AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0247030

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 34 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCCTCAAATGGGTGTTC+TGG 0.276233 2_2:-28910291 None:intergenic
AAACTTCCGTTTGAGAAGTA+TGG 0.319264 2_2:+28910261 Msa0247030:five_prime_UTR
GATGCAAAATCTTCCTCAAA+TGG 0.353751 2_2:-28910300 None:intergenic
TGAGCCTTTCTGTAGCTTGT+TGG 0.361255 2_2:+28910515 Msa0247030:CDS
TAACCCACAAAGGCCATGTT+TGG 0.399285 2_2:-28910866 None:intergenic
GATGTTGTTCTCCTTGCAAC+TGG 0.404208 2_2:+28910456 Msa0247030:CDS
GATTCCAAACATGGCCTTTG+TGG 0.425206 2_2:+28910862 Msa0247030:CDS
AATTGTGTTTACCTGTATAG+TGG 0.425289 2_2:-28910558 None:intergenic
CTCCTTGCAACTGGTTATGA+TGG 0.429093 2_2:+28910465 Msa0247030:CDS
TTCAATCCATACTTCTCAAA+CGG 0.458388 2_2:-28910267 None:intergenic
CTGGTACCATGCCACTATAC+AGG 0.469016 2_2:+28910547 Msa0247030:CDS
ATTCCAAACATGGCCTTTGT+GGG 0.477703 2_2:+28910863 Msa0247030:CDS
GAAACCAGAACACCCATTTG+AGG 0.486081 2_2:+28910287 Msa0247030:five_prime_UTR
ATGCAAAATCTTCCTCAAAT+GGG 0.488179 2_2:-28910299 None:intergenic
CCATCCATCGATTCCAAACA+TGG 0.506030 2_2:+28910853 Msa0247030:CDS
TCCCATCATAACCAGTTGCA+AGG 0.534071 2_2:-28910467 None:intergenic
AAGCCACATGGAACGTATCT+CGG 0.538091 2_2:-28910918 None:intergenic
TCCTTGCAACTGGTTATGAT+GGG 0.545738 2_2:+28910466 Msa0247030:CDS
AAGGCCATGTTTGGAATCGA+TGG 0.546006 2_2:-28910857 None:intergenic
AACAAGCTACAGAAAGGCTC+AGG 0.566868 2_2:-28910513 None:intergenic
TCATAGAGTCCTACTTGCTG+TGG 0.569108 2_2:+28910238 Msa0247030:five_prime_UTR
AGCTTGTTGGAATACCCTAC+TGG 0.573175 2_2:+28910528 Msa0247030:CDS
TATAGTGGCATGGTACCAGT+AGG 0.579959 2_2:-28910543 None:intergenic
CCATGTTTGGAATCGATGGA+TGG 0.583448 2_2:-28910853 None:intergenic
TCAAAAGAGCATCAAAGTGG+TGG 0.590237 2_2:+28910385 Msa0247030:five_prime_UTR
TATTCCAACAAGCTACAGAA+AGG 0.603701 2_2:-28910519 None:intergenic
TGTTTACCTGTATAGTGGCA+TGG 0.612113 2_2:-28910553 None:intergenic
CGGAAGTTTCCACAGCAAGT+AGG 0.614813 2_2:-28910247 None:intergenic
ATGATATTAAACAGAGACGT+GGG 0.621879 2_2:+28910205 Msa0247030:five_prime_UTR
TCTTCAAAAGAGCATCAAAG+TGG 0.668843 2_2:+28910382 Msa0247030:five_prime_UTR
ACTCTCAACATAACCCACAA+AGG 0.682237 2_2:-28910876 None:intergenic
ATAGTGGCATGGTACCAGTA+GGG 0.697965 2_2:-28910542 None:intergenic
AATGATATTAAACAGAGACG+TGG 0.716066 2_2:+28910204 Msa0247030:five_prime_UTR
CATCCGAGATACGTTCCATG+TGG 0.741395 2_2:+28910915 Msa0247030:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTCGATATATTTTTGAC+AGG + chr2_2:28910822-28910841 Msa0247030:intron 20.0%
!!! ATTTCGATATATTTTTGACA+GGG + chr2_2:28910823-28910842 Msa0247030:intron 20.0%
!!! AATTTCGATATATTTTTGAC+AGG + chr2_2:28910822-28910841 Msa0247030:intron 20.0%
!!! ATTTCGATATATTTTTGACA+GGG + chr2_2:28910823-28910842 Msa0247030:intron 20.0%
!!! ATAATATTCTAAAGCGAACA+CGG + chr2_2:28910614-28910633 Msa0247030:intron 25.0%
!!! TTTCGATATATTTTTGACAG+GGG + chr2_2:28910824-28910843 Msa0247030:intron 25.0%
!!! ATAATATTCTAAAGCGAACA+CGG + chr2_2:28910614-28910633 Msa0247030:intron 25.0%
!!! TTTCGATATATTTTTGACAG+GGG + chr2_2:28910824-28910843 Msa0247030:intron 25.0%
AATGATATTAAACAGAGACG+TGG + chr2_2:28910204-28910223 Msa0247030:five_prime_UTR 30.0%
ATGATATTAAACAGAGACGT+GGG + chr2_2:28910205-28910224 Msa0247030:five_prime_UTR 30.0%
TTCAATCCATACTTCTCAAA+CGG - chr2_2:28910270-28910289 None:intergenic 30.0%
ATGCAAAATCTTCCTCAAAT+GGG - chr2_2:28910302-28910321 None:intergenic 30.0%
!!! TTTTTTCAATGAGGCTGATA+AGG + chr2_2:28910350-28910369 Msa0247030:five_prime_UTR 30.0%
!! TTTTTCAATGAGGCTGATAA+GGG + chr2_2:28910351-28910370 Msa0247030:five_prime_UTR 30.0%
AATTGTGTTTACCTGTATAG+TGG - chr2_2:28910561-28910580 None:intergenic 30.0%
!! GTGTTCGCTTTAGAATATTA+TGG - chr2_2:28910615-28910634 None:intergenic 30.0%
ATTCTCAACAATGCTTAGAA+AGG - chr2_2:28910793-28910812 None:intergenic 30.0%
AATGATATTAAACAGAGACG+TGG + chr2_2:28910204-28910223 Msa0247030:five_prime_UTR 30.0%
ATGATATTAAACAGAGACGT+GGG + chr2_2:28910205-28910224 Msa0247030:five_prime_UTR 30.0%
TTCAATCCATACTTCTCAAA+CGG - chr2_2:28910270-28910289 None:intergenic 30.0%
ATGCAAAATCTTCCTCAAAT+GGG - chr2_2:28910302-28910321 None:intergenic 30.0%
!!! TTTTTTCAATGAGGCTGATA+AGG + chr2_2:28910350-28910369 Msa0247030:five_prime_UTR 30.0%
!! TTTTTCAATGAGGCTGATAA+GGG + chr2_2:28910351-28910370 Msa0247030:five_prime_UTR 30.0%
AATTGTGTTTACCTGTATAG+TGG - chr2_2:28910561-28910580 None:intergenic 30.0%
!! GTGTTCGCTTTAGAATATTA+TGG - chr2_2:28910615-28910634 None:intergenic 30.0%
ATTCTCAACAATGCTTAGAA+AGG - chr2_2:28910793-28910812 None:intergenic 30.0%
AAACTTCCGTTTGAGAAGTA+TGG + chr2_2:28910261-28910280 Msa0247030:five_prime_UTR 35.0%
GATGCAAAATCTTCCTCAAA+TGG - chr2_2:28910303-28910322 None:intergenic 35.0%
!!! ACCAGAGAGTTTTTTCAATG+AGG + chr2_2:28910341-28910360 Msa0247030:five_prime_UTR 35.0%
!! TCTTCAAAAGAGCATCAAAG+TGG + chr2_2:28910382-28910401 Msa0247030:five_prime_UTR 35.0%
!!! AAGTGGTGGTTTTGTAATGA+AGG + chr2_2:28910399-28910418 Msa0247030:exon 35.0%
TATTCCAACAAGCTACAGAA+AGG - chr2_2:28910522-28910541 None:intergenic 35.0%
TGCTTGTAGATAATGACAAC+AGG - chr2_2:28910644-28910663 None:intergenic 35.0%
TACAAGCAATCATGTCATCA+GGG + chr2_2:28910656-28910675 Msa0247030:intron 35.0%
AAACTTCCGTTTGAGAAGTA+TGG + chr2_2:28910261-28910280 Msa0247030:five_prime_UTR 35.0%
GATGCAAAATCTTCCTCAAA+TGG - chr2_2:28910303-28910322 None:intergenic 35.0%
!!! ACCAGAGAGTTTTTTCAATG+AGG + chr2_2:28910341-28910360 Msa0247030:five_prime_UTR 35.0%
!! TCTTCAAAAGAGCATCAAAG+TGG + chr2_2:28910382-28910401 Msa0247030:five_prime_UTR 35.0%
!!! AAGTGGTGGTTTTGTAATGA+AGG + chr2_2:28910399-28910418 Msa0247030:exon 35.0%
TATTCCAACAAGCTACAGAA+AGG - chr2_2:28910522-28910541 None:intergenic 35.0%
TGCTTGTAGATAATGACAAC+AGG - chr2_2:28910644-28910663 None:intergenic 35.0%
TACAAGCAATCATGTCATCA+GGG + chr2_2:28910656-28910675 Msa0247030:intron 35.0%
GCCTCATTGAAAAAACTCTC+TGG - chr2_2:28910345-28910364 None:intergenic 40.0%
!! TCAAAAGAGCATCAAAGTGG+TGG + chr2_2:28910385-28910404 Msa0247030:five_prime_UTR 40.0%
TCCTTGCAACTGGTTATGAT+GGG + chr2_2:28910466-28910485 Msa0247030:CDS 40.0%
TGTTTACCTGTATAGTGGCA+TGG - chr2_2:28910556-28910575 None:intergenic 40.0%
CTACAAGCAATCATGTCATC+AGG + chr2_2:28910655-28910674 Msa0247030:intron 40.0%
TGCAACCAATCATGTAACGA+GGG - chr2_2:28910737-28910756 None:intergenic 40.0%
TTGCAACCAATCATGTAACG+AGG - chr2_2:28910738-28910757 None:intergenic 40.0%
ATTCCAAACATGGCCTTTGT+GGG + chr2_2:28910863-28910882 Msa0247030:CDS 40.0%
ACTCTCAACATAACCCACAA+AGG - chr2_2:28910879-28910898 None:intergenic 40.0%
GCCTCATTGAAAAAACTCTC+TGG - chr2_2:28910345-28910364 None:intergenic 40.0%
!! TCAAAAGAGCATCAAAGTGG+TGG + chr2_2:28910385-28910404 Msa0247030:five_prime_UTR 40.0%
TCCTTGCAACTGGTTATGAT+GGG + chr2_2:28910466-28910485 Msa0247030:CDS 40.0%
TGTTTACCTGTATAGTGGCA+TGG - chr2_2:28910556-28910575 None:intergenic 40.0%
CTACAAGCAATCATGTCATC+AGG + chr2_2:28910655-28910674 Msa0247030:intron 40.0%
TGCAACCAATCATGTAACGA+GGG - chr2_2:28910737-28910756 None:intergenic 40.0%
TTGCAACCAATCATGTAACG+AGG - chr2_2:28910738-28910757 None:intergenic 40.0%
ATTCCAAACATGGCCTTTGT+GGG + chr2_2:28910863-28910882 Msa0247030:CDS 40.0%
ACTCTCAACATAACCCACAA+AGG - chr2_2:28910879-28910898 None:intergenic 40.0%
! TCATAGAGTCCTACTTGCTG+TGG + chr2_2:28910238-28910257 Msa0247030:five_prime_UTR 45.0%
GAAACCAGAACACCCATTTG+AGG + chr2_2:28910287-28910306 Msa0247030:five_prime_UTR 45.0%
TCTTCCTCAAATGGGTGTTC+TGG - chr2_2:28910294-28910313 None:intergenic 45.0%
GATGTTGTTCTCCTTGCAAC+TGG + chr2_2:28910456-28910475 Msa0247030:CDS 45.0%
CTCCTTGCAACTGGTTATGA+TGG + chr2_2:28910465-28910484 Msa0247030:CDS 45.0%
TCCCATCATAACCAGTTGCA+AGG - chr2_2:28910470-28910489 None:intergenic 45.0%
AACAAGCTACAGAAAGGCTC+AGG - chr2_2:28910516-28910535 None:intergenic 45.0%
! TGAGCCTTTCTGTAGCTTGT+TGG + chr2_2:28910515-28910534 Msa0247030:CDS 45.0%
!! AGCTTGTTGGAATACCCTAC+TGG + chr2_2:28910528-28910547 Msa0247030:CDS 45.0%
ATAGTGGCATGGTACCAGTA+GGG - chr2_2:28910545-28910564 None:intergenic 45.0%
TATAGTGGCATGGTACCAGT+AGG - chr2_2:28910546-28910565 None:intergenic 45.0%
GATCTCCCTCGTTACATGAT+TGG + chr2_2:28910729-28910748 Msa0247030:intron 45.0%
ACAATGCTTAGAAAGGAGCG+CGG - chr2_2:28910786-28910805 None:intergenic 45.0%
! CCATGTTTGGAATCGATGGA+TGG - chr2_2:28910856-28910875 None:intergenic 45.0%
!! CCATCCATCGATTCCAAACA+TGG + chr2_2:28910853-28910872 Msa0247030:CDS 45.0%
! AAGGCCATGTTTGGAATCGA+TGG - chr2_2:28910860-28910879 None:intergenic 45.0%
GATTCCAAACATGGCCTTTG+TGG + chr2_2:28910862-28910881 Msa0247030:CDS 45.0%
TAACCCACAAAGGCCATGTT+TGG - chr2_2:28910869-28910888 None:intergenic 45.0%
AAGCCACATGGAACGTATCT+CGG - chr2_2:28910921-28910940 None:intergenic 45.0%
! TCATAGAGTCCTACTTGCTG+TGG + chr2_2:28910238-28910257 Msa0247030:five_prime_UTR 45.0%
GAAACCAGAACACCCATTTG+AGG + chr2_2:28910287-28910306 Msa0247030:five_prime_UTR 45.0%
TCTTCCTCAAATGGGTGTTC+TGG - chr2_2:28910294-28910313 None:intergenic 45.0%
GATGTTGTTCTCCTTGCAAC+TGG + chr2_2:28910456-28910475 Msa0247030:CDS 45.0%
CTCCTTGCAACTGGTTATGA+TGG + chr2_2:28910465-28910484 Msa0247030:CDS 45.0%
TCCCATCATAACCAGTTGCA+AGG - chr2_2:28910470-28910489 None:intergenic 45.0%
AACAAGCTACAGAAAGGCTC+AGG - chr2_2:28910516-28910535 None:intergenic 45.0%
! TGAGCCTTTCTGTAGCTTGT+TGG + chr2_2:28910515-28910534 Msa0247030:CDS 45.0%
!! AGCTTGTTGGAATACCCTAC+TGG + chr2_2:28910528-28910547 Msa0247030:CDS 45.0%
ATAGTGGCATGGTACCAGTA+GGG - chr2_2:28910545-28910564 None:intergenic 45.0%
TATAGTGGCATGGTACCAGT+AGG - chr2_2:28910546-28910565 None:intergenic 45.0%
GATCTCCCTCGTTACATGAT+TGG + chr2_2:28910729-28910748 Msa0247030:intron 45.0%
ACAATGCTTAGAAAGGAGCG+CGG - chr2_2:28910786-28910805 None:intergenic 45.0%
! CCATGTTTGGAATCGATGGA+TGG - chr2_2:28910856-28910875 None:intergenic 45.0%
!! CCATCCATCGATTCCAAACA+TGG + chr2_2:28910853-28910872 Msa0247030:CDS 45.0%
! AAGGCCATGTTTGGAATCGA+TGG - chr2_2:28910860-28910879 None:intergenic 45.0%
GATTCCAAACATGGCCTTTG+TGG + chr2_2:28910862-28910881 Msa0247030:CDS 45.0%
TAACCCACAAAGGCCATGTT+TGG - chr2_2:28910869-28910888 None:intergenic 45.0%
AAGCCACATGGAACGTATCT+CGG - chr2_2:28910921-28910940 None:intergenic 45.0%
CGGAAGTTTCCACAGCAAGT+AGG - chr2_2:28910250-28910269 None:intergenic 50.0%
CTGGTACCATGCCACTATAC+AGG + chr2_2:28910547-28910566 Msa0247030:CDS 50.0%
CATCCGAGATACGTTCCATG+TGG + chr2_2:28910915-28910934 Msa0247030:CDS 50.0%
GAGATACGTTCCATGTGGCT+TGG + chr2_2:28910920-28910939 Msa0247030:CDS 50.0%
CGGAAGTTTCCACAGCAAGT+AGG - chr2_2:28910250-28910269 None:intergenic 50.0%
CTGGTACCATGCCACTATAC+AGG + chr2_2:28910547-28910566 Msa0247030:CDS 50.0%
CATCCGAGATACGTTCCATG+TGG + chr2_2:28910915-28910934 Msa0247030:CDS 50.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 28910169 28910941 28910169 ID=Msa0247030;Name=Msa0247030
chr2_2 mRNA 28910169 28910941 28910169 ID=Msa0247030-mRNA-1;Parent=Msa0247030;Name=Msa0247030-mRNA-1;_AED=0.01;_eAED=0.01;_QI=246|1|0.5|1|1|0.5|2|0|84
chr2_2 exon 28910169 28910568 28910169 ID=Msa0247030-mRNA-1:exon:10326;Parent=Msa0247030-mRNA-1
chr2_2 exon 28910844 28910941 28910844 ID=Msa0247030-mRNA-1:exon:10327;Parent=Msa0247030-mRNA-1
chr2_2 five_prime_UTR 28910169 28910414 28910169 ID=Msa0247030-mRNA-1:five_prime_utr;Parent=Msa0247030-mRNA-1
chr2_2 CDS 28910415 28910568 28910415 ID=Msa0247030-mRNA-1:cds;Parent=Msa0247030-mRNA-1
chr2_2 CDS 28910844 28910941 28910844 ID=Msa0247030-mRNA-1:cds;Parent=Msa0247030-mRNA-1
Gene Sequence

>Msa0247030

ATGAAGGAATTGAATTTGATGACAACACTAAAATTGATGCTGATGTTGTTCTCCTTGCAACTGGTTATGATGGGAAAAAGAAGCTCAAAACACTTTTGCCTGAGCCTTTCTGTAGCTTGTTGGAATACCCTACTGGTACCATGCCACTATACAGGGGAACTGTCCATCCATCGATTCCAAACATGGCCTTTGTGGGTTATGTTGAGAGTGTTTCAAATCTTTACACATCCGAGATACGTTCCATGTGGCTTG
Protein sequence

>Msa0247030

MKELNLMTTLKLMLMLFSLQLVMMGKRSSKHFCLSLSVACWNTLLVPCHYTGELSIHRFQTWPLWVMLRVFQIFTHPRYVPCGL