AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015156

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015156.t1 MTR_5g017210 91.270 252 15 3 1 250 1 247 2.97e-139 391
MS.gene015156.t1 MTR_3g101810 54.067 209 78 7 25 215 40 248 2.02e-57 184
MS.gene015156.t1 MTR_8g093500 75.824 91 22 0 113 203 87 177 3.32e-46 155
MS.gene015156.t1 MTR_2g100490 56.489 131 49 3 83 206 227 356 6.53e-32 120
MS.gene015156.t1 MTR_8g015450 62.626 99 33 1 112 206 296 394 6.36e-29 113
MS.gene015156.t1 MTR_7g069590 70.690 58 17 0 146 203 32 89 2.97e-23 92.4
MS.gene015156.t1 MTR_5g079500 54.430 79 34 1 126 202 202 280 2.97e-20 88.2
MS.gene015156.t1 MTR_1g106460 55.224 67 30 0 136 202 234 300 7.21e-18 81.6
MS.gene015156.t1 MTR_1g018090 64.815 54 19 0 149 202 283 336 2.09e-17 80.9
MS.gene015156.t1 MTR_5g005110 64.815 54 19 0 149 202 233 286 3.11e-17 80.1
MS.gene015156.t1 MTR_1g106470 53.247 77 31 2 131 202 182 258 5.21e-17 79.0
MS.gene015156.t1 MTR_3g103030 57.143 63 27 0 140 202 229 291 1.74e-16 77.8
MS.gene015156.t1 MTR_4g131160 42.574 101 48 3 121 211 175 275 1.06e-14 73.2
MS.gene015156.t1 MTR_4g131160 42.574 101 48 3 121 211 172 272 1.10e-14 73.2
MS.gene015156.t1 MTR_1g080890 50.000 70 35 0 133 202 186 255 1.57e-14 72.4
MS.gene015156.t1 MTR_1g106480 66.667 45 15 0 158 202 87 131 6.30e-14 67.8
MS.gene015156.t1 MTR_2g067000 45.333 75 34 1 136 203 146 220 1.53e-12 66.2
MS.gene015156.t1 MTR_4g033295 52.308 65 30 1 141 204 119 183 3.15e-12 63.9
MS.gene015156.t1 MTR_4g033295 51.515 66 31 1 141 205 119 184 5.49e-12 63.2
MS.gene015156.t1 MTR_1g060700 55.556 54 24 0 150 203 357 410 6.36e-12 65.1
MS.gene015156.t1 MTR_2g089070 48.148 54 28 0 150 203 146 199 6.71e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015156.t1 AT5G67060 56.250 192 71 3 17 204 4 186 1.58e-50 166
MS.gene015156.t1 AT3G50330 57.000 200 57 6 14 204 4 183 1.30e-49 163
MS.gene015156.t1 AT5G67060 55.738 183 69 2 25 204 1 174 1.45e-47 157
MS.gene015156.t1 AT4G00120 65.625 96 30 1 115 207 87 182 6.00e-39 134
MS.gene015156.t1 AT3G21330 53.659 123 49 1 91 205 212 334 5.91e-38 136
MS.gene015156.t1 AT5G09750 76.667 90 21 0 113 202 92 181 4.01e-35 125
MS.gene015156.t1 AT5G01305 71.186 59 17 0 141 199 38 96 4.02e-22 90.1
MS.gene015156.t1 AT5G43175 52.174 69 33 0 134 202 126 194 4.40e-19 83.2
MS.gene015156.t1 AT4G33880 61.290 62 24 0 141 202 267 328 8.49e-19 84.7
MS.gene015156.t1 AT1G27740 46.067 89 42 2 135 217 162 250 2.12e-18 82.0
MS.gene015156.t1 AT5G37800 54.795 73 26 1 137 202 191 263 4.73e-18 82.0
MS.gene015156.t1 AT1G66470 65.455 55 19 0 148 202 203 257 6.82e-18 81.3
MS.gene015156.t1 AT2G14760 59.677 62 25 0 141 202 238 299 8.43e-18 81.6
MS.gene015156.t1 AT4G30980 39.130 115 69 1 88 202 79 192 8.84e-17 78.6
MS.gene015156.t1 AT4G30980 38.400 125 76 1 78 202 117 240 1.92e-16 78.2
MS.gene015156.t1 AT2G24260 51.351 74 30 1 135 202 24 97 1.97e-16 76.6
MS.gene015156.t1 AT2G24260 51.351 74 30 1 135 202 127 200 4.37e-16 77.0
MS.gene015156.t1 AT5G58010 53.030 66 31 0 137 202 96 161 1.19e-14 72.4
MS.gene015156.t1 AT2G14760 49.333 75 25 1 141 202 238 312 1.97e-14 72.0
MS.gene015156.t1 AT4G09180 44.444 81 44 1 123 202 167 247 4.17e-11 62.0

Find 58 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGTGGTTTAATGGTTTC+TGG 0.032783 5.1:-9466436 None:intergenic
CTTTCTCTTTGGTGGTTTAA+TGG 0.129321 5.1:-9466443 None:intergenic
ACAAACAATGATTTCCCTTA+TGG 0.235794 5.1:+9466184 MS.gene015156:CDS
ATCTTCACATTCTTTCTCTT+TGG 0.246196 5.1:-9466454 None:intergenic
AATTATTCTTCTTTGCTTAG+AGG 0.258079 5.1:+9466715 MS.gene015156:CDS
GAGATTGAGAGTGTTGTTAT+TGG 0.283226 5.1:-9466155 None:intergenic
TTATTGGTGTTGCTATAAAA+AGG 0.298991 5.1:-9466139 None:intergenic
TTGGTGGTTTAATGGTTTCT+GGG 0.314323 5.1:-9466435 None:intergenic
AAAGAATCAGTGAACGAATA+AGG 0.317487 5.1:+9466518 MS.gene015156:CDS
TGCCATTGAATTCTTCTTCT+CGG 0.319338 5.1:-9466359 None:intergenic
TGTCTTGCTGCTACACTTTG+TGG 0.337683 5.1:-9466487 None:intergenic
TTCACATTCTTTCTCTTTGG+TGG 0.352271 5.1:-9466451 None:intergenic
TTCAAACGTTGGAACAAGTT+GGG 0.366857 5.1:+9466635 MS.gene015156:CDS
TGAAGACATACTGAAAACTT+TGG 0.382012 5.1:+9466045 MS.gene015156:CDS
GTTTCTGGGTCTATGTTAAT+CGG 0.384832 5.1:-9466421 None:intergenic
TGATGGGATTTGAACTCTGT+TGG 0.387374 5.1:-9466305 None:intergenic
GCCATTGAATTCTTCTTCTC+GGG 0.399282 5.1:-9466358 None:intergenic
ACTAAGCATTTGTTTGGAAG+TGG 0.402015 5.1:-9466767 None:intergenic
AATAGACCTTTGAATGTTGT+TGG 0.403761 5.1:+9466661 MS.gene015156:CDS
GTTACATTTGAGTTTCCATA+AGG 0.409196 5.1:-9466199 None:intergenic
TTGAATGTTGTTGGGTTTCA+CGG 0.412650 5.1:+9466670 MS.gene015156:CDS
TGGAAGTGGGACCCACCATT+TGG 0.414540 5.1:-9466753 None:intergenic
GATGGGATTTGAACTCTGTT+GGG 0.418955 5.1:-9466304 None:intergenic
GTGTCAACTAAGCATTTGTT+TGG 0.421668 5.1:-9466773 None:intergenic
GAAGACATACTGAAAACTTT+GGG 0.432163 5.1:+9466046 MS.gene015156:CDS
TTCATCACCTTGCCAAATGG+TGG 0.447650 5.1:+9466741 MS.gene015156:CDS
ATAGACCTTTGAATGTTGTT+GGG 0.458742 5.1:+9466662 MS.gene015156:CDS
TGAATTCTTCTTCTCGGGAT+AGG 0.459318 5.1:-9466353 None:intergenic
AGCGACGGCGGTGGTGTCAT+TGG 0.462107 5.1:-9466277 None:intergenic
ATTCAAACGTTGGAACAAGT+TGG 0.463361 5.1:+9466634 MS.gene015156:CDS
ATAGGAGAATGAAGAATTGT+TGG 0.474836 5.1:-9466335 None:intergenic
TTACATTTGAGTTTCCATAA+GGG 0.484501 5.1:-9466198 None:intergenic
GATGACAATGATGATGCAAA+TGG 0.498844 5.1:+9466093 MS.gene015156:CDS
AATTGTTGGTTCTTCCTGAT+GGG 0.499420 5.1:-9466321 None:intergenic
GAATTGTTGGTTCTTCCTGA+TGG 0.503297 5.1:-9466322 None:intergenic
TTGTTCATCACCTTGCCAAA+TGG 0.505893 5.1:+9466738 MS.gene015156:CDS
AACAGAGTTCAAATCCCATC+AGG 0.513806 5.1:+9466307 MS.gene015156:CDS
GAAGAAACAAATTCAAACGT+TGG 0.519580 5.1:+9466624 MS.gene015156:CDS
CTAAGCATTTGTTTGGAAGT+GGG 0.548242 5.1:-9466766 None:intergenic
TTGGGTTGAAGCGACGGCGG+TGG 0.553364 5.1:-9466286 None:intergenic
TCATCACCTTGCCAAATGGT+GGG 0.555921 5.1:+9466742 MS.gene015156:CDS
TGAAACCCAACAACATTCAA+AGG 0.562813 5.1:-9466667 None:intergenic
TCAAACGTTGGAACAAGTTG+GGG 0.565356 5.1:+9466636 MS.gene015156:CDS
ACTCTGTTGGGTTGAAGCGA+CGG 0.575367 5.1:-9466292 None:intergenic
GAGAGAGATGATATTTCGAA+TGG 0.580908 5.1:+9466387 MS.gene015156:CDS
GGTGTCATTGGTTGTTGAAG+AGG 0.589982 5.1:-9466265 None:intergenic
AAAGAATGTGAAGATTTCAA+AGG 0.590303 5.1:+9466462 MS.gene015156:CDS
TGAAGAGGATAAGACAATGG+TGG 0.592428 5.1:-9466250 None:intergenic
TCCCGAGAAGAAGAATTCAA+TGG 0.593246 5.1:+9466357 MS.gene015156:CDS
TGTTGTTGGGTTTCACGGAG+TGG 0.605278 5.1:+9466675 MS.gene015156:CDS
AGAGATGATATTTCGAATGG+CGG 0.620797 5.1:+9466390 MS.gene015156:CDS
AATGGTGGATTGATCAATGA+AGG 0.629442 5.1:-9466235 None:intergenic
GTGGGACCCACCATTTGGCA+AGG 0.634945 5.1:-9466748 None:intergenic
GGGAAATGTTGAAAGCAACA+TGG 0.641963 5.1:+9466066 MS.gene015156:CDS
CTGTTGGGTTGAAGCGACGG+CGG 0.671897 5.1:-9466289 None:intergenic
ATATTACAAAGATTAGTACC+TGG 0.683168 5.1:+9466541 MS.gene015156:CDS
TTACAAAGATTAGTACCTGG+TGG 0.689802 5.1:+9466544 MS.gene015156:CDS
TGTTGAAGAGGATAAGACAA+TGG 0.700529 5.1:-9466253 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAAAGGTTCATATGAATCA+GGG - chr5.1:9466126-9466145 None:intergenic 25.0%
! AAAGAATGTGAAGATTTCAA+AGG + chr5.1:9466462-9466481 MS.gene015156:CDS 25.0%
! AATTATTCTTCTTTGCTTAG+AGG + chr5.1:9466715-9466734 MS.gene015156:CDS 25.0%
! ATATTACAAAGATTAGTACC+TGG + chr5.1:9466541-9466560 MS.gene015156:CDS 25.0%
! TAAAAAGGTTCATATGAATC+AGG - chr5.1:9466127-9466146 None:intergenic 25.0%
!! TTACATTTGAGTTTCCATAA+GGG - chr5.1:9466201-9466220 None:intergenic 25.0%
!!! TTATTGGTGTTGCTATAAAA+AGG - chr5.1:9466142-9466161 None:intergenic 25.0%
AAAGAATCAGTGAACGAATA+AGG + chr5.1:9466518-9466537 MS.gene015156:CDS 30.0%
AATAGACCTTTGAATGTTGT+TGG + chr5.1:9466661-9466680 MS.gene015156:CDS 30.0%
ACAAACAATGATTTCCCTTA+TGG + chr5.1:9466184-9466203 MS.gene015156:CDS 30.0%
ATAGACCTTTGAATGTTGTT+GGG + chr5.1:9466662-9466681 MS.gene015156:CDS 30.0%
ATAGGAGAATGAAGAATTGT+TGG - chr5.1:9466338-9466357 None:intergenic 30.0%
ATCTTCACATTCTTTCTCTT+TGG - chr5.1:9466457-9466476 None:intergenic 30.0%
GAAGAAACAAATTCAAACGT+TGG + chr5.1:9466624-9466643 MS.gene015156:CDS 30.0%
GAAGACATACTGAAAACTTT+GGG + chr5.1:9466046-9466065 MS.gene015156:CDS 30.0%
TGAAGACATACTGAAAACTT+TGG + chr5.1:9466045-9466064 MS.gene015156:CDS 30.0%
! GTTACATTTGAGTTTCCATA+AGG - chr5.1:9466202-9466221 None:intergenic 30.0%
ACTAAGCATTTGTTTGGAAG+TGG - chr5.1:9466770-9466789 None:intergenic 35.0%
AGAGATGATATTTCGAATGG+CGG + chr5.1:9466390-9466409 MS.gene015156:CDS 35.0%
ATTCAAACGTTGGAACAAGT+TGG + chr5.1:9466634-9466653 MS.gene015156:CDS 35.0%
CTAAGCATTTGTTTGGAAGT+GGG - chr5.1:9466769-9466788 None:intergenic 35.0%
GAGAGAGATGATATTTCGAA+TGG + chr5.1:9466387-9466406 MS.gene015156:CDS 35.0%
TGAAACCCAACAACATTCAA+AGG - chr5.1:9466670-9466689 None:intergenic 35.0%
TGCCATTGAATTCTTCTTCT+CGG - chr5.1:9466362-9466381 None:intergenic 35.0%
TGTTGAAGAGGATAAGACAA+TGG - chr5.1:9466256-9466275 None:intergenic 35.0%
TTACAAAGATTAGTACCTGG+TGG + chr5.1:9466544-9466563 MS.gene015156:CDS 35.0%
TTCAAACGTTGGAACAAGTT+GGG + chr5.1:9466635-9466654 MS.gene015156:CDS 35.0%
TTCACATTCTTTCTCTTTGG+TGG - chr5.1:9466454-9466473 None:intergenic 35.0%
TTGAATGTTGTTGGGTTTCA+CGG + chr5.1:9466670-9466689 MS.gene015156:CDS 35.0%
! CTTTCTCTTTGGTGGTTTAA+TGG - chr5.1:9466446-9466465 None:intergenic 35.0%
! GATGACAATGATGATGCAAA+TGG + chr5.1:9466093-9466112 MS.gene015156:CDS 35.0%
! GTTTCTGGGTCTATGTTAAT+CGG - chr5.1:9466424-9466443 None:intergenic 35.0%
! TTGGTGGTTTAATGGTTTCT+GGG - chr5.1:9466438-9466457 None:intergenic 35.0%
! TTTGGTGGTTTAATGGTTTC+TGG - chr5.1:9466439-9466458 None:intergenic 35.0%
!! AATGGTGGATTGATCAATGA+AGG - chr5.1:9466238-9466257 None:intergenic 35.0%
!! AATTGTTGGTTCTTCCTGAT+GGG - chr5.1:9466324-9466343 None:intergenic 35.0%
!! GAGATTGAGAGTGTTGTTAT+TGG - chr5.1:9466158-9466177 None:intergenic 35.0%
AACAGAGTTCAAATCCCATC+AGG + chr5.1:9466307-9466326 MS.gene015156:CDS 40.0%
AGTACCTGGTGGAACAAAAA+TGG + chr5.1:9466555-9466574 MS.gene015156:CDS 40.0%
GATGGGATTTGAACTCTGTT+GGG - chr5.1:9466307-9466326 None:intergenic 40.0%
GCCATTGAATTCTTCTTCTC+GGG - chr5.1:9466361-9466380 None:intergenic 40.0%
GGGAAATGTTGAAAGCAACA+TGG + chr5.1:9466066-9466085 MS.gene015156:CDS 40.0%
TCAAACGTTGGAACAAGTTG+GGG + chr5.1:9466636-9466655 MS.gene015156:CDS 40.0%
TCCCGAGAAGAAGAATTCAA+TGG + chr5.1:9466357-9466376 MS.gene015156:CDS 40.0%
TGAAGAGGATAAGACAATGG+TGG - chr5.1:9466253-9466272 None:intergenic 40.0%
TGAATTCTTCTTCTCGGGAT+AGG - chr5.1:9466356-9466375 None:intergenic 40.0%
TGATGGGATTTGAACTCTGT+TGG - chr5.1:9466308-9466327 None:intergenic 40.0%
TTGTTCATCACCTTGCCAAA+TGG + chr5.1:9466738-9466757 MS.gene015156:CDS 40.0%
!! GAATTGTTGGTTCTTCCTGA+TGG - chr5.1:9466325-9466344 None:intergenic 40.0%
TCATCACCTTGCCAAATGGT+GGG + chr5.1:9466742-9466761 MS.gene015156:CDS 45.0%
TGTCTTGCTGCTACACTTTG+TGG - chr5.1:9466490-9466509 None:intergenic 45.0%
TTCATCACCTTGCCAAATGG+TGG + chr5.1:9466741-9466760 MS.gene015156:CDS 45.0%
!! GGTGTCATTGGTTGTTGAAG+AGG - chr5.1:9466268-9466287 None:intergenic 45.0%
!! GTGTCCATTTTTGTTCCACC+AGG - chr5.1:9466562-9466581 None:intergenic 45.0%
TGTTGTTGGGTTTCACGGAG+TGG + chr5.1:9466675-9466694 MS.gene015156:CDS 50.0%
!! ACTCTGTTGGGTTGAAGCGA+CGG - chr5.1:9466295-9466314 None:intergenic 50.0%
TGGAAGTGGGACCCACCATT+TGG - chr5.1:9466756-9466775 None:intergenic 55.0%
GTGGGACCCACCATTTGGCA+AGG - chr5.1:9466751-9466770 None:intergenic 60.0%
!! CTGTTGGGTTGAAGCGACGG+CGG - chr5.1:9466292-9466311 None:intergenic 60.0%
!! AGCGACGGCGGTGGTGTCAT+TGG - chr5.1:9466280-9466299 None:intergenic 65.0%
!! TTGGGTTGAAGCGACGGCGG+TGG - chr5.1:9466289-9466308 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 9466040 9466792 9466040 ID=MS.gene015156
chr5.1 mRNA 9466040 9466792 9466040 ID=MS.gene015156.t1;Parent=MS.gene015156
chr5.1 exon 9466040 9466792 9466040 ID=MS.gene015156.t1.exon1;Parent=MS.gene015156.t1
chr5.1 CDS 9466040 9466792 9466040 ID=cds.MS.gene015156.t1;Parent=MS.gene015156.t1
Gene Sequence

>MS.gene015156

ATGGATGAAGACATACTGAAAACTTTGGGAAATGTTGAAAGCAACATGGACATGATGACAATGATGATGCAAATGGAAAAGTTCCCTGATTCATATGAACCTTTTTATAGCAACACCAATAACAACACTCTCAATCTCAATCTCACAAACAATGATTTCCCTTATGGAAACTCAAATGTAACTTCATCACTCACACCTTCATTGATCAATCCACCATTGTCTTATCCTCTTCAACAACCAATGACACCACCGCCGTCGCTTCAACCCAACAGAGTTCAAATCCCATCAGGAAGAACCAACAATTCTTCATTCTCCTATCCCGAGAAGAAGAATTCAATGGCAGCAATGAGAGAGATGATATTTCGAATGGCGGTTATGCAACCGATTAACATAGACCCAGAAACCATTAAACCACCAAAGAGAAAGAATGTGAAGATTTCAAAGGATCCACAAAGTGTAGCAGCAAGACATAGAAGAGAAAGAATCAGTGAACGAATAAGGATATTACAAAGATTAGTACCTGGTGGAACAAAAATGGACACTGCTTCTATGTTAGATGAAGCAATACATTATGTGAAGTTTTTGAAGAAACAAATTCAAACGTTGGAACAAGTTGGGGCAAATAGACCTTTGAATGTTGTTGGGTTTCACGGAGTGGTTTCTAATGCTAATTATAATTATTCTTCTTTGCTTAGAGGTTGTTCATCACCTTGCCAAATGGTGGGTCCCACTTCCAAACAAATGCTTAGTTGA
Protein sequence

>MS.gene015156.t1

MDEDILKTLGNVESNMDMMTMMMQMEKFPDSYEPFYSNTNNNTLNLNLTNNDFPYGNSNVTSSLTPSLINPPLSYPLQQPMTPPPSLQPNRVQIPSGRTNNSSFSYPEKKNSMAAMREMIFRMAVMQPINIDPETIKPPKRKNVKISKDPQSVAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKKQIQTLEQVGANRPLNVVGFHGVVSNANYNYSSLLRGCSSPCQMVGPTSKQMLS