AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0563400

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0563400 MtrunA17_Chr4g0045061 97.059 68 2 0 1 68 560 627 1.07e-41 143
Msa0563400 MtrunA17_Chr4g0045041 92.537 67 5 0 1 67 560 626 4.95e-39 135
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0563400 AT1G49670.1 71.642 67 19 0 1 67 556 622 1.73e-29 109
Msa0563400 AT1G49670.2 71.642 67 19 0 1 67 579 645 2.47e-29 108

Find 39 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCACTTGAAGTCAAATTT+AGG 0.193871 4_1:-63774265 Msa0563400:three_prime_UTR
GAAAATCAACAAATTATAAA+TGG 0.204878 4_1:+63774197 None:intergenic
CATCGGTGAATCCTTAAAAT+TGG 0.228356 4_1:-63774238 Msa0563400:three_prime_UTR
CTTCAAATGATTGTGCTAAT+TGG 0.247718 4_1:-63774337 Msa0563400:three_prime_UTR
TGCAGGCCTATAAATTTCTT+TGG 0.261878 4_1:+63774830 None:intergenic
ACTATTTGACCTTTACTCTA+AGG 0.265584 4_1:-63775009 Msa0563400:CDS
GTGGATCCAAAGAAATTTAT+AGG 0.294001 4_1:-63774836 Msa0563400:CDS
TAAAATTGGGGACCATATTA+TGG 0.299833 4_1:-63774224 Msa0563400:three_prime_UTR
AAATAGCTGCTGAAATATTC+TGG 0.300048 4_1:-63774580 Msa0563400:three_prime_UTR
ACCACTTGAAGTCAAATTTA+GGG 0.329652 4_1:-63774264 Msa0563400:three_prime_UTR
ATCGGTGAATCCTTAAAATT+GGG 0.379227 4_1:-63774237 Msa0563400:three_prime_UTR
TATCGCATCTAACCTGCATA+TGG 0.387142 4_1:-63774130 Msa0563400:three_prime_UTR
GCTGTTGAGTATCTCCATTC+AGG 0.393415 4_1:-63774794 Msa0563400:CDS
GAAGTGGGCATTTGTATTGA+TGG 0.402907 4_1:-63774170 Msa0563400:three_prime_UTR
GCAACTTGATTAACAAGGTT+GGG 0.406143 4_1:+63774652 None:intergenic
TGGCCAGCCCTTAAAATTGA+AGG 0.439856 4_1:-63774295 Msa0563400:three_prime_UTR
TGCAACTTGATTAACAAGGT+TGG 0.450677 4_1:+63774651 None:intergenic
ATAAATGGGAGACCATAATA+TGG 0.457719 4_1:+63774212 None:intergenic
TCCATTCAGGCAAAAGTGTT+GGG 0.459013 4_1:-63774781 Msa0563400:CDS
AAAATCAACAAATTATAAAT+GGG 0.470854 4_1:+63774198 None:intergenic
CTATTTGACCTTTACTCTAA+GGG 0.474026 4_1:-63775008 Msa0563400:CDS
CTCCATTCAGGCAAAAGTGT+TGG 0.484489 4_1:-63774782 Msa0563400:CDS
CCCCTAAATTTGACTTCAAG+TGG 0.503209 4_1:+63774263 None:intergenic
TTTGTTCACACAGGTTGCTG+TGG 0.516926 4_1:-63774855 Msa0563400:intron
ATCGCATCTAACCTGCATAT+GGG 0.540447 4_1:-63774129 Msa0563400:three_prime_UTR
CAGCATCTGCAACAGAATGC+AGG 0.558315 4_1:+63774813 None:intergenic
TCACAGTCACACCCATATGC+AGG 0.565109 4_1:+63774118 None:intergenic
TTTGACTTCAAGTGGTAATG+TGG 0.570123 4_1:+63774271 None:intergenic
ACATATCAGCAGAACAAAGC+GGG 0.571093 4_1:-63774482 Msa0563400:three_prime_UTR
TCTCTAGGTGGTTGTCTGCG+TGG 0.575446 4_1:-63774676 Msa0563400:intron
TTCAGGCAAAAGTGTTGGGA+AGG 0.577859 4_1:-63774777 Msa0563400:intron
CTATAGCGCAAACATAAACT+CGG 0.591837 4_1:+63774508 None:intergenic
AAAAGTGACTGTATTGCACC+AGG 0.609047 4_1:+63775051 None:intergenic
TTACTCTAAGGGAAAACTGA+AGG 0.610562 4_1:-63774997 Msa0563400:intron
CCACTTGAAGTCAAATTTAG+GGG 0.613895 4_1:-63774263 Msa0563400:three_prime_UTR
AGTCAAATTTAGGGGACCAT+CGG 0.620449 4_1:-63774255 Msa0563400:three_prime_UTR
GTGGGCATTTGTATTGATGG+AGG 0.669013 4_1:-63774167 Msa0563400:three_prime_UTR
TCGGTGAATCCTTAAAATTG+GGG 0.687876 4_1:-63774236 Msa0563400:three_prime_UTR
CACATATCAGCAGAACAAAG+CGG 0.706950 4_1:-63774483 Msa0563400:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATCAACAAATTATAAAT+GGG + chr4_1:63774958-63774977 None:intergenic 10.0%
!! AAAATCAACAAATTATAAAT+GGG + chr4_1:63774958-63774977 None:intergenic 10.0%
!!! AAAGTTTTTTTATTGATGAA+AGG + chr4_1:63774736-63774755 None:intergenic 15.0%
!! GAAAATCAACAAATTATAAA+TGG + chr4_1:63774959-63774978 None:intergenic 15.0%
!!! AAAGTTTTTTTATTGATGAA+AGG + chr4_1:63774736-63774755 None:intergenic 15.0%
!! GAAAATCAACAAATTATAAA+TGG + chr4_1:63774959-63774978 None:intergenic 15.0%
!!! TTATATGCATTTTATTTCTG+TGG - chr4_1:63774183-63774202 Msa0563400:three_prime_UTR 20.0%
!! TGGATCAATAAAAAAATGTA+AGG - chr4_1:63774203-63774222 Msa0563400:three_prime_UTR 20.0%
!! TAAAAAAATGTAAGGCATAT+TGG - chr4_1:63774211-63774230 Msa0563400:three_prime_UTR 20.0%
!! TCTAATTATATCATTTCTCT+AGG - chr4_1:63774462-63774481 Msa0563400:three_prime_UTR 20.0%
!!! TTATATGCATTTTATTTCTG+TGG - chr4_1:63774183-63774202 Msa0563400:three_prime_UTR 20.0%
!! TGGATCAATAAAAAAATGTA+AGG - chr4_1:63774203-63774222 Msa0563400:three_prime_UTR 20.0%
!! TAAAAAAATGTAAGGCATAT+TGG - chr4_1:63774211-63774230 Msa0563400:three_prime_UTR 20.0%
!! TCTAATTATATCATTTCTCT+AGG - chr4_1:63774462-63774481 Msa0563400:three_prime_UTR 20.0%
! ACAAACTTTAAACCTTATGA+AGG + chr4_1:63774259-63774278 None:intergenic 25.0%
! AATTATATCATTTCTCTAGG+TGG - chr4_1:63774465-63774484 Msa0563400:three_prime_UTR 25.0%
!! ATTTTGCAACTTGATTAACA+AGG + chr4_1:63774509-63774528 None:intergenic 25.0%
!! TTTTGAACAAAGCAAATACA+AGG + chr4_1:63774783-63774802 None:intergenic 25.0%
! GTTTCCAATGTTGAAAAATT+TGG - chr4_1:63774838-63774857 Msa0563400:CDS 25.0%
!!! TTGTTGATTTTCTTATGAAG+TGG - chr4_1:63774967-63774986 Msa0563400:intron 25.0%
!!! TGTTGATTTTCTTATGAAGT+GGG - chr4_1:63774968-63774987 Msa0563400:intron 25.0%
! ACAAACTTTAAACCTTATGA+AGG + chr4_1:63774259-63774278 None:intergenic 25.0%
! AATTATATCATTTCTCTAGG+TGG - chr4_1:63774465-63774484 Msa0563400:three_prime_UTR 25.0%
!! ATTTTGCAACTTGATTAACA+AGG + chr4_1:63774509-63774528 None:intergenic 25.0%
!! TTTTGAACAAAGCAAATACA+AGG + chr4_1:63774783-63774802 None:intergenic 25.0%
! GTTTCCAATGTTGAAAAATT+TGG - chr4_1:63774838-63774857 Msa0563400:CDS 25.0%
!!! TTGTTGATTTTCTTATGAAG+TGG - chr4_1:63774967-63774986 Msa0563400:intron 25.0%
!!! TGTTGATTTTCTTATGAAGT+GGG - chr4_1:63774968-63774987 Msa0563400:intron 25.0%
ACTATTTGACCTTTACTCTA+AGG - chr4_1:63774144-63774163 Msa0563400:three_prime_UTR 30.0%
CTATTTGACCTTTACTCTAA+GGG - chr4_1:63774145-63774164 Msa0563400:three_prime_UTR 30.0%
! TTTTTCTCATTTGTTCACAC+AGG - chr4_1:63774289-63774308 Msa0563400:three_prime_UTR 30.0%
GTGGATCCAAAGAAATTTAT+AGG - chr4_1:63774317-63774336 Msa0563400:three_prime_UTR 30.0%
AAATAGCTGCTGAAATATTC+TGG - chr4_1:63774573-63774592 Msa0563400:three_prime_UTR 30.0%
!!! TCTGGATGCTTTTTCATTTT+TGG - chr4_1:63774591-63774610 Msa0563400:three_prime_UTR 30.0%
CTTCAAATGATTGTGCTAAT+TGG - chr4_1:63774816-63774835 Msa0563400:CDS 30.0%
! ATGTGGTCCTTCAATTTTAA+GGG + chr4_1:63774868-63774887 None:intergenic 30.0%
! AATGTGGTCCTTCAATTTTA+AGG + chr4_1:63774869-63774888 None:intergenic 30.0%
TACCACTTGAAGTCAAATTT+AGG - chr4_1:63774888-63774907 Msa0563400:intron 30.0%
ACCACTTGAAGTCAAATTTA+GGG - chr4_1:63774889-63774908 Msa0563400:intron 30.0%
ATCGGTGAATCCTTAAAATT+GGG - chr4_1:63774916-63774935 Msa0563400:intron 30.0%
! TAATATGGTCCCCAATTTTA+AGG + chr4_1:63774929-63774948 None:intergenic 30.0%
TAAAATTGGGGACCATATTA+TGG - chr4_1:63774929-63774948 Msa0563400:intron 30.0%
ATAAATGGGAGACCATAATA+TGG + chr4_1:63774944-63774963 None:intergenic 30.0%
! GATGCGATATATTTTCTAAG+AGG + chr4_1:63775012-63775031 None:intergenic 30.0%
ACTATTTGACCTTTACTCTA+AGG - chr4_1:63774144-63774163 Msa0563400:three_prime_UTR 30.0%
CTATTTGACCTTTACTCTAA+GGG - chr4_1:63774145-63774164 Msa0563400:three_prime_UTR 30.0%
! TTTTTCTCATTTGTTCACAC+AGG - chr4_1:63774289-63774308 Msa0563400:three_prime_UTR 30.0%
GTGGATCCAAAGAAATTTAT+AGG - chr4_1:63774317-63774336 Msa0563400:three_prime_UTR 30.0%
AAATAGCTGCTGAAATATTC+TGG - chr4_1:63774573-63774592 Msa0563400:three_prime_UTR 30.0%
!!! TCTGGATGCTTTTTCATTTT+TGG - chr4_1:63774591-63774610 Msa0563400:three_prime_UTR 30.0%
CTTCAAATGATTGTGCTAAT+TGG - chr4_1:63774816-63774835 Msa0563400:CDS 30.0%
! ATGTGGTCCTTCAATTTTAA+GGG + chr4_1:63774868-63774887 None:intergenic 30.0%
! AATGTGGTCCTTCAATTTTA+AGG + chr4_1:63774869-63774888 None:intergenic 30.0%
TACCACTTGAAGTCAAATTT+AGG - chr4_1:63774888-63774907 Msa0563400:intron 30.0%
ACCACTTGAAGTCAAATTTA+GGG - chr4_1:63774889-63774908 Msa0563400:intron 30.0%
ATCGGTGAATCCTTAAAATT+GGG - chr4_1:63774916-63774935 Msa0563400:intron 30.0%
! TAATATGGTCCCCAATTTTA+AGG + chr4_1:63774929-63774948 None:intergenic 30.0%
TAAAATTGGGGACCATATTA+TGG - chr4_1:63774929-63774948 Msa0563400:intron 30.0%
ATAAATGGGAGACCATAATA+TGG + chr4_1:63774944-63774963 None:intergenic 30.0%
! GATGCGATATATTTTCTAAG+AGG + chr4_1:63775012-63775031 None:intergenic 30.0%
! TCAGTTTTCCCTTAGAGTAA+AGG + chr4_1:63774156-63774175 None:intergenic 35.0%
! TTACTCTAAGGGAAAACTGA+AGG - chr4_1:63774156-63774175 Msa0563400:three_prime_UTR 35.0%
TGCAGGCCTATAAATTTCTT+TGG + chr4_1:63774326-63774345 None:intergenic 35.0%
GCAACTTGATTAACAAGGTT+GGG + chr4_1:63774504-63774523 None:intergenic 35.0%
TGCAACTTGATTAACAAGGT+TGG + chr4_1:63774505-63774524 None:intergenic 35.0%
CTATAGCGCAAACATAAACT+CGG + chr4_1:63774648-63774667 None:intergenic 35.0%
!! CTGGCCAAATTTTTCAACAT+TGG + chr4_1:63774845-63774864 None:intergenic 35.0%
! TTTGACTTCAAGTGGTAATG+TGG + chr4_1:63774885-63774904 None:intergenic 35.0%
CCACTTGAAGTCAAATTTAG+GGG - chr4_1:63774890-63774909 Msa0563400:intron 35.0%
!! CAATTTTAAGGATTCACCGA+TGG + chr4_1:63774917-63774936 None:intergenic 35.0%
CATCGGTGAATCCTTAAAAT+TGG - chr4_1:63774915-63774934 Msa0563400:intron 35.0%
TCGGTGAATCCTTAAAATTG+GGG - chr4_1:63774917-63774936 Msa0563400:intron 35.0%
! TCAGTTTTCCCTTAGAGTAA+AGG + chr4_1:63774156-63774175 None:intergenic 35.0%
! TTACTCTAAGGGAAAACTGA+AGG - chr4_1:63774156-63774175 Msa0563400:three_prime_UTR 35.0%
TGCAGGCCTATAAATTTCTT+TGG + chr4_1:63774326-63774345 None:intergenic 35.0%
GCAACTTGATTAACAAGGTT+GGG + chr4_1:63774504-63774523 None:intergenic 35.0%
TGCAACTTGATTAACAAGGT+TGG + chr4_1:63774505-63774524 None:intergenic 35.0%
CTATAGCGCAAACATAAACT+CGG + chr4_1:63774648-63774667 None:intergenic 35.0%
!! CTGGCCAAATTTTTCAACAT+TGG + chr4_1:63774845-63774864 None:intergenic 35.0%
! TTTGACTTCAAGTGGTAATG+TGG + chr4_1:63774885-63774904 None:intergenic 35.0%
CCACTTGAAGTCAAATTTAG+GGG - chr4_1:63774890-63774909 Msa0563400:intron 35.0%
!! CAATTTTAAGGATTCACCGA+TGG + chr4_1:63774917-63774936 None:intergenic 35.0%
CATCGGTGAATCCTTAAAAT+TGG - chr4_1:63774915-63774934 Msa0563400:intron 35.0%
TCGGTGAATCCTTAAAATTG+GGG - chr4_1:63774917-63774936 Msa0563400:intron 35.0%
AAAAGTGACTGTATTGCACC+AGG + chr4_1:63774105-63774124 None:intergenic 40.0%
GCTAGTCGTTATCCTTCATA+AGG - chr4_1:63774244-63774263 Msa0563400:three_prime_UTR 40.0%
!! TCCATTCAGGCAAAAGTGTT+GGG - chr4_1:63774372-63774391 Msa0563400:three_prime_UTR 40.0%
CACATATCAGCAGAACAAAG+CGG - chr4_1:63774670-63774689 Msa0563400:CDS 40.0%
ACATATCAGCAGAACAAAGC+GGG - chr4_1:63774671-63774690 Msa0563400:CDS 40.0%
! CCCCTAAATTTGACTTCAAG+TGG + chr4_1:63774893-63774912 None:intergenic 40.0%
AGTCAAATTTAGGGGACCAT+CGG - chr4_1:63774898-63774917 Msa0563400:intron 40.0%
GAAGTGGGCATTTGTATTGA+TGG - chr4_1:63774983-63775002 Msa0563400:intron 40.0%
TATCGCATCTAACCTGCATA+TGG - chr4_1:63775023-63775042 Msa0563400:CDS 40.0%
ATCGCATCTAACCTGCATAT+GGG - chr4_1:63775024-63775043 Msa0563400:CDS 40.0%
AAAAGTGACTGTATTGCACC+AGG + chr4_1:63774105-63774124 None:intergenic 40.0%
GCTAGTCGTTATCCTTCATA+AGG - chr4_1:63774244-63774263 Msa0563400:three_prime_UTR 40.0%
!! TCCATTCAGGCAAAAGTGTT+GGG - chr4_1:63774372-63774391 Msa0563400:three_prime_UTR 40.0%
CACATATCAGCAGAACAAAG+CGG - chr4_1:63774670-63774689 Msa0563400:CDS 40.0%
ACATATCAGCAGAACAAAGC+GGG - chr4_1:63774671-63774690 Msa0563400:CDS 40.0%
! CCCCTAAATTTGACTTCAAG+TGG + chr4_1:63774893-63774912 None:intergenic 40.0%
AGTCAAATTTAGGGGACCAT+CGG - chr4_1:63774898-63774917 Msa0563400:intron 40.0%
GAAGTGGGCATTTGTATTGA+TGG - chr4_1:63774983-63775002 Msa0563400:intron 40.0%
TATCGCATCTAACCTGCATA+TGG - chr4_1:63775023-63775042 Msa0563400:CDS 40.0%
ATCGCATCTAACCTGCATAT+GGG - chr4_1:63775024-63775043 Msa0563400:CDS 40.0%
TTTGTTCACACAGGTTGCTG+TGG - chr4_1:63774298-63774317 Msa0563400:three_prime_UTR 45.0%
GCTGTTGAGTATCTCCATTC+AGG - chr4_1:63774359-63774378 Msa0563400:three_prime_UTR 45.0%
! CTCCATTCAGGCAAAAGTGT+TGG - chr4_1:63774371-63774390 Msa0563400:three_prime_UTR 45.0%
! TCCCAACACTTTTGCCTGAA+TGG + chr4_1:63774376-63774395 None:intergenic 45.0%
!! TTCAGGCAAAAGTGTTGGGA+AGG - chr4_1:63774376-63774395 Msa0563400:three_prime_UTR 45.0%
TGGCCAGCCCTTAAAATTGA+AGG - chr4_1:63774858-63774877 Msa0563400:intron 45.0%
!! GGTCCTTCAATTTTAAGGGC+TGG + chr4_1:63774864-63774883 None:intergenic 45.0%
! GTGGGCATTTGTATTGATGG+AGG - chr4_1:63774986-63775005 Msa0563400:intron 45.0%
TTTGTTCACACAGGTTGCTG+TGG - chr4_1:63774298-63774317 Msa0563400:three_prime_UTR 45.0%
GCTGTTGAGTATCTCCATTC+AGG - chr4_1:63774359-63774378 Msa0563400:three_prime_UTR 45.0%
! CTCCATTCAGGCAAAAGTGT+TGG - chr4_1:63774371-63774390 Msa0563400:three_prime_UTR 45.0%
! TCCCAACACTTTTGCCTGAA+TGG + chr4_1:63774376-63774395 None:intergenic 45.0%
!! TTCAGGCAAAAGTGTTGGGA+AGG - chr4_1:63774376-63774395 Msa0563400:three_prime_UTR 45.0%
TGGCCAGCCCTTAAAATTGA+AGG - chr4_1:63774858-63774877 Msa0563400:intron 45.0%
!! GGTCCTTCAATTTTAAGGGC+TGG + chr4_1:63774864-63774883 None:intergenic 45.0%
! GTGGGCATTTGTATTGATGG+AGG - chr4_1:63774986-63775005 Msa0563400:intron 45.0%
CAGCATCTGCAACAGAATGC+AGG + chr4_1:63774343-63774362 None:intergenic 50.0%
TCACAGTCACACCCATATGC+AGG + chr4_1:63775038-63775057 None:intergenic 50.0%
CAGCATCTGCAACAGAATGC+AGG + chr4_1:63774343-63774362 None:intergenic 50.0%
TCACAGTCACACCCATATGC+AGG + chr4_1:63775038-63775057 None:intergenic 50.0%
TCTCTAGGTGGTTGTCTGCG+TGG - chr4_1:63774477-63774496 Msa0563400:three_prime_UTR 55.0%
TCTCTAGGTGGTTGTCTGCG+TGG - chr4_1:63774477-63774496 Msa0563400:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 63774091 63775084 63774091 ID=Msa0563400;Name=Msa0563400
chr4_1 mRNA 63774091 63775084 63774091 ID=Msa0563400-mRNA-1;Parent=Msa0563400;Name=Msa0563400-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|0.5|0.33|0.66|1|0.66|3|535|79
chr4_1 exon 63774091 63774691 63774091 ID=Msa0563400-mRNA-1:exon:20315;Parent=Msa0563400-mRNA-1
chr4_1 exon 63774778 63774864 63774778 ID=Msa0563400-mRNA-1:exon:20314;Parent=Msa0563400-mRNA-1
chr4_1 exon 63774998 63775084 63774998 ID=Msa0563400-mRNA-1:exon:20313;Parent=Msa0563400-mRNA-1
chr4_1 CDS 63774998 63775084 63774998 ID=Msa0563400-mRNA-1:cds;Parent=Msa0563400-mRNA-1
chr4_1 CDS 63774778 63774864 63774778 ID=Msa0563400-mRNA-1:cds;Parent=Msa0563400-mRNA-1
chr4_1 CDS 63774626 63774691 63774626 ID=Msa0563400-mRNA-1:cds;Parent=Msa0563400-mRNA-1
chr4_1 three_prime_UTR 63774091 63774625 63774091 ID=Msa0563400-mRNA-1:three_prime_utr;Parent=Msa0563400-mRNA-1
Gene Sequence

>Msa0563400

GCTGGCTTTTTCCTGGTGCAATACAGTCACTTTTATCAAGAACATCTTGATAGACTATTTGACCTTTACTCTAAGGGAAAACTGAAGGTTGCTGTGGATCCAAAGAAATTTATAGGCCTGCATTCTGTTGCAGATGCTGTTGAGTATCTCCATTCAGGCAAAAGTGTTGGGAAGGTGGTTGTCTGCGTGGACCCAACCTTGTTAATCAAGTTGCAAAATTATGAGTCAACACATGTCTAA
Protein sequence

>Msa0563400

AGFFLVQYSHFYQEHLDRLFDLYSKGKLKVAVDPKKFIGLHSVADAVEYLHSGKSVGKVVVCVDPTLLIKLQNYESTHV*