AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene67394

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67394.t1 MTR_6g034975 100.000 181 0 0 1 181 1 181 2.31e-130 364
MS.gene67394.t1 MTR_1g099010 80.108 186 28 3 2 181 6 188 4.82e-95 275
MS.gene67394.t1 MTR_4g094325 62.032 187 60 4 1 180 27 209 1.53e-66 203
MS.gene67394.t1 MTR_4g094332 62.570 179 64 2 5 180 16 194 1.89e-66 202
MS.gene67394.t1 MTR_4g094328 65.089 169 57 1 14 180 26 194 6.69e-66 201
MS.gene67394.t1 MTR_4g094330 65.089 169 57 1 14 180 26 194 6.69e-66 201
MS.gene67394.t1 MTR_0119s0010 68.323 161 44 1 20 180 29 182 9.22e-63 193
MS.gene67394.t1 MTR_0119s0020 68.323 161 44 1 20 180 29 182 9.22e-63 193
MS.gene67394.t1 MTR_2g008110 68.323 161 44 1 20 180 29 182 9.63e-63 193
MS.gene67394.t1 MTR_4g094335 56.111 180 74 1 5 179 20 199 1.65e-54 172
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67394.t1 AT3G43660 68.333 180 45 2 1 180 1 168 1.81e-84 248
MS.gene67394.t1 AT1G21140 75.294 170 33 3 15 181 8 171 4.50e-79 234
MS.gene67394.t1 AT3G43630 76.471 170 31 3 14 180 4 167 5.42e-79 234
MS.gene67394.t1 AT1G76800 72.781 169 32 2 11 179 11 165 3.71e-72 216
MS.gene67394.t1 AT3G25190 58.152 184 70 2 1 177 1 184 6.01e-57 178

Find 18 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGATCATATTTGGCTTGT+TGG 0.261485 6.1:-15549556 None:intergenic
GGCTACCAACCCGGCAAAAC+CGG 0.371040 6.1:-15549747 None:intergenic
GGTTGGTTAGGGGCTGTGTT+GGG 0.375737 6.1:+15550046 MS.gene67394:CDS
TGGTTGGTTAGGGGCTGTGT+TGG 0.391725 6.1:+15550045 MS.gene67394:CDS
GTTAGGGGCTGTGTTGGGTA+AGG 0.394809 6.1:+15550051 MS.gene67394:CDS
CTCCACAGCTTCGCTAATGA+TGG 0.415096 6.1:+15549682 MS.gene67394:CDS
ATCAAAGCAATGATCTTAAC+CGG 0.418707 6.1:+15549728 MS.gene67394:CDS
GGTGCATGCAGCATGGCAAT+AGG 0.426664 6.1:+15549770 MS.gene67394:CDS
ATGAAAAGAGAGAAAGAAAG+AGG 0.469828 6.1:+15549839 MS.gene67394:CDS
GCTGCAGCTTGTAGAGGATT+AGG 0.482303 6.1:-15549899 None:intergenic
GCATGCACCGGCTACCAACC+CGG 0.522518 6.1:-15549756 None:intergenic
TATTGCCATGCTGCATGCAC+CGG 0.557551 6.1:-15549768 None:intergenic
AGGGATTATAAGGTGAGAGT+TGG 0.562126 6.1:+15549983 MS.gene67394:CDS
GGTAGCCGGTGCATGCAGCA+TGG 0.575221 6.1:+15549763 MS.gene67394:CDS
ACCCATCATTAGCGAAGCTG+TGG 0.580136 6.1:-15549684 None:intergenic
TCCACAGCTTCGCTAATGAT+GGG 0.583720 6.1:+15549683 MS.gene67394:CDS
GAAGCTGCTGCAGCTTGTAG+AGG 0.586901 6.1:-15549905 None:intergenic
GCTTCGCTAATGATGGGTGT+CGG 0.616336 6.1:+15549689 MS.gene67394:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTCATAAGGGATTATA+AGG + chr6.1:15549973-15549992 MS.gene67394:CDS 20.0%
! ATAATCCCTTATGAAAAAAG+CGG - chr6.1:15549972-15549991 None:intergenic 25.0%
!! ATTTTGCTCAAGATCATATT+TGG - chr6.1:15549567-15549586 None:intergenic 25.0%
!!! AATCTTTTGTTTCAACTTCT+AGG - chr6.1:15549598-15549617 None:intergenic 25.0%
!!! ATCTTTTGTTTCAACTTCTA+GGG - chr6.1:15549597-15549616 None:intergenic 25.0%
ACTACTCAAAAAGATCACAA+TGG + chr6.1:15549621-15549640 MS.gene67394:CDS 30.0%
ATCAAAGCAATGATCTTAAC+CGG + chr6.1:15549728-15549747 MS.gene67394:CDS 30.0%
ATGAAAAGAGAGAAAGAAAG+AGG + chr6.1:15549839-15549858 MS.gene67394:CDS 30.0%
!! AGTTTTGCTTTGCTTGTTTT+TGG + chr6.1:15550025-15550044 MS.gene67394:CDS 30.0%
!!! TCAGCTTTAGCTTTTTCTAT+TGG + chr6.1:15549926-15549945 MS.gene67394:CDS 30.0%
ATGAAAAAAGCGGCAAGTAA+TGG - chr6.1:15549962-15549981 None:intergenic 35.0%
!! AGCTTTTTCTATTGGTGCAA+TGG + chr6.1:15549934-15549953 MS.gene67394:CDS 35.0%
!! CAAGATCATATTTGGCTTGT+TGG - chr6.1:15549559-15549578 None:intergenic 35.0%
!!! ACTTGCCGCTTTTTTCATAA+GGG + chr6.1:15549964-15549983 MS.gene67394:CDS 35.0%
!!! TACTTGCCGCTTTTTTCATA+AGG + chr6.1:15549963-15549982 MS.gene67394:CDS 35.0%
!!! TGCTTGTTTTTGGTTGGTTA+GGG + chr6.1:15550035-15550054 MS.gene67394:CDS 35.0%
!!! TTGCTTGTTTTTGGTTGGTT+AGG + chr6.1:15550034-15550053 MS.gene67394:CDS 35.0%
!!! TTGCTTTGCTTGTTTTTGGT+TGG + chr6.1:15550029-15550048 MS.gene67394:CDS 35.0%
AGGGATTATAAGGTGAGAGT+TGG + chr6.1:15549983-15550002 MS.gene67394:CDS 40.0%
!! ATGATCTTAACCGGTTTTGC+CGG + chr6.1:15549737-15549756 MS.gene67394:CDS 40.0%
!!! GCTTGTTTTTGGTTGGTTAG+GGG + chr6.1:15550036-15550055 MS.gene67394:CDS 40.0%
TCCACAGCTTCGCTAATGAT+GGG + chr6.1:15549683-15549702 MS.gene67394:CDS 45.0%
!! TGATCTTAACCGGTTTTGCC+GGG + chr6.1:15549738-15549757 MS.gene67394:CDS 45.0%
!! TGGCTAAGAGCAGCTGTTTT+AGG + chr6.1:15549641-15549660 MS.gene67394:CDS 45.0%
!!! GCTGTTTTAGGAGCTAACGA+CGG + chr6.1:15549653-15549672 MS.gene67394:CDS 45.0%
ACCCATCATTAGCGAAGCTG+TGG - chr6.1:15549687-15549706 None:intergenic 50.0%
CTCCACAGCTTCGCTAATGA+TGG + chr6.1:15549682-15549701 MS.gene67394:CDS 50.0%
GCTGCAGCTTGTAGAGGATT+AGG - chr6.1:15549902-15549921 None:intergenic 50.0%
TATTGCCATGCTGCATGCAC+CGG - chr6.1:15549771-15549790 None:intergenic 50.0%
!! GCTTCGCTAATGATGGGTGT+CGG + chr6.1:15549689-15549708 MS.gene67394:CDS 50.0%
GAAGCTGCTGCAGCTTGTAG+AGG - chr6.1:15549908-15549927 None:intergenic 55.0%
GGTGCATGCAGCATGGCAAT+AGG + chr6.1:15549770-15549789 MS.gene67394:CDS 55.0%
GTTAGGGGCTGTGTTGGGTA+AGG + chr6.1:15550051-15550070 MS.gene67394:CDS 55.0%
! GGTTGGTTAGGGGCTGTGTT+GGG + chr6.1:15550046-15550065 MS.gene67394:CDS 55.0%
! TGGTTGGTTAGGGGCTGTGT+TGG + chr6.1:15550045-15550064 MS.gene67394:CDS 55.0%
!! CTTAACCGGTTTTGCCGGGT+TGG + chr6.1:15549742-15549761 MS.gene67394:CDS 55.0%
GGCTACCAACCCGGCAAAAC+CGG - chr6.1:15549750-15549769 None:intergenic 60.0%
!!! GGTTTTGCCGGGTTGGTAGC+CGG + chr6.1:15549749-15549768 MS.gene67394:CDS 60.0%
GGTAGCCGGTGCATGCAGCA+TGG + chr6.1:15549763-15549782 MS.gene67394:CDS 65.0%
!! GCATGCACCGGCTACCAACC+CGG - chr6.1:15549759-15549778 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 15549542 15550086 15549542 ID=MS.gene67394
chr6.1 mRNA 15549542 15550086 15549542 ID=MS.gene67394.t1;Parent=MS.gene67394
chr6.1 exon 15549542 15550086 15549542 ID=MS.gene67394.t1.exon1;Parent=MS.gene67394.t1
chr6.1 CDS 15549542 15550086 15549542 ID=cds.MS.gene67394.t1;Parent=MS.gene67394.t1
Gene Sequence

>MS.gene67394

ATGGCATCACTAAACCAACAAGCCAAATATGATCTTGAGCAAAATTCAACAACCCTAGAAGTTGAAACAAAAGATTTTGACTACTCAAAAAGATCACAATGGCTAAGAGCAGCTGTTTTAGGAGCTAACGACGGATTAGTCTCCACAGCTTCGCTAATGATGGGTGTCGGTGCAGTCAAGCAAGACATCAAAGCAATGATCTTAACCGGTTTTGCCGGGTTGGTAGCCGGTGCATGCAGCATGGCAATAGGTGAATTTGTCTCTGTATACTCACAATTAGACATTGAAGTTGCTCAAATGAAAAGAGAGAAAGAAAGAGGAAGAGAAATCAATGATGATGAAGAGAAAGAAAGTTTGCCTAATCCTCTACAAGCTGCAGCAGCTTCAGCTTTAGCTTTTTCTATTGGTGCAATGGTGCCATTACTTGCCGCTTTTTTCATAAGGGATTATAAGGTGAGAGTTGGTGTTGTTGTAGCTGCAGTTAGTTTTGCTTTGCTTGTTTTTGGTTGGTTAGGGGCTGTGTTGGGTAAGGCTCCAATTTTTAG
Protein sequence

>MS.gene67394.t1

MASLNQQAKYDLEQNSTTLEVETKDFDYSKRSQWLRAAVLGANDGLVSTASLMMGVGAVKQDIKAMILTGFAGLVAGACSMAIGEFVSVYSQLDIEVAQMKREKERGREINDDEEKESLPNPLQAAAASALAFSIGAMVPLLAAFFIRDYKVRVGVVVAAVSFALLVFGWLGAVLGKAPIF