168 2.38e-20 86.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24222.t1 AT1G75520 52.564 234 87 6 11 228 121 346 7.05e-73 225
MS.gene24222.t1 AT3G51060 50.424 236 90 4 13 228 142 370 5.30e-70 219
MS.gene24222.t1 AT1G19790 50.410 244 103 7 1 227 102 344 5.81e-69 215
MS.gene24222.t1 AT1G19790 50.410 244 103 7 1 227 102 344 5.81e-69 215
MS.gene24222.t1 AT5G66350 49.554 224 91 6 15 228 120 331 2.26e-63 200
MS.gene24222.t1 AT5G66350 48.402 219 91 6 15 223 120 326 1.05e-60 193
MS.gene24222.t1 AT5G66350 49.296 213 86 6 15 217 120 320 2.18e-59 190
MS.gene24222.t1 AT2G21400 42.991 214 83 6 12 222 7 184 1.96e-48 157
MS.gene24222.t1 AT2G21400 42.991 214 83 6 12 222 6 183 2.29e-48 157
MS.gene24222.t1 AT2G21400 42.180 211 74 6 12 222 7 169 2.20e-46 152
MS.gene24222.t1 AT2G21400 42.180 211 74 6 12 222 6 168 2.54e-46 152
MS.gene24222.t1 AT4G36260 52.500 160 60 5 13 161 92 246 4.23e-46 155
MS.gene24222.t1 AT2G18120 47.436 156 56 3 13 161 70 206 1.60e-41 141
MS.gene24222.t1 AT2G18120 48.344 151 60 2 13 161 70 204 5.03e-39 134
MS.gene24222.t1 AT5G12330 47.500 160 71 2 15 161 112 271 1.05e-36 131
MS.gene24222.t1 AT5G12330 47.500 160 71 2 15 161 112 271 1.05e-36 131
MS.gene24222.t1 AT5G12330 47.500 160 71 2 15 161 199 358 1.55e-36 132
MS.gene24222.t1 AT5G33210 61.538 91 32 1 13 103 15 102 8.41e-33 115
MS.gene24222.t1 AT5G33210 49.206 126 54 3 13 138 50 165 1.40e-32 116
MS.gene24222.t1 AT3G54430 34.783 161 82 4 11 167 37 178 9.14e-24 94.4
MS.gene24222.t1 AT5G12330 82.609 46 8 0 15 60 112 157 9.40e-22 90.1

Find 59 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGATCCCTCTGGAGCTTC+TGG 0.278538 1.2:+1736171 MS.gene24222:CDS
AGCTCCTCTTAATGCTTTCA+TGG 0.295162 1.2:+1737038 MS.gene24222:CDS
CACTCATGTCTTTAGGATCT+TGG 0.300540 1.2:-1737084 None:intergenic
TGAATTCACCGGCGGTGTTC+AGG 0.312818 1.2:+1736758 MS.gene24222:CDS
TATATACCTGTGGTAGTAAT+AGG 0.332609 1.2:-1736216 None:intergenic
GGTGGTGGCGAGGGTTCTTC+CGG 0.367254 1.2:+1736922 MS.gene24222:CDS
AGGTCTTCGAGTGGTGGTTT+AGG 0.382996 1.2:+1735916 MS.gene24222:CDS
CCACCACCAGCAGCAGCATT+TGG 0.392576 1.2:-1736907 None:intergenic
CGTTCGCGGCGTTTAGCAGC+TGG 0.397352 1.2:-1736066 None:intergenic
CCTCTTAATGCTTTCATGGC+TGG 0.408461 1.2:+1737042 MS.gene24222:CDS
GTGGACAATCTTTCTTAGCT+TGG 0.415642 1.2:-1735972 None:intergenic
TGAGTTGTTGCTGCCGTTCG+CGG 0.429437 1.2:-1736080 None:intergenic
GGCGAGGGTTCTTCCGGTGG+TGG 0.430350 1.2:+1736928 MS.gene24222:CDS
TTGAAATTAGGGTTGGAGTT+GGG 0.437119 1.2:+1736718 MS.gene24222:intron
GGTTCTTCCGGTGGTGGCAG+CGG 0.446891 1.2:+1736934 MS.gene24222:CDS
TTCGCCACCGCTGCCACCAC+CGG 0.449406 1.2:-1736941 None:intergenic
CCAAATGCTGCTGCTGGTGG+TGG 0.457278 1.2:+1736907 MS.gene24222:CDS
AAACTCATGTGAAAAGTACT+TGG 0.464467 1.2:+1736040 MS.gene24222:CDS
TGCTGCTGCTGGTGGTGGCG+AGG 0.465038 1.2:+1736912 MS.gene24222:CDS
TTGTATGATCAAGGACTTGA+AGG 0.474373 1.2:+1736871 MS.gene24222:CDS
GAAAATCAAAATGATCCCTC+TGG 0.474468 1.2:+1736162 MS.gene24222:CDS
TGTCTTTAGGATCTTGGAGG+TGG 0.488834 1.2:-1737078 None:intergenic
GCTGCTGCTGGTGGTGGCGA+GGG 0.489260 1.2:+1736913 MS.gene24222:CDS
TCATGTCTTTAGGATCTTGG+AGG 0.489282 1.2:-1737081 None:intergenic
TATAGTGAAGAATACTCAAA+TGG 0.492700 1.2:-1737012 None:intergenic
AGTGGTGGTTTAGGTGGTGG+TGG 0.496649 1.2:+1735925 MS.gene24222:CDS
ATGAAAGCATTAAGAGGAGC+TGG 0.499046 1.2:-1737036 None:intergenic
CCTGTGGTAGTAATAGGTAC+TGG 0.504192 1.2:-1736210 None:intergenic
TCTTCCGGTGGTGGCAGCGG+TGG 0.515802 1.2:+1736937 MS.gene24222:CDS
AGTAATAGGTACTGGAGTAC+AGG 0.518362 1.2:-1736202 None:intergenic
CCAGCCATGAAAGCATTAAG+AGG 0.523927 1.2:-1737042 None:intergenic
TTTGAAATTAGGGTTGGAGT+TGG 0.534737 1.2:+1736717 MS.gene24222:intron
TCGAGTGGTGGTTTAGGTGG+TGG 0.538002 1.2:+1735922 MS.gene24222:CDS
GGTGGTGGCAGCGGTGGCGA+AGG 0.539736 1.2:+1736943 MS.gene24222:CDS
TTTACACACCTGAACACCGC+CGG 0.552531 1.2:-1736766 None:intergenic
TCCACCGGAGCTGAATTCAC+CGG 0.555263 1.2:+1736747 MS.gene24222:CDS
GAACTTGTTGCAAGAGTCGA+GGG 0.557726 1.2:+1736007 MS.gene24222:CDS
CAGCTGCTAAACGCCGCGAA+CGG 0.557914 1.2:+1736067 MS.gene24222:CDS
ATTGTTAACATTTGTTGTCG+TGG 0.557983 1.2:-1736989 None:intergenic
GTCTTTAGGATCTTGGAGGT+GGG 0.561171 1.2:-1737077 None:intergenic
CCAGTACCTATTACTACCAC+AGG 0.564967 1.2:+1736210 MS.gene24222:CDS
CAAACTGCTGTGAACATAGG+AGG 0.565014 1.2:+1736829 MS.gene24222:CDS
ACTAGTCCAAATGCTGCTGC+TGG 0.565581 1.2:+1736901 MS.gene24222:CDS
GTGATGAGGTCTTCGAGTGG+TGG 0.569075 1.2:+1735910 None:intergenic
GCCGGTGAATTCAGCTCCGG+TGG 0.569608 1.2:-1736748 None:intergenic
TCTTCGAGTGGTGGTTTAGG+TGG 0.570569 1.2:+1735919 MS.gene24222:CDS
TATCAAACTGCTGTGAACAT+AGG 0.572121 1.2:+1736826 MS.gene24222:CDS
GGTGGCGAGGGTTCTTCCGG+TGG 0.572206 1.2:+1736925 MS.gene24222:CDS
ACCGCCGGTGAATTCAGCTC+CGG 0.574562 1.2:-1736751 None:intergenic
TAGAGAACCAGAAGCTCCAG+AGG 0.578477 1.2:-1736178 None:intergenic
AGTCCAAATGCTGCTGCTGG+TGG 0.584415 1.2:+1736904 MS.gene24222:CDS
AACTCATGTGAAAAGTACTT+GGG 0.591492 1.2:+1736041 MS.gene24222:CDS
AGAACTTGTTGCAAGAGTCG+AGG 0.603647 1.2:+1736006 MS.gene24222:CDS
CAAGTTCTACATCTAAGATG+TGG 0.632750 1.2:-1735991 None:intergenic
GGAATGAACTGTCAAGATTG+TGG 0.658447 1.2:+1735946 MS.gene24222:CDS
ACCGGAGCTGAATTCACCGG+CGG 0.668533 1.2:+1736750 MS.gene24222:CDS
AGAGAACCAGAAGCTCCAGA+GGG 0.671479 1.2:-1736177 None:intergenic
GTGTGTAAAAGTGAGTGCAA+TGG 0.678715 1.2:+1736780 MS.gene24222:CDS
ACAGTGATGAGGTCTTCGAG+TGG 0.727572 1.2:+1735907 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTTGATTTGAAATTA+GGG + chr1.2:1736707-1736726 MS.gene24222:intron 10.0%
!!! TTTTTATTTGATTTGAAATT+AGG + chr1.2:1736706-1736725 MS.gene24222:intron 10.0%
!! ATAGAATATATAGACTAATT+AGG - chr1.2:1736492-1736511 None:intergenic 15.0%
!!! TCTTTTTGAATTTTTTGATT+TGG + chr1.2:1736672-1736691 MS.gene24222:intron 15.0%
!! AAAATGAAAAGATATTACGA+GGG + chr1.2:1736339-1736358 MS.gene24222:intron 20.0%
!! TAAAATGAAAAGATATTACG+AGG + chr1.2:1736338-1736357 MS.gene24222:intron 20.0%
!! TCTATGAATCTATGATAAAT+AGG + chr1.2:1736463-1736482 MS.gene24222:intron 20.0%
!!! TAGTTTTTTGATATATAGCT+AGG + chr1.2:1736378-1736397 MS.gene24222:intron 20.0%
! TAGCTATATAGAAACAATTG+AGG + chr1.2:1736645-1736664 MS.gene24222:intron 25.0%
! TATAGTGAAGAATACTCAAA+TGG - chr1.2:1737015-1737034 None:intergenic 25.0%
! TGAAAAAATTGTTAGGTAAG+TGG + chr1.2:1736593-1736612 MS.gene24222:intron 25.0%
! TGAAGGATGAAAAAATTGTT+AGG + chr1.2:1736586-1736605 MS.gene24222:intron 25.0%
! TTTCTACATATATATACCTG+TGG - chr1.2:1736229-1736248 None:intergenic 25.0%
!!! ATTTGATTTGAAATTAGGGT+TGG + chr1.2:1736711-1736730 MS.gene24222:intron 25.0%
ATCCTTCAGAAGAAAAGAAA+GGG - chr1.2:1736574-1736593 None:intergenic 30.0%
TATATACCTGTGGTAGTAAT+AGG - chr1.2:1736219-1736238 None:intergenic 30.0%
TTGATAGAGTATGAAAGGAA+TGG - chr1.2:1736519-1736538 None:intergenic 30.0%
! AAGGGAATTTTGTATGATCA+AGG + chr1.2:1736862-1736881 MS.gene24222:CDS 30.0%
!! AAACTCATGTGAAAAGTACT+TGG + chr1.2:1736040-1736059 MS.gene24222:CDS 30.0%
!! AACTCATGTGAAAAGTACTT+GGG + chr1.2:1736041-1736060 MS.gene24222:CDS 30.0%
!! ATTGTTAACATTTGTTGTCG+TGG - chr1.2:1736992-1737011 None:intergenic 30.0%
!! CTAAGTTGATAGAGTATGAA+AGG - chr1.2:1736524-1736543 None:intergenic 30.0%
CATCCTTCAGAAGAAAAGAA+AGG - chr1.2:1736575-1736594 None:intergenic 35.0%
GAAAATCAAAATGATCCCTC+TGG + chr1.2:1736162-1736181 MS.gene24222:CDS 35.0%
TATCAAACTGCTGTGAACAT+AGG + chr1.2:1736826-1736845 MS.gene24222:CDS 35.0%
TTGAAATTAGGGTTGGAGTT+GGG + chr1.2:1736718-1736737 MS.gene24222:intron 35.0%
TTGTATGATCAAGGACTTGA+AGG + chr1.2:1736871-1736890 MS.gene24222:CDS 35.0%
! ATAGGAGGAAGAGTTTTCAA+GGG + chr1.2:1736844-1736863 MS.gene24222:CDS 35.0%
! CAAGTTCTACATCTAAGATG+TGG - chr1.2:1735994-1736013 None:intergenic 35.0%
! TTCCCTTTCTTTTCTTCTGA+AGG + chr1.2:1736569-1736588 MS.gene24222:intron 35.0%
! TTTGAAATTAGGGTTGGAGT+TGG + chr1.2:1736717-1736736 MS.gene24222:intron 35.0%
AGCTCCTCTTAATGCTTTCA+TGG + chr1.2:1737038-1737057 MS.gene24222:CDS 40.0%
GGAATGAACTGTCAAGATTG+TGG + chr1.2:1735946-1735965 MS.gene24222:CDS 40.0%
GTGGACAATCTTTCTTAGCT+TGG - chr1.2:1735975-1735994 None:intergenic 40.0%
GTGTGTAAAAGTGAGTGCAA+TGG + chr1.2:1736780-1736799 MS.gene24222:CDS 40.0%
! CATAGGAGGAAGAGTTTTCA+AGG + chr1.2:1736843-1736862 MS.gene24222:CDS 40.0%
!! AGTAATAGGTACTGGAGTAC+AGG - chr1.2:1736205-1736224 None:intergenic 40.0%
!! ATGAAAGCATTAAGAGGAGC+TGG - chr1.2:1737039-1737058 None:intergenic 40.0%
CAAACTGCTGTGAACATAGG+AGG + chr1.2:1736829-1736848 MS.gene24222:CDS 45.0%
CCAGTACCTATTACTACCAC+AGG + chr1.2:1736210-1736229 MS.gene24222:CDS 45.0%
CCTCTTAATGCTTTCATGGC+TGG + chr1.2:1737042-1737061 MS.gene24222:CDS 45.0%
CCTGTGGTAGTAATAGGTAC+TGG - chr1.2:1736213-1736232 None:intergenic 45.0%
GCTTAGTGATAGAGATCTCG+AGG + chr1.2:1736427-1736446 MS.gene24222:intron 45.0%
! GGAGTTGGGAAATTTTCCAC+CGG + chr1.2:1736732-1736751 MS.gene24222:CDS 45.0%
!! AGAACTTGTTGCAAGAGTCG+AGG + chr1.2:1736006-1736025 MS.gene24222:CDS 45.0%
!! CCAGCCATGAAAGCATTAAG+AGG - chr1.2:1737045-1737064 None:intergenic 45.0%
!! GAACTTGTTGCAAGAGTCGA+GGG + chr1.2:1736007-1736026 MS.gene24222:CDS 45.0%
ACTAGTCCAAATGCTGCTGC+TGG + chr1.2:1736901-1736920 MS.gene24222:CDS 50.0%
AGAGAACCAGAAGCTCCAGA+GGG - chr1.2:1736180-1736199 None:intergenic 50.0%
AGGTCTTCGAGTGGTGGTTT+AGG + chr1.2:1735916-1735935 MS.gene24222:CDS 50.0%
TAGAGAACCAGAAGCTCCAG+AGG - chr1.2:1736181-1736200 None:intergenic 50.0%
TCTTCGAGTGGTGGTTTAGG+TGG + chr1.2:1735919-1735938 MS.gene24222:CDS 50.0%
TTTACACACCTGAACACCGC+CGG - chr1.2:1736769-1736788 None:intergenic 50.0%
!! AATGATCCCTCTGGAGCTTC+TGG + chr1.2:1736171-1736190 MS.gene24222:CDS 50.0%
AGTCCAAATGCTGCTGCTGG+TGG + chr1.2:1736904-1736923 MS.gene24222:CDS 55.0%
TCCACCGGAGCTGAATTCAC+CGG + chr1.2:1736747-1736766 MS.gene24222:CDS 55.0%
TCGAGTGGTGGTTTAGGTGG+TGG + chr1.2:1735922-1735941 MS.gene24222:CDS 55.0%
TGAATTCACCGGCGGTGTTC+AGG + chr1.2:1736758-1736777 MS.gene24222:CDS 55.0%
TGAGTTGTTGCTGCCGTTCG+CGG - chr1.2:1736083-1736102 None:intergenic 55.0%
! AGTGGTGGTTTAGGTGGTGG+TGG + chr1.2:1735925-1735944 MS.gene24222:CDS 55.0%
ACCGCCGGTGAATTCAGCTC+CGG - chr1.2:1736754-1736773 None:intergenic 60.0%
ACCGGAGCTGAATTCACCGG+CGG + chr1.2:1736750-1736769 MS.gene24222:CDS 60.0%
CAGCTGCTAAACGCCGCGAA+CGG + chr1.2:1736067-1736086 MS.gene24222:CDS 60.0%
CCAAATGCTGCTGCTGGTGG+TGG + chr1.2:1736907-1736926 MS.gene24222:CDS 60.0%
CCACCACCAGCAGCAGCATT+TGG - chr1.2:1736910-1736929 None:intergenic 60.0%
CGTTCGCGGCGTTTAGCAGC+TGG - chr1.2:1736069-1736088 None:intergenic 65.0%
GCCGGTGAATTCAGCTCCGG+TGG - chr1.2:1736751-1736770 None:intergenic 65.0%
! GGTGGTGGCGAGGGTTCTTC+CGG + chr1.2:1736922-1736941 MS.gene24222:CDS 65.0%
! GGTTCTTCCGGTGGTGGCAG+CGG + chr1.2:1736934-1736953 MS.gene24222:CDS 65.0%
GGCGAGGGTTCTTCCGGTGG+TGG + chr1.2:1736928-1736947 MS.gene24222:CDS 70.0%
GGTGGCGAGGGTTCTTCCGG+TGG + chr1.2:1736925-1736944 MS.gene24222:CDS 70.0%
TTCGCCACCGCTGCCACCAC+CGG - chr1.2:1736944-1736963 None:intergenic 70.0%
! TCTTCCGGTGGTGGCAGCGG+TGG + chr1.2:1736937-1736956 MS.gene24222:CDS 70.0%
!! GCTGCTGCTGGTGGTGGCGA+GGG + chr1.2:1736913-1736932 MS.gene24222:CDS 70.0%
!! TGCTGCTGCTGGTGGTGGCG+AGG + chr1.2:1736912-1736931 MS.gene24222:CDS 70.0%
! GGTGGTGGCAGCGGTGGCGA+AGG + chr1.2:1736943-1736962 MS.gene24222:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 1735913 1737095 1735913 ID=MS.gene24222
chr1.2 mRNA 1735913 1737095 1735913 ID=MS.gene24222.t1;Parent=MS.gene24222
chr1.2 exon 1735913 1736231 1735913 ID=MS.gene24222.t1.exon1;Parent=MS.gene24222.t1
chr1.2 CDS 1735913 1736231 1735913 ID=cds.MS.gene24222.t1;Parent=MS.gene24222.t1
chr1.2 exon 1736728 1737095 1736728 ID=MS.gene24222.t1.exon2;Parent=MS.gene24222.t1
chr1.2 CDS 1736728 1737095 1736728 ID=cds.MS.gene24222.t1;Parent=MS.gene24222.t1
Gene Sequence

>MS.gene24222

ATGAGGTCTTCGAGTGGTGGTTTAGGTGGTGGTGGAATGAACTGTCAAGATTGTGGTAACCAAGCTAAGAAAGATTGTCCACATCTTAGATGTAGAACTTGTTGCAAGAGTCGAGGGTTTCAGTGTCAAACTCATGTGAAAAGTACTTGGGTTCCAGCTGCTAAACGCCGCGAACGGCAGCAACAACTCACGTCGTTGCAGCAACAAAATCAGCAGCAGCAACAACAGTTTCACTCAAGAAGACACAGAGAAAATCAAAATGATCCCTCTGGAGCTTCTGGTTCTCTAACCTGTACTCCAGTACCTATTACTACCACAGGTATATATATGTAGAAATATAAACTTTTGAACGATATACATCAACTTTCTTTGACTCACTTGTGTTTTTATTTCTTTACAGAAGAGTCGTTGAAAGAGAGAGTATATAAAATGAAAAGATATTACGAGGGTTTGAATTATAGTGTTTAGTTTTTTGATATATAGCTAGGTCAGTGACGAATTTTCAAACTATATAGCTTAGTGATAGAGATCTCGAGGAGAAACTATAGTTTCTATGAATCTATGATAAATAGGATACCTAATTAGTCTATATATTCTATATATCCATTCCTTTCATACTCTATCAACTTAGTTTTTTTCTTTTCTCTCTCTCTTTTTTCCCTTTCTTTTCTTCTGAAGGATGAAAAAATTGTTAGGTAAGTGGTTCTTTCTTTCTTTTAAATTTGAAAATGATAGCTATATAGAAACAATTGAGGTTTCTCTTTTTGAATTTTTTGATTTGGATTTAATTTTTTTTTTATTTGATTTGAAATTAGGGTTGGAGTTGGGAAATTTTCCACCGGAGCTGAATTCACCGGCGGTGTTCAGGTGTGTAAAAGTGAGTGCAATGGATGCACAAGATGAACGTTATGCTTATCAAACTGCTGTGAACATAGGAGGAAGAGTTTTCAAGGGAATTTTGTATGATCAAGGACTTGAAGGTAGCTACACTAGTCCAAATGCTGCTGCTGGTGGTGGCGAGGGTTCTTCCGGTGGTGGCAGCGGTGGCGAAGGAAATCAACAAAATCTCATAACAACCACGACAACAAATGTTAACAATCCATTTGAGTATTCTTCACTATATCCAGCTCCTCTTAATGCTTTCATGGCTGGTACGCAATTCTTCCCACCTCCAAGATCCTAA
Protein sequence

>MS.gene24222.t1

MRSSSGGLGGGGMNCQDCGNQAKKDCPHLRCRTCCKSRGFQCQTHVKSTWVPAAKRRERQQQLTSLQQQNQQQQQQFHSRRHRENQNDPSGASGSLTCTPVPITTTGLELGNFPPELNSPAVFRCVKVSAMDAQDERYAYQTAVNIGGRVFKGILYDQGLEGSYTSPNAAAGGGEGSSGGGSGGEGNQQNLITTTTTNVNNPFEYSSLYPAPLNAFMAGTQFFPPPRS