AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028407

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028407.t1 MTR_4g119428 65.198 227 69 4 1 219 2 226 8.20e-94 275
MS.gene028407.t1 MTR_1g057270 56.140 228 91 2 1 219 1 228 2.23e-72 220
MS.gene028407.t1 MTR_7g106000 39.091 220 117 4 1 213 1 210 1.08e-48 159
MS.gene028407.t1 MTR_7g106010 39.450 218 119 3 5 218 4 212 2.22e-48 158
MS.gene028407.t1 MTR_7g105870 46.411 209 105 2 4 211 5 207 2.91e-47 155
MS.gene028407.t1 MTR_7g106030 36.530 219 125 4 5 218 7 216 2.71e-41 140
MS.gene028407.t1 MTR_7g105970 36.036 222 125 4 1 215 1 212 1.49e-37 130
MS.gene028407.t1 MTR_1g057400 35.714 182 112 2 38 214 11 192 1.56e-34 122
MS.gene028407.t1 MTR_6g071410 36.207 174 101 6 45 211 9 179 2.24e-25 99.0
MS.gene028407.t1 MTR_6g070890 36.207 174 101 6 45 211 9 179 2.24e-25 99.0
MS.gene028407.t1 MTR_6g471090 35.979 189 103 8 30 212 2 178 6.38e-25 97.8
MS.gene028407.t1 MTR_6g070900 34.483 174 103 6 47 211 8 179 3.22e-22 90.5
MS.gene028407.t1 MTR_6g071400 34.483 174 103 6 47 211 8 179 3.22e-22 90.5
MS.gene028407.t1 MTR_4g094322 75.510 49 12 0 171 219 2 50 1.43e-20 82.4
MS.gene028407.t1 MTR_2g011350 29.252 147 103 1 59 205 35 180 4.50e-20 84.7
MS.gene028407.t1 MTR_1g057290 39.333 150 86 2 72 216 52 201 1.40e-19 83.6
MS.gene028407.t1 MTR_6g471080 37.647 170 98 6 48 211 7 174 1.13e-17 78.6
MS.gene028407.t1 MTR_3g078800 29.814 161 110 3 51 209 73 232 2.65e-17 78.6
MS.gene028407.t1 MTR_2g048270 38.686 137 76 5 87 218 3 136 4.67e-17 75.9
MS.gene028407.t1 MTR_5g087760 25.234 214 132 8 15 214 41 240 1.07e-16 76.6
MS.gene028407.t1 MTR_5g076170 32.051 156 102 4 63 216 96 249 1.49e-16 76.3
MS.gene028407.t1 MTR_3g063310 30.137 146 98 3 66 209 87 230 6.33e-16 74.3
MS.gene028407.t1 MTR_7g106100 32.203 118 73 3 42 153 64 180 1.93e-13 67.8
MS.gene028407.t1 MTR_2g100060 25.170 147 108 2 61 206 78 223 2.57e-13 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028407.t1 AT2G35460 38.182 220 128 3 4 215 3 222 2.73e-55 176
MS.gene028407.t1 AT2G35980 38.679 212 120 3 2 211 3 206 3.80e-53 171
MS.gene028407.t1 AT3G11650 37.443 219 129 3 6 217 8 225 1.13e-51 167
MS.gene028407.t1 AT5G06320 39.450 218 127 3 1 215 1 216 2.82e-48 158
MS.gene028407.t1 AT1G32270 33.775 151 98 1 69 217 1 151 7.82e-22 92.0
MS.gene028407.t1 AT1G32270 33.775 151 98 1 69 217 1 151 1.91e-21 91.7
MS.gene028407.t1 AT5G22870 25.767 163 117 3 46 205 24 185 3.66e-16 74.3
MS.gene028407.t1 AT4G01410 25.625 160 119 0 48 207 44 203 1.31e-15 73.2
MS.gene028407.t1 AT4G05220 22.051 195 149 3 16 209 14 206 2.29e-15 72.8
MS.gene028407.t1 AT5G53730 28.402 169 108 4 61 217 40 207 7.95e-15 70.9
MS.gene028407.t1 AT3G52470 28.000 150 106 2 34 182 5 153 8.71e-15 70.9
MS.gene028407.t1 AT2G27080 25.248 202 133 6 15 209 49 239 1.08e-14 71.2
MS.gene028407.t1 AT2G27080 25.248 202 133 6 15 209 49 239 1.08e-14 71.2
MS.gene028407.t1 AT5G21130 25.743 202 132 6 15 209 70 260 8.55e-13 66.2
MS.gene028407.t1 AT4G09590 25.000 160 118 2 48 206 22 180 1.25e-12 64.7
MS.gene028407.t1 AT1G65690 25.444 169 122 4 49 215 71 237 5.46e-12 63.5
MS.gene028407.t1 AT1G61760 23.780 164 122 3 47 209 43 204 2.40e-11 61.6
MS.gene028407.t1 AT5G36970 25.000 152 109 4 60 209 78 226 7.80e-11 60.5

Find 43 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATAATTGGTTTCCTCTTT+TGG 0.148150 4.2:-18634331 MS.gene028407:CDS
GCAAAACACTTGTATTCTTA+TGG 0.189397 4.2:+18634087 None:intergenic
CAAAACACTTGTATTCTTAT+GGG 0.307477 4.2:+18634088 None:intergenic
TTCAAATCGCAATGAAGTTT+AGG 0.324721 4.2:+18633909 None:intergenic
CAAGGGATTCATTTGAGTTC+AGG 0.328368 4.2:-18634044 MS.gene028407:CDS
ATTGTCATAGTAGCAATAAT+TGG 0.352334 4.2:-18634344 MS.gene028407:CDS
TAAACTTCATTGCGATTTGA+AGG 0.374826 4.2:-18633907 MS.gene028407:CDS
CGCTGGGCTTGTTTAGGTCT+AGG 0.393225 4.2:-18633941 MS.gene028407:CDS
CTTCACTAACGCTGAATTTG+AGG 0.395049 4.2:+18634288 None:intergenic
TCTAAATTTGAGGTGTACGC+TGG 0.411534 4.2:-18633958 MS.gene028407:CDS
GGTGTACGCTGGGCTTGTTT+AGG 0.415997 4.2:-18633947 MS.gene028407:CDS
AAGTTTGTTTCTCAAACCTT+AGG 0.419715 4.2:-18634125 MS.gene028407:CDS
TCAAATGTCAGAGTTCAATA+AGG 0.431524 4.2:-18634021 MS.gene028407:CDS
GCAGAAGCCGCAACCATTGT+TGG 0.436398 4.2:+18634430 None:intergenic
CAAAACCCTAATCGAAAAGT+TGG 0.457401 4.2:-18634194 MS.gene028407:CDS
TGCAGTTGCTTCAGAGGATG+TGG 0.464777 4.2:-18634410 MS.gene028407:CDS
CGGTTAGATTTCGACGGCGA+GGG 0.468702 4.2:+18634464 None:intergenic
TTCGACGGCGAGGGGATGGA+AGG 0.471157 4.2:+18634473 None:intergenic
ACGCTGAATTTGAGGACGTA+GGG 0.476124 4.2:+18634296 None:intergenic
AGATTTCGACGGCGAGGGGA+TGG 0.478535 4.2:+18634469 None:intergenic
AACCATTGTTGGTGTGGCGT+CGG 0.479384 4.2:+18634441 None:intergenic
GGCTTCTGCAGTTGCTTCAG+AGG 0.506618 4.2:-18634416 MS.gene028407:CDS
AACAATGGAACTTCTTCGTA+GGG 0.531313 4.2:-18633870 None:intergenic
GTTCCATTGTTTGATGTCAA+CGG 0.541893 4.2:+18633882 None:intergenic
CTAAATTTGAGGTGTACGCT+GGG 0.543006 4.2:-18633957 MS.gene028407:CDS
CGCCACACCAACAATGGTTG+CGG 0.544206 4.2:-18634437 MS.gene028407:CDS
AAACAATGGAACTTCTTCGT+AGG 0.544398 4.2:-18633871 None:intergenic
AAAACACTTGTATTCTTATG+GGG 0.553234 4.2:+18634089 None:intergenic
CATTGTTGGTGTGGCGTCGG+CGG 0.554135 4.2:+18634444 None:intergenic
GGCGCACAATAAACCAAAAG+AGG 0.561827 4.2:+18634318 None:intergenic
CGCCGACGCCACACCAACAA+TGG 0.563040 4.2:-18634443 MS.gene028407:CDS
AGCCGCAACCATTGTTGGTG+TGG 0.573197 4.2:+18634435 None:intergenic
TCGACGGCGAGGGGATGGAA+GGG 0.573313 4.2:+18634474 None:intergenic
CAACTCCACAATGCTTACTA+CGG 0.575454 4.2:-18634497 MS.gene028407:CDS
GGTTAGATTTCGACGGCGAG+GGG 0.578761 4.2:+18634465 None:intergenic
CGTCGGCGGTTAGATTTCGA+CGG 0.597925 4.2:+18634458 None:intergenic
GCGGTTAGATTTCGACGGCG+AGG 0.619749 4.2:+18634463 None:intergenic
TGCTACTATGACAATGATTG+TGG 0.622752 4.2:+18634352 None:intergenic
CGCTGAATTTGAGGACGTAG+GGG 0.649005 4.2:+18634297 None:intergenic
AGTTGCTTCAGAGGATGTGG+TGG 0.654726 4.2:-18634407 MS.gene028407:CDS
AAGGGCCGTAGTAAGCATTG+TGG 0.684765 4.2:+18634492 None:intergenic
GTTCCGTTGACATCAAACAA+TGG 0.691708 4.2:-18633885 MS.gene028407:CDS
AACGCTGAATTTGAGGACGT+AGG 0.716355 4.2:+18634295 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAACACTTGTATTCTTATG+GGG + chr4.2:18634295-18634314 None:intergenic 25.0%
! ATTGTCATAGTAGCAATAAT+TGG - chr4.2:18634037-18634056 MS.gene028407:CDS 25.0%
! CAAAACACTTGTATTCTTAT+GGG + chr4.2:18634296-18634315 None:intergenic 25.0%
! TTCAATAAGGAGAAAAATGA+TGG - chr4.2:18634373-18634392 MS.gene028407:CDS 25.0%
!! ATAAGAATACAAGTGTTTTG+CGG - chr4.2:18634296-18634315 MS.gene028407:CDS 25.0%
!! TGAAGGTTTTTCTAAATTTG+AGG - chr4.2:18634413-18634432 MS.gene028407:CDS 25.0%
GCAAAACACTTGTATTCTTA+TGG + chr4.2:18634297-18634316 None:intergenic 30.0%
TAAACTTCATTGCGATTTGA+AGG - chr4.2:18634474-18634493 MS.gene028407:CDS 30.0%
TCAAATGTCAGAGTTCAATA+AGG - chr4.2:18634360-18634379 MS.gene028407:CDS 30.0%
TTCAAATCGCAATGAAGTTT+AGG + chr4.2:18634475-18634494 None:intergenic 30.0%
! AAGTTTGTTTCTCAAACCTT+AGG - chr4.2:18634256-18634275 MS.gene028407:CDS 30.0%
! TAAGAATACAAGTGTTTTGC+GGG - chr4.2:18634297-18634316 MS.gene028407:CDS 30.0%
!! CAATAATTGGTTTCCTCTTT+TGG - chr4.2:18634050-18634069 MS.gene028407:CDS 30.0%
CAAAACCCTAATCGAAAAGT+TGG - chr4.2:18634187-18634206 MS.gene028407:CDS 35.0%
GTTCCATTGTTTGATGTCAA+CGG + chr4.2:18634502-18634521 None:intergenic 35.0%
TGCTACTATGACAATGATTG+TGG + chr4.2:18634032-18634051 None:intergenic 35.0%
! CAACTTTTCGATTAGGGTTT+TGG + chr4.2:18634189-18634208 None:intergenic 35.0%
! CGATACCAACTTTTCGATTA+GGG + chr4.2:18634195-18634214 None:intergenic 35.0%
! GGGTTGAAAGAATTTTCCTA+AGG + chr4.2:18634275-18634294 None:intergenic 35.0%
! TCGATACCAACTTTTCGATT+AGG + chr4.2:18634196-18634215 None:intergenic 35.0%
!! CTGCTTTTAAAGGTAAGCAA+GGG - chr4.2:18634320-18634339 MS.gene028407:CDS 35.0%
!! GAGAAAAATGATGGCGTTTT+TGG - chr4.2:18634382-18634401 MS.gene028407:CDS 35.0%
!!! CGTTTTTGGAATTGACTTGA+AGG - chr4.2:18634396-18634415 MS.gene028407:CDS 35.0%
CAACTCCACAATGCTTACTA+CGG - chr4.2:18633884-18633903 MS.gene028407:CDS 40.0%
CTTCACTAACGCTGAATTTG+AGG + chr4.2:18634096-18634115 None:intergenic 40.0%
GTTCCGTTGACATCAAACAA+TGG - chr4.2:18634496-18634515 MS.gene028407:CDS 40.0%
! CAAGGGATTCATTTGAGTTC+AGG - chr4.2:18634337-18634356 MS.gene028407:CDS 40.0%
! CTAAATTTGAGGTGTACGCT+GGG - chr4.2:18634424-18634443 MS.gene028407:CDS 40.0%
! TCTAAATTTGAGGTGTACGC+TGG - chr4.2:18634423-18634442 MS.gene028407:CDS 40.0%
!!! GCTGCTTTTAAAGGTAAGCA+AGG - chr4.2:18634319-18634338 MS.gene028407:CDS 40.0%
AACGCTGAATTTGAGGACGT+AGG + chr4.2:18634089-18634108 None:intergenic 45.0%
ACGCTGAATTTGAGGACGTA+GGG + chr4.2:18634088-18634107 None:intergenic 45.0%
GGCGCACAATAAACCAAAAG+AGG + chr4.2:18634066-18634085 None:intergenic 45.0%
!!! GTTTTGCGGGCTGCTTTTAA+AGG - chr4.2:18634310-18634329 MS.gene028407:CDS 45.0%
AACCATTGTTGGTGTGGCGT+CGG + chr4.2:18633943-18633962 None:intergenic 50.0%
AGTTGCTTCAGAGGATGTGG+TGG - chr4.2:18633974-18633993 MS.gene028407:CDS 50.0%
CGCTGAATTTGAGGACGTAG+GGG + chr4.2:18634087-18634106 None:intergenic 50.0%
TGCAGTTGCTTCAGAGGATG+TGG - chr4.2:18633971-18633990 MS.gene028407:CDS 50.0%
! AAGGGCCGTAGTAAGCATTG+TGG + chr4.2:18633892-18633911 None:intergenic 50.0%
AGCCGCAACCATTGTTGGTG+TGG + chr4.2:18633949-18633968 None:intergenic 55.0%
CGCCACACCAACAATGGTTG+CGG - chr4.2:18633944-18633963 MS.gene028407:CDS 55.0%
CGGTTAGATTTCGACGGCGA+GGG + chr4.2:18633920-18633939 None:intergenic 55.0%
CGTCGGCGGTTAGATTTCGA+CGG + chr4.2:18633926-18633945 None:intergenic 55.0%
GCAGAAGCCGCAACCATTGT+TGG + chr4.2:18633954-18633973 None:intergenic 55.0%
GGCTTCTGCAGTTGCTTCAG+AGG - chr4.2:18633965-18633984 MS.gene028407:CDS 55.0%
GGTTAGATTTCGACGGCGAG+GGG + chr4.2:18633919-18633938 None:intergenic 55.0%
! CGCTGGGCTTGTTTAGGTCT+AGG - chr4.2:18634440-18634459 MS.gene028407:CDS 55.0%
! GGTGTACGCTGGGCTTGTTT+AGG - chr4.2:18634434-18634453 MS.gene028407:CDS 55.0%
AGATTTCGACGGCGAGGGGA+TGG + chr4.2:18633915-18633934 None:intergenic 60.0%
GCGGTTAGATTTCGACGGCG+AGG + chr4.2:18633921-18633940 None:intergenic 60.0%
! CATTGTTGGTGTGGCGTCGG+CGG + chr4.2:18633940-18633959 None:intergenic 60.0%
CGCCGACGCCACACCAACAA+TGG - chr4.2:18633938-18633957 MS.gene028407:CDS 65.0%
TCGACGGCGAGGGGATGGAA+GGG + chr4.2:18633910-18633929 None:intergenic 65.0%
TTCGACGGCGAGGGGATGGA+AGG + chr4.2:18633911-18633930 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 18633872 18634531 18633872 ID=MS.gene028407
chr4.2 mRNA 18633872 18634531 18633872 ID=MS.gene028407.t1;Parent=MS.gene028407
chr4.2 exon 18633872 18634531 18633872 ID=MS.gene028407.t1.exon1;Parent=MS.gene028407.t1
chr4.2 CDS 18633872 18634531 18633872 ID=cds.MS.gene028407.t1;Parent=MS.gene028407.t1
Gene Sequence

>MS.gene028407

ATGGCAGATAATCAACTCCACAATGCTTACTACGGCCCTTCCATCCCCTCGCCGTCGAAATCTAACCGCCGACGCCACACCAACAATGGTTGCGGCTTCTGCAGTTGCTTCAGAGGATGTGGTGGTTGCATCTTCAGCTTCTTATGCAAAATCATTACCACAATCATTGTCATAGTAGCAATAATTGGTTTCCTCTTTTGGTTTATTGTGCGCCCCTACGTCCTCAAATTCAGCGTTAGTGAAGCATCACTTACACTATTCAATTTCACAAACAACAACACATTTAACTATGATCTTTCTGTCAACATATCGATCCAAAACCCTAATCGAAAAGTTGGTATCGATTATGAAGACATCGAAATGTTTGCATTTTATAAAGATCTTAAGTTTGTTTCTCAAACCTTAGGAAAATTCTTTCAACCCCATAAGAATACAAGTGTTTTGCGGGCTGCTTTTAAAGGTAAGCAAGGGATTCATTTGAGTTCAGGTCAAATGTCAGAGTTCAATAAGGAGAAAAATGATGGCGTTTTTGGAATTGACTTGAAGGTTTTTCTAAATTTGAGGTGTACGCTGGGCTTGTTTAGGTCTAGGAATGTGAAACCTAAACTTCATTGCGATTTGAAGGTTCCGTTGACATCAAACAATGGAACTTCTTCGTAG
Protein sequence

>MS.gene028407.t1

MADNQLHNAYYGPSIPSPSKSNRRRHTNNGCGFCSCFRGCGGCIFSFLCKIITTIIVIVAIIGFLFWFIVRPYVLKFSVSEASLTLFNFTNNNTFNYDLSVNISIQNPNRKVGIDYEDIEMFAFYKDLKFVSQTLGKFFQPHKNTSVLRAAFKGKQGIHLSSGQMSEFNKEKNDGVFGIDLKVFLNLRCTLGLFRSRNVKPKLHCDLKVPLTSNNGTSS