AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene056417

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene056417.t1 MTR_2g076780 55.204 221 82 4 23 231 21 236 1.37e-74 226
MS.gene056417.t1 MTR_8g069080 53.636 220 84 5 24 231 54 267 1.65e-69 214
MS.gene056417.t1 MTR_8g069380 87.255 102 6 1 131 232 21 115 1.83e-57 178
MS.gene056417.t1 MTR_5g032600 46.330 218 76 7 36 232 75 272 1.74e-47 158
MS.gene056417.t1 MTR_3g100650 45.972 211 85 6 37 232 78 274 1.26e-46 155
MS.gene056417.t1 MTR_5g065440 38.039 255 121 5 5 232 24 268 2.18e-46 155
MS.gene056417.t1 MTR_1g077020 38.679 212 81 4 37 231 7 186 7.70e-43 143
MS.gene056417.t1 MTR_5g020510 36.893 206 108 3 39 231 99 295 8.88e-43 146
MS.gene056417.t1 MTR_6g012280 39.423 208 97 5 39 231 91 284 1.20e-37 134
MS.gene056417.t1 MTR_8g442330 48.750 160 47 5 48 206 14 139 1.30e-37 128
MS.gene056417.t1 MTR_7g010300 36.667 210 105 5 37 231 86 282 2.69e-36 130
MS.gene056417.t1 MTR_8g051480 57.895 114 37 4 123 231 21 128 1.58e-33 117
MS.gene056417.t1 MTR_6g073013 29.319 191 84 3 39 227 19 160 4.51e-28 105
MS.gene056417.t1 MTR_4g134580 65.079 63 22 0 169 231 284 346 1.79e-22 94.4
MS.gene056417.t1 MTR_4g134580 45.652 92 47 1 7 95 78 169 2.34e-19 85.9
MS.gene056417.t1 MTR_8g467340 53.968 63 29 0 169 231 271 333 1.04e-16 78.6
MS.gene056417.t1 MTR_8g467340 52.542 59 26 1 32 88 57 115 2.04e-14 72.0
MS.gene056417.t1 MTR_3g039810 57.692 52 22 0 37 88 18 69 2.25e-16 72.0
MS.gene056417.t1 MTR_8g032100 68.182 44 14 0 176 219 125 168 5.00e-13 65.5
MS.gene056417.t1 MTR_6g012220 53.125 64 26 2 37 100 19 78 7.94e-13 62.4
MS.gene056417.t1 MTR_8g032050 65.909 44 15 0 176 219 125 168 2.05e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene056417.t1 AT4G24660 41.709 199 90 3 36 232 46 220 3.23e-48 158
MS.gene056417.t1 AT4G24660 40.513 195 90 3 36 228 46 216 5.36e-45 150
MS.gene056417.t1 AT2G02540 36.986 219 95 5 37 231 85 284 5.84e-43 147
MS.gene056417.t1 AT2G02540 36.986 219 95 5 37 231 85 284 5.84e-43 147
MS.gene056417.t1 AT5G65410 40.609 197 103 3 36 232 72 254 2.01e-42 145
MS.gene056417.t1 AT1G14440 38.537 205 104 4 37 231 88 280 3.04e-40 140
MS.gene056417.t1 AT1G14440 38.537 205 104 4 37 231 88 280 3.04e-40 140
MS.gene056417.t1 AT5G15210 39.437 213 103 6 22 225 40 235 5.24e-40 139
MS.gene056417.t1 AT2G18350 38.889 198 103 4 36 231 79 260 2.96e-38 134
MS.gene056417.t1 AT1G69600 35.217 230 120 7 11 228 3 215 2.49e-36 128
MS.gene056417.t1 AT3G50890 37.374 198 103 6 39 230 60 242 1.42e-35 126
MS.gene056417.t1 AT3G28920 37.143 210 108 5 36 228 49 251 1.30e-32 120
MS.gene056417.t1 AT5G60480 36.683 199 98 6 32 226 30 204 3.83e-29 109
MS.gene056417.t1 AT5G42780 32.323 198 105 5 38 228 63 238 3.58e-22 91.7
MS.gene056417.t1 AT1G75240 59.701 67 27 0 166 232 237 303 1.29e-21 91.3
MS.gene056417.t1 AT1G74660 64.151 53 19 0 37 89 37 89 1.26e-19 80.9
MS.gene056417.t1 AT1G74660 64.151 53 19 0 37 89 37 89 1.94e-19 80.5
MS.gene056417.t1 AT5G39760 53.125 64 30 0 168 231 199 262 1.55e-17 80.5
MS.gene056417.t1 AT3G28917 56.604 53 22 1 37 88 31 83 4.88e-16 71.6
MS.gene056417.t1 AT1G18835 56.604 53 20 1 37 89 24 73 1.95e-14 67.0

Find 45 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAATCTAAGAAGAGATTC+AGG 0.367997 8.2:-33734581 MS.gene056417:CDS
GGTGGTATTGGTGGTGGTGG+TGG 0.379831 8.2:-33734618 MS.gene056417:CDS
CAACAATAGTTTCCTTCCTA+TGG 0.387746 8.2:+33734826 None:intergenic
TTCTGAAGCAAATAGTTTCC+AGG 0.399589 8.2:-33734991 MS.gene056417:CDS
CAAAGATAGAGGTGGAGAAT+TGG 0.404534 8.2:+33734713 None:intergenic
CCACCTCTATCTTTGTATGA+AGG 0.411052 8.2:-33734705 MS.gene056417:CDS
CTAAGAAGAGATTCAGGTCT+AGG 0.422419 8.2:-33734575 MS.gene056417:CDS
CCAATACCACCAATATTGAT+AGG 0.424085 8.2:+33734630 None:intergenic
CCTATCAATATTGGTGGTAT+TGG 0.426127 8.2:-33734630 MS.gene056417:CDS
AAGAACCATGCTTCCAGCAT+TGG 0.428212 8.2:-33734948 MS.gene056417:CDS
CATCACTTCGTTGACTTTGG+TGG 0.429801 8.2:+33735067 None:intergenic
CACCTCTATCTTTGTATGAA+GGG 0.435863 8.2:-33734704 MS.gene056417:CDS
ATCAATATTGGTGGTATTGG+TGG 0.443160 8.2:-33734627 MS.gene056417:CDS
GTTGTTGAGCCTATCAATAT+TGG 0.447727 8.2:-33734639 MS.gene056417:CDS
AATATTGGTGGTATTGGTGG+TGG 0.452356 8.2:-33734624 MS.gene056417:CDS
ATTGGAGGTTATGCCGTTGA+TGG 0.455927 8.2:-33734930 MS.gene056417:CDS
ACTCATCACTTCGTTGACTT+TGG 0.456189 8.2:+33735064 None:intergenic
CTTGGTGCTCCAGTCGTAGA+AGG 0.459839 8.2:+33734744 None:intergenic
ATTGGTGGTATTGGTGGTGG+TGG 0.462716 8.2:-33734621 MS.gene056417:CDS
CGAGATAGGAGTCATATCTC+TGG 0.469386 8.2:+33734800 None:intergenic
CATGGATCACTAAACGAGAT+AGG 0.482608 8.2:+33734786 None:intergenic
ACCTCTATCTTTGTATGAAG+GGG 0.485817 8.2:-33734703 MS.gene056417:CDS
GGAGAATTGGTTGTGCCCCT+TGG 0.489769 8.2:+33734726 None:intergenic
AACGGCATAACCTCCAATGC+TGG 0.490028 8.2:+33734935 None:intergenic
AACATTCCTTAAAATTTACC+TGG 0.498095 8.2:+33734973 None:intergenic
AGGTTGGAAGATTCCGAAAA+GGG 0.512733 8.2:-33734505 MS.gene056417:CDS
CATAATAACAAGCATACCCT+TGG 0.523934 8.2:-33734414 MS.gene056417:CDS
TAGAAGGAGTAACTGCTTGA+GGG 0.527054 8.2:+33734760 None:intergenic
AACCATGCTTCCAGCATTGG+AGG 0.529576 8.2:-33734945 MS.gene056417:CDS
GAGGTTGGAAGATTCCGAAA+AGG 0.538054 8.2:-33734506 MS.gene056417:CDS
AACCTCCAATGCTGGAAGCA+TGG 0.548110 8.2:+33734943 None:intergenic
TTCTACGACTGGAGCACCAA+GGG 0.559075 8.2:-33734742 MS.gene056417:CDS
GCAGTTACTCCTTCTACGAC+TGG 0.562065 8.2:-33734753 MS.gene056417:CDS
GTAGAAGGAGTAACTGCTTG+AGG 0.569241 8.2:+33734759 None:intergenic
AATGTACCTTCATCTCCAGC+AGG 0.574198 8.2:+33734891 None:intergenic
GTAACTGCTTGAGGGAGGCA+TGG 0.581241 8.2:+33734768 None:intergenic
GTTGAGCCTATCAATATTGG+TGG 0.591055 8.2:-33734636 MS.gene056417:CDS
CAGCAAAGAAAAGATGGTGA+TGG 0.612071 8.2:-33735090 None:intergenic
AAACTCACAACAACCATCAA+CGG 0.619715 8.2:+33734917 None:intergenic
AAGGGATGAGAATGTTGTCA+AGG 0.636812 8.2:-33734487 MS.gene056417:CDS
CTTCTACGACTGGAGCACCA+AGG 0.637408 8.2:-33734743 MS.gene056417:CDS
CCTTCATACAAAGATAGAGG+TGG 0.648904 8.2:+33734705 None:intergenic
CCTCTATCTTTGTATGAAGG+GGG 0.651375 8.2:-33734702 MS.gene056417:CDS
AAGGAGTAACTGCTTGAGGG+AGG 0.663240 8.2:+33734763 None:intergenic
TCTACGACTGGAGCACCAAG+GGG 0.703811 8.2:-33734741 MS.gene056417:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACATTAGAGTTTTTTAAATG+TGG - chr8.2:33734605-33734624 MS.gene056417:CDS 20.0%
! AACATTCCTTAAAATTTACC+TGG + chr8.2:33734508-33734527 None:intergenic 25.0%
! ATTGTCATAAAAACTTCCAT+AGG - chr8.2:33734636-33734655 MS.gene056417:CDS 25.0%
!! TAGTTTCCAGGTAAATTTTA+AGG - chr8.2:33734499-33734518 MS.gene056417:CDS 25.0%
TCATAAAAACTTCCATAGGA+AGG - chr8.2:33734640-33734659 MS.gene056417:CDS 30.0%
! AAAAGATGCTTGATTTTGCT+TGG - chr8.2:33734945-33734964 MS.gene056417:CDS 30.0%
! AAAGATGCTTGATTTTGCTT+GGG - chr8.2:33734946-33734965 MS.gene056417:CDS 30.0%
!! AAGGAGTTTTGTAATGAGAT+TGG - chr8.2:33735010-33735029 MS.gene056417:CDS 30.0%
!! AGGAGTTTTGTAATGAGATT+GGG - chr8.2:33735011-33735030 MS.gene056417:CDS 30.0%
!!! AGCTTCAAGTTTTTAAGGTT+TGG - chr8.2:33735038-33735057 MS.gene056417:CDS 30.0%
!!! GCTTCAAGTTTTTAAGGTTT+GGG - chr8.2:33735039-33735058 MS.gene056417:CDS 30.0%
AAACTCACAACAACCATCAA+CGG + chr8.2:33734564-33734583 None:intergenic 35.0%
ACCTCTATCTTTGTATGAAG+GGG - chr8.2:33734775-33734794 MS.gene056417:CDS 35.0%
CAACAATAGTTTCCTTCCTA+TGG + chr8.2:33734655-33734674 None:intergenic 35.0%
CACAATCTAAGAAGAGATTC+AGG - chr8.2:33734897-33734916 MS.gene056417:CDS 35.0%
CACCTCTATCTTTGTATGAA+GGG - chr8.2:33734774-33734793 MS.gene056417:CDS 35.0%
CATAATAACAAGCATACCCT+TGG - chr8.2:33735064-33735083 MS.gene056417:CDS 35.0%
CCAATACCACCAATATTGAT+AGG + chr8.2:33734851-33734870 None:intergenic 35.0%
GTTGTTGAGCCTATCAATAT+TGG - chr8.2:33734839-33734858 MS.gene056417:CDS 35.0%
! ACAACATTCTCATCCCTTTT+CGG + chr8.2:33734989-33735008 None:intergenic 35.0%
! ATCAATATTGGTGGTATTGG+TGG - chr8.2:33734851-33734870 MS.gene056417:CDS 35.0%
! CCTATCAATATTGGTGGTAT+TGG - chr8.2:33734848-33734867 MS.gene056417:CDS 35.0%
!! GGAGTTTTGTAATGAGATTG+GGG - chr8.2:33735012-33735031 MS.gene056417:CDS 35.0%
!! GGTGAAGCTTCAAGTTTTTA+AGG - chr8.2:33735033-33735052 MS.gene056417:CDS 35.0%
!! TTCTGAAGCAAATAGTTTCC+AGG - chr8.2:33734487-33734506 MS.gene056417:CDS 35.0%
AAGGGATGAGAATGTTGTCA+AGG - chr8.2:33734991-33735010 MS.gene056417:CDS 40.0%
AGGTTGGAAGATTCCGAAAA+GGG - chr8.2:33734973-33734992 MS.gene056417:CDS 40.0%
CAAAGATAGAGGTGGAGAAT+TGG + chr8.2:33734768-33734787 None:intergenic 40.0%
CATGGATCACTAAACGAGAT+AGG + chr8.2:33734695-33734714 None:intergenic 40.0%
CCACCTCTATCTTTGTATGA+AGG - chr8.2:33734773-33734792 MS.gene056417:CDS 40.0%
CCTCTATCTTTGTATGAAGG+GGG - chr8.2:33734776-33734795 MS.gene056417:CDS 40.0%
CCTTCATACAAAGATAGAGG+TGG + chr8.2:33734776-33734795 None:intergenic 40.0%
CTAAGAAGAGATTCAGGTCT+AGG - chr8.2:33734903-33734922 MS.gene056417:CDS 40.0%
GTTGAGCCTATCAATATTGG+TGG - chr8.2:33734842-33734861 MS.gene056417:CDS 40.0%
TAGAAGGAGTAACTGCTTGA+GGG + chr8.2:33734721-33734740 None:intergenic 40.0%
! ATGAAGGGGGCTATATTTTG+AGG - chr8.2:33734789-33734808 MS.gene056417:CDS 40.0%
! TGTTGTGAGTTTTTACCTGC+TGG - chr8.2:33734572-33734591 MS.gene056417:CDS 40.0%
! TTTTTACCTGCTGGAGATGA+AGG - chr8.2:33734581-33734600 MS.gene056417:CDS 40.0%
!! AATATTGGTGGTATTGGTGG+TGG - chr8.2:33734854-33734873 MS.gene056417:CDS 40.0%
!! ACTCATCACTTCGTTGACTT+TGG + chr8.2:33734417-33734436 None:intergenic 40.0%
!! TGAAGGGGGCTATATTTTGA+GGG - chr8.2:33734790-33734809 MS.gene056417:CDS 40.0%
AAGAACCATGCTTCCAGCAT+TGG - chr8.2:33734530-33734549 MS.gene056417:CDS 45.0%
AATGTACCTTCATCTCCAGC+AGG + chr8.2:33734590-33734609 None:intergenic 45.0%
ATTGGAGGTTATGCCGTTGA+TGG - chr8.2:33734548-33734567 MS.gene056417:CDS 45.0%
CCCCCTTCATACAAAGATAG+AGG + chr8.2:33734779-33734798 None:intergenic 45.0%
CGAGATAGGAGTCATATCTC+TGG + chr8.2:33734681-33734700 None:intergenic 45.0%
GAGGTTGGAAGATTCCGAAA+AGG - chr8.2:33734972-33734991 MS.gene056417:CDS 45.0%
GTAGAAGGAGTAACTGCTTG+AGG + chr8.2:33734722-33734741 None:intergenic 45.0%
!! CATCACTTCGTTGACTTTGG+TGG + chr8.2:33734414-33734433 None:intergenic 45.0%
AACCTCCAATGCTGGAAGCA+TGG + chr8.2:33734538-33734557 None:intergenic 50.0%
AACGGCATAACCTCCAATGC+TGG + chr8.2:33734546-33734565 None:intergenic 50.0%
AAGGAGTAACTGCTTGAGGG+AGG + chr8.2:33734718-33734737 None:intergenic 50.0%
GCAGTTACTCCTTCTACGAC+TGG - chr8.2:33734725-33734744 MS.gene056417:CDS 50.0%
! AACCATGCTTCCAGCATTGG+AGG - chr8.2:33734533-33734552 MS.gene056417:CDS 50.0%
! ATTTTGCTTGGGCACGAGGT+TGG - chr8.2:33734957-33734976 MS.gene056417:CDS 50.0%
! CTTGATTTTGCTTGGGCACG+AGG - chr8.2:33734953-33734972 MS.gene056417:CDS 50.0%
! TTCTACGACTGGAGCACCAA+GGG - chr8.2:33734736-33734755 MS.gene056417:CDS 50.0%
!! AGGGGGCTATATTTTGAGGG+AGG - chr8.2:33734793-33734812 MS.gene056417:CDS 50.0%
!! ATTGGTGGTATTGGTGGTGG+TGG - chr8.2:33734857-33734876 MS.gene056417:CDS 50.0%
GGAGAATTGGTTGTGCCCCT+TGG + chr8.2:33734755-33734774 None:intergenic 55.0%
GTAACTGCTTGAGGGAGGCA+TGG + chr8.2:33734713-33734732 None:intergenic 55.0%
! CTTCTACGACTGGAGCACCA+AGG - chr8.2:33734735-33734754 MS.gene056417:CDS 55.0%
! TCTACGACTGGAGCACCAAG+GGG - chr8.2:33734737-33734756 MS.gene056417:CDS 55.0%
!! CTTGGTGCTCCAGTCGTAGA+AGG + chr8.2:33734737-33734756 None:intergenic 55.0%
!! GGTATTGGTGGTGGTGGTGG+TGG - chr8.2:33734863-33734882 MS.gene056417:CDS 60.0%
!! GGTGGTATTGGTGGTGGTGG+TGG - chr8.2:33734860-33734879 MS.gene056417:CDS 60.0%
!! GTGGTGGTGGTGGTGGAGAA+GGG - chr8.2:33734870-33734889 MS.gene056417:CDS 60.0%
!! GGTGGTGGTGGTGGTGGAGA+AGG - chr8.2:33734869-33734888 MS.gene056417:CDS 65.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 33734401 33735099 33734401 ID=MS.gene056417
chr8.2 mRNA 33734401 33735099 33734401 ID=MS.gene056417.t1;Parent=MS.gene056417
chr8.2 exon 33734401 33735099 33734401 ID=MS.gene056417.t1.exon1;Parent=MS.gene056417.t1
chr8.2 CDS 33734401 33735099 33734401 ID=cds.MS.gene056417.t1;Parent=MS.gene056417.t1
Gene Sequence

>MS.gene056417

ATGGTGATGGCCACCAAAGTCAACGAAGTGATGAGTAGCACATCACAAGAGAAAATATCAACTCGAGTAGAAGAATCTCATATGAATTCTGAAGCAAATAGTTTCCAGGTAAATTTTAAGGAATGTTTGAAGAACCATGCTTCCAGCATTGGAGGTTATGCCGTTGATGGTTGTTGTGAGTTTTTACCTGCTGGAGATGAAGGTACATTAGAGTTTTTTAAATGTGGTGCTTGTCATTGTCATAAAAACTTCCATAGGAAGGAAACTATTGTTGTTTCCAGAGATATGACTCCTATCTCGTTTAGTGATCCATGCCTCCCTCAAGCAGTTACTCCTTCTACGACTGGAGCACCAAGGGGCACAACCAATTCTCCACCTCTATCTTTGTATGAAGGGGGCTATATTTTGAGGGAGGATCTTGAACAAAATGTTCATCATGTTGTTGAGCCTATCAATATTGGTGGTATTGGTGGTGGTGGTGGTGGAGAAGGGTCATCACAATCTAAGAAGAGATTCAGGTCTAGGTTCACACATGAACAAAGAGAAAAGATGCTTGATTTTGCTTGGGCACGAGGTTGGAAGATTCCGAAAAGGGATGAGAATGTTGTCAAGGAGTTTTGTAATGAGATTGGGGTGAAGCTTCAAGTTTTTAAGGTTTGGGTTCATAATAACAAGCATACCCTTGGTAAAAAGCCCTAA
Protein sequence

>MS.gene056417.t1

MVMATKVNEVMSSTSQEKISTRVEESHMNSEANSFQVNFKECLKNHASSIGGYAVDGCCEFLPAGDEGTLEFFKCGACHCHKNFHRKETIVVSRDMTPISFSDPCLPQAVTPSTTGAPRGTTNSPPLSLYEGGYILREDLEQNVHHVVEPINIGGIGGGGGGEGSSQSKKRFRSRFTHEQREKMLDFAWARGWKIPKRDENVVKEFCNEIGVKLQVFKVWVHNNKHTLGKKP