AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene000219

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000219.t1 MTR_6g034975 100.000 210 0 0 1 210 1 210 2.39e-152 421
MS.gene000219.t1 MTR_1g099010 80.465 215 33 3 2 210 6 217 3.86e-114 325
MS.gene000219.t1 MTR_4g094332 64.593 209 71 2 5 210 16 224 3.64e-85 251
MS.gene000219.t1 MTR_4g094328 66.332 199 65 1 14 210 26 224 1.08e-83 248
MS.gene000219.t1 MTR_4g094330 66.332 199 65 1 14 210 26 224 1.08e-83 248
MS.gene000219.t1 MTR_4g094325 62.212 217 71 4 1 210 27 239 7.27e-81 241
MS.gene000219.t1 MTR_2g008110 68.817 186 51 1 20 205 29 207 1.76e-77 231
MS.gene000219.t1 MTR_0119s0010 68.817 186 51 1 20 205 29 207 1.84e-77 231
MS.gene000219.t1 MTR_0119s0020 68.817 186 51 1 20 205 29 207 1.84e-77 231
MS.gene000219.t1 MTR_4g094335 57.075 212 85 2 5 210 20 231 1.42e-67 207
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000219.t1 AT3G43660 67.619 210 56 2 1 210 1 198 1.47e-100 290
MS.gene000219.t1 AT1G21140 74.372 199 42 3 15 210 8 200 7.10e-95 275
MS.gene000219.t1 AT3G43630 74.747 198 41 3 14 208 4 195 1.51e-93 272
MS.gene000219.t1 AT1G76800 72.500 200 41 2 11 210 11 196 7.71e-89 259
MS.gene000219.t1 AT3G25190 57.143 217 86 2 1 210 1 217 1.17e-67 207

Find 23 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCTATGTCCATTACTTT+TGG 0.207489 6.3:+26420737 MS.gene000219:CDS
CAAGATCATATTTGGCTTGT+TGG 0.261485 6.3:-26420175 None:intergenic
TTTGGGCTTACTAAGTTGAT+TGG 0.343858 6.3:+26420755 MS.gene000219:CDS
GGCTACCAACCCGGCAAAAC+CGG 0.371040 6.3:-26420366 None:intergenic
GGTTGGTTAGGGGCTGTGTT+GGG 0.375737 6.3:+26420665 MS.gene000219:CDS
TGGTTGGTTAGGGGCTGTGT+TGG 0.391725 6.3:+26420664 MS.gene000219:CDS
GTTAGGGGCTGTGTTGGGTA+AGG 0.394809 6.3:+26420670 MS.gene000219:CDS
CTCCACAGCTTCGCTAATGA+TGG 0.415096 6.3:+26420301 MS.gene000219:CDS
ATCAAAGCAATGATCTTAAC+CGG 0.418707 6.3:+26420347 MS.gene000219:CDS
GGTGCATGCAGCATGGCAAT+AGG 0.426664 6.3:+26420389 MS.gene000219:CDS
TTGGGCTTACTAAGTTGATT+GGG 0.437883 6.3:+26420756 MS.gene000219:CDS
ATGAAAAGAGAGAAAGAAAG+AGG 0.469828 6.3:+26420458 MS.gene000219:CDS
CTTAGTAAGCCCAAAAGTAA+TGG 0.481590 6.3:-26420747 None:intergenic
GCTGCAGCTTGTAGAGGATT+AGG 0.482303 6.3:-26420518 None:intergenic
GCATGCACCGGCTACCAACC+CGG 0.522518 6.3:-26420375 None:intergenic
TATTGCCATGCTGCATGCAC+CGG 0.557551 6.3:-26420387 None:intergenic
AGGGATTATAAGGTGAGAGT+TGG 0.562126 6.3:+26420602 MS.gene000219:CDS
GGTAGCCGGTGCATGCAGCA+TGG 0.575221 6.3:+26420382 MS.gene000219:CDS
ACCCATCATTAGCGAAGCTG+TGG 0.580136 6.3:-26420303 None:intergenic
TCCACAGCTTCGCTAATGAT+GGG 0.583720 6.3:+26420302 MS.gene000219:CDS
GAAGCTGCTGCAGCTTGTAG+AGG 0.586901 6.3:-26420524 None:intergenic
ACTAAGTTGATTGGGACAAG+TGG 0.608678 6.3:+26420764 MS.gene000219:CDS
GCTTCGCTAATGATGGGTGT+CGG 0.616336 6.3:+26420308 MS.gene000219:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTTAGGTCTGTTTTAA+GGG + chr6.3:26420697-26420716 MS.gene000219:CDS 20.0%
!!! TTTTTTCATAAGGGATTATA+AGG + chr6.3:26420592-26420611 MS.gene000219:CDS 20.0%
! ATAATCCCTTATGAAAAAAG+CGG - chr6.3:26420591-26420610 None:intergenic 25.0%
! CTTAAAACAGACCTAAAAAT+TGG - chr6.3:26420698-26420717 None:intergenic 25.0%
!! ATTTTGCTCAAGATCATATT+TGG - chr6.3:26420186-26420205 None:intergenic 25.0%
!!! AATCTTTTGTTTCAACTTCT+AGG - chr6.3:26420217-26420236 None:intergenic 25.0%
!!! ATCTTTTGTTTCAACTTCTA+GGG - chr6.3:26420216-26420235 None:intergenic 25.0%
!!! CAATTTTTAGGTCTGTTTTA+AGG + chr6.3:26420696-26420715 MS.gene000219:CDS 25.0%
ACTACTCAAAAAGATCACAA+TGG + chr6.3:26420240-26420259 MS.gene000219:CDS 30.0%
ATCAAAGCAATGATCTTAAC+CGG + chr6.3:26420347-26420366 MS.gene000219:CDS 30.0%
ATGAAAAGAGAGAAAGAAAG+AGG + chr6.3:26420458-26420477 MS.gene000219:CDS 30.0%
!! AGTTTTGCTTTGCTTGTTTT+TGG + chr6.3:26420644-26420663 MS.gene000219:CDS 30.0%
!!! TCAGCTTTAGCTTTTTCTAT+TGG + chr6.3:26420545-26420564 MS.gene000219:CDS 30.0%
!!! TCTGTTTTAAGGGTTTTGTT+TGG + chr6.3:26420707-26420726 MS.gene000219:CDS 30.0%
ATGAAAAAAGCGGCAAGTAA+TGG - chr6.3:26420581-26420600 None:intergenic 35.0%
CTTAGTAAGCCCAAAAGTAA+TGG - chr6.3:26420750-26420769 None:intergenic 35.0%
! ATGGCTATGTCCATTACTTT+TGG + chr6.3:26420737-26420756 MS.gene000219:CDS 35.0%
!! AGCTTTTTCTATTGGTGCAA+TGG + chr6.3:26420553-26420572 MS.gene000219:CDS 35.0%
!! CAAGATCATATTTGGCTTGT+TGG - chr6.3:26420178-26420197 None:intergenic 35.0%
!! TGGCTATGTCCATTACTTTT+GGG + chr6.3:26420738-26420757 MS.gene000219:CDS 35.0%
!! TTGGGCTTACTAAGTTGATT+GGG + chr6.3:26420756-26420775 MS.gene000219:CDS 35.0%
!! TTTGGGCTTACTAAGTTGAT+TGG + chr6.3:26420755-26420774 MS.gene000219:CDS 35.0%
!!! ACTTGCCGCTTTTTTCATAA+GGG + chr6.3:26420583-26420602 MS.gene000219:CDS 35.0%
!!! GTTTTAAGGGTTTTGTTTGG+TGG + chr6.3:26420710-26420729 MS.gene000219:CDS 35.0%
!!! TACTTGCCGCTTTTTTCATA+AGG + chr6.3:26420582-26420601 MS.gene000219:CDS 35.0%
!!! TGCTTGTTTTTGGTTGGTTA+GGG + chr6.3:26420654-26420673 MS.gene000219:CDS 35.0%
!!! TTGCTTGTTTTTGGTTGGTT+AGG + chr6.3:26420653-26420672 MS.gene000219:CDS 35.0%
!!! TTGCTTTGCTTGTTTTTGGT+TGG + chr6.3:26420648-26420667 MS.gene000219:CDS 35.0%
AGGGATTATAAGGTGAGAGT+TGG + chr6.3:26420602-26420621 MS.gene000219:CDS 40.0%
! TGGGTAAGGCTCCAATTTTT+AGG + chr6.3:26420684-26420703 MS.gene000219:CDS 40.0%
!! ACTAAGTTGATTGGGACAAG+TGG + chr6.3:26420764-26420783 MS.gene000219:CDS 40.0%
!! ATGATCTTAACCGGTTTTGC+CGG + chr6.3:26420356-26420375 MS.gene000219:CDS 40.0%
!!! GCTTGTTTTTGGTTGGTTAG+GGG + chr6.3:26420655-26420674 MS.gene000219:CDS 40.0%
!!! TAAGGGTTTTGTTTGGTGGT+TGG + chr6.3:26420714-26420733 MS.gene000219:CDS 40.0%
TCCACAGCTTCGCTAATGAT+GGG + chr6.3:26420302-26420321 MS.gene000219:CDS 45.0%
!! TGATCTTAACCGGTTTTGCC+GGG + chr6.3:26420357-26420376 MS.gene000219:CDS 45.0%
!! TGGCTAAGAGCAGCTGTTTT+AGG + chr6.3:26420260-26420279 MS.gene000219:CDS 45.0%
!!! GCTGTTTTAGGAGCTAACGA+CGG + chr6.3:26420272-26420291 MS.gene000219:CDS 45.0%
!!! GGTTTTGTTTGGTGGTTGGA+TGG + chr6.3:26420718-26420737 MS.gene000219:CDS 45.0%
ACCCATCATTAGCGAAGCTG+TGG - chr6.3:26420306-26420325 None:intergenic 50.0%
CTCCACAGCTTCGCTAATGA+TGG + chr6.3:26420301-26420320 MS.gene000219:CDS 50.0%
GCTGCAGCTTGTAGAGGATT+AGG - chr6.3:26420521-26420540 None:intergenic 50.0%
TATTGCCATGCTGCATGCAC+CGG - chr6.3:26420390-26420409 None:intergenic 50.0%
!! GCTTCGCTAATGATGGGTGT+CGG + chr6.3:26420308-26420327 MS.gene000219:CDS 50.0%
GAAGCTGCTGCAGCTTGTAG+AGG - chr6.3:26420527-26420546 None:intergenic 55.0%
GGTGCATGCAGCATGGCAAT+AGG + chr6.3:26420389-26420408 MS.gene000219:CDS 55.0%
GTTAGGGGCTGTGTTGGGTA+AGG + chr6.3:26420670-26420689 MS.gene000219:CDS 55.0%
! GGTTGGTTAGGGGCTGTGTT+GGG + chr6.3:26420665-26420684 MS.gene000219:CDS 55.0%
! TGGTTGGTTAGGGGCTGTGT+TGG + chr6.3:26420664-26420683 MS.gene000219:CDS 55.0%
!! CTTAACCGGTTTTGCCGGGT+TGG + chr6.3:26420361-26420380 MS.gene000219:CDS 55.0%
GGCTACCAACCCGGCAAAAC+CGG - chr6.3:26420369-26420388 None:intergenic 60.0%
!!! GGTTTTGCCGGGTTGGTAGC+CGG + chr6.3:26420368-26420387 MS.gene000219:CDS 60.0%
GGTAGCCGGTGCATGCAGCA+TGG + chr6.3:26420382-26420401 MS.gene000219:CDS 65.0%
!! GCATGCACCGGCTACCAACC+CGG - chr6.3:26420378-26420397 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 26420161 26420793 26420161 ID=MS.gene000219
chr6.3 mRNA 26420161 26420793 26420161 ID=MS.gene000219.t1;Parent=MS.gene000219
chr6.3 exon 26420161 26420793 26420161 ID=MS.gene000219.t1.exon1;Parent=MS.gene000219.t1
chr6.3 CDS 26420161 26420793 26420161 ID=cds.MS.gene000219.t1;Parent=MS.gene000219.t1
Gene Sequence

>MS.gene000219

ATGGCATCACTAAACCAACAAGCCAAATATGATCTTGAGCAAAATTCAACAACCCTAGAAGTTGAAACAAAAGATTTTGACTACTCAAAAAGATCACAATGGCTAAGAGCAGCTGTTTTAGGAGCTAACGACGGATTAGTCTCCACAGCTTCGCTAATGATGGGTGTCGGTGCAGTCAAGCAAGACATCAAAGCAATGATCTTAACCGGTTTTGCCGGGTTGGTAGCCGGTGCATGCAGCATGGCAATAGGTGAATTTGTCTCTGTATACTCACAATTAGACATTGAAGTTGCTCAAATGAAAAGAGAGAAAGAAAGAGGAAGAGAAATCAATGATGATGAAGAGAAAGAAAGTTTGCCTAATCCTCTACAAGCTGCAGCAGCTTCAGCTTTAGCTTTTTCTATTGGTGCAATGGTGCCATTACTTGCCGCTTTTTTCATAAGGGATTATAAGGTGAGAGTTGGTGTTGTTGTAGCTGCAGTTAGTTTTGCTTTGCTTGTTTTTGGTTGGTTAGGGGCTGTGTTGGGTAAGGCTCCAATTTTTAGGTCTGTTTTAAGGGTTTTGTTTGGTGGTTGGATGGCTATGTCCATTACTTTTGGGCTTACTAAGTTGATTGGGACAAGTGGACTTTAG
Protein sequence

>MS.gene000219.t1

MASLNQQAKYDLEQNSTTLEVETKDFDYSKRSQWLRAAVLGANDGLVSTASLMMGVGAVKQDIKAMILTGFAGLVAGACSMAIGEFVSVYSQLDIEVAQMKREKERGREINDDEEKESLPNPLQAAAASALAFSIGAMVPLLAAFFIRDYKVRVGVVVAAVSFALLVFGWLGAVLGKAPIFRSVLRVLFGGWMAMSITFGLTKLIGTSGL