AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38708

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38708.t1 MTR_3g101810 97.426 272 4 3 1 270 1 271 0.0 531
MS.gene38708.t1 MTR_5g017210 65.714 140 45 2 110 248 75 212 9.65e-47 156
MS.gene38708.t1 MTR_8g093500 75.824 91 22 0 144 234 87 177 7.91e-46 155
MS.gene38708.t1 MTR_2g100490 63.441 93 33 1 143 234 261 353 1.56e-27 109
MS.gene38708.t1 MTR_8g015450 55.769 104 42 1 143 242 296 399 3.28e-27 109
MS.gene38708.t1 MTR_7g069590 68.519 54 17 0 177 230 32 85 1.76e-21 88.2
MS.gene38708.t1 MTR_5g079500 62.500 56 21 0 178 233 225 280 1.55e-18 84.0
MS.gene38708.t1 MTR_1g018090 62.963 54 20 0 180 233 283 336 9.21e-18 82.4
MS.gene38708.t1 MTR_1g106460 50.746 67 33 0 167 233 234 300 2.11e-17 80.9
MS.gene38708.t1 MTR_1g106470 46.914 81 43 0 180 260 205 285 2.26e-17 80.1
MS.gene38708.t1 MTR_5g005110 61.111 54 21 0 180 233 233 286 4.23e-17 80.1
MS.gene38708.t1 MTR_3g103030 53.968 63 29 0 171 233 229 291 4.78e-16 77.0
MS.gene38708.t1 MTR_4g131160 54.545 66 29 1 178 242 203 268 6.95e-15 74.3
MS.gene38708.t1 MTR_4g131160 54.545 66 29 1 178 242 206 271 7.02e-15 74.3
MS.gene38708.t1 MTR_1g080890 46.250 80 42 1 164 242 186 265 1.17e-14 73.2
MS.gene38708.t1 MTR_1g106480 58.000 50 21 0 184 233 82 131 1.27e-13 67.4
MS.gene38708.t1 MTR_2g067000 48.684 76 32 1 166 234 145 220 3.00e-13 68.6
MS.gene38708.t1 MTR_1g060700 57.407 54 23 0 181 234 357 410 2.71e-12 66.6
MS.gene38708.t1 MTR_4g033295 56.140 57 24 1 181 236 128 184 7.40e-12 63.2
MS.gene38708.t1 MTR_1g052470 41.304 92 49 2 146 236 277 364 8.63e-12 65.1
MS.gene38708.t1 MTR_2g089070 51.852 54 26 0 181 234 146 199 1.57e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38708.t1 AT3G50330 60.000 165 55 3 99 252 37 201 3.02e-48 160
MS.gene38708.t1 AT5G67060 86.170 94 13 0 144 237 83 176 1.25e-45 153
MS.gene38708.t1 AT5G67060 86.170 94 13 0 144 237 95 188 1.83e-45 153
MS.gene38708.t1 AT3G21330 65.217 92 32 0 143 234 241 332 8.06e-37 134
MS.gene38708.t1 AT4G00120 68.539 89 28 0 146 234 87 175 8.93e-37 129
MS.gene38708.t1 AT5G09750 74.444 90 23 0 144 233 92 181 8.61e-34 122
MS.gene38708.t1 AT5G01305 67.797 59 19 0 172 230 38 96 3.43e-21 88.2
MS.gene38708.t1 AT5G43175 50.725 69 34 0 165 233 126 194 1.26e-18 82.4
MS.gene38708.t1 AT4G33880 64.815 54 19 0 180 233 275 328 1.72e-18 84.3
MS.gene38708.t1 AT5G37800 53.333 75 28 1 166 233 189 263 3.44e-18 82.8
MS.gene38708.t1 AT1G27740 52.941 68 32 0 166 233 162 229 4.12e-18 82.0
MS.gene38708.t1 AT1G66470 63.636 55 20 0 179 233 203 257 5.61e-18 82.0
MS.gene38708.t1 AT2G14760 62.963 54 20 0 180 233 246 299 1.82e-17 81.3
MS.gene38708.t1 AT4G30980 53.947 76 34 1 168 242 127 202 2.91e-16 77.4
MS.gene38708.t1 AT2G24260 53.086 81 30 3 169 242 28 107 3.42e-16 76.3
MS.gene38708.t1 AT4G30980 53.247 77 35 1 167 242 174 250 6.06e-16 77.0
MS.gene38708.t1 AT2G24260 50.000 84 35 2 166 242 127 210 8.38e-16 76.6
MS.gene38708.t1 AT5G58010 51.316 76 36 1 168 242 96 171 6.30e-15 73.6
MS.gene38708.t1 AT2G14760 50.746 67 20 1 180 233 246 312 3.77e-14 71.6

Find 54 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTGACGTTTCTTCTCTT+TGG 0.218574 3.3:+84294392 None:intergenic
ACAGTTGCTGGTTCAGGATT+AGG 0.247420 3.3:-84294167 MS.gene38708:CDS
GATTCTGGGTCTATGTAAAT+TGG 0.284997 3.3:+84294425 None:intergenic
CCGTTAGATGAAGAAAATTC+AGG 0.301231 3.3:+84294818 None:intergenic
GATCGTAATGTTGATCGTTA+TGG 0.304956 3.3:-84294113 MS.gene38708:CDS
GTTTGTTGTTGGAACATTAA+TGG 0.311513 3.3:+84294584 None:intergenic
AACAGGACAGTTGCTGGTTC+AGG 0.321831 3.3:-84294173 MS.gene38708:CDS
CAGTTGCTGGTTCAGGATTA+GGG 0.322129 3.3:-84294166 MS.gene38708:CDS
GAAGACCATGGTATTTGATT+AGG 0.333202 3.3:+84294686 None:intergenic
TAATGGTGTAGAGTTGTTAT+TGG 0.339297 3.3:+84294601 None:intergenic
AGAGATTGTGTTTGTGTTTG+TGG 0.340639 3.3:+84294628 None:intergenic
TCACTGCAGGAACGTGCTTC+AGG 0.355705 3.3:-84294206 MS.gene38708:CDS
CCGTCAGATCAACAATTCTA+TGG 0.368765 3.3:-84294764 MS.gene38708:CDS
TAAGGCTTAGGCAATGAAAC+AGG 0.373028 3.3:+84294140 None:intergenic
CTTCAGGAGCCAACAGTAAC+AGG 0.378388 3.3:-84294190 MS.gene38708:CDS
ATCGTAATGTTGATCGTTAT+GGG 0.398296 3.3:-84294112 MS.gene38708:CDS
ATGATGAAGATGACTTTAAC+TGG 0.403724 3.3:+84294888 None:intergenic
GCTCCGAATGCGAACCATTA+CGG 0.404632 3.3:-84294524 MS.gene38708:CDS
TTGACGTTTCTTCTCTTTGG+TGG 0.422338 3.3:+84294395 None:intergenic
AACGATCAACATTACGATCT+TGG 0.428866 3.3:+84294117 None:intergenic
CTCGAATTTGAAAACATTAG+CGG 0.440870 3.3:+84294557 None:intergenic
GACCATGGTATTTGATTAGG+AGG 0.444146 3.3:+84294689 None:intergenic
AACAGTAACAGGACAGTTGC+TGG 0.445444 3.3:-84294179 MS.gene38708:CDS
ATCGAGTTTCGTTTCTCTGA+TGG 0.446419 3.3:+84294491 None:intergenic
TTAGCGGTGTTGTTTGTTGT+TGG 0.484736 3.3:+84294573 None:intergenic
GTACCGTAATGGTTCGCATT+CGG 0.489297 3.3:+84294521 None:intergenic
CGTTAGATGAAGAAAATTCA+GGG 0.499125 3.3:+84294819 None:intergenic
AATAAGAATACTGCAAAGAA+TGG 0.517132 3.3:-84294312 MS.gene38708:CDS
TGTGTTTGTGGTGGATTGTG+AGG 0.519086 3.3:+84294640 None:intergenic
GGTACCAGGTGGAACTAAGA+TGG 0.521420 3.3:-84294291 MS.gene38708:CDS
GTGTTTGTGGTGGATTGTGA+GGG 0.523310 3.3:+84294641 None:intergenic
TGACGGTGGAAATTGATTGA+TGG 0.535291 3.3:+84294781 None:intergenic
GATTGTGTTTGTGTTTGTGG+TGG 0.537734 3.3:+84294631 None:intergenic
TTACGATCTTGGTAAGGCTT+AGG 0.545623 3.3:+84294128 None:intergenic
ATGGCGATGCAGTACCGTAA+TGG 0.554413 3.3:+84294510 None:intergenic
GATGGATACTGCATCAATGT+TGG 0.564818 3.3:-84294273 MS.gene38708:CDS
GAAACTCGATGGCGACGATG+AGG 0.573917 3.3:-84294478 MS.gene38708:CDS
TCAACATTACGATCTTGGTA+AGG 0.575828 3.3:+84294122 None:intergenic
GACACAACTTAAGTCACTGC+AGG 0.578655 3.3:-84294219 MS.gene38708:CDS
AGCAACTGTCCTGTTACTGT+TGG 0.580375 3.3:+84294181 None:intergenic
ACCATGGTATTTGATTAGGA+GGG 0.602997 3.3:+84294690 None:intergenic
AAACTCGATGGCGACGATGA+GGG 0.604342 3.3:-84294477 MS.gene38708:CDS
ATCAGAGAAACGAAACTCGA+TGG 0.615534 3.3:-84294489 MS.gene38708:CDS
GTCATCTTCATCATCATCAG+AGG 0.630073 3.3:-84294879 MS.gene38708:CDS
TGTCTAGCTGCTATACTCTG+AGG 0.634069 3.3:+84294359 None:intergenic
TTATCTATTAAATCTGCAAG+AGG 0.636966 3.3:+84294713 None:intergenic
GTATCCATCTTAGTTCCACC+TGG 0.642640 3.3:+84294287 None:intergenic
CCATAGAATTGTTGATCTGA+CGG 0.644487 3.3:+84294764 None:intergenic
AAGGCTTAGGCAATGAAACA+GGG 0.655130 3.3:+84294141 None:intergenic
ACCCTCCTAATCAAATACCA+TGG 0.671083 3.3:-84294691 MS.gene38708:CDS
ATACTGCAAAGAATGGTACC+AGG 0.680757 3.3:-84294305 MS.gene38708:CDS
CTGCAAAGAATGGTACCAGG+TGG 0.704915 3.3:-84294302 MS.gene38708:CDS
TAGAATTGTTGATCTGACGG+TGG 0.709109 3.3:+84294767 None:intergenic
AATGATGAAGATGAAGACCA+TGG 0.757666 3.3:+84294674 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATAAGAATACTGCAAAGAA+TGG - chr3.3:84294696-84294715 MS.gene38708:CDS 25.0%
! TTATCTATTAAATCTGCAAG+AGG + chr3.3:84294298-84294317 None:intergenic 25.0%
ATCGTAATGTTGATCGTTAT+GGG - chr3.3:84294896-84294915 MS.gene38708:CDS 30.0%
ATGATGAAGATGACTTTAAC+TGG + chr3.3:84294123-84294142 None:intergenic 30.0%
CGTTAGATGAAGAAAATTCA+GGG + chr3.3:84294192-84294211 None:intergenic 30.0%
CTCGAATTTGAAAACATTAG+CGG + chr3.3:84294454-84294473 None:intergenic 30.0%
TAATGGTGTAGAGTTGTTAT+TGG + chr3.3:84294410-84294429 None:intergenic 30.0%
! CCTGAATTTTCTTCATCTAA+CGG - chr3.3:84294190-84294209 MS.gene38708:CDS 30.0%
!! GTTTGTTGTTGGAACATTAA+TGG + chr3.3:84294427-84294446 None:intergenic 30.0%
AACGATCAACATTACGATCT+TGG + chr3.3:84294894-84294913 None:intergenic 35.0%
AATGATGAAGATGAAGACCA+TGG + chr3.3:84294337-84294356 None:intergenic 35.0%
ACCATGGTATTTGATTAGGA+GGG + chr3.3:84294321-84294340 None:intergenic 35.0%
AGAGATTGTGTTTGTGTTTG+TGG + chr3.3:84294383-84294402 None:intergenic 35.0%
ATCTTGACGTTTCTTCTCTT+TGG + chr3.3:84294619-84294638 None:intergenic 35.0%
CCATAGAATTGTTGATCTGA+CGG + chr3.3:84294247-84294266 None:intergenic 35.0%
CCGTTAGATGAAGAAAATTC+AGG + chr3.3:84294193-84294212 None:intergenic 35.0%
GAAGACCATGGTATTTGATT+AGG + chr3.3:84294325-84294344 None:intergenic 35.0%
GATCGTAATGTTGATCGTTA+TGG - chr3.3:84294895-84294914 MS.gene38708:CDS 35.0%
GATTCTGGGTCTATGTAAAT+TGG + chr3.3:84294586-84294605 None:intergenic 35.0%
TCAACATTACGATCTTGGTA+AGG + chr3.3:84294889-84294908 None:intergenic 35.0%
!!! TTGGTGGTTTTACTGATTCT+GGG + chr3.3:84294600-84294619 None:intergenic 35.0%
!!! TTTGGTGGTTTTACTGATTC+TGG + chr3.3:84294601-84294620 None:intergenic 35.0%
AAGGCTTAGGCAATGAAACA+GGG + chr3.3:84294870-84294889 None:intergenic 40.0%
ACCCTCCTAATCAAATACCA+TGG - chr3.3:84294317-84294336 MS.gene38708:CDS 40.0%
ATACTGCAAAGAATGGTACC+AGG - chr3.3:84294703-84294722 MS.gene38708:CDS 40.0%
ATCAGAGAAACGAAACTCGA+TGG - chr3.3:84294519-84294538 MS.gene38708:CDS 40.0%
ATCGAGTTTCGTTTCTCTGA+TGG + chr3.3:84294520-84294539 None:intergenic 40.0%
CCGTCAGATCAACAATTCTA+TGG - chr3.3:84294244-84294263 MS.gene38708:CDS 40.0%
GACCATGGTATTTGATTAGG+AGG + chr3.3:84294322-84294341 None:intergenic 40.0%
GATGGATACTGCATCAATGT+TGG - chr3.3:84294735-84294754 MS.gene38708:CDS 40.0%
GATTGTGTTTGTGTTTGTGG+TGG + chr3.3:84294380-84294399 None:intergenic 40.0%
GTCATCTTCATCATCATCAG+AGG - chr3.3:84294129-84294148 MS.gene38708:CDS 40.0%
TAAGGCTTAGGCAATGAAAC+AGG + chr3.3:84294871-84294890 None:intergenic 40.0%
TAGAATTGTTGATCTGACGG+TGG + chr3.3:84294244-84294263 None:intergenic 40.0%
TGACGGTGGAAATTGATTGA+TGG + chr3.3:84294230-84294249 None:intergenic 40.0%
TTACGATCTTGGTAAGGCTT+AGG + chr3.3:84294883-84294902 None:intergenic 40.0%
TTGACGTTTCTTCTCTTTGG+TGG + chr3.3:84294616-84294635 None:intergenic 40.0%
!! TTAGCGGTGTTGTTTGTTGT+TGG + chr3.3:84294438-84294457 None:intergenic 40.0%
AACAGTAACAGGACAGTTGC+TGG - chr3.3:84294829-84294848 MS.gene38708:CDS 45.0%
AGCAACTGTCCTGTTACTGT+TGG + chr3.3:84294830-84294849 None:intergenic 45.0%
GACACAACTTAAGTCACTGC+AGG - chr3.3:84294789-84294808 MS.gene38708:CDS 45.0%
GTACCGTAATGGTTCGCATT+CGG + chr3.3:84294490-84294509 None:intergenic 45.0%
GTATCCATCTTAGTTCCACC+TGG + chr3.3:84294724-84294743 None:intergenic 45.0%
TGTCTAGCTGCTATACTCTG+AGG + chr3.3:84294652-84294671 None:intergenic 45.0%
!! ACAGTTGCTGGTTCAGGATT+AGG - chr3.3:84294841-84294860 MS.gene38708:CDS 45.0%
!! CAGTTGCTGGTTCAGGATTA+GGG - chr3.3:84294842-84294861 MS.gene38708:CDS 45.0%
!! GTGTTTGTGGTGGATTGTGA+GGG + chr3.3:84294370-84294389 None:intergenic 45.0%
!! TGTGTTTGTGGTGGATTGTG+AGG + chr3.3:84294371-84294390 None:intergenic 45.0%
AAACTCGATGGCGACGATGA+GGG - chr3.3:84294531-84294550 MS.gene38708:CDS 50.0%
ATGGCGATGCAGTACCGTAA+TGG + chr3.3:84294501-84294520 None:intergenic 50.0%
CTGCAAAGAATGGTACCAGG+TGG - chr3.3:84294706-84294725 MS.gene38708:CDS 50.0%
CTTCAGGAGCCAACAGTAAC+AGG - chr3.3:84294818-84294837 MS.gene38708:CDS 50.0%
GCTCCGAATGCGAACCATTA+CGG - chr3.3:84294484-84294503 MS.gene38708:CDS 50.0%
GGTACCAGGTGGAACTAAGA+TGG - chr3.3:84294717-84294736 MS.gene38708:CDS 50.0%
!! AACAGGACAGTTGCTGGTTC+AGG - chr3.3:84294835-84294854 MS.gene38708:CDS 50.0%
GAAACTCGATGGCGACGATG+AGG - chr3.3:84294530-84294549 MS.gene38708:CDS 55.0%
TCACTGCAGGAACGTGCTTC+AGG - chr3.3:84294802-84294821 MS.gene38708:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 84294109 84294921 84294109 ID=MS.gene38708
chr3.3 mRNA 84294109 84294921 84294109 ID=MS.gene38708.t1;Parent=MS.gene38708
chr3.3 exon 84294109 84294921 84294109 ID=MS.gene38708.t1.exon1;Parent=MS.gene38708.t1
chr3.3 CDS 84294109 84294921 84294109 ID=cds.MS.gene38708.t1;Parent=MS.gene38708.t1
Gene Sequence

>MS.gene38708

ATGGACTGTAACCAGTTAAAGTCATCTTCATCATCATCAGAGGATCAAATTGACATGATGTTAATGATGATGATGCAACTCCCTGAATTTTCTTCATCTAACGGTAATAACAACAACACCATCAATCAATTTCCACCGTCAGATCAACAATTCTATGGCACTTCAAATGCTTCTAACAATACACGTCCTCTTGCAGATTTAATAGATAACCCTCCTAATCAAATACCATGGTCTTCATCTTCATCATTCACTCACTTACCCTCACAATCCACCACAAACACAAACACAATCTCTTTCACCAATAACAACTCTACACCATTAATGTTCCAACAACAAACAACACCGCTAATGTTTTCAAATTCGAGCAACGAGATTGCTCCGAATGCGAACCATTACGGTACTGCATCGCCATCAGAGAAACGAAACTCGATGGCGACGATGAGGGAGATGATATTCAGAATAGCAGCTATGCAACCAATTTACATAGACCCAGAATCAGTAAAACCACCAAAGAGAAGAAACGTCAAGATTTCAAAAGATCCTCAGAGTATAGCAGCTAGACACAGAAGAGAAAGAATAAGCGAGAAAATAAGAATACTGCAAAGAATGGTACCAGGTGGAACTAAGATGGATACTGCATCAATGTTGGATGAAGCTATTCATTATGTTAAGTTTCTCAAGACACAACTTAAGTCACTGCAGGAACGTGCTTCAGGAGCCAACAGTAACAGGACAGTTGCTGGTTCAGGATTAGGGTTCCCTGTTTCATTGCCTAAGCCTTACCAAGATCGTAATGTTGATCGTTATGGGTGA
Protein sequence

>MS.gene38708.t1

MDCNQLKSSSSSSEDQIDMMLMMMMQLPEFSSSNGNNNNTINQFPPSDQQFYGTSNASNNTRPLADLIDNPPNQIPWSSSSSFTHLPSQSTTNTNTISFTNNNSTPLMFQQQTTPLMFSNSSNEIAPNANHYGTASPSEKRNSMATMREMIFRIAAMQPIYIDPESVKPPKRRNVKISKDPQSIAARHRRERISEKIRILQRMVPGGTKMDTASMLDEAIHYVKFLKTQLKSLQERASGANSNRTVAGSGLGFPVSLPKPYQDRNVDRYG