AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96409

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96409.t1 MTR_0160s0030 97.345 339 6 1 1 336 23 361 0.0 672
MS.gene96409.t1 MTR_4g100860 42.268 291 126 9 47 330 60 315 2.44e-58 191
MS.gene96409.t1 MTR_4g027440 44.949 396 113 16 1 334 24 376 2.93e-54 182
MS.gene96409.t1 MTR_4g109340 39.241 158 53 4 205 321 340 495 8.36e-25 105
MS.gene96409.t1 MTR_5g012630 36.946 203 96 7 38 237 67 240 1.18e-23 98.6
MS.gene96409.t1 MTR_1g067640 40.476 126 60 4 215 326 38 162 6.08e-21 88.6
MS.gene96409.t1 MTR_1g067650 41.880 117 53 4 215 317 39 154 6.62e-21 88.6
MS.gene96409.t1 MTR_7g100100 40.136 147 70 9 188 319 6 149 7.31e-21 88.2
MS.gene96409.t1 MTR_1g106730 36.628 172 77 8 176 316 29 199 1.61e-19 86.7
MS.gene96409.t1 MTR_4g028610 31.624 234 88 7 144 315 159 382 2.21e-19 89.0
MS.gene96409.t1 MTR_2g096540 35.664 143 68 5 187 319 1 129 4.81e-18 79.7
MS.gene96409.t1 MTR_3g102980 38.889 162 71 6 185 320 57 216 1.47e-17 80.9
MS.gene96409.t1 MTR_1g018420 33.155 187 80 7 141 312 37 193 2.33e-16 77.4
MS.gene96409.t1 MTR_1g067660 38.583 127 60 6 215 326 35 158 5.18e-16 75.1
MS.gene96409.t1 MTR_5g062300 41.176 102 40 3 214 295 118 219 6.86e-16 76.6
MS.gene96409.t1 MTR_7g023560 40.367 109 53 4 181 283 6 108 1.84e-15 73.9
MS.gene96409.t1 MTR_4g057230 33.333 165 55 4 215 326 113 275 4.71e-15 74.7
MS.gene96409.t1 MTR_4g082980 52.459 61 21 2 261 316 393 450 6.52e-14 72.8
MS.gene96409.t1 MTR_1g115345 42.683 82 38 2 207 283 41 118 1.98e-13 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96409.t1 AT3G60580 43.333 330 113 11 1 322 23 286 8.89e-59 191
MS.gene96409.t1 AT2G45120 43.072 332 135 11 1 322 23 310 5.78e-50 169
MS.gene96409.t1 AT1G02030 40.071 282 108 10 57 320 25 263 2.25e-34 127
MS.gene96409.t1 AT3G53600 38.760 129 66 4 215 333 49 174 1.44e-21 90.5
MS.gene96409.t1 AT3G19580 31.019 216 79 7 140 319 64 245 2.21e-21 92.4
MS.gene96409.t1 AT3G19580 31.019 216 79 7 140 319 64 245 2.21e-21 92.4
MS.gene96409.t1 AT2G37430 42.623 122 44 6 214 317 46 159 1.31e-18 82.4
MS.gene96409.t1 AT2G28200 34.416 154 45 5 215 316 115 264 3.49e-18 84.0
MS.gene96409.t1 AT5G61470 46.667 75 40 0 211 285 224 298 1.13e-17 82.8
MS.gene96409.t1 AT5G43170 35.333 150 51 3 142 291 45 148 3.02e-17 79.3
MS.gene96409.t1 AT4G35280 36.719 128 57 4 214 327 161 278 1.04e-16 79.7
MS.gene96409.t1 AT1G49900 47.887 71 35 1 215 283 750 820 1.81e-16 80.9
MS.gene96409.t1 AT1G49900 44.000 75 36 1 215 283 193 267 7.66e-14 73.2
MS.gene96409.t1 AT5G03510 35.616 146 52 4 213 316 116 261 2.33e-16 78.6
MS.gene96409.t1 AT2G28710 38.333 120 53 6 215 319 34 147 3.89e-16 75.1
MS.gene96409.t1 AT3G49930 41.739 115 47 4 215 320 94 197 1.76e-15 74.7
MS.gene96409.t1 AT2G17180 38.017 121 48 3 214 317 147 257 1.79e-15 75.9
MS.gene96409.t1 AT1G27730 33.654 208 63 9 140 319 48 208 2.86e-15 74.3
MS.gene96409.t1 AT5G67450 40.217 92 30 2 215 283 97 186 2.97e-15 74.7
MS.gene96409.t1 AT3G46090 41.739 115 42 6 215 310 40 148 3.85e-15 72.8
MS.gene96409.t1 AT5G59820 53.623 69 29 2 215 283 39 104 4.69e-15 72.4
MS.gene96409.t1 AT1G26610 59.016 61 20 2 259 316 397 455 5.32e-15 75.9
MS.gene96409.t1 AT3G46080 47.368 76 28 3 215 283 37 107 1.50e-14 70.9
MS.gene96409.t1 AT5G04340 41.176 85 31 2 215 283 89 170 9.63e-14 70.5
MS.gene96409.t1 AT3G46070 42.308 78 40 2 211 283 31 108 4.50e-13 67.0
MS.gene96409.t1 AT4G16610 36.441 118 58 4 43 157 52 155 7.96e-12 64.3

Find 40 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGAAAAGGGTCTTAATTA+TGG 0.263811 7.1:+56270362 MS.gene96409:CDS
TTCTCTTTGGATTCTCTCTA+AGG 0.279891 7.1:-56270385 None:intergenic
ACGAGACGAATGCTTCTCTT+TGG 0.315457 7.1:-56270398 None:intergenic
AATTGAAATCGAAAGATCTT+TGG 0.317289 7.1:+56270787 MS.gene96409:CDS
AACAACCGAAGAATCATTCT+TGG 0.327984 7.1:-56270603 None:intergenic
AAAAGAACACATGTGATTCA+TGG 0.392470 7.1:+56271073 MS.gene96409:CDS
AGATGATGACGTTGATGAAA+AGG 0.399134 7.1:+56270349 MS.gene96409:CDS
CTAACTTCATCATCATCAAT+TGG 0.412597 7.1:-56271172 None:intergenic
ACAAAATGCAACATCTTCTT+CGG 0.417782 7.1:-56270663 None:intergenic
TTCAAATCTTATCAAGCATT+GGG 0.429788 7.1:+56270905 MS.gene96409:CDS
GCATCAGAAACCGAACTAAC+AGG 0.435004 7.1:-56270635 None:intergenic
GTTCAAATCTTATCAAGCAT+TGG 0.444666 7.1:+56270904 MS.gene96409:CDS
CTTCTTGCTTTGTAACAAGA+AGG 0.459791 7.1:-56270256 None:intergenic
TGAACATGAACCTGTTAGTT+CGG 0.475159 7.1:+56270625 MS.gene96409:CDS
GATTCTTCCACCGTTATGTT+CGG 0.482402 7.1:-56270959 None:intergenic
GATGATGACGTTGATGAAAA+GGG 0.491203 7.1:+56270350 MS.gene96409:CDS
TGCAGTTGTCGAGAGACAAA+TGG 0.497909 7.1:+56270690 MS.gene96409:CDS
TTCTATATCTTGAAGAATCA+CGG 0.508062 7.1:-56270459 None:intergenic
AAAGAAAGTTCATGAATGTC+CGG 0.517315 7.1:+56271006 MS.gene96409:CDS
AATAATAATAAAGTACGTAA+AGG 0.519533 7.1:+56270851 MS.gene96409:CDS
CAACTCGGAAAAGATCCAAA+AGG 0.530550 7.1:+56270510 MS.gene96409:CDS
TTTAATTCGGGACAAGCACT+TGG 0.537402 7.1:+56271043 MS.gene96409:CDS
AAAGGGTGTGGAAAATTCGC+GGG 0.538446 7.1:+56270528 MS.gene96409:CDS
TGATGACGACGAAGCTGAAG+AGG 0.541596 7.1:+56270754 MS.gene96409:CDS
AACTCGGAAAAGATCCAAAA+GGG 0.553686 7.1:+56270511 MS.gene96409:CDS
TCATCATCATCAATTGGAGC+AGG 0.554191 7.1:-56271166 None:intergenic
AAAAGGGTGTGGAAAATTCG+CGG 0.559838 7.1:+56270527 MS.gene96409:CDS
AATTCGGGACAAGCACTTGG+TGG 0.563519 7.1:+56271046 MS.gene96409:CDS
ACGGAACTTGTATCCACTTG+TGG 0.567540 7.1:-56270440 None:intergenic
GGAAAAGATCCAAAAGGGTG+TGG 0.567774 7.1:+56270516 MS.gene96409:CDS
GAAGATTAAACCGAACATAA+CGG 0.578318 7.1:+56270949 MS.gene96409:CDS
CATCGAAGAATAATCCAACT+CGG 0.596368 7.1:+56270495 MS.gene96409:CDS
TTAAATACTCGAAAACATAC+CGG 0.600102 7.1:-56271025 None:intergenic
ATAATAAAGTACGTAAAGGA+AGG 0.605908 7.1:+56270855 MS.gene96409:CDS
CATCATCAATTGGAGCAGGA+AGG 0.614177 7.1:-56271162 None:intergenic
AAATCTTATCAAGCATTGGG+TGG 0.639931 7.1:+56270908 MS.gene96409:CDS
AGAAGAAGAATCATCGCGAA+CGG 0.649326 7.1:+56270274 MS.gene96409:CDS
TCTGATGACGATGATGAAGA+CGG 0.688378 7.1:-56270326 None:intergenic
GATTAAACCGAACATAACGG+TGG 0.692339 7.1:+56270952 MS.gene96409:CDS
AAATGAACAATATGAAGACG+TGG 0.705726 7.1:+56270721 MS.gene96409:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATAATAAAGTACGTAA+AGG + chr7.1:56270851-56270870 MS.gene96409:CDS 15.0%
!!! ATGTTTTCGAGTATTTAATT+CGG + chr7.1:56271030-56271049 MS.gene96409:CDS 20.0%
! AATTGAAATCGAAAGATCTT+TGG + chr7.1:56270787-56270806 MS.gene96409:CDS 25.0%
! ATAATAAAGTACGTAAAGGA+AGG + chr7.1:56270855-56270874 MS.gene96409:CDS 25.0%
! TTAAATACTCGAAAACATAC+CGG - chr7.1:56271028-56271047 None:intergenic 25.0%
! TTCAAATCTTATCAAGCATT+GGG + chr7.1:56270905-56270924 MS.gene96409:CDS 25.0%
! TTCTATATCTTGAAGAATCA+CGG - chr7.1:56270462-56270481 None:intergenic 25.0%
!! TTTTACCAAGAATGATTCTT+CGG + chr7.1:56270598-56270617 MS.gene96409:CDS 25.0%
!!! TGTTTTCGAGTATTTAATTC+GGG + chr7.1:56271031-56271050 MS.gene96409:CDS 25.0%
AAAAGAACACATGTGATTCA+TGG + chr7.1:56271073-56271092 MS.gene96409:CDS 30.0%
AAAGAAAGTTCATGAATGTC+CGG + chr7.1:56271006-56271025 MS.gene96409:CDS 30.0%
AAATGAACAATATGAAGACG+TGG + chr7.1:56270721-56270740 MS.gene96409:CDS 30.0%
ACAAAATGCAACATCTTCTT+CGG - chr7.1:56270666-56270685 None:intergenic 30.0%
CTAACTTCATCATCATCAAT+TGG - chr7.1:56271175-56271194 None:intergenic 30.0%
GAAGATTAAACCGAACATAA+CGG + chr7.1:56270949-56270968 MS.gene96409:CDS 30.0%
GATGAAAAGGGTCTTAATTA+TGG + chr7.1:56270362-56270381 MS.gene96409:CDS 30.0%
GTTCAAATCTTATCAAGCAT+TGG + chr7.1:56270904-56270923 MS.gene96409:CDS 30.0%
! TTTTCAACAACTTCGAATTC+TGG - chr7.1:56270989-56271008 None:intergenic 30.0%
!! ACTCTTTTTGAGCTGAAAAT+TGG - chr7.1:56271118-56271137 None:intergenic 30.0%
AACAACCGAAGAATCATTCT+TGG - chr7.1:56270606-56270625 None:intergenic 35.0%
AACTCGGAAAAGATCCAAAA+GGG + chr7.1:56270511-56270530 MS.gene96409:CDS 35.0%
CATCGAAGAATAATCCAACT+CGG + chr7.1:56270495-56270514 MS.gene96409:CDS 35.0%
CTTCTTGCTTTGTAACAAGA+AGG - chr7.1:56270259-56270278 None:intergenic 35.0%
TGAACATGAACCTGTTAGTT+CGG + chr7.1:56270625-56270644 MS.gene96409:CDS 35.0%
TTCTCTTTGGATTCTCTCTA+AGG - chr7.1:56270388-56270407 None:intergenic 35.0%
! AGAGTTTTCTTTTCCACAAG+TGG + chr7.1:56270427-56270446 MS.gene96409:CDS 35.0%
! AGATGATGACGTTGATGAAA+AGG + chr7.1:56270349-56270368 MS.gene96409:CDS 35.0%
! GATGATGACGTTGATGAAAA+GGG + chr7.1:56270350-56270369 MS.gene96409:CDS 35.0%
!! AAATCTTATCAAGCATTGGG+TGG + chr7.1:56270908-56270927 MS.gene96409:CDS 35.0%
AGAAGAAGAATCATCGCGAA+CGG + chr7.1:56270274-56270293 MS.gene96409:CDS 40.0%
CAACTCGGAAAAGATCCAAA+AGG + chr7.1:56270510-56270529 MS.gene96409:CDS 40.0%
GATTAAACCGAACATAACGG+TGG + chr7.1:56270952-56270971 MS.gene96409:CDS 40.0%
GATTCTTCCACCGTTATGTT+CGG - chr7.1:56270962-56270981 None:intergenic 40.0%
TCATCATCATCAATTGGAGC+AGG - chr7.1:56271169-56271188 None:intergenic 40.0%
TTTAATTCGGGACAAGCACT+TGG + chr7.1:56271043-56271062 MS.gene96409:CDS 40.0%
! AAAAGGGTGTGGAAAATTCG+CGG + chr7.1:56270527-56270546 MS.gene96409:CDS 40.0%
! CTTTTGGATCTTTTCCGAGT+TGG - chr7.1:56270512-56270531 None:intergenic 40.0%
! TCTGATGACGATGATGAAGA+CGG - chr7.1:56270329-56270348 None:intergenic 40.0%
ACGAGACGAATGCTTCTCTT+TGG - chr7.1:56270401-56270420 None:intergenic 45.0%
ACGGAACTTGTATCCACTTG+TGG - chr7.1:56270443-56270462 None:intergenic 45.0%
CATCATCAATTGGAGCAGGA+AGG - chr7.1:56271165-56271184 None:intergenic 45.0%
GCATCAGAAACCGAACTAAC+AGG - chr7.1:56270638-56270657 None:intergenic 45.0%
GGAAAAGATCCAAAAGGGTG+TGG + chr7.1:56270516-56270535 MS.gene96409:CDS 45.0%
TGCAGTTGTCGAGAGACAAA+TGG + chr7.1:56270690-56270709 MS.gene96409:CDS 45.0%
! AAAGGGTGTGGAAAATTCGC+GGG + chr7.1:56270528-56270547 MS.gene96409:CDS 45.0%
! GCGAATTTTCCACACCCTTT+TGG - chr7.1:56270528-56270547 None:intergenic 45.0%
AATTCGGGACAAGCACTTGG+TGG + chr7.1:56271046-56271065 MS.gene96409:CDS 50.0%
! TGATGACGACGAAGCTGAAG+AGG + chr7.1:56270754-56270773 MS.gene96409:CDS 50.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 56270236 56271246 56270236 ID=MS.gene96409
chr7.1 mRNA 56270236 56271246 56270236 ID=MS.gene96409.t1;Parent=MS.gene96409
chr7.1 exon 56270236 56271246 56270236 ID=MS.gene96409.t1.exon1;Parent=MS.gene96409.t1
chr7.1 CDS 56270236 56271246 56270236 ID=cds.MS.gene96409.t1;Parent=MS.gene96409.t1
Gene Sequence

>MS.gene96409

ATGAGATCTCATATGATGAACCTTCTTGTTACAAAGCAAGAAGAAGAATCATCGCGAACGGTTCAACTTAGTTTCGAAGCTGAATCAGCACCGTCTTCATCATCGTCATCAGAAGATGATGACGTTGATGAAAAGGGTCTTAATTATGGCCTTAGAGAGAATCCAAAGAGAAGCATTCGTCTCGTAGATCAAGAGTTTTCTTTTCCACAAGTGGATACAAGTTCCGTGATTCTTCAAGATATAGAAAGCGAAACTGAATCATCGAAGAATAATCCAACTCGGAAAAGATCCAAAAGGGTGTGGAAAATTCGCGGGTTTGAACAAAAGTATTACAATGAATCTGCTACGAAGAAAATGAAATTTTTTACCAAGAATGATTCTTCGGTTGTTGAACATGAACCTGTTAGTTCGGTTTCTGATGCAACAACCGAAGAAGATGTTGCATTTTGTCTAATGCAGTTGTCGAGAGACAAATGGAATAGACAAAATGAACAATATGAAGACGTGGAAGAAGAAGATGATGACGACGAAGCTGAAGAGGAAGAAGATGAAATTGAAATCGAAAGATCTTTGGAAGATAGTGATGAATCTCAAGAGCTACTAAAAGTATGCAAGAATAATAATAAAGTACGTAAAGGAAGGTACAAATGTGAAACATGTAATAAAGTGTTCAAATCTTATCAAGCATTGGGTGGTCATAGAGCAAGTCACAAGAAGATTAAACCGAACATAACGGTGGAAGAATCGTCGCCAGAATTCGAAGTTGTTGAAAAGAAAGTTCATGAATGTCCGGTATGTTTTCGAGTATTTAATTCGGGACAAGCACTTGGTGGACACAAAAGAACACATGTGATTCATGGATCATCATCAACAACAGTTCCAATTTTCAGCTCAAAAAGAGTTGCAAAAAGTGTTATAGATCTTAACCTTCCTGCTCCAATTGATGATGATGAAGTTAGTCAAATTGAAAATTCTGCTGTTTCTGATGCAGAATTTGTCAAAACTCGTTAA
Protein sequence

>MS.gene96409.t1

MRSHMMNLLVTKQEEESSRTVQLSFEAESAPSSSSSSEDDDVDEKGLNYGLRENPKRSIRLVDQEFSFPQVDTSSVILQDIESETESSKNNPTRKRSKRVWKIRGFEQKYYNESATKKMKFFTKNDSSVVEHEPVSSVSDATTEEDVAFCLMQLSRDKWNRQNEQYEDVEEEDDDDEAEEEEDEIEIERSLEDSDESQELLKVCKNNNKVRKGRYKCETCNKVFKSYQALGGHRASHKKIKPNITVEESSPEFEVVEKKVHECPVCFRVFNSGQALGGHKRTHVIHGSSSTTVPIFSSKRVAKSVIDLNLPAPIDDDEVSQIENSAVSDAEFVKTR