AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41212

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41212.t1 MTR_1g049370 96.996 233 7 0 1 233 1 233 1.73e-172 474
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41212.t1 AT2G39020 68.018 222 68 2 12 232 15 234 4.99e-106 306
MS.gene41212.t1 AT2G39030 61.712 222 83 1 7 228 3 222 2.08e-101 294

Find 68 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGACTCACTGGGGAGAATT+TGG 0.144921 1.4:+36248789 MS.gene41212:CDS
TGGCGTGGGAGGGAGGTTTC+TGG 0.225083 1.4:-36248184 None:intergenic
GAGGTTTCTGGCATGGTTGA+TGG 0.307668 1.4:-36248172 None:intergenic
TGTTATAGAAGGAAAGGATT+TGG 0.322014 1.4:+36248622 MS.gene41212:CDS
GTTATAGAAGGAAAGGATTT+GGG 0.325583 1.4:+36248623 MS.gene41212:CDS
GGGGAGAATTTGGAGGCTTA+TGG 0.326367 1.4:+36248799 MS.gene41212:CDS
TGCGAAACAAGCTGTGAAAA+TGG 0.330688 1.4:+36248666 MS.gene41212:CDS
AGACGGATGCGTGTGAAAAC+TGG 0.343289 1.4:-36248208 None:intergenic
TTTGTGATGGGTTTGTAAAA+TGG 0.346829 1.4:-36248436 None:intergenic
TCTTTCTCTGGGTCATCGAT+TGG 0.358639 1.4:-36248478 None:intergenic
TTGAATGGGTTGTTCTTGAT+TGG 0.376314 1.4:+36248701 MS.gene41212:CDS
AAAATGGGTCGTTGTCGAAA+TGG 0.382151 1.4:-36248420 None:intergenic
CTTTCTCTGGGTCATCGATT+GGG 0.385676 1.4:-36248477 None:intergenic
GGAGGTTCTGTCGGTGGTGG+TGG 0.390585 1.4:-36248151 None:intergenic
TTGTGATGGGTTTGTAAAAT+GGG 0.394107 1.4:-36248435 None:intergenic
TGGAGGCTTTGCAGACTCAC+TGG 0.419524 1.4:+36248778 MS.gene41212:CDS
GGAGAAGAGAGTGGAGGAGT+AGG 0.423379 1.4:-36248326 None:intergenic
TTGTGAGAGAGTGTTATAGA+AGG 0.433799 1.4:+36248611 MS.gene41212:CDS
GAGGATGGTGGTGGAATGGA+AGG 0.442348 1.4:-36248362 None:intergenic
GGTTCTGTCGGTGGTGGTGG+CGG 0.442536 1.4:-36248148 None:intergenic
CCATTTGATGCATTAGTTTG+TGG 0.444519 1.4:-36248258 None:intergenic
AAATGGGTCGTTGTCGAAAT+GGG 0.450614 1.4:-36248419 None:intergenic
TGGTGGTGGCGGTGCTGCGG+CGG 0.464382 1.4:-36248137 None:intergenic
GCGAAACAAGCTGTGAAAAT+GGG 0.467825 1.4:+36248667 MS.gene41212:CDS
TGAAAACTGGGTGGCGTGGG+AGG 0.468784 1.4:-36248195 None:intergenic
GGATGAGGATGGTGGTGGAA+TGG 0.477208 1.4:-36248366 None:intergenic
CCACAAACTAATGCATCAAA+TGG 0.477989 1.4:+36248258 MS.gene41212:CDS
AGAGAGTGTTATAGAAGGAA+AGG 0.484459 1.4:+36248616 MS.gene41212:CDS
TGGATGTAGGGAACGTCGGA+AGG 0.497082 1.4:-36248238 None:intergenic
TGGGGTATGGAAGAGTTGAA+TGG 0.498138 1.4:+36248686 MS.gene41212:CDS
GATGGAGGTTCTGTCGGTGG+TGG 0.500496 1.4:-36248154 None:intergenic
CGTCGGAAGGGGTGGCTAGA+CGG 0.500858 1.4:-36248225 None:intergenic
CGAAATGGGTATCGGTGAAA+GGG 0.509100 1.4:-36248405 None:intergenic
TGGGAGGGAGGTTTCTGGCA+TGG 0.510483 1.4:-36248179 None:intergenic
GGAGGCTTTGCAGACTCACT+GGG 0.510969 1.4:+36248779 MS.gene41212:CDS
TTTGAGAGACTTCAAGGATG+AGG 0.512897 1.4:-36248381 None:intergenic
GAAAACTGGGTGGCGTGGGA+GGG 0.513063 1.4:-36248194 None:intergenic
GGGGTATGGAAGAGTTGAAT+GGG 0.513899 1.4:+36248687 MS.gene41212:CDS
TCGAAATGGGTATCGGTGAA+AGG 0.517532 1.4:-36248406 None:intergenic
ACTCACTGGGGAGAATTTGG+AGG 0.518312 1.4:+36248792 MS.gene41212:CDS
TGCATTAGTTTGTGGATGTA+GGG 0.523176 1.4:-36248250 None:intergenic
CGGTGGTGGTGGCGGTGCTG+CGG 0.526205 1.4:-36248140 None:intergenic
GATGTAGGGAACGTCGGAAG+GGG 0.527743 1.4:-36248236 None:intergenic
ATGCATTAGTTTGTGGATGT+AGG 0.527995 1.4:-36248251 None:intergenic
AACTGGGTGGCGTGGGAGGG+AGG 0.528341 1.4:-36248191 None:intergenic
GTAGGGAACGTCGGAAGGGG+TGG 0.529853 1.4:-36248233 None:intergenic
ATGGTTGATGGAGGTTCTGT+CGG 0.539956 1.4:-36248160 None:intergenic
CAAGCTGTGAAAATGGGGTA+TGG 0.543716 1.4:+36248673 MS.gene41212:CDS
GTTTCTGGCATGGTTGATGG+AGG 0.545304 1.4:-36248169 None:intergenic
ATGTGTGAGTTGTTCGAAAA+CGG 0.552949 1.4:-36248281 None:intergenic
GTGTGAAAACTGGGTGGCGT+GGG 0.564107 1.4:-36248198 None:intergenic
TTCAAGGATGAGGATGGTGG+TGG 0.566001 1.4:-36248371 None:intergenic
TTCAGGGGAGAAGAGAGTGG+AGG 0.567933 1.4:-36248332 None:intergenic
GTCGTTGTCGAAATGGGTAT+CGG 0.570206 1.4:-36248413 None:intergenic
GGATGTAGGGAACGTCGGAA+GGG 0.582464 1.4:-36248237 None:intergenic
GACGGATGCGTGTGAAAACT+GGG 0.582552 1.4:-36248207 None:intergenic
AGAGACTTCAAGGATGAGGA+TGG 0.590756 1.4:-36248377 None:intergenic
CGTGTGAAAACTGGGTGGCG+TGG 0.593886 1.4:-36248199 None:intergenic
CGAAACAAGCTGTGAAAATG+GGG 0.605125 1.4:+36248668 MS.gene41212:CDS
TTTGTGGATGTAGGGAACGT+CGG 0.617809 1.4:-36248242 None:intergenic
GTTGATGGAGGTTCTGTCGG+TGG 0.625153 1.4:-36248157 None:intergenic
GACTTCAAGGATGAGGATGG+TGG 0.644873 1.4:-36248374 None:intergenic
AGGATGGTGGTGGAATGGAA+GGG 0.647470 1.4:-36248361 None:intergenic
GGAGGAGTAGGAAGCTTCTG+TGG 0.649662 1.4:-36248314 None:intergenic
GAAAACTTCAAAACTCAACA+TGG 0.690199 1.4:+36248499 MS.gene41212:CDS
GGAGTAGGAAGCTTCTGTGG+CGG 0.698830 1.4:-36248311 None:intergenic
GAGGCTTTGCAGACTCACTG+GGG 0.729456 1.4:+36248780 MS.gene41212:CDS
GGATGCGTGTGAAAACTGGG+TGG 0.835632 1.4:-36248204 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAAGTTTTATGAAGATAT+GGG + chr1.4:36248736-36248755 MS.gene41212:CDS 15.0%
!!! TATAAAGTTTTATGAAGATA+TGG + chr1.4:36248735-36248754 MS.gene41212:CDS 15.0%
!!! AAGTTGATAGTTTTTGTGAT+GGG - chr1.4:36248451-36248470 None:intergenic 25.0%
!!! TTTTGAAGTTTTCTTTCTCT+GGG - chr1.4:36248492-36248511 None:intergenic 25.0%
CATCACAAAAACTATCAACT+TGG + chr1.4:36248450-36248469 MS.gene41212:CDS 30.0%
GAAAACTTCAAAACTCAACA+TGG + chr1.4:36248499-36248518 MS.gene41212:CDS 30.0%
GTTATAGAAGGAAAGGATTT+GGG + chr1.4:36248623-36248642 MS.gene41212:CDS 30.0%
TGTTATAGAAGGAAAGGATT+TGG + chr1.4:36248622-36248641 MS.gene41212:CDS 30.0%
! GTAATGAAGTTTTTGTTGCT+GGG + chr1.4:36248521-36248540 MS.gene41212:CDS 30.0%
!! TTGTGATGGGTTTGTAAAAT+GGG - chr1.4:36248438-36248457 None:intergenic 30.0%
!! TTTGTGATGGGTTTGTAAAA+TGG - chr1.4:36248439-36248458 None:intergenic 30.0%
!!! CAAGTTGATAGTTTTTGTGA+TGG - chr1.4:36248452-36248471 None:intergenic 30.0%
!!! CCTAACTACTCAACTTTTTT+GGG + chr1.4:36248559-36248578 MS.gene41212:CDS 30.0%
!!! CTAACTACTCAACTTTTTTG+GGG + chr1.4:36248560-36248579 MS.gene41212:CDS 30.0%
!!! GTTTTGAAGTTTTCTTTCTC+TGG - chr1.4:36248493-36248512 None:intergenic 30.0%
!!! TCCTAACTACTCAACTTTTT+TGG + chr1.4:36248558-36248577 MS.gene41212:CDS 30.0%
ATGTGTGAGTTGTTCGAAAA+CGG - chr1.4:36248284-36248303 None:intergenic 35.0%
CCACAAACTAATGCATCAAA+TGG + chr1.4:36248258-36248277 MS.gene41212:CDS 35.0%
CCCAAAAAAGTTGAGTAGTT+AGG - chr1.4:36248562-36248581 None:intergenic 35.0%
! CCATTTGATGCATTAGTTTG+TGG - chr1.4:36248261-36248280 None:intergenic 35.0%
! GGTAATGAAGTTTTTGTTGC+TGG + chr1.4:36248520-36248539 MS.gene41212:CDS 35.0%
!! AATGGAAGGGTTTGTTTTCA+GGG - chr1.4:36248351-36248370 None:intergenic 35.0%
!! AGAGAGTGTTATAGAAGGAA+AGG + chr1.4:36248616-36248635 MS.gene41212:CDS 35.0%
!! ATGCATTAGTTTGTGGATGT+AGG - chr1.4:36248254-36248273 None:intergenic 35.0%
!! TGCATTAGTTTGTGGATGTA+GGG - chr1.4:36248253-36248272 None:intergenic 35.0%
!! TTGAATGGGTTGTTCTTGAT+TGG + chr1.4:36248701-36248720 MS.gene41212:CDS 35.0%
!! TTGTGAGAGAGTGTTATAGA+AGG + chr1.4:36248611-36248630 MS.gene41212:CDS 35.0%
!!! CAACTTTTTTGGGGAAACAT+GGG + chr1.4:36248569-36248588 MS.gene41212:CDS 35.0%
!!! TCAACTTTTTTGGGGAAACA+TGG + chr1.4:36248568-36248587 MS.gene41212:CDS 35.0%
AAAATGGGTCGTTGTCGAAA+TGG - chr1.4:36248423-36248442 None:intergenic 40.0%
AAATGGGTCGTTGTCGAAAT+GGG - chr1.4:36248422-36248441 None:intergenic 40.0%
CGAAACAAGCTGTGAAAATG+GGG + chr1.4:36248668-36248687 MS.gene41212:CDS 40.0%
GCGAAACAAGCTGTGAAAAT+GGG + chr1.4:36248667-36248686 MS.gene41212:CDS 40.0%
TGCGAAACAAGCTGTGAAAA+TGG + chr1.4:36248666-36248685 MS.gene41212:CDS 40.0%
TTTGAGAGACTTCAAGGATG+AGG - chr1.4:36248384-36248403 None:intergenic 40.0%
! CTAAGATTTTGCAGGAATGG+AGG + chr1.4:36248761-36248780 MS.gene41212:CDS 40.0%
! GTGCTAAGATTTTGCAGGAA+TGG + chr1.4:36248758-36248777 MS.gene41212:CDS 40.0%
! TATGGGTGCTAAGATTTTGC+AGG + chr1.4:36248753-36248772 MS.gene41212:CDS 40.0%
!! ATGGAAGGGTTTGTTTTCAG+GGG - chr1.4:36248350-36248369 None:intergenic 40.0%
!! GAATGGAAGGGTTTGTTTTC+AGG - chr1.4:36248352-36248371 None:intergenic 40.0%
!!! AAGGGTTTTGAGAGACTTCA+AGG - chr1.4:36248390-36248409 None:intergenic 40.0%
AGAGACTTCAAGGATGAGGA+TGG - chr1.4:36248380-36248399 None:intergenic 45.0%
CAAGCTGTGAAAATGGGGTA+TGG + chr1.4:36248673-36248692 MS.gene41212:CDS 45.0%
GGGGTATGGAAGAGTTGAAT+GGG + chr1.4:36248687-36248706 MS.gene41212:CDS 45.0%
GTCGTTGTCGAAATGGGTAT+CGG - chr1.4:36248416-36248435 None:intergenic 45.0%
TCTTTCTCTGGGTCATCGAT+TGG - chr1.4:36248481-36248500 None:intergenic 45.0%
TGGGGTATGGAAGAGTTGAA+TGG + chr1.4:36248686-36248705 MS.gene41212:CDS 45.0%
TTTGTGGATGTAGGGAACGT+CGG - chr1.4:36248245-36248264 None:intergenic 45.0%
! CTTTCTCTGGGTCATCGATT+GGG - chr1.4:36248480-36248499 None:intergenic 45.0%
!! ATGGTTGATGGAGGTTCTGT+CGG - chr1.4:36248163-36248182 None:intergenic 45.0%
!! CGAAATGGGTATCGGTGAAA+GGG - chr1.4:36248408-36248427 None:intergenic 45.0%
!! TCGAAATGGGTATCGGTGAA+AGG - chr1.4:36248409-36248428 None:intergenic 45.0%
ACTCACTGGGGAGAATTTGG+AGG + chr1.4:36248792-36248811 MS.gene41212:CDS 50.0%
AGACGGATGCGTGTGAAAAC+TGG - chr1.4:36248211-36248230 None:intergenic 50.0%
CAGACTCACTGGGGAGAATT+TGG + chr1.4:36248789-36248808 MS.gene41212:CDS 50.0%
GACGGATGCGTGTGAAAACT+GGG - chr1.4:36248210-36248229 None:intergenic 50.0%
GACTTCAAGGATGAGGATGG+TGG - chr1.4:36248377-36248396 None:intergenic 50.0%
GGGGAGAATTTGGAGGCTTA+TGG + chr1.4:36248799-36248818 MS.gene41212:CDS 50.0%
! TTCAAGGATGAGGATGGTGG+TGG - chr1.4:36248374-36248393 None:intergenic 50.0%
!! AGGATGGTGGTGGAATGGAA+GGG - chr1.4:36248364-36248383 None:intergenic 50.0%
!! GAGGTTTCTGGCATGGTTGA+TGG - chr1.4:36248175-36248194 None:intergenic 50.0%
!! GTTTCTGGCATGGTTGATGG+AGG - chr1.4:36248172-36248191 None:intergenic 50.0%
!! GTTTTCAGGGGAGAAGAGAG+TGG - chr1.4:36248338-36248357 None:intergenic 50.0%
GAGGCTTTGCAGACTCACTG+GGG + chr1.4:36248780-36248799 MS.gene41212:CDS 55.0%
GATGTAGGGAACGTCGGAAG+GGG - chr1.4:36248239-36248258 None:intergenic 55.0%
GGAGAAGAGAGTGGAGGAGT+AGG - chr1.4:36248329-36248348 None:intergenic 55.0%
GGAGGAGTAGGAAGCTTCTG+TGG - chr1.4:36248317-36248336 None:intergenic 55.0%
GGAGGCTTTGCAGACTCACT+GGG + chr1.4:36248779-36248798 MS.gene41212:CDS 55.0%
GGAGTAGGAAGCTTCTGTGG+CGG - chr1.4:36248314-36248333 None:intergenic 55.0%
GGATGCGTGTGAAAACTGGG+TGG - chr1.4:36248207-36248226 None:intergenic 55.0%
GGATGTAGGGAACGTCGGAA+GGG - chr1.4:36248240-36248259 None:intergenic 55.0%
GTGTGAAAACTGGGTGGCGT+GGG - chr1.4:36248201-36248220 None:intergenic 55.0%
TGGAGGCTTTGCAGACTCAC+TGG + chr1.4:36248778-36248797 MS.gene41212:CDS 55.0%
TGGATGTAGGGAACGTCGGA+AGG - chr1.4:36248241-36248260 None:intergenic 55.0%
TTCAGGGGAGAAGAGAGTGG+AGG - chr1.4:36248335-36248354 None:intergenic 55.0%
! GTTGATGGAGGTTCTGTCGG+TGG - chr1.4:36248160-36248179 None:intergenic 55.0%
!! GAGGATGGTGGTGGAATGGA+AGG - chr1.4:36248365-36248384 None:intergenic 55.0%
!! GGATGAGGATGGTGGTGGAA+TGG - chr1.4:36248369-36248388 None:intergenic 55.0%
CGTGTGAAAACTGGGTGGCG+TGG - chr1.4:36248202-36248221 None:intergenic 60.0%
GAAAACTGGGTGGCGTGGGA+GGG - chr1.4:36248197-36248216 None:intergenic 60.0%
GATGGAGGTTCTGTCGGTGG+TGG - chr1.4:36248157-36248176 None:intergenic 60.0%
TGAAAACTGGGTGGCGTGGG+AGG - chr1.4:36248198-36248217 None:intergenic 60.0%
!! TGGGAGGGAGGTTTCTGGCA+TGG - chr1.4:36248182-36248201 None:intergenic 60.0%
CGTCGGAAGGGGTGGCTAGA+CGG - chr1.4:36248228-36248247 None:intergenic 65.0%
GTAGGGAACGTCGGAAGGGG+TGG - chr1.4:36248236-36248255 None:intergenic 65.0%
TGGCGTGGGAGGGAGGTTTC+TGG - chr1.4:36248187-36248206 None:intergenic 65.0%
! GGAGGTTCTGTCGGTGGTGG+TGG - chr1.4:36248154-36248173 None:intergenic 65.0%
!! GGTTCTGTCGGTGGTGGTGG+CGG - chr1.4:36248151-36248170 None:intergenic 65.0%
AACTGGGTGGCGTGGGAGGG+AGG - chr1.4:36248194-36248213 None:intergenic 70.0%
!! CGGTGGTGGTGGCGGTGCTG+CGG - chr1.4:36248143-36248162 None:intergenic 75.0%
!! TGGTGGTGGCGGTGCTGCGG+CGG - chr1.4:36248140-36248159 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 36248133 36248834 36248133 ID=MS.gene41212
chr1.4 mRNA 36248133 36248834 36248133 ID=MS.gene41212.t1;Parent=MS.gene41212
chr1.4 exon 36248133 36248834 36248133 ID=MS.gene41212.t1.exon1;Parent=MS.gene41212.t1
chr1.4 CDS 36248133 36248834 36248133 ID=cds.MS.gene41212.t1;Parent=MS.gene41212.t1
Gene Sequence

>MS.gene41212

ATGGCCGCCGCAGCACCGCCACCACCACCGACAGAACCTCCATCAACCATGCCAGAAACCTCCCTCCCACGCCACCCAGTTTTCACACGCATCCGTCTAGCCACCCCTTCCGACGTTCCCTACATCCACAAACTAATGCATCAAATGGCCGTTTTCGAACAACTCACACATCTCATGACCGCCACAGAAGCTTCCTACTCCTCCACTCTCTTCTCCCCTGAAAACAAACCCTTCCATTCCACCACCATCCTCATCCTTGAAGTCTCTCAAAACCCTTTCACCGATACCCATTTCGACAACGACCCATTTTACAAACCCATCACAAAAACTATCAACTTGGATCTCCCAATCGATGACCCAGAGAAAGAAAACTTCAAAACTCAACATGGTAATGAAGTTTTTGTTGCTGGGTTTGTTTTGTTTTTTCCTAACTACTCAACTTTTTTGGGGAAACATGGGTTTTATGTTGAAGATCTGTTTGTGAGAGAGTGTTATAGAAGGAAAGGATTTGGGAAGATGTTGCTTACTGCTGTTGCGAAACAAGCTGTGAAAATGGGGTATGGAAGAGTTGAATGGGTTGTTCTTGATTGGAATGTTAATGCTATAAAGTTTTATGAAGATATGGGTGCTAAGATTTTGCAGGAATGGAGGCTTTGCAGACTCACTGGGGAGAATTTGGAGGCTTATGGAGCTATTGAGTAA
Protein sequence

>MS.gene41212.t1

MAAAAPPPPPTEPPSTMPETSLPRHPVFTRIRLATPSDVPYIHKLMHQMAVFEQLTHLMTATEASYSSTLFSPENKPFHSTTILILEVSQNPFTDTHFDNDPFYKPITKTINLDLPIDDPEKENFKTQHGNEVFVAGFVLFFPNYSTFLGKHGFYVEDLFVRECYRRKGFGKMLLTAVAKQAVKMGYGRVEWVVLDWNVNAIKFYEDMGAKILQEWRLCRLTGENLEAYGAIE