AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0916690

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 38 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGAGATATAATTTATTTC+TGG 0.147351 6_2:+38776764 None:intergenic
GTGAAAATTTATACAAAATA+TGG 0.181864 6_2:-38776177 Msa0916690:five_prime_UTR
CCTTTGGGTGCTGGTTGTTC+AGG 0.222091 6_2:-38776018 Msa0916690:CDS
TACTGATCTTGGATCTCCTT+TGG 0.276419 6_2:-38776034 Msa0916690:CDS
CTTGGATCTCCTTTGGGTGC+TGG 0.302719 6_2:-38776027 Msa0916690:CDS
GTAGAATTGTTTACTGATCT+TGG 0.316602 6_2:-38776045 Msa0916690:CDS
ACTGATCTTGGATCTCCTTT+GGG 0.322297 6_2:-38776033 Msa0916690:CDS
TTTACTTGATCTGCTATGAT+TGG 0.350556 6_2:-38776102 Msa0916690:exon
TGAAAATTTATACAAAATAT+GGG 0.407943 6_2:-38776176 Msa0916690:five_prime_UTR
AAAATTAGAATCTAGAATAG+TGG 0.415671 6_2:+38775222 None:intergenic
CTCTGCCATGTTCAATTCGT+TGG 0.419055 6_2:-38776559 Msa0916690:five_prime_UTR
TTCAAGAAACAAGAGTTTAG+TGG 0.420423 6_2:-38776073 Msa0916690:CDS
TATTCAGTGTACAATATATA+TGG 0.435028 6_2:-38775259 Msa0916690:CDS
CAACCTAACCTCAAACCCTC+GGG 0.488472 6_2:-38775293 Msa0916690:CDS
CCGAGGGTTTGAGGTTAGGT+TGG 0.488550 6_2:+38775294 None:intergenic
CACGGATCAAAGGTGACAAT+CGG 0.503183 6_2:+38776587 None:intergenic
TTCCACTCATCTCCGATCCA+TGG 0.503803 6_2:-38776664 Msa0916690:five_prime_UTR
GCTGGTTGTTCAGGTTCACT+TGG 0.503863 6_2:-38776009 Msa0916690:intron
AAATTAGAATCTAGAATAGT+GGG 0.508107 6_2:+38775223 None:intergenic
CTCCATCTCTCACCTTTGAT+CGG 0.528502 6_2:-38776638 Msa0916690:five_prime_UTR
GGTGAGAGATGGAGATTCCA+TGG 0.528725 6_2:+38776647 None:intergenic
TGACGACGAACACCGATCAA+AGG 0.561423 6_2:+38776626 None:intergenic
CACCGATCAAAGGTGAGAGA+TGG 0.565535 6_2:+38776636 None:intergenic
CCAACCTAACCTCAAACCCT+CGG 0.568478 6_2:-38775294 Msa0916690:CDS
TTAACCATCTTAGCAATGCT+AGG 0.589611 6_2:+38775193 None:intergenic
CAGAGGCAAACACGGATCAA+AGG 0.591554 6_2:+38776577 None:intergenic
TTCTGATATATAGACCAAGT+TGG 0.595176 6_2:-38776199 Msa0916690:five_prime_UTR
TTCCATGGATCGGAGATGAG+TGG 0.601493 6_2:+38776662 None:intergenic
AATTACCAACGAATTGAACA+TGG 0.605246 6_2:+38776554 None:intergenic
AAGAAACAAGAGTTTAGTGG+AGG 0.611839 6_2:-38776070 Msa0916690:CDS
GAGATGGAGATTCCATGGAT+CGG 0.615536 6_2:+38776652 None:intergenic
TCAAAGGTGACAATCGGTGA+CGG 0.618089 6_2:+38776593 None:intergenic
CAACGAATTGAACATGGCAG+AGG 0.619897 6_2:+38776560 None:intergenic
GAACATGGCAGAGGCAAACA+CGG 0.626760 6_2:+38776569 None:intergenic
CCTGAACAACCAGCACCCAA+AGG 0.656297 6_2:+38776018 None:intergenic
AACCTAACCTCAAACCCTCG+GGG 0.660027 6_2:-38775292 Msa0916690:CDS
ACCTAACCTCAAACCCTCGG+GGG 0.693945 6_2:-38775291 Msa0916690:CDS
TGTTTGATGAAATGCATGTG+AGG 0.696932 6_2:-38776131 Msa0916690:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAAATTTATACAAAATAT+GGG - chr6_2:38775806-38775825 Msa0916690:intron 10.0%
!! AAAGAGATATAATTTATTTC+TGG + chr6_2:38775221-38775240 None:intergenic 15.0%
!!! ATTAGGTTTCAATTTTAATT+AGG - chr6_2:38775535-38775554 Msa0916690:intron 15.0%
!! AAATATTACTTTCAAAAACT+AGG + chr6_2:38775641-38775660 None:intergenic 15.0%
!! GTGAAAATTTATACAAAATA+TGG - chr6_2:38775805-38775824 Msa0916690:intron 15.0%
!! TTTATCTTAATCTGTTAAAA+TGG - chr6_2:38776270-38776289 Msa0916690:intron 15.0%
!! TAATTGAAATTGAAACCTAA+TGG + chr6_2:38775493-38775512 None:intergenic 20.0%
!! ATTAGGTTTCAATTTCAATT+AGG - chr6_2:38775492-38775511 Msa0916690:intron 20.0%
!! CAATACATTCATGATTAATT+AGG - chr6_2:38775518-38775537 Msa0916690:intron 20.0%
!!! TGGTAAATAAATATTTGTTG+TGG - chr6_2:38776159-38776178 Msa0916690:five_prime_UTR 20.0%
!!! ACGTTAATCTTATTTATGTT+TGG - chr6_2:38776543-38776562 Msa0916690:intron 20.0%
!!! TCTTATTTATGTTTGGTATA+TGG - chr6_2:38776550-38776569 Msa0916690:intron 20.0%
!! TATTCAGTGTACAATATATA+TGG - chr6_2:38776723-38776742 Msa0916690:five_prime_UTR 20.0%
!!! AAATTAGAATCTAGAATAGT+GGG + chr6_2:38776762-38776781 None:intergenic 20.0%
!!! AAAATTAGAATCTAGAATAG+TGG + chr6_2:38776763-38776782 None:intergenic 20.0%
! TTAGAGCAAAATTGGAAAAT+TGG - chr6_2:38775678-38775697 Msa0916690:intron 25.0%
! ATTATACCTGAAATTGATGA+TGG + chr6_2:38775743-38775762 None:intergenic 25.0%
!! TGTATAAATTTTCACCAACT+TGG + chr6_2:38775800-38775819 None:intergenic 25.0%
! TATAGTATAGATCATGTATG+TGG + chr6_2:38776058-38776077 None:intergenic 25.0%
! CTTGTTACAAAATGAAGATT+TGG - chr6_2:38776139-38776158 Msa0916690:five_prime_UTR 25.0%
!!! AAATAAATATTTGTTGTGGC+TGG - chr6_2:38776163-38776182 Msa0916690:five_prime_UTR 25.0%
! TTAATGGTTGTCATGAAATT+GGG - chr6_2:38776186-38776205 Msa0916690:five_prime_UTR 25.0%
! TGCATATAGTTTATATGATG+AGG - chr6_2:38776306-38776325 Msa0916690:intron 25.0%
! ACTAAAGTTTGAATTATCAC+TGG + chr6_2:38776368-38776387 None:intergenic 25.0%
! TTAGTCTAAGTTGTTGAATA+TGG - chr6_2:38776383-38776402 Msa0916690:intron 25.0%
AATTACCAACGAATTGAACA+TGG + chr6_2:38775431-38775450 None:intergenic 30.0%
! TAATGCTTGTTAAGTGTTTG+AGG - chr6_2:38775598-38775617 Msa0916690:intron 30.0%
! GATGCTATTTAGAGCAAAAT+TGG - chr6_2:38775670-38775689 Msa0916690:intron 30.0%
TTCTGATATATAGACCAAGT+TGG - chr6_2:38775783-38775802 Msa0916690:intron 30.0%
TTTACTTGATCTGCTATGAT+TGG - chr6_2:38775880-38775899 Msa0916690:intron 30.0%
TTCAAGAAACAAGAGTTTAG+TGG - chr6_2:38775909-38775928 Msa0916690:intron 30.0%
GTAGAATTGTTTACTGATCT+TGG - chr6_2:38775937-38775956 Msa0916690:intron 30.0%
! CTTGGTAAGATTTAGAATCA+TGG - chr6_2:38775991-38776010 Msa0916690:intron 30.0%
GTTAATGGTTGTCATGAAAT+TGG - chr6_2:38776185-38776204 Msa0916690:five_prime_UTR 30.0%
! TGTTGAATATGGTCTTTTTC+AGG - chr6_2:38776394-38776413 Msa0916690:intron 30.0%
CATCTTATCTTATGAGCTTT+AGG + chr6_2:38776473-38776492 None:intergenic 30.0%
CGTAAACGTATCATAACAAA+GGG + chr6_2:38776526-38776545 None:intergenic 30.0%
ACGTAAACGTATCATAACAA+AGG + chr6_2:38776527-38776546 None:intergenic 30.0%
TTCATGATTCACGATCCATT+AGG - chr6_2:38775475-38775494 Msa0916690:intron 35.0%
! TTGCTCTAAATAGCATCACA+GGG + chr6_2:38775667-38775686 None:intergenic 35.0%
! TTTGCTCTAAATAGCATCAC+AGG + chr6_2:38775668-38775687 None:intergenic 35.0%
CTTTCTCCATCATCAATTTC+AGG - chr6_2:38775734-38775753 Msa0916690:intron 35.0%
TGTTTGATGAAATGCATGTG+AGG - chr6_2:38775851-38775870 Msa0916690:intron 35.0%
AAGAAACAAGAGTTTAGTGG+AGG - chr6_2:38775912-38775931 Msa0916690:intron 35.0%
CTTCAGATTCTTCTCTTTCT+AGG - chr6_2:38776021-38776040 Msa0916690:CDS 35.0%
!! TATTTGTTGTGGCTGGTTAA+TGG - chr6_2:38776170-38776189 Msa0916690:five_prime_UTR 35.0%
! AGGCACAAGAATAGAAGTTT+TGG - chr6_2:38776217-38776236 Msa0916690:five_prime_UTR 35.0%
TTGAATTATCACTGGAAGTG+TGG + chr6_2:38776360-38776379 None:intergenic 35.0%
!! TATGAGCTTTAGGTACTTTC+TGG + chr6_2:38776463-38776482 None:intergenic 35.0%
ACAAAGGGACAATAAACAAG+TGG + chr6_2:38776511-38776530 None:intergenic 35.0%
GTATGCATGTATGATTCTGT+AGG - chr6_2:38776572-38776591 Msa0916690:five_prime_UTR 35.0%
! TGCTCTAAATAGCATCACAG+GGG + chr6_2:38775666-38775685 None:intergenic 40.0%
TACTGATCTTGGATCTCCTT+TGG - chr6_2:38775948-38775967 Msa0916690:intron 40.0%
ACTGATCTTGGATCTCCTTT+GGG - chr6_2:38775949-38775968 Msa0916690:intron 40.0%
CATGAAATTGGGTGAGATGT+AGG - chr6_2:38776197-38776216 Msa0916690:five_prime_UTR 40.0%
TCAATTCCATCATCCAACAG+TGG - chr6_2:38776630-38776649 Msa0916690:five_prime_UTR 40.0%
!! CAATGATTTGCTTCCACTGT+TGG + chr6_2:38776646-38776665 None:intergenic 40.0%
GAGATGGAGATTCCATGGAT+CGG + chr6_2:38775333-38775352 None:intergenic 45.0%
CTCCATCTCTCACCTTTGAT+CGG - chr6_2:38775344-38775363 Msa0916690:intron 45.0%
TCAAAGGTGACAATCGGTGA+CGG + chr6_2:38775392-38775411 None:intergenic 45.0%
CACGGATCAAAGGTGACAAT+CGG + chr6_2:38775398-38775417 None:intergenic 45.0%
CAACGAATTGAACATGGCAG+AGG + chr6_2:38775425-38775444 None:intergenic 45.0%
CTCTGCCATGTTCAATTCGT+TGG - chr6_2:38775423-38775442 Msa0916690:intron 45.0%
TTGCTTCCACTGTTGGATGA+TGG + chr6_2:38776639-38776658 None:intergenic 45.0%
TTCCACTCATCTCCGATCCA+TGG - chr6_2:38775318-38775337 Msa0916690:intron 50.0%
TTCCATGGATCGGAGATGAG+TGG + chr6_2:38775323-38775342 None:intergenic 50.0%
GGTGAGAGATGGAGATTCCA+TGG + chr6_2:38775338-38775357 None:intergenic 50.0%
CACCGATCAAAGGTGAGAGA+TGG + chr6_2:38775349-38775368 None:intergenic 50.0%
TGACGACGAACACCGATCAA+AGG + chr6_2:38775359-38775378 None:intergenic 50.0%
CAGAGGCAAACACGGATCAA+AGG + chr6_2:38775408-38775427 None:intergenic 50.0%
GAACATGGCAGAGGCAAACA+CGG + chr6_2:38775416-38775435 None:intergenic 50.0%
! GCTGGTTGTTCAGGTTCACT+TGG - chr6_2:38775973-38775992 Msa0916690:intron 50.0%
CCAACCTAACCTCAAACCCT+CGG - chr6_2:38776688-38776707 Msa0916690:five_prime_UTR 50.0%
CAACCTAACCTCAAACCCTC+GGG - chr6_2:38776689-38776708 Msa0916690:five_prime_UTR 50.0%
AACCTAACCTCAAACCCTCG+GGG - chr6_2:38776690-38776709 Msa0916690:five_prime_UTR 50.0%
CTTGGATCTCCTTTGGGTGC+TGG - chr6_2:38775955-38775974 Msa0916690:intron 55.0%
CCTGAACAACCAGCACCCAA+AGG + chr6_2:38775967-38775986 None:intergenic 55.0%
!! CCTTTGGGTGCTGGTTGTTC+AGG - chr6_2:38775964-38775983 Msa0916690:intron 55.0%
! CCGAGGGTTTGAGGTTAGGT+TGG + chr6_2:38776691-38776710 None:intergenic 55.0%
ACCTAACCTCAAACCCTCGG+GGG - chr6_2:38776691-38776710 Msa0916690:five_prime_UTR 55.0%
AATACCTTCTCAGCCCCCGA+GGG + chr6_2:38776707-38776726 None:intergenic 55.0%
GAATACCTTCTCAGCCCCCG+AGG + chr6_2:38776708-38776727 None:intergenic 60.0%
! GCCCCCGAGGGTTTGAGGTT+AGG + chr6_2:38776695-38776714 None:intergenic 65.0%
TCTCAGCCCCCGAGGGTTTG+AGG + chr6_2:38776700-38776719 None:intergenic 65.0%
CAAACCCTCGGGGGCTGAGA+AGG - chr6_2:38776700-38776719 Msa0916690:five_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 38775201 38776803 38775201 ID=Msa0916690;Name=Msa0916690
chr6_2 mRNA 38775201 38776803 38775201 ID=Msa0916690-mRNA-1;Parent=Msa0916690;Name=Msa0916690-mRNA-1;_AED=0.31;_eAED=0.31;_QI=392|0.5|0.66|1|0|0|3|0|73
chr6_2 exon 38775201 38775319 38775201 ID=Msa0916690-mRNA-1:exon:6431;Parent=Msa0916690-mRNA-1
chr6_2 exon 38776010 38776248 38776010 ID=Msa0916690-mRNA-1:exon:6430;Parent=Msa0916690-mRNA-1
chr6_2 exon 38776551 38776803 38776551 ID=Msa0916690-mRNA-1:exon:6429;Parent=Msa0916690-mRNA-1
chr6_2 five_prime_UTR 38776551 38776803 38776551 ID=Msa0916690-mRNA-1:five_prime_utr;Parent=Msa0916690-mRNA-1
chr6_2 five_prime_UTR 38776110 38776248 38776110 ID=Msa0916690-mRNA-1:five_prime_utr;Parent=Msa0916690-mRNA-1
chr6_2 CDS 38776010 38776109 38776010 ID=Msa0916690-mRNA-1:cds;Parent=Msa0916690-mRNA-1
chr6_2 CDS 38775201 38775319 38775201 ID=Msa0916690-mRNA-1:cds;Parent=Msa0916690-mRNA-1
Gene Sequence

>Msa0916690

ATGATTGGTGTTGTTTCAAGAAACAAGAGTTTAGTGGAGGTTGTAGAATTGTTTACTGATCTTGGATCTCCTTTGGGTGCTGGTTGTTCAGGTTCACTTGTTTCCAACCTAACCTCAAACCCTCGGGGGCTGAGAAGGTATTCAGTGTACAATATATATGGTCTAATAATATATCCCACTATTCTAGATTCTAATTTTTCATTTCCTAGCATTGCTAAG
Protein sequence

>Msa0916690

MIGVVSRNKSLVEVVELFTDLGSPLGAGCSGSLVSNLTSNPRGLRRYSVYNIYGLIIYPTILDSNFSFPSIAK