AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480022712.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480022712.01.T01 MTR_4g094380 97.279 147 4 0 1 147 1 147 2.43e-104 295
MsG0480022712.01.T01 MTR_4g094380 98.571 140 2 0 1 140 1 140 1.52e-99 285
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480022712.01.T01 AT3G60360 64.085 142 51 0 1 142 1 142 3.60e-65 198

Find 32 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCTTCAAAGTGAGAAAA+AGG 0.290672 4:-75740231 MsG0480022712.01.T01:intron
ACGCTCTTTGTGAGCAGGTC+TGG 0.296864 4:+75741373 None:intergenic
GCACCAAGATTAAAATTATC+AGG 0.330125 4:+75741529 None:intergenic
ATGTGAAAGAAGACACTTTA+CGG 0.340011 4:-75741195 MsG0480022712.01.T01:CDS
ATTGATGAAGACACAAGATA+TGG 0.356282 4:-75740267 MsG0480022712.01.T01:CDS
ATGATCAATCAAGTGCAAAT+TGG 0.364827 4:+75740090 None:intergenic
CGCTCTTTGTGAGCAGGTCT+GGG 0.369189 4:+75741374 None:intergenic
TGTTTCAATCACAGGTACTT+AGG 0.379172 4:-75741093 MsG0480022712.01.T01:intron
CTGAAACCACGATGTTTAGT+AGG 0.387112 4:+75741486 None:intergenic
GGTCTTCGAGGAAGAAATTC+GGG 0.397372 4:-75741264 MsG0480022712.01.T01:CDS
AGGTCTTCGAGGAAGAAATT+CGG 0.408654 4:-75741265 MsG0480022712.01.T01:CDS
TGTGAAAGAAGACACTTTAC+GGG 0.432035 4:-75741194 MsG0480022712.01.T01:intron
CACGGTGATTTCTACGGTGG+AGG 0.441233 4:+75741440 None:intergenic
GTTTCAATCACAGGTACTTA+GGG 0.442736 4:-75741092 MsG0480022712.01.T01:intron
ATTTCTACGGTGGAGGGTGG+TGG 0.448143 4:+75741447 None:intergenic
CAGAGAAGACATGTCGTATC+GGG 0.455443 4:+75741409 None:intergenic
TGAGGACGCTCTTTGTGAGC+AGG 0.462799 4:+75741368 None:intergenic
ATGTTTACTTTGCTGACGAC+AGG 0.476056 4:-75740051 MsG0480022712.01.T01:CDS
AGTGTCTTCTTTCACATGAA+AGG 0.479919 4:+75741201 None:intergenic
TTACTTCACGGTGATTTCTA+CGG 0.482839 4:+75741434 None:intergenic
CCATTATTATTAGGTCTTCG+AGG 0.508365 4:-75741276 MsG0480022712.01.T01:intron
TTGATGAAGACACAAGATAT+GGG 0.519917 4:-75740266 MsG0480022712.01.T01:CDS
GAGAAAGAGAGTTACGGTTG+AGG 0.524326 4:+75741350 None:intergenic
TGAAACCACGATGTTTAGTA+GGG 0.527276 4:+75741487 None:intergenic
AAGTAAACATGCTTGTTCGC+TGG 0.531696 4:+75740064 None:intergenic
ACGGTGATTTCTACGGTGGA+GGG 0.559484 4:+75741441 None:intergenic
TCAGAGAAGACATGTCGTAT+CGG 0.571231 4:+75741408 None:intergenic
CTTCACGGTGATTTCTACGG+TGG 0.591836 4:+75741437 None:intergenic
TTTGTGAGCAGGTCTGGGAA+CGG 0.611566 4:+75741379 None:intergenic
GTGATTTCTACGGTGGAGGG+TGG 0.614851 4:+75741444 None:intergenic
TAAAACCCTACTAAACATCG+TGG 0.665068 4:-75741492 MsG0480022712.01.T01:five_prime_UTR
AAAAGCTGCTAATAGAAACG+AGG 0.712242 4:-75741068 MsG0480022712.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATGTATAAATTGTTAATGT+AGG - Chr4:75741388-75741407 MsG0480022712.01.T01:CDS 15.0%
!! TAGTATATTTACGTAGTTTA+GGG - Chr4:75740839-75740858 MsG0480022712.01.T01:intron 20.0%
!! TTAGTATATTTACGTAGTTT+AGG - Chr4:75740838-75740857 MsG0480022712.01.T01:intron 20.0%
!!! ATTTTATGATTGTTAGTTGT+TGG - Chr4:75741213-75741232 MsG0480022712.01.T01:CDS 20.0%
!!! CTTTTTATAAGTTTTGACTA+AGG - Chr4:75740737-75740756 MsG0480022712.01.T01:intron 20.0%
!!! GACAGATTTTATATAGTTTA+GGG - Chr4:75740810-75740829 MsG0480022712.01.T01:intron 20.0%
!!! TGACAGATTTTATATAGTTT+AGG - Chr4:75740809-75740828 MsG0480022712.01.T01:intron 20.0%
!!! TTTTTCTCTCCATTATTATT+AGG - Chr4:75740268-75740287 MsG0480022712.01.T01:CDS 20.0%
! GTTAATTCAAAAACTGTTGA+TGG - Chr4:75740528-75740547 MsG0480022712.01.T01:intron 25.0%
!! GAAGCTATCTTTTCTTATAA+AGG - Chr4:75741535-75741554 MsG0480022712.01.T01:five_prime_UTR 25.0%
!! TAACTACTTTCTATCCTTTT+CGG - Chr4:75740575-75740594 MsG0480022712.01.T01:intron 25.0%
!!! GGATGAGTTTTATTTTAAGA+TGG - Chr4:75740506-75740525 MsG0480022712.01.T01:intron 25.0%
!!! TTTTTGTTTGTTTCAATCAC+AGG - Chr4:75740452-75740471 MsG0480022712.01.T01:intron 25.0%
AAAGCTTCAAAGTGAGAAAA+AGG - Chr4:75741322-75741341 MsG0480022712.01.T01:intron 30.0%
AACTAGCCACATAAAAATCA+AGG + Chr4:75741192-75741211 None:intergenic 30.0%
AAGTAGTTAGTTACATACAC+TGG + Chr4:75740564-75740583 None:intergenic 30.0%
AAGTGAAATATTGCAGAGAA+AGG + Chr4:75740405-75740424 None:intergenic 30.0%
ACTAGCCACATAAAAATCAA+GGG + Chr4:75741191-75741210 None:intergenic 30.0%
AGTGAAATATTGCAGAGAAA+GGG + Chr4:75740404-75740423 None:intergenic 30.0%
ATAAAAATCAAGGGTCTGTT+TGG + Chr4:75741182-75741201 None:intergenic 30.0%
ATGATCAATCAAGTGCAAAT+TGG + Chr4:75741466-75741485 None:intergenic 30.0%
ATGCTATAAGCTGCAAATTA+AGG + Chr4:75740973-75740992 None:intergenic 30.0%
ATGTGAAAGAAGACACTTTA+CGG - Chr4:75740358-75740377 MsG0480022712.01.T01:intron 30.0%
ATTGATGAAGACACAAGATA+TGG - Chr4:75741286-75741305 MsG0480022712.01.T01:intron 30.0%
CAATAGATAAGCTTCAAACA+TGG - Chr4:75740779-75740798 MsG0480022712.01.T01:intron 30.0%
GAAGAAATAAGTATGTGAAG+AGG + Chr4:75740231-75740250 None:intergenic 30.0%
GCACCAAGATTAAAATTATC+AGG + Chr4:75740027-75740046 None:intergenic 30.0%
TTGATGAAGACACAAGATAT+GGG - Chr4:75741287-75741306 MsG0480022712.01.T01:intron 30.0%
! CATGTTTGAAGCTTATCTAT+TGG + Chr4:75740781-75740800 None:intergenic 30.0%
! GTTTTTCTTTTGTAGGAATG+AGG - Chr4:75741235-75741254 MsG0480022712.01.T01:CDS 30.0%
! TGACTACTTTCTATCCTTTT+CGG - Chr4:75740930-75740949 MsG0480022712.01.T01:intron 30.0%
! TTAAGGTGTTTATCCAAACA+TGG + Chr4:75740956-75740975 None:intergenic 30.0%
!! AGGCCTGATAATTTTAATCT+TGG - Chr4:75740021-75740040 MsG0480022712.01.T01:CDS 30.0%
!! GATAATTTTAATCTTGGTGC+TGG - Chr4:75740027-75740046 MsG0480022712.01.T01:CDS 30.0%
!! GCTATTTTCGTAAGATATCT+CGG - Chr4:75740665-75740684 MsG0480022712.01.T01:intron 30.0%
!!! GTTGTTGGTTTTTCTTTTGT+AGG - Chr4:75741228-75741247 MsG0480022712.01.T01:CDS 30.0%
AAAAGCTGCTAATAGAAACG+AGG - Chr4:75740485-75740504 MsG0480022712.01.T01:intron 35.0%
AGTGTCTTCTTTCACATGAA+AGG + Chr4:75740355-75740374 None:intergenic 35.0%
CCATTATTATTAGGTCTTCG+AGG - Chr4:75740277-75740296 MsG0480022712.01.T01:CDS 35.0%
CCTCGAAGACCTAATAATAA+TGG + Chr4:75740280-75740299 None:intergenic 35.0%
GTTTCAATCACAGGTACTTA+GGG - Chr4:75740461-75740480 MsG0480022712.01.T01:intron 35.0%
TAAAACCCTACTAAACATCG+TGG - Chr4:75740061-75740080 MsG0480022712.01.T01:CDS 35.0%
TAAGATATCTCGGCAAGTTT+GGG - Chr4:75740675-75740694 MsG0480022712.01.T01:intron 35.0%
TAGGGACTAAATTGAAGTGT+AGG - Chr4:75740857-75740876 MsG0480022712.01.T01:intron 35.0%
TGAAACCACGATGTTTAGTA+GGG + Chr4:75740069-75740088 None:intergenic 35.0%
TGTGAAAGAAGACACTTTAC+GGG - Chr4:75740359-75740378 MsG0480022712.01.T01:intron 35.0%
TGTTTCAATCACAGGTACTT+AGG - Chr4:75740460-75740479 MsG0480022712.01.T01:intron 35.0%
TTACTTCACGGTGATTTCTA+CGG + Chr4:75740122-75740141 None:intergenic 35.0%
TTTATGAGACATCTCCGAAA+AGG + Chr4:75740592-75740611 None:intergenic 35.0%
TTTCATAAGCTATCTTGGTG+AGG - Chr4:75741043-75741062 MsG0480022712.01.T01:CDS 35.0%
! ACAGACCCTTGATTTTTATG+TGG - Chr4:75741183-75741202 MsG0480022712.01.T01:intron 35.0%
! AGCTGTTTCATAAGCTATCT+TGG - Chr4:75741038-75741057 MsG0480022712.01.T01:CDS 35.0%
! TAGCTTTTCAACTTTCTGCA+AGG + Chr4:75741439-75741458 None:intergenic 35.0%
AAGTAAACATGCTTGTTCGC+TGG + Chr4:75741492-75741511 None:intergenic 40.0%
ACTGATGCTAACCATCAACT+TGG + Chr4:75740885-75740904 None:intergenic 40.0%
AGGATAGAAAGTAGTCACAC+TGG + Chr4:75740927-75740946 None:intergenic 40.0%
AGGTCTTCGAGGAAGAAATT+CGG - Chr4:75740288-75740307 MsG0480022712.01.T01:CDS 40.0%
ATGTTTACTTTGCTGACGAC+AGG - Chr4:75741502-75741521 MsG0480022712.01.T01:five_prime_UTR 40.0%
CTGAAACCACGATGTTTAGT+AGG + Chr4:75740070-75740089 None:intergenic 40.0%
GAGGAAGAGAAAGAGAGTTA+CGG + Chr4:75740212-75740231 None:intergenic 40.0%
GTAAGATATCTCGGCAAGTT+TGG - Chr4:75740674-75740693 MsG0480022712.01.T01:intron 40.0%
TCAGAGAAGACATGTCGTAT+CGG + Chr4:75740148-75740167 None:intergenic 40.0%
TCGGCAAGTTTGGGAAAATA+AGG - Chr4:75740684-75740703 MsG0480022712.01.T01:intron 40.0%
TTATCCAAACATGGCCGAAA+AGG + Chr4:75740947-75740966 None:intergenic 40.0%
! TCGTATCGGGTTTTACTTCA+CGG + Chr4:75740134-75740153 None:intergenic 40.0%
ACTCAGTCGAGCTTATCTAC+TGG + Chr4:75741155-75741174 None:intergenic 45.0%
CAGAGAAGACATGTCGTATC+GGG + Chr4:75740147-75740166 None:intergenic 45.0%
GAGAAAGAGAGTTACGGTTG+AGG + Chr4:75740206-75740225 None:intergenic 45.0%
GGTCTTCGAGGAAGAAATTC+GGG - Chr4:75740289-75740308 MsG0480022712.01.T01:CDS 45.0%
! AAGTGTAGGCACCAAGTTGA+TGG - Chr4:75740871-75740890 MsG0480022712.01.T01:intron 45.0%
! CTATCCTTTTCGGCCATGTT+TGG - Chr4:75740940-75740959 MsG0480022712.01.T01:intron 45.0%
ACGGTGATTTCTACGGTGGA+GGG + Chr4:75740115-75740134 None:intergenic 50.0%
CTTCACGGTGATTTCTACGG+TGG + Chr4:75740119-75740138 None:intergenic 50.0%
TTTGTGAGCAGGTCTGGGAA+CGG + Chr4:75740177-75740196 None:intergenic 50.0%
ACGCTCTTTGTGAGCAGGTC+TGG + Chr4:75740183-75740202 None:intergenic 55.0%
ATTTCTACGGTGGAGGGTGG+TGG + Chr4:75740109-75740128 None:intergenic 55.0%
CACGGTGATTTCTACGGTGG+AGG + Chr4:75740116-75740135 None:intergenic 55.0%
CGCTCTTTGTGAGCAGGTCT+GGG + Chr4:75740182-75740201 None:intergenic 55.0%
GTGATTTCTACGGTGGAGGG+TGG + Chr4:75740112-75740131 None:intergenic 55.0%
TGAGGACGCTCTTTGTGAGC+AGG + Chr4:75740188-75740207 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
Chr4 gene 75740021 75741554 75740021 ID=MsG0480022712.01;Name=MsG0480022712.01
Chr4 mRNA 75740021 75741554 75740021 ID=MsG0480022712.01.T01;Parent=MsG0480022712.01;Name=MsG0480022712.01.T01;_AED=0.49;_eAED=0.51;_QI=134|1|0.8|1|1|1|5|0|147
Chr4 exon 75740021 75740131 75740021 ID=MsG0480022712.01.T01:exon:8528;Parent=MsG0480022712.01.T01
Chr4 exon 75740232 75740325 75740232 ID=MsG0480022712.01.T01:exon:8527;Parent=MsG0480022712.01.T01
Chr4 exon 75741010 75741101 75741010 ID=MsG0480022712.01.T01:exon:8526;Parent=MsG0480022712.01.T01
Chr4 exon 75741195 75741285 75741195 ID=MsG0480022712.01.T01:exon:8525;Parent=MsG0480022712.01.T01
Chr4 exon 75741365 75741554 75741365 ID=MsG0480022712.01.T01:exon:8524;Parent=MsG0480022712.01.T01
Chr4 five_prime_UTR 75741421 75741554 75741421 ID=MsG0480022712.01.T01:five_prime_utr;Parent=MsG0480022712.01.T01
Chr4 CDS 75741365 75741420 75741365 ID=MsG0480022712.01.T01:cds;Parent=MsG0480022712.01.T01
Chr4 CDS 75741195 75741285 75741195 ID=MsG0480022712.01.T01:cds;Parent=MsG0480022712.01.T01
Chr4 CDS 75741010 75741101 75741010 ID=MsG0480022712.01.T01:cds;Parent=MsG0480022712.01.T01
Chr4 CDS 75740232 75740325 75740232 ID=MsG0480022712.01.T01:cds;Parent=MsG0480022712.01.T01
Chr4 CDS 75740021 75740131 75740021 ID=MsG0480022712.01.T01:cds;Parent=MsG0480022712.01.T01
Gene Sequence

>MsG0480022712.01.T01

ATGTCTTCTCTGAGAAACGCCGTTCCCAGACCTGCTCACAAAGAGCGTCCTCAACCGTCTTCGAGGAAGAAATTCGGGATACTCGAAAAGCACAAAGACTATGTCGAACGTGCTAAAGCCTTTCATGTGAAAGAAGACACTTTACGGGTACTTAGGGAAAAAGCTGCTAATAGAAACGAGGATGAGTTTTATTTTAAGATGGTTAATTCAAAAACTGTTGATGGAGTTCATAGACCAGTGAATGAGGATAACAAGTATACTCAAGATGAACTTATATTGATGAAGACACAAGATATGGGATATGTTCTTCAAAAGCTTCAAAGTGAGAAAAAGAAAGTTGAAAAGCTATCTGCCAATTTGCACTTGATTGATCATAAGCCAGCGAACAAGCATGTTTACTTTGCTGACGACAGGTTTGAGTTTCGAAGCTATCTTTTCTTATAA
Protein sequence

>MsG0480022712.01.T01

MSSLRNAVPRPAHKERPQPSSRKKFGILEKHKDYVERAKAFHVKEDTLRVLREKAANRNEDEFYFKMVNSKTVDGVHRPVNEDNKYTQDELILMKTQDMGYVLQKLQSEKKKVEKLSANLHLIDHKPANKHVYFADDRFEFRSYLFL*