AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene064031

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064031.t1 MTR_6g091690 69.811 159 32 2 45 187 643 801 6.44e-65 214
MS.gene064031.t1 MTR_6g091690 69.811 159 32 2 45 187 708 866 1.19e-64 214
MS.gene064031.t1 MTR_6g091710 64.286 98 27 2 26 121 50 141 7.71e-33 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGATCTGGTTTCAGTATT+AGG 0.243148 6.1:+79323928 None:intergenic
GCCTGATGTTGTAGAGTTAT+TGG 0.246788 6.1:+79323954 None:intergenic
TCAGTATCCTCAAAATTATT+AGG 0.251875 6.1:+79323730 None:intergenic
ATTTCTATTTCCTCGGCTTT+CGG 0.284663 6.1:+79323489 None:intergenic
TCTGATGTATTCTTAATATA+AGG 0.320184 6.1:+79323616 None:intergenic
GATGTATATTTGTCCTGAAC+AGG 0.381263 6.1:+79323511 None:intergenic
GTTGAAGATGGTTCATTAGT+TGG 0.397624 6.1:+79323778 None:intergenic
AATACTGAAACCAGATCTTC+AGG 0.417052 6.1:-79323925 MS.gene064031:intron
GCCAATAACTCTACAACATC+AGG 0.419000 6.1:-79323955 MS.gene064031:CDS
CTGAACAGGAGCATCAAAAC+TGG 0.438709 6.1:+79323525 None:intergenic
AGCCGACATTTCTATTTCCT+CGG 0.444211 6.1:+79323482 None:intergenic
GAGTTTCTTCCTGTTGAAGA+TGG 0.444220 6.1:+79323766 None:intergenic
CATTCTGAATGTGAAGTTCA+TGG 0.449411 6.1:+79323401 None:intergenic
AAACGATTTACAACACAGTC+AGG 0.467267 6.1:+79324362 None:intergenic
ACTAATGAACCATCTTCAAC+AGG 0.475523 6.1:-79323775 MS.gene064031:CDS
TGATTCTGATAGCTACGATC+TGG 0.490408 6.1:-79323437 MS.gene064031:CDS
ATTAAGCTACAGAACGTTGA+AGG 0.508639 6.1:-79323671 MS.gene064031:CDS
GAGAAATCTTGCGTAGAAAG+TGG 0.543489 6.1:-79323700 MS.gene064031:CDS
AGATGATGTTTCAACTTCAG+TGG 0.545104 6.1:-79323596 MS.gene064031:CDS
GATGATGTTTCAACTTCAGT+GGG 0.546176 6.1:-79323595 MS.gene064031:CDS
CTGCACACAATCTTTCACTC+TGG 0.560209 6.1:+79323560 None:intergenic
GAGTAGGTCAAGTGCTGCTG+AGG 0.588842 6.1:+79324385 None:intergenic
GATGTATTCTTAATATAAGG+TGG 0.589065 6.1:+79323619 None:intergenic
AGCCGAGGAAATAGAAATGT+CGG 0.590279 6.1:-79323484 MS.gene064031:CDS
ATCTTGCGTAGAAAGTGGCA+TGG 0.614247 6.1:-79323695 MS.gene064031:CDS
AGCTACAGAACGTTGAAGGG+TGG 0.614968 6.1:-79323667 MS.gene064031:CDS
TTAAGCTACAGAACGTTGAA+GGG 0.632705 6.1:-79323670 MS.gene064031:CDS
TAGCATACGATGTCAAAGCA+AGG 0.635240 6.1:-79324419 None:intergenic
AACGATTTACAACACAGTCA+GGG 0.666758 6.1:+79324363 None:intergenic
TTACAACACAGTCAGGGAGT+AGG 0.670169 6.1:+79324369 None:intergenic
AAATATACATCCGAAAGCCG+AGG 0.671474 6.1:-79323499 MS.gene064031:CDS
GTGAAAGATTGTGTGCAGTG+AGG 0.767939 6.1:-79323555 MS.gene064031:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTATCAAAATAAACTA+GGG + chr6.1:79323602-79323621 None:intergenic 10.0%
!!! TTTTTTTATCAAAATAAACT+AGG + chr6.1:79323603-79323622 None:intergenic 10.0%
!! AAAAGAATCTCAAATAATTC+AGG + chr6.1:79323964-79323983 None:intergenic 20.0%
!! ACTATTTATATGTTAAGGTT+GGG - chr6.1:79323651-79323670 MS.gene064031:CDS 20.0%
!! TCTGATGTATTCTTAATATA+AGG + chr6.1:79324193-79324212 None:intergenic 20.0%
!! TTGACACTATTTATATGTTA+AGG - chr6.1:79323646-79323665 MS.gene064031:CDS 20.0%
! ATTTGGAGATAATCATACAA+AGG - chr6.1:79323543-79323562 MS.gene064031:CDS 25.0%
! CACTATTTATATGTTAAGGT+TGG - chr6.1:79323650-79323669 MS.gene064031:CDS 25.0%
! GATGTATTCTTAATATAAGG+TGG + chr6.1:79324190-79324209 None:intergenic 25.0%
! GTGGAAGTCAAAAAAAATTA+TGG - chr6.1:79323992-79324011 MS.gene064031:intron 25.0%
! TCAGTATCCTCAAAATTATT+AGG + chr6.1:79324079-79324098 None:intergenic 25.0%
ATAAAAATACTGTCTAGCTG+AGG - chr6.1:79323492-79323511 MS.gene064031:CDS 30.0%
ATGATTATCTCCAAATGACT+TGG + chr6.1:79323539-79323558 None:intergenic 30.0%
TGATTATCTCCAAATGACTT+GGG + chr6.1:79323538-79323557 None:intergenic 30.0%
TTGTGTTGTAGATGTGAAAT+AGG + chr6.1:79323759-79323778 None:intergenic 30.0%
TTTGTATATGCATCATGCAT+TGG + chr6.1:79323788-79323807 None:intergenic 30.0%
! TGAGGAGCATAATATCAAAT+GGG - chr6.1:79323510-79323529 MS.gene064031:CDS 30.0%
!! GACAGTATTTTTATCTTCGT+TGG + chr6.1:79323486-79323505 None:intergenic 30.0%
!! TAAAAAAGTACCTGAAGATC+TGG + chr6.1:79323894-79323913 None:intergenic 30.0%
!! TTATTTGAGATTCTTTTCGC+AGG - chr6.1:79323967-79323986 MS.gene064031:intron 30.0%
!! TTTTGAGGATACTGAAACTT+TGG - chr6.1:79324084-79324103 MS.gene064031:intron 30.0%
AAACGATTTACAACACAGTC+AGG + chr6.1:79323447-79323466 None:intergenic 35.0%
AACGATTTACAACACAGTCA+GGG + chr6.1:79323446-79323465 None:intergenic 35.0%
AATACTGAAACCAGATCTTC+AGG - chr6.1:79323881-79323900 MS.gene064031:intron 35.0%
ACTAATGAACCATCTTCAAC+AGG - chr6.1:79324031-79324050 MS.gene064031:intron 35.0%
AGATGATGTTTCAACTTCAG+TGG - chr6.1:79324210-79324229 MS.gene064031:intron 35.0%
ATTAAGCTACAGAACGTTGA+AGG - chr6.1:79324135-79324154 MS.gene064031:intron 35.0%
ATTTCTATTTCCTCGGCTTT+CGG + chr6.1:79324320-79324339 None:intergenic 35.0%
CATTCTGAATGTGAAGTTCA+TGG + chr6.1:79324408-79324427 None:intergenic 35.0%
GATGATGTTTCAACTTCAGT+GGG - chr6.1:79324211-79324230 MS.gene064031:intron 35.0%
GATGTATATTTGTCCTGAAC+AGG + chr6.1:79324298-79324317 None:intergenic 35.0%
GGTAGAACATGAACTTGAAA+AGG + chr6.1:79323711-79323730 None:intergenic 35.0%
GTTGAAGATGGTTCATTAGT+TGG + chr6.1:79324031-79324050 None:intergenic 35.0%
TGACTGTGTTGTAAATCGTT+TGG - chr6.1:79323446-79323465 MS.gene064031:CDS 35.0%
TGTTGTAGATGTGAAATAGG+AGG + chr6.1:79323756-79323775 None:intergenic 35.0%
TTAAGCTACAGAACGTTGAA+GGG - chr6.1:79324136-79324155 MS.gene064031:intron 35.0%
! CTGAGGAGCATAATATCAAA+TGG - chr6.1:79323509-79323528 MS.gene064031:CDS 35.0%
! GAAGATCTGGTTTCAGTATT+AGG + chr6.1:79323881-79323900 None:intergenic 35.0%
! GCAGTCACCTAATAATTTTG+AGG - chr6.1:79324069-79324088 MS.gene064031:intron 35.0%
! TCTAAATACTGCTGCTTGAA+AGG - chr6.1:79323823-79323842 MS.gene064031:intron 35.0%
!! TATGCATCATGCATTGGTTT+AGG + chr6.1:79323782-79323801 None:intergenic 35.0%
AAATATACATCCGAAAGCCG+AGG - chr6.1:79324307-79324326 MS.gene064031:intron 40.0%
AAATGGGAACCCAAGTCATT+TGG - chr6.1:79323526-79323545 MS.gene064031:CDS 40.0%
AATCGTTTGGCAAGTTTCTC+TGG - chr6.1:79323459-79323478 MS.gene064031:CDS 40.0%
AGCCGACATTTCTATTTCCT+CGG + chr6.1:79324327-79324346 None:intergenic 40.0%
AGCCGAGGAAATAGAAATGT+CGG - chr6.1:79324322-79324341 MS.gene064031:intron 40.0%
CTTGAAAATGCCTGCTTATG+AGG - chr6.1:79323683-79323702 MS.gene064031:CDS 40.0%
GAGAAATCTTGCGTAGAAAG+TGG - chr6.1:79324106-79324125 MS.gene064031:intron 40.0%
GAGTTTCTTCCTGTTGAAGA+TGG + chr6.1:79324043-79324062 None:intergenic 40.0%
GCCAATAACTCTACAACATC+AGG - chr6.1:79323851-79323870 MS.gene064031:intron 40.0%
GCCTGATGTTGTAGAGTTAT+TGG + chr6.1:79323855-79323874 None:intergenic 40.0%
TGAAAAGGTTCCTCATAAGC+AGG + chr6.1:79323696-79323715 None:intergenic 40.0%
TGATTCTGATAGCTACGATC+TGG - chr6.1:79324369-79324388 MS.gene064031:CDS 40.0%
TTATATGTTAAGGTTGGGCC+AGG - chr6.1:79323656-79323675 MS.gene064031:CDS 40.0%
! AAGGGTGGTTTTCGCAATAA+AGG - chr6.1:79324154-79324173 MS.gene064031:intron 40.0%
!! TTTGAGATTCTTTTCGCAGG+AGG - chr6.1:79323970-79323989 MS.gene064031:intron 40.0%
AAAGGCTTCTCAAGACTTGC+TGG - chr6.1:79323561-79323580 MS.gene064031:CDS 45.0%
ATCTTGCGTAGAAAGTGGCA+TGG - chr6.1:79324111-79324130 MS.gene064031:intron 45.0%
CTGCACACAATCTTTCACTC+TGG + chr6.1:79324249-79324268 None:intergenic 45.0%
GTGAAAGATTGTGTGCAGTG+AGG - chr6.1:79324251-79324270 MS.gene064031:intron 45.0%
TTACAACACAGTCAGGGAGT+AGG + chr6.1:79323440-79323459 None:intergenic 45.0%
! CGCTTTTCATCATGAACAGG+TGG + chr6.1:79323732-79323751 None:intergenic 45.0%
! GGACGCTTTTCATCATGAAC+AGG + chr6.1:79323735-79323754 None:intergenic 45.0%
!! CAGTTTTGATGCTCCTGTTC+AGG - chr6.1:79324282-79324301 MS.gene064031:intron 45.0%
!! CTGAACAGGAGCATCAAAAC+TGG + chr6.1:79324284-79324303 None:intergenic 45.0%
!!! CAGGCATTTTCAAGAGTACC+TGG + chr6.1:79323677-79323696 None:intergenic 45.0%
AGCTACAGAACGTTGAAGGG+TGG - chr6.1:79324139-79324158 MS.gene064031:intron 50.0%
! GAGATTCTTTTCGCAGGAGG+TGG - chr6.1:79323973-79323992 MS.gene064031:intron 50.0%
!! GCTTCTCAAGACTTGCTGGT+AGG - chr6.1:79323565-79323584 MS.gene064031:CDS 50.0%
! GAGTAGGTCAAGTGCTGCTG+AGG + chr6.1:79323424-79323443 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 79323396 79324432 79323396 ID=MS.gene064031
chr6.1 mRNA 79323396 79324432 79323396 ID=MS.gene064031.t1;Parent=MS.gene064031
chr6.1 exon 79324366 79324432 79324366 ID=MS.gene064031.t1.exon1;Parent=MS.gene064031.t1
chr6.1 CDS 79324366 79324432 79324366 ID=cds.MS.gene064031.t1;Parent=MS.gene064031.t1
chr6.1 exon 79323926 79323978 79323926 ID=MS.gene064031.t1.exon2;Parent=MS.gene064031.t1
chr6.1 CDS 79323926 79323978 79323926 ID=cds.MS.gene064031.t1;Parent=MS.gene064031.t1
chr6.1 exon 79323396 79323839 79323396 ID=MS.gene064031.t1.exon3;Parent=MS.gene064031.t1
chr6.1 CDS 79323396 79323839 79323396 ID=cds.MS.gene064031.t1;Parent=MS.gene064031.t1
Gene Sequence

>MS.gene064031

ATGTCAAAGCAAGGAAAAGAATTTACCTCAGCAGCACTTGACCTACTCCCTGACTGTGTTGTAAATCGTTTGGCAAGTTTCTCTGGTCCAACGAAGATAAAAATACTGTCTAGCTGAGGAGCATAATATCAAATGGGAACCCAAGTCATTTGGAGATAATCATACAAAGGCTTCTCAAGACTTGCTGGTAGGATTTGTTTATTCCCTAGTTTATTTTGATAAAAAAAAGTTGTTACTATAGTTTATCATTTTGACACTATTTATATGTTAAGGTTGGGCCAGGTACTCTTGAAAATGCCTGCTTATGAGGAACCTTTTCAAGTTCATGTTCTACCACCTGTTCATGATGAAAAGCGTCCTCCTATTTCACATCTACAACACAACCTAAACCAATGCATGATGCATATACAAATTCGTTTGAGCAGAGTCTAAATACTGCTGCTTGAAAGGATAGTGCCAATAACTCTACAACATCAGGCATGCCTAATACTGAAACCAGATCTTCAGGTACTTTTTTAAAGAAAGTCATTACAATTGAATATCTAAGCTTCTTTTTTGTTCTTTACCTGAATTATTTGAGATTCTTTTCGCAGGAGGTGGAAGTCAAAAAAAATTATGGTTACGATGACTTGCCAACTAATGAACCATCTTCAACAGGAAGAAACTCGACATTGCAGTCACCTAATAATTTTGAGGATACTGAAACTTTGGAGAAATCTTGCGTAGAAAGTGGCATGGAATTAAGCTACAGAACGTTGAAGGGTGGTTTTCGCAATAAAGGTTGTACACAACCACCTTATATTAAGAATACATCAGATGATGTTTCAACTTCAGTGGGAAACATTTCAATCCAGAGTGAAAGATTGTGTGCAGTGAGGATTTCAACCAGTTTTGATGCTCCTGTTCAGGACAAATATACATCCGAAAGCCGAGGAAATAGAAATGTCGGCTTGAAAGCACACAACAAATCTTCTGATTCTGATAGCTACGATCTGGTTGCAGACTCACACCATGAACTTCACATTCAGAATGAGTAG
Protein sequence

>MS.gene064031.t1

MSKQGKEFTSAALDLLPDCVVNLPITLQHQACLILKPDLQEVEVKKNYGYDDLPTNEPSSTGRNSTLQSPNNFEDTETLEKSCVESGMELSYRTLKGGFRNKGCTQPPYIKNTSDDVSTSVGNISIQSERLCAVRISTSFDAPVQDKYTSESRGNRNVGLKAHNKSSDSDSYDLVADSHHELHIQNE