AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908260


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 40 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGCCTTTCGGCCTGATCTT+AGG 0.275595 6_2:-9511299 Msa0908260:CDS
CGCGCGGGTACTTCGTTCTA+AGG 0.329525 6_2:-9511152 None:intergenic
TCGTCCACGGAGGGTGAGTC+AGG 0.342961 6_2:+9511275 None:intergenic
ACCTAGCCTCCTCCGTCCCT+CGG 0.407009 6_2:-9511369 Msa0908260:intron
AACGAAGTACCCGCGCGAGC+AGG 0.426901 6_2:+9511158 None:intergenic
ATTCCTGTACTACCCCTTGT+TGG 0.431214 6_2:+9511344 None:intergenic
CCCTTGTTGGTCCCGAGGGA+CGG 0.434382 6_2:+9511357 None:intergenic
GTGAGTCAGGGCCTAAGATC+AGG 0.453368 6_2:+9511288 None:intergenic
AGGCGTAGTCGATGGACAAC+AGG 0.473069 6_2:+9511316 None:intergenic
TACATGGTCTTACGACTTTG+CGG 0.476001 6_2:-9511737 Msa0908260:CDS
TGTCCATCGACTACGCCTTT+CGG 0.477754 6_2:-9511311 Msa0908260:CDS
TCCAATGCCCCGAAAACCTA+AGG 0.481914 6_2:+9511237 None:intergenic
CCTAGCCTCCTCCGTCCCTC+GGG 0.487169 6_2:-9511368 Msa0908260:intron
TCCGTCCCTCGGGACCAACA+AGG 0.498430 6_2:-9511358 Msa0908260:CDS
TTCGTCCAACCCTGCTCGCG+CGG 0.503688 6_2:-9511168 Msa0908260:CDS
AACCTTGCGGAGGAACCCTT+AGG 0.515988 6_2:-9511253 Msa0908260:CDS
CCGTCCCTCGGGACCAACAA+GGG 0.520911 6_2:-9511357 Msa0908260:CDS
TTGGTCCCGAGGGACGGAGG+AGG 0.522310 6_2:+9511363 None:intergenic
TCGTCCAACCCTGCTCGCGC+GGG 0.525250 6_2:-9511167 Msa0908260:CDS
AGTACCCGCGCGAGCAGGGT+TGG 0.535281 6_2:+9511163 None:intergenic
CTACCCCTTGTTGGTCCCGA+GGG 0.555675 6_2:+9511353 None:intergenic
AACCTAAGGGTTCCTCCGCA+AGG 0.559471 6_2:+9511251 None:intergenic
ACGAAGTACCCGCGCGAGCA+GGG 0.565436 6_2:+9511159 None:intergenic
GGACCAACAAGGGGTAGTAC+AGG 0.569765 6_2:-9511347 Msa0908260:CDS
AGGCCGAAAGGCGTAGTCGA+TGG 0.572797 6_2:+9511308 None:intergenic
TCCTCCGCAAGGTTCGTCCA+CGG 0.575439 6_2:+9511262 None:intergenic
CCGCAAGGTTCGTCCACGGA+GGG 0.579950 6_2:+9511266 None:intergenic
CGTCCACGGAGGGTGAGTCA+GGG 0.596173 6_2:+9511276 None:intergenic
TTGTTGGTCCCGAGGGACGG+AGG 0.609698 6_2:+9511360 None:intergenic
GGCTTGAGTAACGCAAACAT+TGG 0.611831 6_2:+9511208 None:intergenic
CGTCCCTCGGGACCAACAAG+GGG 0.613145 6_2:-9511356 Msa0908260:CDS
ACTACCCCTTGTTGGTCCCG+AGG 0.625318 6_2:+9511352 None:intergenic
GCGAGCAGGGTTGGACGAAG+CGG 0.626879 6_2:+9511172 None:intergenic
GGGCCTAAGATCAGGCCGAA+AGG 0.628716 6_2:+9511296 None:intergenic
CCAATGCCCCGAAAACCTAA+GGG 0.629622 6_2:+9511238 None:intergenic
CCCTCCGTGGACGAACCTTG+CGG 0.633512 6_2:-9511266 Msa0908260:CDS
TCCGCAAGGTTCGTCCACGG+AGG 0.633907 6_2:+9511265 None:intergenic
CGAAGCGGAAGCGAGAATGT+CGG 0.648690 6_2:+9511187 None:intergenic
AGGCCCTGACTCACCCTCCG+TGG 0.655611 6_2:-9511279 Msa0908260:CDS
TCCGTGGACGAACCTTGCGG+AGG 0.674144 6_2:-9511263 Msa0908260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTTTTTCAGGGTAAGAAG+GGG + chr6_2:9511456-9511475 None:intergenic 35.0%
!!! CTGTTTTTTCAGGGTAAGAA+GGG + chr6_2:9511457-9511476 None:intergenic 35.0%
CTTCTTACCCTGAAAAAACA+GGG - chr6_2:9511456-9511475 Msa0908260:intron 35.0%
TTCTTACCCTGAAAAAACAG+GGG - chr6_2:9511457-9511476 Msa0908260:intron 35.0%
TTGAACCGATAACCATCTTT+CGG - chr6_2:9511493-9511512 Msa0908260:intron 35.0%
CGACTGTTTACCAAAAACAC+AGG + chr6_2:9511180-9511199 None:intergenic 40.0%
! ACAACTCTCTCTAAGGAACT+CGG + chr6_2:9511273-9511292 None:intergenic 40.0%
! TACAGGTACCCTTTTGTTGA+AGG - chr6_2:9511341-9511360 Msa0908260:CDS 40.0%
TCGAACGACCTTCAACAAAA+GGG + chr6_2:9511352-9511371 None:intergenic 40.0%
!!! CCTGTTTTTTCAGGGTAAGA+AGG + chr6_2:9511458-9511477 None:intergenic 40.0%
CCTTCTTACCCTGAAAAAAC+AGG - chr6_2:9511455-9511474 Msa0908260:intron 40.0%
!! GTTATCGGTTCAAGAACACA+AGG + chr6_2:9511486-9511505 None:intergenic 40.0%
GTTAGCCGAAAGATGGTTAT+CGG + chr6_2:9511501-9511520 None:intergenic 40.0%
! TTTGCGGAGACCTGTGTTTT+TGG - chr6_2:9511167-9511186 Msa0908260:CDS 45.0%
!!! GTTTTTGGTAAACAGTCGCC+CGG - chr6_2:9511182-9511201 Msa0908260:CDS 45.0%
!! TTTTTGGTAAACAGTCGCCC+GGG - chr6_2:9511183-9511202 Msa0908260:CDS 45.0%
CAAAATAGCCCCGTAACTTC+GGG + chr6_2:9511250-9511269 None:intergenic 45.0%
GCAAAATAGCCCCGTAACTT+CGG + chr6_2:9511251-9511270 None:intergenic 45.0%
GGTAGGTAGAGAATACCTAG+GGG + chr6_2:9511302-9511321 None:intergenic 45.0%
GGGTAGGTAGAGAATACCTA+GGG + chr6_2:9511303-9511322 None:intergenic 45.0%
TGGGTAGGTAGAGAATACCT+AGG + chr6_2:9511304-9511323 None:intergenic 45.0%
CTCGAACGACCTTCAACAAA+AGG + chr6_2:9511353-9511372 None:intergenic 45.0%
GTAATTGATGCCATACTCCC+AGG + chr6_2:9511381-9511400 None:intergenic 45.0%
!!! AGGTGACCCCTGTTTTTTCA+GGG + chr6_2:9511466-9511485 None:intergenic 45.0%
!!! AAGGTGACCCCTGTTTTTTC+AGG + chr6_2:9511467-9511486 None:intergenic 45.0%
ATTCCTGTACTACCCCTTGT+TGG + chr6_2:9511547-9511566 None:intergenic 45.0%
GGCTTGAGTAACGCAAACAT+TGG + chr6_2:9511683-9511702 None:intergenic 45.0%
! AAGGTCGTTCGAGCTTTTCC+TGG - chr6_2:9511360-9511379 Msa0908260:CDS 50.0%
! AGGTCGTTCGAGCTTTTCCT+GGG - chr6_2:9511361-9511380 Msa0908260:CDS 50.0%
! TCGAGCTTTTCCTGGGAGTA+TGG - chr6_2:9511368-9511387 Msa0908260:intron 50.0%
GGCATCAATTACTTCAGCGC+CGG - chr6_2:9511389-9511408 Msa0908260:intron 50.0%
AGAGAAAATGCCTCCAGCCA+AGG + chr6_2:9511432-9511451 None:intergenic 50.0%
! AGGCTAGGTTAGCCGAAAGA+TGG + chr6_2:9511508-9511527 None:intergenic 50.0%
! TGTCCATCGACTACGCCTTT+CGG - chr6_2:9511577-9511596 Msa0908260:intron 50.0%
! CGGAGGAACCCTTAGGTTTT+CGG - chr6_2:9511642-9511661 Msa0908260:intron 50.0%
! GGAGGAACCCTTAGGTTTTC+GGG - chr6_2:9511643-9511662 Msa0908260:intron 50.0%
! GAGGAACCCTTAGGTTTTCG+GGG - chr6_2:9511644-9511663 Msa0908260:intron 50.0%
CCAATGCCCCGAAAACCTAA+GGG + chr6_2:9511653-9511672 None:intergenic 50.0%
TCCAATGCCCCGAAAACCTA+AGG + chr6_2:9511654-9511673 None:intergenic 50.0%
!! AAGGGGTGCCTCCTCACAAA+GGG + chr6_2:9511225-9511244 None:intergenic 55.0%
CACCCCTTCTCCCGAAGTTA+CGG - chr6_2:9511237-9511256 Msa0908260:CDS 55.0%
ACCCCTTCTCCCGAAGTTAC+GGG - chr6_2:9511238-9511257 Msa0908260:CDS 55.0%
GCGCGAGACAACTCTCTCTA+AGG + chr6_2:9511280-9511299 None:intergenic 55.0%
CTCTACCTACCCACCTGTGT+CGG - chr6_2:9511311-9511330 Msa0908260:CDS 55.0%
!! CTACCCACCTGTGTCGGTTT+CGG - chr6_2:9511317-9511336 Msa0908260:CDS 55.0%
!! TACCCACCTGTGTCGGTTTC+GGG - chr6_2:9511318-9511337 Msa0908260:CDS 55.0%
TACCCGAAACCGACACAGGT+GGG + chr6_2:9511323-9511342 None:intergenic 55.0%
GGACCAACAAGGGGTAGTAC+AGG - chr6_2:9511541-9511560 Msa0908260:intron 55.0%
AGGCGTAGTCGATGGACAAC+AGG + chr6_2:9511575-9511594 None:intergenic 55.0%
ACGCCTTTCGGCCTGATCTT+AGG - chr6_2:9511589-9511608 Msa0908260:intron 55.0%
GTGAGTCAGGGCCTAAGATC+AGG + chr6_2:9511603-9511622 None:intergenic 55.0%
AACCTTGCGGAGGAACCCTT+AGG - chr6_2:9511635-9511654 Msa0908260:intron 55.0%
AACCTAAGGGTTCCTCCGCA+AGG + chr6_2:9511640-9511659 None:intergenic 55.0%
!! CCCTTAGGTTTTCGGGGCAT+TGG - chr6_2:9511650-9511669 Msa0908260:intron 55.0%
CGAAGCGGAAGCGAGAATGT+CGG + chr6_2:9511704-9511723 None:intergenic 55.0%
TCACTGCGACCCCCTTTGTG+AGG - chr6_2:9511211-9511230 Msa0908260:CDS 60.0%
!! AGGGGTGCCTCCTCACAAAG+GGG + chr6_2:9511224-9511243 None:intergenic 60.0%
!! GAAGGGGTGCCTCCTCACAA+AGG + chr6_2:9511226-9511245 None:intergenic 60.0%
CCCCGTAACTTCGGGAGAAG+GGG + chr6_2:9511242-9511261 None:intergenic 60.0%
CCCCTTCTCCCGAAGTTACG+GGG - chr6_2:9511239-9511258 Msa0908260:CDS 60.0%
GCCCCGTAACTTCGGGAGAA+GGG + chr6_2:9511243-9511262 None:intergenic 60.0%
AGCCCCGTAACTTCGGGAGA+AGG + chr6_2:9511244-9511263 None:intergenic 60.0%
CGAAACCGACACAGGTGGGT+AGG + chr6_2:9511319-9511338 None:intergenic 60.0%
GTACCCGAAACCGACACAGG+TGG + chr6_2:9511324-9511343 None:intergenic 60.0%
CCTGTACCCGAAACCGACAC+AGG + chr6_2:9511327-9511346 None:intergenic 60.0%
!! CCTGTGTCGGTTTCGGGTAC+AGG - chr6_2:9511324-9511343 Msa0908260:CDS 60.0%
AGCGCCTGGTACTCGAACCT+TGG - chr6_2:9511412-9511431 Msa0908260:intron 60.0%
CCAGCCAAGGTTCGAGTACC+AGG + chr6_2:9511419-9511438 None:intergenic 60.0%
CCTGGTACTCGAACCTTGGC+TGG - chr6_2:9511416-9511435 Msa0908260:intron 60.0%
GGTACTCGAACCTTGGCTGG+AGG - chr6_2:9511419-9511438 Msa0908260:intron 60.0%
CTACCCCTTGTTGGTCCCGA+GGG + chr6_2:9511538-9511557 None:intergenic 60.0%
ACTACCCCTTGTTGGTCCCG+AGG + chr6_2:9511539-9511558 None:intergenic 60.0%
! AGGCCGAAAGGCGTAGTCGA+TGG + chr6_2:9511583-9511602 None:intergenic 60.0%
GGGCCTAAGATCAGGCCGAA+AGG + chr6_2:9511595-9511614 None:intergenic 60.0%
TCCTCCGCAAGGTTCGTCCA+CGG + chr6_2:9511629-9511648 None:intergenic 60.0%
CAAAGGGGGTCGCAGTGACC+AGG + chr6_2:9511209-9511228 None:intergenic 65.0%
CTGCGACCCCCTTTGTGAGG+AGG - chr6_2:9511214-9511233 Msa0908260:CDS 65.0%
! GGGGTGCCTCCTCACAAAGG+GGG + chr6_2:9511223-9511242 None:intergenic 65.0%
GAGAGTTGTCTCGCGCCCCT+AGG - chr6_2:9511284-9511303 Msa0908260:CDS 65.0%
GGTTCGAGTACCAGGCGCTC+CGG + chr6_2:9511411-9511430 None:intergenic 65.0%
ACCTAGCCTCCTCCGTCCCT+CGG - chr6_2:9511519-9511538 Msa0908260:intron 65.0%
TTGTTGGTCCCGAGGGACGG+AGG + chr6_2:9511531-9511550 None:intergenic 65.0%
TCCGTCCCTCGGGACCAACA+AGG - chr6_2:9511530-9511549 Msa0908260:intron 65.0%
CCCTTGTTGGTCCCGAGGGA+CGG + chr6_2:9511534-9511553 None:intergenic 65.0%
CCGTCCCTCGGGACCAACAA+GGG - chr6_2:9511531-9511550 Msa0908260:intron 65.0%
CGTCCCTCGGGACCAACAAG+GGG - chr6_2:9511532-9511551 Msa0908260:intron 65.0%
CGTCCACGGAGGGTGAGTCA+GGG + chr6_2:9511615-9511634 None:intergenic 65.0%
TCGTCCACGGAGGGTGAGTC+AGG + chr6_2:9511616-9511635 None:intergenic 65.0%
CCGCAAGGTTCGTCCACGGA+GGG + chr6_2:9511625-9511644 None:intergenic 65.0%
CCCTCCGTGGACGAACCTTG+CGG - chr6_2:9511622-9511641 Msa0908260:intron 65.0%
TCCGCAAGGTTCGTCCACGG+AGG + chr6_2:9511626-9511645 None:intergenic 65.0%
TCCGTGGACGAACCTTGCGG+AGG - chr6_2:9511625-9511644 Msa0908260:intron 65.0%
GCGAGCAGGGTTGGACGAAG+CGG + chr6_2:9511719-9511738 None:intergenic 65.0%
TTCGTCCAACCCTGCTCGCG+CGG - chr6_2:9511720-9511739 Msa0908260:intron 65.0%
! ACGAAGTACCCGCGCGAGCA+GGG + chr6_2:9511732-9511751 None:intergenic 65.0%
! AACGAAGTACCCGCGCGAGC+AGG + chr6_2:9511733-9511752 None:intergenic 65.0%
GGTAAACAGTCGCCCGGGCC+TGG - chr6_2:9511188-9511207 Msa0908260:CDS 70.0%
! TACTTCAGCGCCGGAGCGCC+TGG - chr6_2:9511398-9511417 Msa0908260:intron 70.0%
CCTAGCCTCCTCCGTCCCTC+GGG - chr6_2:9511520-9511539 Msa0908260:intron 70.0%
TTGGTCCCGAGGGACGGAGG+AGG + chr6_2:9511528-9511547 None:intergenic 70.0%
AGGCCCTGACTCACCCTCCG+TGG - chr6_2:9511609-9511628 Msa0908260:intron 70.0%
TCGTCCAACCCTGCTCGCGC+GGG - chr6_2:9511721-9511740 Msa0908260:intron 70.0%
AGTACCCGCGCGAGCAGGGT+TGG + chr6_2:9511728-9511747 None:intergenic 70.0%
GGGTCGCAGTGACCAGGCCC+GGG + chr6_2:9511203-9511222 None:intergenic 75.0%
GGGGTCGCAGTGACCAGGCC+CGG + chr6_2:9511204-9511223 None:intergenic 75.0%
CCCGAGGGACGGAGGAGGCT+AGG + chr6_2:9511523-9511542 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9511154 9511756 9511154 ID=Msa0908260;Name=Msa0908260
chr6_2 mRNA 9511154 9511756 9511154 ID=Msa0908260-mRNA-1;Parent=Msa0908260;Name=Msa0908260-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0|0|1|0|0|2|0|85
chr6_2 exon 9511731 9511756 9511731 ID=Msa0908260-mRNA-1:exon:2335;Parent=Msa0908260-mRNA-1
chr6_2 exon 9511154 9511385 9511154 ID=Msa0908260-mRNA-1:exon:2334;Parent=Msa0908260-mRNA-1
chr6_2 CDS 9511731 9511756 9511731 ID=Msa0908260-mRNA-1:cds;Parent=Msa0908260-mRNA-1
chr6_2 CDS 9511154 9511385 9511154 ID=Msa0908260-mRNA-1:cds;Parent=Msa0908260-mRNA-1
Gene Sequence

>Msa0908260

ATGGTCTTACGACTTTGCGGAGACCTCCTCCTCCGTCCCTCGGGACCAACAAGGGGTAGTACAGGAATATTCACCTGTTGTCCATCGACTACGCCTTTCGGCCTGATCTTAGGCCCTGACTCACCCTCCGTGGACGAACCTTGCGGAGGAACCCTTAGGTTTTCGGGGCATTGGATTCTCACCAATGTTTGCGTTACTCAAGCCGACATTCTCGCTTCCGCTTCGTCCAACCCTGCTCGCGCGGGTACTTCGTTCTAA

Protein sequence

>Msa0908260

MVLRLCGDLLLRPSGPTRGSTGIFTCCPSTTPFGLILGPDSPSVDEPCGGTLRFSGHWILTNVCVTQADILASASSNPARAGTSF*