AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene82232

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82232.t1 MTR_4g028930 93.750 256 14 2 17 270 127 382 9.97e-152 429
MS.gene82232.t1 MTR_7g072875 54.015 274 64 11 27 268 42 285 1.51e-73 226
MS.gene82232.t1 MTR_7g072630 54.182 275 62 12 27 268 104 347 1.94e-72 226
MS.gene82232.t1 MTR_5g075210 45.455 209 84 9 77 268 151 346 3.46e-42 147
MS.gene82232.t1 MTR_2g018030 39.865 148 74 3 135 270 201 345 4.79e-26 105
MS.gene82232.t1 MTR_8g087530 55.224 67 30 0 203 269 259 325 2.44e-21 92.0
MS.gene82232.t1 MTR_0907s0020 46.377 69 37 0 195 263 95 163 6.84e-16 73.9
MS.gene82232.t1 MTR_4g132740 47.761 67 35 0 200 266 79 145 4.12e-15 71.2
MS.gene82232.t1 MTR_8g103520 52.459 61 29 0 203 263 225 285 6.69e-15 73.6
MS.gene82232.t1 MTR_4g052040 49.180 61 31 0 203 263 100 160 2.15e-13 67.0
MS.gene82232.t1 MTR_7g105790 45.000 60 33 0 204 263 112 171 9.32e-13 65.9
MS.gene82232.t1 MTR_3g111780 37.374 99 60 1 165 263 163 259 9.58e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82232.t1 AT1G06920 54.206 107 43 1 160 266 207 307 3.87e-30 115
MS.gene82232.t1 AT2G30400 53.719 121 52 3 150 269 202 319 1.33e-29 114
MS.gene82232.t1 AT5G01840 36.406 217 71 5 51 266 112 262 9.52e-28 108
MS.gene82232.t1 AT5G58360 31.229 301 159 9 1 268 5 290 2.70e-25 102
MS.gene82232.t1 AT4G18830 37.267 161 82 3 122 266 189 346 2.61e-20 89.4
MS.gene82232.t1 AT5G19650 53.125 64 30 0 203 266 155 218 1.28e-15 74.3
MS.gene82232.t1 AT3G52525 46.154 65 35 0 201 265 65 129 1.20e-14 70.1
MS.gene82232.t1 AT2G18500 45.312 64 35 0 203 266 227 290 2.97e-13 68.9
MS.gene82232.t1 AT4G04025 46.053 76 34 1 187 262 105 173 6.34e-13 65.9
MS.gene82232.t1 AT2G36026 50.000 56 28 0 208 263 92 147 1.37e-12 65.1

Find 42 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACACGGTCGGTCCTGAATTC+AGG 0.231482 4.2:-75084282 None:intergenic
TCAAGGTATTCAAGCAAATA+TGG 0.240278 4.2:+75084898 MS.gene82232:CDS
ATCTATATTGTTGTTATTGT+TGG 0.260502 4.2:-75084379 None:intergenic
TGGTTTGATTTGACTGAAAC+AGG 0.278617 4.2:+75084918 MS.gene82232:CDS
TGATGAAACTGAACAATTCT+TGG 0.299759 4.2:-75084657 None:intergenic
CATAAGAGCATCAAAGGATT+TGG 0.303549 4.2:+75084818 MS.gene82232:CDS
CTTGAGAGACTCTTCTTTGA+TGG 0.320524 4.2:-75084541 None:intergenic
AGTCCCCTGACCCTGAATTC+AGG 0.363541 4.2:+75084271 MS.gene82232:CDS
TGAACCATCATTCGATGAAA+TGG 0.382649 4.2:+75084317 MS.gene82232:CDS
AGCTTGTAAAACCAAGCATT+GGG 0.421130 4.2:-75083853 None:intergenic
CAGATATGATTCCCAATGCT+TGG 0.444868 4.2:+75083842 MS.gene82232:CDS
AATGGTTCTGTAAATTCTCC+TGG 0.454172 4.2:+75084612 MS.gene82232:CDS
TAGCTTGTAAAACCAAGCAT+TGG 0.457451 4.2:-75083854 None:intergenic
GTGTCATCAACGGTGACTTC+CGG 0.457835 4.2:+75084693 MS.gene82232:CDS
TTGAGAGACTCTTCTTTGAT+GGG 0.463202 4.2:-75084540 None:intergenic
TCGGTCCTGAATTCAGGGTC+AGG 0.466344 4.2:-75084276 None:intergenic
GAAACCATTTCATCGAATGA+TGG 0.486121 4.2:-75084321 None:intergenic
TCATCGAATGATGGTTCAGT+TGG 0.490192 4.2:-75084312 None:intergenic
AGAATTGTTCAGTTTCATCA+TGG 0.500576 4.2:+75084660 MS.gene82232:CDS
CAACGGTGACTTCCGGCTAT+CGG 0.501903 4.2:+75084700 MS.gene82232:CDS
GGCTATCGGAGAAGCTTCTC+CGG 0.501925 4.2:+75084714 MS.gene82232:CDS
TTGTTCAGTTTCATCATGGC+CGG 0.517006 4.2:+75084664 MS.gene82232:CDS
GTTGCAAGAACAAGAAGAAG+TGG 0.529061 4.2:-75084349 None:intergenic
TTTATACGAAGTTTCACTCC+AGG 0.530998 4.2:-75084630 None:intergenic
CGGTCCTGAATTCAGGGTCA+GGG 0.533564 4.2:-75084275 None:intergenic
CACGGTCGGTCCTGAATTCA+GGG 0.533725 4.2:-75084281 None:intergenic
GAATAACATAAGAGCATCAA+AGG 0.542179 4.2:+75084812 MS.gene82232:CDS
GTATCATGATCTTATTATCA+AGG 0.547052 4.2:+75084881 MS.gene82232:CDS
TGATTTGACTGAAACAGGGT+AGG 0.547431 4.2:+75084923 MS.gene82232:CDS
GATTTGACTGAAACAGGGTA+GGG 0.553104 4.2:+75084924 MS.gene82232:CDS
CTTCACTATTGCTAGACTAC+CGG 0.553123 4.2:-75084733 None:intergenic
GGAGAAGCTTCTCCGATAGC+CGG 0.561715 4.2:-75084712 None:intergenic
GTCAATGGTGGAGATGATTG+TGG 0.584914 4.2:+75084788 MS.gene82232:CDS
GAAAAGATGATAAACTTGAA+AGG 0.588535 4.2:+75084436 MS.gene82232:CDS
GACTCTCTAAAATCCTTCTG+AGG 0.593112 4.2:-75084768 None:intergenic
GGTCCTGAATTCAGGGTCAG+GGG 0.604260 4.2:-75084274 None:intergenic
GATTCAGTTAAACTATCAAG+TGG 0.609478 4.2:-75084246 None:intergenic
CCGGAAAAGTGTGTCATCAA+CGG 0.613406 4.2:+75084683 MS.gene82232:CDS
AGTTGGTATCAGAACACGGT+CGG 0.669498 4.2:-75084295 None:intergenic
GGTTTGATTTGACTGAAACA+GGG 0.673887 4.2:+75084919 MS.gene82232:CDS
GAACGACGCTTGAATCAGTG+TGG 0.678886 4.2:+75084184 MS.gene82232:CDS
GTTCAGTTGGTATCAGAACA+CGG 0.691441 4.2:-75084299 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCTATATTGTTGTTATTGT+TGG - chr4.2:75084382-75084401 None:intergenic 20.0%
!!! ATTTTCTAGGATTATTACAT+TGG - chr4.2:75083996-75084015 None:intergenic 20.0%
!!! ATTTTTTGATGTTAATGTTG+TGG - chr4.2:75084109-75084128 None:intergenic 20.0%
!!! TTTTACAAGCTAAAAGAAAT+AGG + chr4.2:75083865-75083884 MS.gene82232:intron 20.0%
! AAGAACAAGAAGAAGAAAAA+TGG + chr4.2:75084594-75084613 MS.gene82232:CDS 25.0%
! GAAAAGATGATAAACTTGAA+AGG + chr4.2:75084436-75084455 MS.gene82232:CDS 25.0%
! GTATCATGATCTTATTATCA+AGG + chr4.2:75084881-75084900 MS.gene82232:CDS 25.0%
!! TCTTTTTCTTGTTCTGTTTT+TGG - chr4.2:75084082-75084101 None:intergenic 25.0%
!!! AAAAGGTTGTTTTTTCTTCT+TGG - chr4.2:75083923-75083942 None:intergenic 25.0%
!!! TTTGTGGTGTTTTTGTTTTT+GGG - chr4.2:75084053-75084072 None:intergenic 25.0%
!!! TTTTTGTTTTTGGGTTGTTT+TGG - chr4.2:75084044-75084063 None:intergenic 25.0%
ACAAAAGAGGTAACATGTTT+CGG - chr4.2:75084144-75084163 None:intergenic 30.0%
AGAATTGTTCAGTTTCATCA+TGG + chr4.2:75084660-75084679 MS.gene82232:CDS 30.0%
GATTCAGTTAAACTATCAAG+TGG - chr4.2:75084249-75084268 None:intergenic 30.0%
GTTGTTGAGGATAATGAAAA+AGG - chr4.2:75083940-75083959 None:intergenic 30.0%
TGATGAAACTGAACAATTCT+TGG - chr4.2:75084660-75084679 None:intergenic 30.0%
! CTAGGATTATTACATTGGTT+GGG - chr4.2:75083991-75084010 None:intergenic 30.0%
! GTGAAGTAGTAAGATTTTCT+AGG - chr4.2:75084009-75084028 None:intergenic 30.0%
! TCAAGGTATTCAAGCAAATA+TGG + chr4.2:75084898-75084917 MS.gene82232:CDS 30.0%
! TCTAGGATTATTACATTGGT+TGG - chr4.2:75083992-75084011 None:intergenic 30.0%
!! GAATAACATAAGAGCATCAA+AGG + chr4.2:75084812-75084831 MS.gene82232:CDS 30.0%
!!! ATAGCTGGTTTTGTAATGAT+AGG - chr4.2:75084504-75084523 None:intergenic 30.0%
!!! GTTTGTGGTGTTTTTGTTTT+TGG - chr4.2:75084054-75084073 None:intergenic 30.0%
!!! TTTCTTGTTCTGTTTTTGGA+TGG - chr4.2:75084078-75084097 None:intergenic 30.0%
AGCTTGTAAAACCAAGCATT+GGG - chr4.2:75083856-75083875 None:intergenic 35.0%
GAAACCATTTCATCGAATGA+TGG - chr4.2:75084324-75084343 None:intergenic 35.0%
TGAACCATCATTCGATGAAA+TGG + chr4.2:75084317-75084336 MS.gene82232:CDS 35.0%
TTGAGAGACTCTTCTTTGAT+GGG - chr4.2:75084543-75084562 None:intergenic 35.0%
TTTATACGAAGTTTCACTCC+AGG - chr4.2:75084633-75084652 None:intergenic 35.0%
! AATGGTTCTGTAAATTCTCC+TGG + chr4.2:75084612-75084631 MS.gene82232:CDS 35.0%
! GAAGAAGAAGAGTTTTCATG+AGG - chr4.2:75084225-75084244 None:intergenic 35.0%
! GATTATTACATTGGTTGGGT+TGG - chr4.2:75083987-75084006 None:intergenic 35.0%
! GTCATCTTTTAATCCTCAGA+AGG + chr4.2:75084755-75084774 MS.gene82232:CDS 35.0%
! TAGCTTGTAAAACCAAGCAT+TGG - chr4.2:75083857-75083876 None:intergenic 35.0%
!! CATAAGAGCATCAAAGGATT+TGG + chr4.2:75084818-75084837 MS.gene82232:CDS 35.0%
!! GAAGGATTTTAGAGAGTCAA+TGG + chr4.2:75084773-75084792 MS.gene82232:CDS 35.0%
!! GGTTTGATTTGACTGAAACA+GGG + chr4.2:75084919-75084938 MS.gene82232:CDS 35.0%
!! TGGTTTGATTTGACTGAAAC+AGG + chr4.2:75084918-75084937 MS.gene82232:CDS 35.0%
!! TTGTGCTCATTTTTCATAGC+TGG - chr4.2:75084519-75084538 None:intergenic 35.0%
!!! GGTTGTTTTTTCTTCTTGGA+AGG - chr4.2:75083919-75083938 None:intergenic 35.0%
CAGATATGATTCCCAATGCT+TGG + chr4.2:75083842-75083861 MS.gene82232:CDS 40.0%
CTTCACTATTGCTAGACTAC+CGG - chr4.2:75084736-75084755 None:intergenic 40.0%
CTTGAGAGACTCTTCTTTGA+TGG - chr4.2:75084544-75084563 None:intergenic 40.0%
GGAATGTGTTGAAGTTGTTG+AGG - chr4.2:75083953-75083972 None:intergenic 40.0%
GTTGCAAGAACAAGAAGAAG+TGG - chr4.2:75084352-75084371 None:intergenic 40.0%
TCATCGAATGATGGTTCAGT+TGG - chr4.2:75084315-75084334 None:intergenic 40.0%
TTGTTCAGTTTCATCATGGC+CGG + chr4.2:75084664-75084683 MS.gene82232:CDS 40.0%
! GTTCAGTTGGTATCAGAACA+CGG - chr4.2:75084302-75084321 None:intergenic 40.0%
!! GACTCTCTAAAATCCTTCTG+AGG - chr4.2:75084771-75084790 None:intergenic 40.0%
!! GGATTTTAGAGAGTCAATGG+TGG + chr4.2:75084776-75084795 MS.gene82232:CDS 40.0%
!! TGTTACCTCTTTTGTTTCCG+CGG + chr4.2:75084149-75084168 MS.gene82232:intron 40.0%
!! TTACATTGGTTGGGTTGGTT+TGG - chr4.2:75083982-75084001 None:intergenic 40.0%
!!! CTGTTTTTGGATGGTGTTTG+TGG - chr4.2:75084069-75084088 None:intergenic 40.0%
!!! GCTGGTTTTGTAATGATAGG+AGG - chr4.2:75084501-75084520 None:intergenic 40.0%
! AGTTGGTATCAGAACACGGT+CGG - chr4.2:75084298-75084317 None:intergenic 45.0%
! CCGGAAAAGTGTGTCATCAA+CGG + chr4.2:75084683-75084702 MS.gene82232:CDS 45.0%
! GTCAATGGTGGAGATGATTG+TGG + chr4.2:75084788-75084807 MS.gene82232:CDS 45.0%
!! GTTACCTCTTTTGTTTCCGC+GGG + chr4.2:75084150-75084169 MS.gene82232:intron 45.0%
!!! CCGTTGATGACACACTTTTC+CGG - chr4.2:75084686-75084705 None:intergenic 45.0%
!!! GTTGGGTTGGTTTGGTTTTG+AGG - chr4.2:75083974-75083993 None:intergenic 45.0%
ACAACCCGCGGAAACAAAAG+AGG - chr4.2:75084157-75084176 None:intergenic 50.0%
GAACGACGCTTGAATCAGTG+TGG + chr4.2:75084184-75084203 MS.gene82232:CDS 50.0%
GTGTCATCAACGGTGACTTC+CGG + chr4.2:75084693-75084712 MS.gene82232:CDS 50.0%
ACACGGTCGGTCCTGAATTC+AGG - chr4.2:75084285-75084304 None:intergenic 55.0%
AGTCCCCTGACCCTGAATTC+AGG + chr4.2:75084271-75084290 MS.gene82232:CDS 55.0%
CAACGGTGACTTCCGGCTAT+CGG + chr4.2:75084700-75084719 MS.gene82232:CDS 55.0%
CACGGTCGGTCCTGAATTCA+GGG - chr4.2:75084284-75084303 None:intergenic 55.0%
CGGTCCTGAATTCAGGGTCA+GGG - chr4.2:75084278-75084297 None:intergenic 55.0%
CGTTCGACAACTACAACCCG+CGG - chr4.2:75084169-75084188 None:intergenic 55.0%
GGAGAAGCTTCTCCGATAGC+CGG - chr4.2:75084715-75084734 None:intergenic 55.0%
GGCTATCGGAGAAGCTTCTC+CGG + chr4.2:75084714-75084733 MS.gene82232:CDS 55.0%
GGTCCTGAATTCAGGGTCAG+GGG - chr4.2:75084277-75084296 None:intergenic 55.0%
TCGGTCCTGAATTCAGGGTC+AGG - chr4.2:75084279-75084298 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 75083817 75084944 75083817 ID=MS.gene82232
chr4.2 mRNA 75083817 75084944 75083817 ID=MS.gene82232.t1;Parent=MS.gene82232
chr4.2 exon 75083817 75083863 75083817 ID=MS.gene82232.t1.exon1;Parent=MS.gene82232.t1
chr4.2 CDS 75083817 75083863 75083817 ID=cds.MS.gene82232.t1;Parent=MS.gene82232.t1
chr4.2 exon 75084179 75084944 75084179 ID=MS.gene82232.t1.exon2;Parent=MS.gene82232.t1
chr4.2 CDS 75084179 75084944 75084179 ID=cds.MS.gene82232.t1;Parent=MS.gene82232.t1
Gene Sequence

>MS.gene82232

ATGAGGAATAACAAGTTTAAGCTATCAGATATGATTCCCAATGCTTGGTTTTACAAGCTAAAAGAAATAGGAAAAACAAAAAAGCAAACATCAACAACACCTTCCAAGAAGAAAAAACAACCTTTTTCATTATCCTCAACAACTTCAACACATTCCTCAAAACCAAACCAACCCAACCAATGTAATAATCCTAGAAAATCTTACTACTTCACTAGAGAACTTAACCAAAACAACCCAAAAACAAAAACACCACAAACACCATCCAAAAACAGAACAAGAAAAAGAAGAACCACAACATTAACATCAAAAAATTCTTCTTCTTCTCCGAAACATGTTACCTCTTTTGTTTCCGCGGGTTGTAGTTGTCGAACGACGCTTGAATCAGTGTGGACAAAATCAGATTCTCCTCATGAAAACTCTTCTTCTTCTCCACTTGATAGTTTAACTGAATCAGAGTCCCCTGACCCTGAATTCAGGACCGACCGTGTTCTGATACCAACTGAACCATCATTCGATGAAATGGTTTCGTTAACCACTTCTTCTTGTTCTTGCAACAAAATCTCCAACAATAACAACAATATAGATATTGTTATTGATGTTGATAAAAATTCTCTAGCTAGAAAAGATGATAAACTTGAAAGGTATGATTATTCATATGATTCTTTTTCAAAGCTTGAACTTCCTCCTATCATTACAAAACCAGCTATGAAAAATGAGCACAAACCCATCAAAGAAGAGTCTCTCAAGATTAAAATCATGAATCAACAACAGAAGCAGAAGAACAAGAAGAAGAAAAATGGTTCTGTAAATTCTCCTGGAGTGAAACTTCGTATAAAATCTCCAAGAATTGTTCAGTTTCATCATGGCCGGAAAAGTGTGTCATCAACGGTGACTTCCGGCTATCGGAGAAGCTTCTCCGGTAGTCTAGCAATAGTGAAGTCATCTTTTAATCCTCAGAAGGATTTTAGAGAGTCAATGGTGGAGATGATTGTGGAGAATAACATAAGAGCATCAAAGGATTTGGAAGATCTTCTTGCTTGTTATCTTTCTTTGAATTCAGATGAGTATCATGATCTTATTATCAAGGTATTCAAGCAAATATGGTTTGATTTGACTGAAACAGGGTAG
Protein sequence

>MS.gene82232.t1

MRNNKFKLSDMIPNACCRTTLESVWTKSDSPHENSSSSPLDSLTESESPDPEFRTDRVLIPTEPSFDEMVSLTTSSCSCNKISNNNNNIDIVIDVDKNSLARKDDKLERYDYSYDSFSKLELPPIITKPAMKNEHKPIKEESLKIKIMNQQQKQKNKKKKNGSVNSPGVKLRIKSPRIVQFHHGRKSVSSTVTSGYRRSFSGSLAIVKSSFNPQKDFRESMVEMIVENNIRASKDLEDLLACYLSLNSDEYHDLIIKVFKQIWFDLTETG