AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24615

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24615.t1 MTR_4g123470 80.930 215 30 1 1 215 22 225 3.66e-130 365
MS.gene24615.t1 MTR_7g025150 29.231 195 127 2 6 200 24 207 7.78e-21 87.0
MS.gene24615.t1 MTR_4g085790 28.283 198 131 2 3 200 21 207 4.45e-20 85.1
MS.gene24615.t1 MTR_1g090753 38.462 104 64 0 8 111 43 146 1.06e-19 82.8
MS.gene24615.t1 MTR_7g039210 24.878 205 136 2 7 193 26 230 3.13e-15 72.4
MS.gene24615.t1 MTR_4g053550 41.772 79 46 0 4 82 45 123 4.26e-15 69.3
MS.gene24615.t1 MTR_7g113060 83.784 37 6 0 177 213 3 39 1.16e-14 69.7
MS.gene24615.t1 MTR_0014s0220 25.616 203 108 4 6 200 642 809 8.59e-14 70.1
MS.gene24615.t1 MTR_8g468550 41.772 79 46 0 11 89 65 143 2.16e-13 65.9
MS.gene24615.t1 MTR_1g054495 27.179 195 125 5 3 194 21 201 3.95e-13 66.2
MS.gene24615.t1 MTR_5g074790 30.392 102 71 0 4 105 169 270 3.77e-12 64.3
MS.gene24615.t1 MTR_1g054485 37.079 89 56 0 10 98 28 116 9.50e-12 62.0
MS.gene24615.t1 MTR_4g069750 36.486 74 47 0 6 79 24 97 3.37e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGATTATTCTACGAGTTTAA+TGG 0.216834 1.2:-49018396 MS.gene24615:CDS
TTGAAGTTCCTATCTGGATA+TGG 0.289906 1.2:-49018242 MS.gene24615:CDS
CACAATGCATGTAGAAAATC+AGG 0.306799 1.2:-49018744 None:intergenic
GTACCTTTGAAGTTCCTATC+TGG 0.333773 1.2:-49018248 MS.gene24615:CDS
AGGAATTTGCCGAAAGTATC+AGG 0.335653 1.2:+49018095 None:intergenic
AATCATGATGTTTCACTCTA+AGG 0.341428 1.2:+49018075 None:intergenic
TAGGAACTACCTGATACTTT+CGG 0.400617 1.2:-49018104 MS.gene24615:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 1.2:+49017989 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 1.2:+49018355 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 1.2:+49017990 None:intergenic
GAGCAATGGCACTTGCTAGA+TGG 0.455163 1.2:-49018495 MS.gene24615:CDS
TTGTGCTGCCAATGGTATTG+AGG 0.463000 1.2:-49017949 MS.gene24615:CDS
CCAAATGTGATGTTCGGAAA+AGG 0.475440 1.2:-49017984 MS.gene24615:CDS
TGCCGCACTCATGGAATGAT+AGG 0.476633 1.2:+49018284 None:intergenic
CCCATACCAAATGTGATGTT+CGG 0.477035 1.2:-49017990 MS.gene24615:CDS
AAATATTTAGCAACGAAGAA+TGG 0.478005 1.2:+49018531 None:intergenic
TCGTCGATCCATATCCAGAT+AGG 0.486078 1.2:+49018234 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 1.2:-49018428 MS.gene24615:CDS
GTCATGCGTTTATCAACGCT+TGG 0.494559 1.2:+49017866 None:intergenic
ACATGATGTTGCCGCACTCA+TGG 0.495582 1.2:+49018275 None:intergenic
TTTGTATATTTGAGTCTCAC+AGG 0.498944 1.2:+49018017 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 1.2:-49017948 MS.gene24615:CDS
TAAATATTTCTACGAGCTAC+CGG 0.507354 1.2:-49018517 MS.gene24615:CDS
ACAGGAATGATATTGTCATA+AGG 0.528831 1.2:+49018035 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 1.2:-49018432 MS.gene24615:CDS
TCTAGCAAGTGCCATTGCTC+CGG 0.534587 1.2:+49018498 None:intergenic
TGATAGGGTGGATAATCAGC+TGG 0.541144 1.2:+49018300 None:intergenic
CGAACATCACATTTGGTATG+GGG 0.552019 1.2:+49017991 None:intergenic
CTGTCTAACTTCTAGGATGT+CGG 0.570416 1.2:-49018564 MS.gene24615:intron
GTCTCCGCCCTCAATACCAT+TGG 0.581950 1.2:+49017941 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.587936 1.2:-49018489 MS.gene24615:CDS
TATCCAGATAGGAACTTCAA+AGG 0.596572 1.2:+49018245 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 1.2:-49017980 MS.gene24615:CDS
GGCACTTGCTAGATGGTGAT+GGG 0.608333 1.2:-49018488 MS.gene24615:CDS
TGTTCAACAAATCAGTTAGT+CGG 0.609582 1.2:-49018449 MS.gene24615:CDS
TCTACGAGCTACCGGAGCAA+TGG 0.612965 1.2:-49018509 MS.gene24615:CDS
CATGATTACGTCATGTTGTG+TGG 0.630019 1.2:-49018059 MS.gene24615:CDS
ACCCTATCATTCCATGAGTG+CGG 0.636716 1.2:-49018286 MS.gene24615:CDS
GCCGCACTCATGGAATGATA+GGG 0.643165 1.2:+49018285 None:intergenic
GCACTCATGGAATGATAGGG+TGG 0.649652 1.2:+49018288 None:intergenic
TTTCAAGTGCAAGTGCGTCG+TGG 0.669986 1.2:-49017910 MS.gene24615:CDS
CTCCAACCATCTGTCAACAA+CGG 0.679074 1.2:+49018426 None:intergenic
TGGATCGACGAAATCACCAA+AGG 0.681312 1.2:-49018222 MS.gene24615:CDS
TTTGAAATCTACTTCCACCA+AGG 0.697820 1.2:+49018349 None:intergenic
GCTGCCAATGGTATTGAGGG+CGG 0.739556 1.2:-49017945 MS.gene24615:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTTTTTTTCTTTTTTT+AGG - chr1.2:49018495-49018514 MS.gene24615:CDS 10.0%
!! GTTTATATATGCTATAATAA+AGG - chr1.2:49018453-49018472 MS.gene24615:CDS 15.0%
!! AAAAAACAATAAACAACCTT+TGG + chr1.2:49018415-49018434 None:intergenic 20.0%
!! TTAGACAGTGTATTAAAAAA+AGG + chr1.2:49018042-49018061 None:intergenic 20.0%
!! TTCTATTTAAATACGATGAA+GGG - chr1.2:49017924-49017943 MS.gene24615:CDS 20.0%
!! TTTCTATTTAAATACGATGA+AGG - chr1.2:49017923-49017942 MS.gene24615:CDS 20.0%
!!! ATGAAAATTAAATCCTCTTT+TGG - chr1.2:49017969-49017988 MS.gene24615:CDS 20.0%
! AAATATTTAGCAACGAAGAA+TGG + chr1.2:49018090-49018109 None:intergenic 25.0%
! ATATTAAATCCAACCAAAAG+AGG + chr1.2:49017985-49018004 None:intergenic 25.0%
!! AAATTAAATCCTCTTTTGGT+TGG - chr1.2:49017973-49017992 MS.gene24615:CDS 25.0%
!! TTTTGATGCTATTCATTTAG+AGG - chr1.2:49018431-49018450 MS.gene24615:CDS 25.0%
AATCATGATGTTTCACTCTA+AGG + chr1.2:49018546-49018565 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG + chr1.2:49018586-49018605 None:intergenic 30.0%
CGATTATTCTACGAGTTTAA+TGG - chr1.2:49018222-49018241 MS.gene24615:CDS 30.0%
TAATACACTGTCTAACTTCT+AGG - chr1.2:49018047-49018066 MS.gene24615:CDS 30.0%
TGTTCAACAAATCAGTTAGT+CGG - chr1.2:49018169-49018188 MS.gene24615:intron 30.0%
TTTGTATATTTGAGTCTCAC+AGG + chr1.2:49018604-49018623 None:intergenic 30.0%
! ATTATTGTTTTCCAGTACCT+TGG - chr1.2:49018252-49018271 MS.gene24615:CDS 30.0%
! TAAATATTTCTACGAGCTAC+CGG - chr1.2:49018101-49018120 MS.gene24615:CDS 30.0%
TAGGAACTACCTGATACTTT+CGG - chr1.2:49018514-49018533 MS.gene24615:CDS 35.0%
TATCCAGATAGGAACTTCAA+AGG + chr1.2:49018376-49018395 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG - chr1.2:49018376-49018395 MS.gene24615:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr1.2:49018272-49018291 None:intergenic 35.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr1.2:49018638-49018657 MS.gene24615:intron 40.0%
CATGATTACGTCATGTTGTG+TGG - chr1.2:49018559-49018578 MS.gene24615:intron 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr1.2:49018634-49018653 MS.gene24615:intron 40.0%
CCCATACCAAATGTGATGTT+CGG - chr1.2:49018628-49018647 MS.gene24615:intron 40.0%
CCGAACATCACATTTGGTAT+GGG + chr1.2:49018631-49018650 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + chr1.2:49018630-49018649 None:intergenic 40.0%
TCCGAACATCACATTTGGTA+TGG + chr1.2:49018632-49018651 None:intergenic 40.0%
! ATTGTTTTCCAGTACCTTGG+TGG - chr1.2:49018255-49018274 MS.gene24615:CDS 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr1.2:49018637-49018656 None:intergenic 40.0%
!! AGGAATTTGCCGAAAGTATC+AGG + chr1.2:49018526-49018545 None:intergenic 40.0%
!! CTGTCTAACTTCTAGGATGT+CGG - chr1.2:49018054-49018073 MS.gene24615:CDS 40.0%
!! GTACCTTTGAAGTTCCTATC+TGG - chr1.2:49018370-49018389 MS.gene24615:CDS 40.0%
ACCCTATCATTCCATGAGTG+CGG - chr1.2:49018332-49018351 MS.gene24615:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr1.2:49018266-49018285 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr1.2:49018195-49018214 None:intergenic 45.0%
TCGTCGATCCATATCCAGAT+AGG + chr1.2:49018387-49018406 None:intergenic 45.0%
TGATAGGGTGGATAATCAGC+TGG + chr1.2:49018321-49018340 None:intergenic 45.0%
TGGATCGACGAAATCACCAA+AGG - chr1.2:49018396-49018415 MS.gene24615:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr1.2:49018669-49018688 MS.gene24615:intron 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr1.2:49018661-49018680 MS.gene24615:intron 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr1.2:49018670-49018689 MS.gene24615:intron 45.0%
ACATGATGTTGCCGCACTCA+TGG + chr1.2:49018346-49018365 None:intergenic 50.0%
GCACTCATGGAATGATAGGG+TGG + chr1.2:49018333-49018352 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + chr1.2:49018336-49018355 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + chr1.2:49018337-49018356 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG - chr1.2:49018123-49018142 MS.gene24615:intron 50.0%
! GGCACTTGCTAGATGGTGAT+GGG - chr1.2:49018130-49018149 MS.gene24615:intron 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG + chr1.2:49018123-49018142 None:intergenic 50.0%
! TGGCACTTGCTAGATGGTGA+TGG - chr1.2:49018129-49018148 MS.gene24615:intron 50.0%
! TTTCAAGTGCAAGTGCGTCG+TGG - chr1.2:49018708-49018727 MS.gene24615:intron 50.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr1.2:49018186-49018205 MS.gene24615:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr1.2:49018190-49018209 MS.gene24615:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr1.2:49018680-49018699 None:intergenic 55.0%
TCTACGAGCTACCGGAGCAA+TGG - chr1.2:49018109-49018128 MS.gene24615:intron 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr1.2:49018673-49018692 MS.gene24615:intron 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 49017878 49018762 49017878 ID=MS.gene24615
chr1.2 mRNA 49017878 49018762 49017878 ID=MS.gene24615.t1;Parent=MS.gene24615
chr1.2 exon 49018745 49018762 49018745 ID=MS.gene24615.t1.exon1;Parent=MS.gene24615.t1
chr1.2 CDS 49018745 49018762 49018745 ID=cds.MS.gene24615.t1;Parent=MS.gene24615.t1
chr1.2 exon 49018188 49018571 49018188 ID=MS.gene24615.t1.exon2;Parent=MS.gene24615.t1
chr1.2 CDS 49018188 49018571 49018188 ID=cds.MS.gene24615.t1;Parent=MS.gene24615.t1
chr1.2 exon 49017878 49018123 49017878 ID=MS.gene24615.t1.exon3;Parent=MS.gene24615.t1
chr1.2 CDS 49017878 49018123 49017878 ID=cds.MS.gene24615.t1;Parent=MS.gene24615.t1
Gene Sequence

>MS.gene24615

ATGCATGTAGAAAATCAGGTTTGTTTCACTTGATGATTTAATCTTTTTCTATTTAAATACGATGAAGGGAGTTCGTAAACGTATTATGTGCATGAAAATTAAATCCTCTTTTGGTTGGATTTAATATTTTGTGTTGTTTAAATCAGCTTGCAGTTGTTTTTCCTTTTTTTAATACACTGTCTAACTTCTAGGATGTCGGAGAACTACAACCATTCTTCGTTGCTAAATATTTCTACGAGCTACCGGAGCAATGGCACTTGCTAGATGGTGATGGGAATACTCATAACGTCATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTGCGATTATTCTACGAGTTTAATGGAAGTAAGATTATTGTTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCATTGTTTTTGCTCATAACATTACTCCAGCTGATTATCCACCCTATCATTCCATGAGTGCGGCAACATCATGTTATTGTACCTTTGAAGTTCCTATCTGGATATGGATCGACGAAATCACCAAAGGTTGTTTATTGTTTTTTGATGCTATTCATTTAGAGGTTTATATATGCTATAATAAAGGATTTATGTATGTCATTAACAGTTTTTTTTTTCTTTTTTTAGGAACTACCTGATACTTTCGGCAAATTCCTTAGAGTGAAACATCATGATTACGTCATGTTGTGTGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAAACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCGTGGTCAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>MS.gene24615.t1

MHVENQDVGELQPFFVAKYFYELPEQWHLLDGDGNTHNVMFNKSVSRPLLTDGWSALRLFYEFNGSKIIVFQYLGGSRFQIIVFAHNITPADYPPYHSMSAATSCYCTFEVPIWIWIDEITKGCLLFFDAIHLEELPDTFGKFLRVKHHDYVMLCGPYDNIIPVRLKYTNDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVVVKKYVIVSKR