AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene60323

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60323.t1 MTR_4g107170 79.863 293 21 2 1 293 1 255 1.70e-168 467
MS.gene60323.t1 MTR_4g045977 54.545 297 104 5 1 293 1 270 1.83e-99 297
MS.gene60323.t1 MTR_2g049610 46.818 220 105 4 1 214 1 214 7.08e-60 191
MS.gene60323.t1 MTR_2g049630 45.320 203 105 4 1 198 1 202 4.97e-53 177
MS.gene60323.t1 MTR_2g049530 50.000 162 78 3 3 162 5 165 3.21e-47 157
MS.gene60323.t1 MTR_1g115290 61.538 117 43 1 38 152 2 118 2.81e-44 148
MS.gene60323.t1 MTR_1g114730 43.226 155 85 1 1 152 1 155 9.50e-37 134
MS.gene60323.t1 MTR_6g018920 38.710 155 92 1 1 152 1 155 3.99e-36 132
MS.gene60323.t1 MTR_6g005440 39.744 156 91 1 1 153 1 156 7.19e-35 128
MS.gene60323.t1 MTR_6g005450 37.419 155 94 1 1 152 1 155 5.15e-30 116
MS.gene60323.t1 MTR_3g466980 31.618 136 87 4 1 135 1 131 2.74e-14 70.9
MS.gene60323.t1 MTR_2g016210 24.074 216 146 4 2 209 3 208 1.58e-13 69.3
MS.gene60323.t1 MTR_3g031240 31.776 107 71 1 1 107 1 105 2.77e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60323.t1 AT5G55690 31.788 151 92 2 1 147 1 144 5.90e-17 79.3
MS.gene60323.t1 AT5G55690 31.788 151 92 2 1 147 1 144 5.90e-17 79.3

Find 48 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTACACTTGTAAGGTCTTC+TGG 0.270047 8.2:+18861713 None:intergenic
AAGTTGTTAATCCTGATTAT+AGG 0.299671 8.2:-18861202 MS.gene60323:CDS
GCACTTTGGATGTATTTCAT+AGG 0.341140 8.2:+18861875 None:intergenic
TCCTGAGATATTTGATGTTA+AGG 0.348371 8.2:-18861648 MS.gene60323:CDS
AGCCCACTAAGTTGGTTTGA+TGG 0.416723 8.2:+18861353 None:intergenic
ACCATCTCACTTGTATAATC+AGG 0.418843 8.2:+18861302 None:intergenic
GATCAACAAGTTGACTAAGT+TGG 0.422061 8.2:+18861123 None:intergenic
GCAAGGAGTTTACACTTGTA+AGG 0.440354 8.2:+18861705 None:intergenic
ACAATCTCACTCCTATAATC+AGG 0.445065 8.2:+18861191 None:intergenic
TATAATCAGGATTAACTACT+TGG 0.446120 8.2:+18861315 None:intergenic
AGTTGGTTTGCTGATGAACT+TGG 0.448642 8.2:+18861140 None:intergenic
AGTTGGTTTGATGGTGAACT+AGG 0.459766 8.2:+18861362 None:intergenic
CTAAAATGTGGATGCCAAGT+TGG 0.479466 8.2:+18861548 None:intergenic
TAAAATGTGGATGCCAAGTT+GGG 0.491000 8.2:+18861549 None:intergenic
GCTTGCTTTATTGTGTATGA+TGG 0.491871 8.2:-18861767 MS.gene60323:CDS
TCATCATCAAACCAACTTAG+TGG 0.501564 8.2:-18861245 MS.gene60323:CDS
TCCTTAACATCAAATATCTC+AGG 0.501707 8.2:+18861647 None:intergenic
TCTCCACAAGCCCACTAAGT+TGG 0.501726 8.2:+18861345 None:intergenic
ACAAATAGAAACTAGCACTT+TGG 0.504283 8.2:-18861429 MS.gene60323:CDS
CTTTGAAAATAAGATAGAAA+AGG 0.507369 8.2:-18861621 MS.gene60323:CDS
TCTCCACAAGCCCACTAAGT+TGG 0.508925 8.2:+18861234 None:intergenic
TTGTAAGAAGTCTGGAGCAA+AGG 0.512867 8.2:-18861789 MS.gene60323:CDS
AACTTGTTGATCTTGATGAC+TGG 0.515181 8.2:-18861112 MS.gene60323:CDS
TCACCATCAAACCAACTTAG+TGG 0.519319 8.2:-18861356 MS.gene60323:CDS
TGATTATAGGAGTGAGATTG+TGG 0.520372 8.2:-18861189 MS.gene60323:CDS
ATTGTGGATTTCACTAGTCT+TGG 0.527589 8.2:-18861173 MS.gene60323:CDS
AGTTGGTTTGATGATGAACT+AGG 0.530891 8.2:+18861251 None:intergenic
TATAATCAGGATTAACAACT+TGG 0.536057 8.2:+18861204 None:intergenic
GAGGATATCTCTCCGCACTT+TGG 0.536952 8.2:+18861583 None:intergenic
AAACCAACTTAGTGGGCTTG+TGG 0.552156 8.2:-18861237 MS.gene60323:CDS
AAACCAACTTAGTGGGCTTG+TGG 0.552156 8.2:-18861348 MS.gene60323:CDS
CATCATCAAACCAACTTAGT+GGG 0.554520 8.2:-18861244 MS.gene60323:CDS
ACTTTCAAACAGAGAAAGCA+TGG 0.556747 8.2:-18861836 MS.gene60323:CDS
AGGTCTTCTGGCCATGTCGT+AGG 0.557005 8.2:+18861725 None:intergenic
TCATCCAAGTTACTAAAATG+TGG 0.567439 8.2:+18861536 None:intergenic
ATGGTGGATTTCACAAGTCT+TGG 0.570027 8.2:-18861284 MS.gene60323:CDS
TGGTTTGCTGATGAACTTGG+AGG 0.570787 8.2:+18861143 None:intergenic
TCAGTAAGATCTACCCAACT+TGG 0.575658 8.2:-18861562 MS.gene60323:CDS
CACCATCAAACCAACTTAGT+GGG 0.576425 8.2:-18861355 MS.gene60323:CDS
ATTCTGATACTCTTGAAGCA+AGG 0.580425 8.2:+18861688 None:intergenic
TGATTATACAAGTGAGATGG+TGG 0.591946 8.2:-18861300 MS.gene60323:CDS
TGGTTTGATGGTGAACTAGG+AGG 0.598871 8.2:+18861365 None:intergenic
TCCTGATTATACAAGTGAGA+TGG 0.603434 8.2:-18861303 MS.gene60323:CDS
TGGATAAATCAACTAGATGA+TGG 0.621105 8.2:-18861092 MS.gene60323:CDS
AAACAAAGATTACCAAAGTG+CGG 0.659281 8.2:-18861595 MS.gene60323:CDS
TGGTTTGATGATGAACTAGG+AGG 0.662339 8.2:+18861254 None:intergenic
ATAATATTGAACCTACGACA+TGG 0.717032 8.2:-18861736 MS.gene60323:CDS
AAGTTGGGTAGATCTTACTG+AGG 0.750378 8.2:+18861564 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAAATAAGATAGAAA+AGG - chr8.2:18861306-18861325 MS.gene60323:CDS 20.0%
! AAGTTGTTAATCCTGATTAT+AGG - chr8.2:18861725-18861744 MS.gene60323:CDS 25.0%
! TATAATCAGGATTAACAACT+TGG + chr8.2:18861726-18861745 None:intergenic 25.0%
! TATAATCAGGATTAACTACT+TGG + chr8.2:18861615-18861634 None:intergenic 25.0%
!!! ATGATTGATTTTTCTGATCT+TGG - chr8.2:18861532-18861551 MS.gene60323:CDS 25.0%
AAACAAAGATTACCAAAGTG+CGG - chr8.2:18861332-18861351 MS.gene60323:CDS 30.0%
ACAAATAGAAACTAGCACTT+TGG - chr8.2:18861498-18861517 MS.gene60323:CDS 30.0%
ATAATATTGAACCTACGACA+TGG - chr8.2:18861191-18861210 MS.gene60323:CDS 30.0%
TCATCCAAGTTACTAAAATG+TGG + chr8.2:18861394-18861413 None:intergenic 30.0%
TCCTGAGATATTTGATGTTA+AGG - chr8.2:18861279-18861298 MS.gene60323:CDS 30.0%
TCCTTAACATCAAATATCTC+AGG + chr8.2:18861283-18861302 None:intergenic 30.0%
TCTTTCCAAAAAAACTCATC+AGG + chr8.2:18861883-18861902 None:intergenic 30.0%
TGGATAAATCAACTAGATGA+TGG - chr8.2:18861835-18861854 MS.gene60323:CDS 30.0%
! TCTGAATTTTGTAAGAAGTC+TGG - chr8.2:18861130-18861149 MS.gene60323:CDS 30.0%
ACAATCTCACTCCTATAATC+AGG + chr8.2:18861739-18861758 None:intergenic 35.0%
ACCATCTCACTTGTATAATC+AGG + chr8.2:18861628-18861647 None:intergenic 35.0%
ACTTTCAAACAGAGAAAGCA+TGG - chr8.2:18861091-18861110 MS.gene60323:CDS 35.0%
ATTCTGATACTCTTGAAGCA+AGG + chr8.2:18861242-18861261 None:intergenic 35.0%
CATCATCAAACCAACTTAGT+GGG - chr8.2:18861683-18861702 MS.gene60323:CDS 35.0%
GCACTTTGGATGTATTTCAT+AGG + chr8.2:18861055-18861074 None:intergenic 35.0%
TAAAATGTGGATGCCAAGTT+GGG + chr8.2:18861381-18861400 None:intergenic 35.0%
TCATCATCAAACCAACTTAG+TGG - chr8.2:18861682-18861701 MS.gene60323:CDS 35.0%
TCCTGATTATACAAGTGAGA+TGG - chr8.2:18861624-18861643 MS.gene60323:CDS 35.0%
TGATTATACAAGTGAGATGG+TGG - chr8.2:18861627-18861646 MS.gene60323:CDS 35.0%
TGATTATAGGAGTGAGATTG+TGG - chr8.2:18861738-18861757 MS.gene60323:CDS 35.0%
TTTACACTTGTAAGGTCTTC+TGG + chr8.2:18861217-18861236 None:intergenic 35.0%
! ATTGTGGATTTCACTAGTCT+TGG - chr8.2:18861754-18861773 MS.gene60323:CDS 35.0%
! GATCAACAAGTTGACTAAGT+TGG + chr8.2:18861807-18861826 None:intergenic 35.0%
! GCTTGCTTTATTGTGTATGA+TGG - chr8.2:18861160-18861179 MS.gene60323:CDS 35.0%
! TTTTGCGAGATTTTGCACTT+TGG + chr8.2:18861069-18861088 None:intergenic 35.0%
!! AACTTGTTGATCTTGATGAC+TGG - chr8.2:18861815-18861834 MS.gene60323:CDS 35.0%
!! AGTTGGTTTGATGATGAACT+AGG + chr8.2:18861679-18861698 None:intergenic 35.0%
!! GCATCCACATTTTAGTAACT+TGG - chr8.2:18861387-18861406 MS.gene60323:CDS 35.0%
!!! GTCAACCTGATGAGTTTTTT+TGG - chr8.2:18861875-18861894 MS.gene60323:CDS 35.0%
AAGTTGGGTAGATCTTACTG+AGG + chr8.2:18861366-18861385 None:intergenic 40.0%
CACCATCAAACCAACTTAGT+GGG - chr8.2:18861572-18861591 MS.gene60323:CDS 40.0%
CTAAAATGTGGATGCCAAGT+TGG + chr8.2:18861382-18861401 None:intergenic 40.0%
GCAAGGAGTTTACACTTGTA+AGG + chr8.2:18861225-18861244 None:intergenic 40.0%
TCACCATCAAACCAACTTAG+TGG - chr8.2:18861571-18861590 MS.gene60323:CDS 40.0%
TCAGTAAGATCTACCCAACT+TGG - chr8.2:18861365-18861384 MS.gene60323:CDS 40.0%
! TTGTAAGAAGTCTGGAGCAA+AGG - chr8.2:18861138-18861157 MS.gene60323:CDS 40.0%
!! AGATGATGGTGTTTTGTGCT+GGG - chr8.2:18861849-18861868 MS.gene60323:CDS 40.0%
!! AGTTGGTTTGATGGTGAACT+AGG + chr8.2:18861568-18861587 None:intergenic 40.0%
!! AGTTGGTTTGCTGATGAACT+TGG + chr8.2:18861790-18861809 None:intergenic 40.0%
!! ATGGTGGATTTCACAAGTCT+TGG - chr8.2:18861643-18861662 MS.gene60323:CDS 40.0%
!! TAGATGATGGTGTTTTGTGC+TGG - chr8.2:18861848-18861867 MS.gene60323:CDS 40.0%
!! TGGTTTGATGATGAACTAGG+AGG + chr8.2:18861676-18861695 None:intergenic 40.0%
!! AAACCAACTTAGTGGGCTTG+TGG - chr8.2:18861579-18861598 MS.gene60323:CDS 45.0%
!! AGCCCACTAAGTTGGTTTGA+TGG + chr8.2:18861577-18861596 None:intergenic 45.0%
!! TGGTTTGATGGTGAACTAGG+AGG + chr8.2:18861565-18861584 None:intergenic 45.0%
!! TGGTTTGCTGATGAACTTGG+AGG + chr8.2:18861787-18861806 None:intergenic 45.0%
GAGGATATCTCTCCGCACTT+TGG + chr8.2:18861347-18861366 None:intergenic 50.0%
TCTCCACAAGCCCACTAAGT+TGG + chr8.2:18861585-18861604 None:intergenic 50.0%
AGGTCTTCTGGCCATGTCGT+AGG + chr8.2:18861205-18861224 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 18861034 18861915 18861034 ID=MS.gene60323
chr8.2 mRNA 18861034 18861915 18861034 ID=MS.gene60323.t1;Parent=MS.gene60323
chr8.2 exon 18861034 18861915 18861034 ID=MS.gene60323.t1.exon1;Parent=MS.gene60323.t1
chr8.2 CDS 18861034 18861915 18861034 ID=cds.MS.gene60323.t1;Parent=MS.gene60323.t1
Gene Sequence

>MS.gene60323

ATGGGTCGCGCAAAAATACCTATGAAATACATCCAAAGTGCAAAATCTCGCAAAATAACTTTCAAACAGAGAAAGCATGGATTAGAAAAGAAAATTTCTGAATTTTGTAAGAAGTCTGGAGCAAAGGCTTGCTTTATTGTGTATGATGGTGATCATAATAATATTGAACCTACGACATGGCCAGAAGACCTTACAAGTGTAAACTCCTTGCTTCAAGAGTATCAGAATCAAAAGATTGAGAAAACTCCTGAGATATTTGATGTTAAGGACTACTTTGAAAATAAGATAGAAAAGGTTGAAACAAAGATTACCAAAGTGCGGAGAGATATCCTCAGTAAGATCTACCCAACTTGGCATCCACATTTTAGTAACTTGGATGAGAATCAACTCAGAGACTTCATTGCTGCAATAAATGCTAAGATTCAAGCTTGCAATCACAAAATTAGCATGTTGAAAAATATGCAACAAATAGAAACTAGCACTTTGGATATATGTGAGATGATTGATTTTTCTGATCTTGGTGATTTTCCTCCTAGTTCACCATCAAACCAACTTAGTGGGCTTGTGGAGATGAATGACCAAGTAGTTAATCCTGATTATACAAGTGAGATGGTGGATTTCACAAGTCTTGGTGATTTGCCTCCTAGTTCATCATCAAACCAACTTAGTGGGCTTGTGGAGATGAGTGACCAAGTTGTTAATCCTGATTATAGGAGTGAGATTGTGGATTTCACTAGTCTTGGTGATTTGCCTCCAAGTTCATCAGCAAACCAACTTAGTCAACTTGTTGATCTTGATGACTGGATAAATCAACTAGATGATGGTGTTTTGTGCTGGGATTGTCAACCTGATGAGTTTTTTTGGAAAGATCTTTCTTTTTAA
Protein sequence

>MS.gene60323.t1

MGRAKIPMKYIQSAKSRKITFKQRKHGLEKKISEFCKKSGAKACFIVYDGDHNNIEPTTWPEDLTSVNSLLQEYQNQKIEKTPEIFDVKDYFENKIEKVETKITKVRRDILSKIYPTWHPHFSNLDENQLRDFIAAINAKIQACNHKISMLKNMQQIETSTLDICEMIDFSDLGDFPPSSPSNQLSGLVEMNDQVVNPDYTSEMVDFTSLGDLPPSSSSNQLSGLVEMSDQVVNPDYRSEIVDFTSLGDLPPSSSANQLSQLVDLDDWINQLDDGVLCWDCQPDEFFWKDLSF