AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1281860


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 13 sgRNAs with CRISPR-Local

Find 142 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATAAAATAACAACCTTT+TGG 0.313884 8_3:-21746323 None:intergenic
TTCGGCTAATGTTGATGTCT+TGG 0.354087 8_3:+21746260 Msa1281860:CDS
ACTAAGTAACATTGAGTTAA+GGG 0.414063 8_3:-21746118 None:intergenic
CAACCTCATTGTTCAGCCTT+GGG 0.443415 8_3:-21746299 None:intergenic
ACAACCTCATTGTTCAGCCT+TGG 0.452193 8_3:-21746300 None:intergenic
GAACAATGAGGTTGTCCAAA+AGG 0.461266 8_3:+21746308 Msa1281860:CDS
CACTAAGTAACATTGAGTTA+AGG 0.471214 8_3:-21746119 None:intergenic
TTAAAGTTGACATTAAAGGC+AGG 0.531244 8_3:-21746352 None:intergenic
TCAAATGAGTCACTATGTGC+AGG 0.551698 8_3:-21746194 None:intergenic
CTCATTGTTCAGCCTTGGGT+AGG 0.565323 8_3:-21746295 None:intergenic
CTTCAAGCAACACCTACCCA+AGG 0.660266 8_3:+21746283 Msa1281860:CDS
CTACCCAAGGCTGAACAATG+AGG 0.671110 8_3:+21746296 Msa1281860:CDS
ATATATCGCTGTGAACACAA+AGG 0.725360 8_3:-21746149 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATTTTCTAAAAAAAAATT+TGG + chr8_3:21745076-21745095 Msa1281860:intron 10.0%
!! TTCATTATAATTATGTTAAA+AGG + chr8_3:21745128-21745147 Msa1281860:intron 10.0%
!!! CAATTTTCTAAAAAAAAATT+TGG + chr8_3:21745076-21745095 Msa1281860:intron 10.0%
!! TTCATTATAATTATGTTAAA+AGG + chr8_3:21745128-21745147 Msa1281860:intron 10.0%
!!! TGATAATTTTTTGTGATATA+AGG + chr8_3:21745032-21745051 Msa1281860:intron 15.0%
!! AACATAATTATAATGAAGAT+TGG - chr8_3:21745125-21745144 None:intergenic 15.0%
!!! TTTGGTTTAATAGTTTTTTT+AGG + chr8_3:21745470-21745489 Msa1281860:intron 15.0%
!!! TTGGTTTAATAGTTTTTTTA+GGG + chr8_3:21745471-21745490 Msa1281860:intron 15.0%
!! TAAAGAGTGAAAATTAAAAA+AGG - chr8_3:21745720-21745739 None:intergenic 15.0%
!!! TTTAGTATTAGTTTCTAAAT+GGG + chr8_3:21745908-21745927 Msa1281860:intron 15.0%
!!! GATTTTTTGTTTTAGTTTTA+TGG + chr8_3:21746034-21746053 Msa1281860:intron 15.0%
!!! TGATAATTTTTTGTGATATA+AGG + chr8_3:21745032-21745051 Msa1281860:intron 15.0%
!! AACATAATTATAATGAAGAT+TGG - chr8_3:21745125-21745144 None:intergenic 15.0%
!!! TTTGGTTTAATAGTTTTTTT+AGG + chr8_3:21745470-21745489 Msa1281860:intron 15.0%
!!! TTGGTTTAATAGTTTTTTTA+GGG + chr8_3:21745471-21745490 Msa1281860:intron 15.0%
!! TAAAGAGTGAAAATTAAAAA+AGG - chr8_3:21745720-21745739 None:intergenic 15.0%
!!! TTTAGTATTAGTTTCTAAAT+GGG + chr8_3:21745908-21745927 Msa1281860:intron 15.0%
!!! GATTTTTTGTTTTAGTTTTA+TGG + chr8_3:21746034-21746053 Msa1281860:intron 15.0%
!! TAATGTGAATTAATGAAGAT+TGG - chr8_3:21745158-21745177 None:intergenic 20.0%
!!! TGGTTTAATAGTTTTTTTAG+GGG + chr8_3:21745472-21745491 Msa1281860:intron 20.0%
!! TAAATAATATACGAAAGTGA+AGG + chr8_3:21745661-21745680 Msa1281860:intron 20.0%
!! ATATTATATGCAATTCTACA+TGG - chr8_3:21745777-21745796 None:intergenic 20.0%
!!! GTTTAGTATTAGTTTCTAAA+TGG + chr8_3:21745907-21745926 Msa1281860:intron 20.0%
!! TAGTTAAAGAATGATTTAGA+TGG - chr8_3:21745959-21745978 None:intergenic 20.0%
!! AACAATTTCTATAATAGATG+AGG + chr8_3:21746095-21746114 Msa1281860:intron 20.0%
!!! TTGATAAAATAACAACCTTT+TGG - chr8_3:21746326-21746345 None:intergenic 20.0%
!! TAATGTGAATTAATGAAGAT+TGG - chr8_3:21745158-21745177 None:intergenic 20.0%
!!! TGGTTTAATAGTTTTTTTAG+GGG + chr8_3:21745472-21745491 Msa1281860:intron 20.0%
!! TAAATAATATACGAAAGTGA+AGG + chr8_3:21745661-21745680 Msa1281860:intron 20.0%
!! ATATTATATGCAATTCTACA+TGG - chr8_3:21745777-21745796 None:intergenic 20.0%
!!! GTTTAGTATTAGTTTCTAAA+TGG + chr8_3:21745907-21745926 Msa1281860:intron 20.0%
!! TAGTTAAAGAATGATTTAGA+TGG - chr8_3:21745959-21745978 None:intergenic 20.0%
!! AACAATTTCTATAATAGATG+AGG + chr8_3:21746095-21746114 Msa1281860:intron 20.0%
!!! TTGATAAAATAACAACCTTT+TGG - chr8_3:21746326-21746345 None:intergenic 20.0%
!! TCTCTAGTCTATTTTATGAA+TGG + chr8_3:21745191-21745210 Msa1281860:intron 25.0%
! TCTAAAGAAAAGACATAAGA+TGG + chr8_3:21745631-21745650 Msa1281860:intron 25.0%
! ATCACTCATTATAGTCTTTA+TGG + chr8_3:21745739-21745758 Msa1281860:intron 25.0%
! ACTAAGTAACATTGAGTTAA+GGG - chr8_3:21746121-21746140 None:intergenic 25.0%
!! TCTCTAGTCTATTTTATGAA+TGG + chr8_3:21745191-21745210 Msa1281860:intron 25.0%
! TCTAAAGAAAAGACATAAGA+TGG + chr8_3:21745631-21745650 Msa1281860:intron 25.0%
! ATCACTCATTATAGTCTTTA+TGG + chr8_3:21745739-21745758 Msa1281860:intron 25.0%
! ACTAAGTAACATTGAGTTAA+GGG - chr8_3:21746121-21746140 None:intergenic 25.0%
ATTGTTGATGCTTCAAACAT+TGG - chr8_3:21745060-21745079 None:intergenic 30.0%
!!! TTATTTGGCTTTGTTTTGTG+TGG + chr8_3:21745373-21745392 Msa1281860:intron 30.0%
CATACCAAAACACAAACATT+GGG - chr8_3:21745420-21745439 None:intergenic 30.0%
TTATTGCTTGTGTTTGTGTA+AGG + chr8_3:21745578-21745597 Msa1281860:intron 30.0%
TGTGTTTGTGTAAGGAAATT+AGG + chr8_3:21745586-21745605 Msa1281860:intron 30.0%
AAAGAAAAGACATAAGATGG+AGG + chr8_3:21745634-21745653 Msa1281860:intron 30.0%
CACTAAGTAACATTGAGTTA+AGG - chr8_3:21746122-21746141 None:intergenic 30.0%
! CATTTTGCAAGCTTTCTTTT+CGG + chr8_3:21746242-21746261 Msa1281860:CDS 30.0%
ATTGTTGATGCTTCAAACAT+TGG - chr8_3:21745060-21745079 None:intergenic 30.0%
!!! TTATTTGGCTTTGTTTTGTG+TGG + chr8_3:21745373-21745392 Msa1281860:intron 30.0%
CATACCAAAACACAAACATT+GGG - chr8_3:21745420-21745439 None:intergenic 30.0%
TTATTGCTTGTGTTTGTGTA+AGG + chr8_3:21745578-21745597 Msa1281860:intron 30.0%
TGTGTTTGTGTAAGGAAATT+AGG + chr8_3:21745586-21745605 Msa1281860:intron 30.0%
AAAGAAAAGACATAAGATGG+AGG + chr8_3:21745634-21745653 Msa1281860:intron 30.0%
CACTAAGTAACATTGAGTTA+AGG - chr8_3:21746122-21746141 None:intergenic 30.0%
! CATTTTGCAAGCTTTCTTTT+CGG + chr8_3:21746242-21746261 Msa1281860:CDS 30.0%
TTCGAATCGAATTCTTCTCT+TGG + chr8_3:21745249-21745268 Msa1281860:intron 35.0%
AATCGAATTCTTCTCTTGGA+GGG + chr8_3:21745253-21745272 Msa1281860:intron 35.0%
TAATAGCTATCTTGTGCTGT+TGG + chr8_3:21745340-21745359 Msa1281860:intron 35.0%
! AATAGCTATCTTGTGCTGTT+GGG + chr8_3:21745341-21745360 Msa1281860:intron 35.0%
!! GTTGGGATTCACTTGTTATT+TGG + chr8_3:21745358-21745377 Msa1281860:intron 35.0%
!!! CTTTGTTTTGTGTGGTTTGT+CGG + chr8_3:21745381-21745400 Msa1281860:intron 35.0%
GCATACCAAAACACAAACAT+TGG - chr8_3:21745421-21745440 None:intergenic 35.0%
! GTTGTTTCAGTTCTGTGTAT+TGG + chr8_3:21745500-21745519 Msa1281860:intron 35.0%
!! TGTATTGGCTCTAGAGTATT+GGG + chr8_3:21745515-21745534 Msa1281860:intron 35.0%
GTTTGTGTAAGGAAATTAGG+AGG + chr8_3:21745589-21745608 Msa1281860:intron 35.0%
TATACGAAAGTGAAGGAGAA+TGG + chr8_3:21745668-21745687 Msa1281860:intron 35.0%
ATATATCGCTGTGAACACAA+AGG - chr8_3:21746152-21746171 None:intergenic 35.0%
TTCGAATCGAATTCTTCTCT+TGG + chr8_3:21745249-21745268 Msa1281860:intron 35.0%
AATCGAATTCTTCTCTTGGA+GGG + chr8_3:21745253-21745272 Msa1281860:intron 35.0%
TAATAGCTATCTTGTGCTGT+TGG + chr8_3:21745340-21745359 Msa1281860:intron 35.0%
! AATAGCTATCTTGTGCTGTT+GGG + chr8_3:21745341-21745360 Msa1281860:intron 35.0%
!! GTTGGGATTCACTTGTTATT+TGG + chr8_3:21745358-21745377 Msa1281860:intron 35.0%
!!! CTTTGTTTTGTGTGGTTTGT+CGG + chr8_3:21745381-21745400 Msa1281860:intron 35.0%
GCATACCAAAACACAAACAT+TGG - chr8_3:21745421-21745440 None:intergenic 35.0%
! GTTGTTTCAGTTCTGTGTAT+TGG + chr8_3:21745500-21745519 Msa1281860:intron 35.0%
!! TGTATTGGCTCTAGAGTATT+GGG + chr8_3:21745515-21745534 Msa1281860:intron 35.0%
GTTTGTGTAAGGAAATTAGG+AGG + chr8_3:21745589-21745608 Msa1281860:intron 35.0%
TATACGAAAGTGAAGGAGAA+TGG + chr8_3:21745668-21745687 Msa1281860:intron 35.0%
ATATATCGCTGTGAACACAA+AGG - chr8_3:21746152-21746171 None:intergenic 35.0%
ACCTGGAGGATAGTTTGAAT+AGG + chr8_3:21745221-21745240 Msa1281860:intron 40.0%
ACCTATTCAAACTATCCTCC+AGG - chr8_3:21745225-21745244 None:intergenic 40.0%
GAATCGAATTCTTCTCTTGG+AGG + chr8_3:21745252-21745271 Msa1281860:intron 40.0%
ATCGAATTCTTCTCTTGGAG+GGG + chr8_3:21745254-21745273 Msa1281860:intron 40.0%
!! AATAGTTTTTGAGCCGTTGC+TGG + chr8_3:21745277-21745296 Msa1281860:intron 40.0%
CTGCTAAAAATCACCAGCAA+CGG - chr8_3:21745293-21745312 None:intergenic 40.0%
AAACATTGGGTGGAAAACAG+AGG - chr8_3:21745407-21745426 None:intergenic 40.0%
! TCCACCCAATGTTTGTGTTT+TGG + chr8_3:21745413-21745432 Msa1281860:intron 40.0%
ACCAAAACACAAACATTGGG+TGG - chr8_3:21745417-21745436 None:intergenic 40.0%
!!! CTAGTGTTGTTTTTGCAGCA+GGG + chr8_3:21745440-21745459 Msa1281860:intron 40.0%
!! GTGTATTGGCTCTAGAGTAT+TGG + chr8_3:21745514-21745533 Msa1281860:intron 40.0%
!! GTATTGGCTCTAGAGTATTG+GGG + chr8_3:21745516-21745535 Msa1281860:intron 40.0%
GAAAGTGAAGGAGAATGGAT+GGG + chr8_3:21745673-21745692 Msa1281860:intron 40.0%
TCAAATGAGTCACTATGTGC+AGG - chr8_3:21746197-21746216 None:intergenic 40.0%
TTCGGCTAATGTTGATGTCT+TGG + chr8_3:21746260-21746279 Msa1281860:CDS 40.0%
GAACAATGAGGTTGTCCAAA+AGG + chr8_3:21746308-21746327 Msa1281860:CDS 40.0%
ACCTGGAGGATAGTTTGAAT+AGG + chr8_3:21745221-21745240 Msa1281860:intron 40.0%
ACCTATTCAAACTATCCTCC+AGG - chr8_3:21745225-21745244 None:intergenic 40.0%
GAATCGAATTCTTCTCTTGG+AGG + chr8_3:21745252-21745271 Msa1281860:intron 40.0%
ATCGAATTCTTCTCTTGGAG+GGG + chr8_3:21745254-21745273 Msa1281860:intron 40.0%
!! AATAGTTTTTGAGCCGTTGC+TGG + chr8_3:21745277-21745296 Msa1281860:intron 40.0%
CTGCTAAAAATCACCAGCAA+CGG - chr8_3:21745293-21745312 None:intergenic 40.0%
AAACATTGGGTGGAAAACAG+AGG - chr8_3:21745407-21745426 None:intergenic 40.0%
! TCCACCCAATGTTTGTGTTT+TGG + chr8_3:21745413-21745432 Msa1281860:intron 40.0%
ACCAAAACACAAACATTGGG+TGG - chr8_3:21745417-21745436 None:intergenic 40.0%
!!! CTAGTGTTGTTTTTGCAGCA+GGG + chr8_3:21745440-21745459 Msa1281860:intron 40.0%
!! GTGTATTGGCTCTAGAGTAT+TGG + chr8_3:21745514-21745533 Msa1281860:intron 40.0%
!! GTATTGGCTCTAGAGTATTG+GGG + chr8_3:21745516-21745535 Msa1281860:intron 40.0%
GAAAGTGAAGGAGAATGGAT+GGG + chr8_3:21745673-21745692 Msa1281860:intron 40.0%
TCAAATGAGTCACTATGTGC+AGG - chr8_3:21746197-21746216 None:intergenic 40.0%
TTCGGCTAATGTTGATGTCT+TGG + chr8_3:21746260-21746279 Msa1281860:CDS 40.0%
GAACAATGAGGTTGTCCAAA+AGG + chr8_3:21746308-21746327 Msa1281860:CDS 40.0%
TTATGAATGGTGCTCGAACC+TGG + chr8_3:21745204-21745223 Msa1281860:intron 45.0%
!!! CGTTGCTGGTGATTTTTAGC+AGG + chr8_3:21745291-21745310 Msa1281860:intron 45.0%
!!! GCTAGTGTTGTTTTTGCAGC+AGG + chr8_3:21745439-21745458 Msa1281860:intron 45.0%
!!! TTGTTTTTGCAGCAGGGTAG+CGG + chr8_3:21745446-21745465 Msa1281860:intron 45.0%
CGAAAGTGAAGGAGAATGGA+TGG + chr8_3:21745672-21745691 Msa1281860:intron 45.0%
CAACCTCATTGTTCAGCCTT+GGG - chr8_3:21746302-21746321 None:intergenic 45.0%
ACAACCTCATTGTTCAGCCT+TGG - chr8_3:21746303-21746322 None:intergenic 45.0%
TTATGAATGGTGCTCGAACC+TGG + chr8_3:21745204-21745223 Msa1281860:intron 45.0%
!!! CGTTGCTGGTGATTTTTAGC+AGG + chr8_3:21745291-21745310 Msa1281860:intron 45.0%
!!! GCTAGTGTTGTTTTTGCAGC+AGG + chr8_3:21745439-21745458 Msa1281860:intron 45.0%
!!! TTGTTTTTGCAGCAGGGTAG+CGG + chr8_3:21745446-21745465 Msa1281860:intron 45.0%
CGAAAGTGAAGGAGAATGGA+TGG + chr8_3:21745672-21745691 Msa1281860:intron 45.0%
CAACCTCATTGTTCAGCCTT+GGG - chr8_3:21746302-21746321 None:intergenic 45.0%
ACAACCTCATTGTTCAGCCT+TGG - chr8_3:21746303-21746322 None:intergenic 45.0%
!!! AATTTTCTAAAAAAAAATTT+GGG + chr8_3:21745077-21745096 Msa1281860:intron 5.0%
!!! AATTTTCTAAAAAAAAATTT+GGG + chr8_3:21745077-21745096 Msa1281860:intron 5.0%
CTTCAAGCAACACCTACCCA+AGG + chr8_3:21746283-21746302 Msa1281860:CDS 50.0%
CTCATTGTTCAGCCTTGGGT+AGG - chr8_3:21746298-21746317 None:intergenic 50.0%
CTACCCAAGGCTGAACAATG+AGG + chr8_3:21746296-21746315 Msa1281860:CDS 50.0%
CTTCAAGCAACACCTACCCA+AGG + chr8_3:21746283-21746302 Msa1281860:CDS 50.0%
CTCATTGTTCAGCCTTGGGT+AGG - chr8_3:21746298-21746317 None:intergenic 50.0%
CTACCCAAGGCTGAACAATG+AGG + chr8_3:21746296-21746315 Msa1281860:CDS 50.0%
TGAATGGTGCTCGAACCTGG+AGG + chr8_3:21745207-21745226 Msa1281860:intron 55.0%
!! TTGCAGCAGGGTAGCGGTTT+TGG + chr8_3:21745452-21745471 Msa1281860:intron 55.0%
!! CTCTAGAGTATTGGGGCGTG+TGG + chr8_3:21745523-21745542 Msa1281860:intron 55.0%
TGAATGGTGCTCGAACCTGG+AGG + chr8_3:21745207-21745226 Msa1281860:intron 55.0%
!! TTGCAGCAGGGTAGCGGTTT+TGG + chr8_3:21745452-21745471 Msa1281860:intron 55.0%
!! CTCTAGAGTATTGGGGCGTG+TGG + chr8_3:21745523-21745542 Msa1281860:intron 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 21745019 21746362 21745019 ID=Msa1281860;Name=Msa1281860
chr8_3 mRNA 21745019 21746362 21745019 ID=Msa1281860-mRNA-1;Parent=Msa1281860;Name=Msa1281860-mRNA-1;_AED=0.55;_eAED=0.96;_QI=0|0|0|0.75|1|1|4|0|89
chr8_3 exon 21745019 21745022 21745019 ID=Msa1281860-mRNA-1:exon:7878;Parent=Msa1281860-mRNA-1
chr8_3 exon 21745054 21745061 21745054 ID=Msa1281860-mRNA-1:exon:7879;Parent=Msa1281860-mRNA-1
chr8_3 exon 21745461 21745467 21745461 ID=Msa1281860-mRNA-1:exon:7880;Parent=Msa1281860-mRNA-1
chr8_3 exon 21746112 21746362 21746112 ID=Msa1281860-mRNA-1:exon:7881;Parent=Msa1281860-mRNA-1
chr8_3 CDS 21745019 21745022 21745019 ID=Msa1281860-mRNA-1:cds;Parent=Msa1281860-mRNA-1
chr8_3 CDS 21745054 21745061 21745054 ID=Msa1281860-mRNA-1:cds;Parent=Msa1281860-mRNA-1
chr8_3 CDS 21745461 21745467 21745461 ID=Msa1281860-mRNA-1:cds;Parent=Msa1281860-mRNA-1
chr8_3 CDS 21746112 21746362 21746112 ID=Msa1281860-mRNA-1:cds;Parent=Msa1281860-mRNA-1
Gene Sequence

>Msa1281860

ATGAGTACCAATGGTAGCGATGAGGCCCTTAACTCAATGTTACTTAGTGTGTGCTACCTTTGTGTTCACAGCGATATATATAATCTCTTTTACACAAGCAACCTGCACATAGTGACTCATTTGATATTTTTCAGCTTCTCAATGCATGTCATTTTGCAAGCTTTCTTTTCGGCTAATGTTGATGTCTTGGCTTCAAGCAACACCTACCCAAGGCTGAACAATGAGGTTGTCCAAAAGGTTGTTATTTTATCAAGCATCGCCTGCCTTTAA

Protein sequence

>Msa1281860

MSTNGSDEALNSMLLSVCYLCVHSDIYNLFYTSNLHIVTHLIFFSFSMHVILQAFFSANVDVLASSNTYPRLNNEVVQKVVILSSIACL*