AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1042690

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 46 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGTGTTTGTTTGCTTATT+AGG 0.170300 7_1:-80689489 Msa1042690:five_prime_UTR
CATACCTTTGTGAAGATAAA+AGG 0.212182 7_1:+80689799 None:intergenic
ATGTTATTATGCAGTTATTT+AGG 0.218335 7_1:+80689674 None:intergenic
CAAACTTATAACATGTTAAA+TGG 0.250440 7_1:-80689718 Msa1042690:five_prime_UTR
GTGTGTTTGTTTGCTTATTA+GGG 0.282917 7_1:-80689488 Msa1042690:five_prime_UTR
AGATGACAATGCTATGATTT+AGG 0.322538 7_1:-80689420 Msa1042690:five_prime_UTR
GTGATCTCATCCAGGATGAT+AGG 0.356626 7_1:+80689084 None:intergenic
CCAGGATGATAGGGTGGATA+GGG 0.403549 7_1:+80689094 None:intergenic
ATGTTGAAGGAGGCAAGAAC+TGG 0.403774 7_1:-80689197 Msa1042690:CDS
TAAGGACGGGAAGGAACATT+TGG 0.428961 7_1:-80689597 Msa1042690:five_prime_UTR
TCAAGGAAATAATCAGTTGT+AGG 0.437408 7_1:+80689532 None:intergenic
GCAAGAGGTGTGATGGCAGC+AGG 0.439246 7_1:+80689153 None:intergenic
AAATGTTCCTTCCCGTCCTT+AGG 0.450368 7_1:+80689599 None:intergenic
TGATGGCAGCAGGGGTAAGT+TGG 0.456592 7_1:+80689163 None:intergenic
CATACTACCTCTGCTAAGAT+TGG 0.469905 7_1:-80689129 Msa1042690:CDS
CCCTATCCACCCTATCATCC+TGG 0.477480 7_1:-80689094 Msa1042690:CDS
ACCATGTTGCAGAATGTTGA+AGG 0.481802 7_1:-80689210 Msa1042690:CDS
TTTAGGATATGTACATATGA+AGG 0.490693 7_1:+80689691 None:intergenic
TAAGATAGTAACATATCCTA+AGG 0.501123 7_1:-80689615 Msa1042690:five_prime_UTR
ATTCTGCAACATGGTGGAAG+GGG 0.513075 7_1:+80689218 None:intergenic
TTGCAGGAGTGATCTCATCC+AGG 0.524797 7_1:+80689076 None:intergenic
TGTCTTTGAACAACAAGTGC+AGG 0.532648 7_1:-80689833 Msa1042690:five_prime_UTR
ACATTCTGCAACATGGTGGA+AGG 0.539324 7_1:+80689216 None:intergenic
GCTATGATTTAGGACACAAA+TGG 0.549496 7_1:-80689410 Msa1042690:exon
TGATCTCATCCAGGATGATA+GGG 0.550931 7_1:+80689085 None:intergenic
TAGTAACATATCCTAAGGAC+GGG 0.551671 7_1:-80689610 Msa1042690:five_prime_UTR
CAGTTGATGGATATGTACTT+AGG 0.555877 7_1:+80689649 None:intergenic
TCCTTCAACATTCTGCAACA+TGG 0.556193 7_1:+80689209 None:intergenic
CATTCTGCAACATGGTGGAA+GGG 0.560478 7_1:+80689217 None:intergenic
AGTATGAGCAAGAGGTGTGA+TGG 0.566077 7_1:+80689146 None:intergenic
ATCATAGCATTGTCATCTTG+TGG 0.571853 7_1:+80689425 None:intergenic
GATGGTCATTGTTGATGCTA+AGG 0.581330 7_1:-80689573 Msa1042690:five_prime_UTR
TCCAGGATGATAGGGTGGAT+AGG 0.585429 7_1:+80689093 None:intergenic
CAAGAGGTGTGATGGCAGCA+GGG 0.589536 7_1:+80689154 None:intergenic
GCAGAGGTAGTATGAGCAAG+AGG 0.599567 7_1:+80689138 None:intergenic
ATAGTAACATATCCTAAGGA+CGG 0.602531 7_1:-80689611 Msa1042690:five_prime_UTR
CGGGAAGGAACATTTGGAGA+TGG 0.612772 7_1:-80689591 Msa1042690:five_prime_UTR
TGTTGAAGGAGGCAAGAACT+GGG 0.613431 7_1:-80689196 Msa1042690:CDS
AAGATGTCATAAATTAGTCA+AGG 0.614511 7_1:+80689515 None:intergenic
AACATATCCTAAGGACGGGA+AGG 0.619664 7_1:-80689606 Msa1042690:five_prime_UTR
CAGGATGATAGGGTGGATAG+GGG 0.620934 7_1:+80689095 None:intergenic
AAGAGGTGTGATGGCAGCAG+GGG 0.623171 7_1:+80689155 None:intergenic
TTCAACATTCTGCAACATGG+TGG 0.658953 7_1:+80689212 None:intergenic
TCTCATCCAGGATGATAGGG+TGG 0.663515 7_1:+80689088 None:intergenic
ACTTGAACCAATCTTAGCAG+AGG 0.665354 7_1:+80689122 None:intergenic
ATGTTGCAGAATGTTGAAGG+AGG 0.685850 7_1:-80689207 Msa1042690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAACTTATAACATGTTAAA+TGG - chr7_1:80689294-80689313 Msa1042690:intron 20.0%
!! ATGTTATTATGCAGTTATTT+AGG + chr7_1:80689341-80689360 None:intergenic 20.0%
!! TAAAAAAAAATAGCAGTTGA+TGG + chr7_1:80689379-80689398 None:intergenic 20.0%
!! ACATATGTTTAAACATATCA+AGG + chr7_1:80689711-80689730 None:intergenic 20.0%
!! CAAACTTATAACATGTTAAA+TGG - chr7_1:80689294-80689313 Msa1042690:intron 20.0%
!! ATGTTATTATGCAGTTATTT+AGG + chr7_1:80689341-80689360 None:intergenic 20.0%
!! TAAAAAAAAATAGCAGTTGA+TGG + chr7_1:80689379-80689398 None:intergenic 20.0%
!! ACATATGTTTAAACATATCA+AGG + chr7_1:80689711-80689730 None:intergenic 20.0%
!! AATTTGTAGTGTTTTCAACT+AGG - chr7_1:80689089-80689108 Msa1042690:CDS 25.0%
!! TTTAGGATATGTACATATGA+AGG + chr7_1:80689324-80689343 None:intergenic 25.0%
! TAAGATAGTAACATATCCTA+AGG - chr7_1:80689397-80689416 Msa1042690:exon 25.0%
! AAGATGTCATAAATTAGTCA+AGG + chr7_1:80689500-80689519 None:intergenic 25.0%
! TCAATTAAGATGATCTACAT+TGG - chr7_1:80689668-80689687 Msa1042690:five_prime_UTR 25.0%
!! AATTTGTAGTGTTTTCAACT+AGG - chr7_1:80689089-80689108 Msa1042690:CDS 25.0%
!! TTTAGGATATGTACATATGA+AGG + chr7_1:80689324-80689343 None:intergenic 25.0%
! TAAGATAGTAACATATCCTA+AGG - chr7_1:80689397-80689416 Msa1042690:exon 25.0%
! AAGATGTCATAAATTAGTCA+AGG + chr7_1:80689500-80689519 None:intergenic 25.0%
! TCAATTAAGATGATCTACAT+TGG - chr7_1:80689668-80689687 Msa1042690:five_prime_UTR 25.0%
! TACTCCTTTTATCTTCACAA+AGG - chr7_1:80689209-80689228 Msa1042690:CDS 30.0%
CATACCTTTGTGAAGATAAA+AGG + chr7_1:80689216-80689235 None:intergenic 30.0%
ATAGTAACATATCCTAAGGA+CGG - chr7_1:80689401-80689420 Msa1042690:exon 30.0%
TCAAGGAAATAATCAGTTGT+AGG + chr7_1:80689483-80689502 None:intergenic 30.0%
TGTGTGTTTGTTTGCTTATT+AGG - chr7_1:80689523-80689542 Msa1042690:five_prime_UTR 30.0%
GTGTGTTTGTTTGCTTATTA+GGG - chr7_1:80689524-80689543 Msa1042690:five_prime_UTR 30.0%
AGATGACAATGCTATGATTT+AGG - chr7_1:80689592-80689611 Msa1042690:five_prime_UTR 30.0%
! CTACATTGGTTATTTATCTG+CGG - chr7_1:80689682-80689701 Msa1042690:five_prime_UTR 30.0%
!!! TTAGAGTAAGAGTTTTTTGC+AGG + chr7_1:80689955-80689974 None:intergenic 30.0%
! TACTCCTTTTATCTTCACAA+AGG - chr7_1:80689209-80689228 Msa1042690:CDS 30.0%
CATACCTTTGTGAAGATAAA+AGG + chr7_1:80689216-80689235 None:intergenic 30.0%
ATAGTAACATATCCTAAGGA+CGG - chr7_1:80689401-80689420 Msa1042690:exon 30.0%
TCAAGGAAATAATCAGTTGT+AGG + chr7_1:80689483-80689502 None:intergenic 30.0%
TGTGTGTTTGTTTGCTTATT+AGG - chr7_1:80689523-80689542 Msa1042690:five_prime_UTR 30.0%
GTGTGTTTGTTTGCTTATTA+GGG - chr7_1:80689524-80689543 Msa1042690:five_prime_UTR 30.0%
AGATGACAATGCTATGATTT+AGG - chr7_1:80689592-80689611 Msa1042690:five_prime_UTR 30.0%
! CTACATTGGTTATTTATCTG+CGG - chr7_1:80689682-80689701 Msa1042690:five_prime_UTR 30.0%
!!! TTAGAGTAAGAGTTTTTTGC+AGG + chr7_1:80689955-80689974 None:intergenic 30.0%
!! CAGTTGATGGATATGTACTT+AGG + chr7_1:80689366-80689385 None:intergenic 35.0%
TAGTAACATATCCTAAGGAC+GGG - chr7_1:80689402-80689421 Msa1042690:exon 35.0%
ATCATAGCATTGTCATCTTG+TGG + chr7_1:80689590-80689609 None:intergenic 35.0%
! GCTATGATTTAGGACACAAA+TGG - chr7_1:80689602-80689621 Msa1042690:five_prime_UTR 35.0%
TAAGAACATGATCTGTCACT+TGG - chr7_1:80689760-80689779 Msa1042690:five_prime_UTR 35.0%
!! CAGTTGATGGATATGTACTT+AGG + chr7_1:80689366-80689385 None:intergenic 35.0%
TAGTAACATATCCTAAGGAC+GGG - chr7_1:80689402-80689421 Msa1042690:exon 35.0%
ATCATAGCATTGTCATCTTG+TGG + chr7_1:80689590-80689609 None:intergenic 35.0%
! GCTATGATTTAGGACACAAA+TGG - chr7_1:80689602-80689621 Msa1042690:five_prime_UTR 35.0%
TAAGAACATGATCTGTCACT+TGG - chr7_1:80689760-80689779 Msa1042690:five_prime_UTR 35.0%
TGTCTTTGAACAACAAGTGC+AGG - chr7_1:80689179-80689198 Msa1042690:CDS 40.0%
GATGGTCATTGTTGATGCTA+AGG - chr7_1:80689439-80689458 Msa1042690:five_prime_UTR 40.0%
TTCAACATTCTGCAACATGG+TGG + chr7_1:80689803-80689822 None:intergenic 40.0%
ACCATGTTGCAGAATGTTGA+AGG - chr7_1:80689802-80689821 Msa1042690:five_prime_UTR 40.0%
TCCTTCAACATTCTGCAACA+TGG + chr7_1:80689806-80689825 None:intergenic 40.0%
ATGTTGCAGAATGTTGAAGG+AGG - chr7_1:80689805-80689824 Msa1042690:five_prime_UTR 40.0%
CATACTACCTCTGCTAAGAT+TGG - chr7_1:80689883-80689902 Msa1042690:five_prime_UTR 40.0%
ACTTGAACCAATCTTAGCAG+AGG + chr7_1:80689893-80689912 None:intergenic 40.0%
TGATCTCATCCAGGATGATA+GGG + chr7_1:80689930-80689949 None:intergenic 40.0%
TGTCTTTGAACAACAAGTGC+AGG - chr7_1:80689179-80689198 Msa1042690:CDS 40.0%
GATGGTCATTGTTGATGCTA+AGG - chr7_1:80689439-80689458 Msa1042690:five_prime_UTR 40.0%
TTCAACATTCTGCAACATGG+TGG + chr7_1:80689803-80689822 None:intergenic 40.0%
ACCATGTTGCAGAATGTTGA+AGG - chr7_1:80689802-80689821 Msa1042690:five_prime_UTR 40.0%
TCCTTCAACATTCTGCAACA+TGG + chr7_1:80689806-80689825 None:intergenic 40.0%
ATGTTGCAGAATGTTGAAGG+AGG - chr7_1:80689805-80689824 Msa1042690:five_prime_UTR 40.0%
CATACTACCTCTGCTAAGAT+TGG - chr7_1:80689883-80689902 Msa1042690:five_prime_UTR 40.0%
ACTTGAACCAATCTTAGCAG+AGG + chr7_1:80689893-80689912 None:intergenic 40.0%
TGATCTCATCCAGGATGATA+GGG + chr7_1:80689930-80689949 None:intergenic 40.0%
AACATATCCTAAGGACGGGA+AGG - chr7_1:80689406-80689425 Msa1042690:exon 45.0%
AAATGTTCCTTCCCGTCCTT+AGG + chr7_1:80689416-80689435 None:intergenic 45.0%
TAAGGACGGGAAGGAACATT+TGG - chr7_1:80689415-80689434 Msa1042690:five_prime_UTR 45.0%
! ATTCTGCAACATGGTGGAAG+GGG + chr7_1:80689797-80689816 None:intergenic 45.0%
! CATTCTGCAACATGGTGGAA+GGG + chr7_1:80689798-80689817 None:intergenic 45.0%
! ACATTCTGCAACATGGTGGA+AGG + chr7_1:80689799-80689818 None:intergenic 45.0%
ATGTTGAAGGAGGCAAGAAC+TGG - chr7_1:80689815-80689834 Msa1042690:five_prime_UTR 45.0%
TGTTGAAGGAGGCAAGAACT+GGG - chr7_1:80689816-80689835 Msa1042690:five_prime_UTR 45.0%
! AGTATGAGCAAGAGGTGTGA+TGG + chr7_1:80689869-80689888 None:intergenic 45.0%
GTGATCTCATCCAGGATGAT+AGG + chr7_1:80689931-80689950 None:intergenic 45.0%
AACATATCCTAAGGACGGGA+AGG - chr7_1:80689406-80689425 Msa1042690:exon 45.0%
AAATGTTCCTTCCCGTCCTT+AGG + chr7_1:80689416-80689435 None:intergenic 45.0%
TAAGGACGGGAAGGAACATT+TGG - chr7_1:80689415-80689434 Msa1042690:five_prime_UTR 45.0%
! ATTCTGCAACATGGTGGAAG+GGG + chr7_1:80689797-80689816 None:intergenic 45.0%
! CATTCTGCAACATGGTGGAA+GGG + chr7_1:80689798-80689817 None:intergenic 45.0%
! ACATTCTGCAACATGGTGGA+AGG + chr7_1:80689799-80689818 None:intergenic 45.0%
ATGTTGAAGGAGGCAAGAAC+TGG - chr7_1:80689815-80689834 Msa1042690:five_prime_UTR 45.0%
TGTTGAAGGAGGCAAGAACT+GGG - chr7_1:80689816-80689835 Msa1042690:five_prime_UTR 45.0%
! AGTATGAGCAAGAGGTGTGA+TGG + chr7_1:80689869-80689888 None:intergenic 45.0%
GTGATCTCATCCAGGATGAT+AGG + chr7_1:80689931-80689950 None:intergenic 45.0%
CGGGAAGGAACATTTGGAGA+TGG - chr7_1:80689421-80689440 Msa1042690:five_prime_UTR 50.0%
AAGTTGCAGATGCAGCACAC+TGG + chr7_1:80689735-80689754 None:intergenic 50.0%
GCAGAGGTAGTATGAGCAAG+AGG + chr7_1:80689877-80689896 None:intergenic 50.0%
CAGGATGATAGGGTGGATAG+GGG + chr7_1:80689920-80689939 None:intergenic 50.0%
CCAGGATGATAGGGTGGATA+GGG + chr7_1:80689921-80689940 None:intergenic 50.0%
TCCAGGATGATAGGGTGGAT+AGG + chr7_1:80689922-80689941 None:intergenic 50.0%
TCTCATCCAGGATGATAGGG+TGG + chr7_1:80689927-80689946 None:intergenic 50.0%
TTGCAGGAGTGATCTCATCC+AGG + chr7_1:80689939-80689958 None:intergenic 50.0%
CGGGAAGGAACATTTGGAGA+TGG - chr7_1:80689421-80689440 Msa1042690:five_prime_UTR 50.0%
AAGTTGCAGATGCAGCACAC+TGG + chr7_1:80689735-80689754 None:intergenic 50.0%
GCAGAGGTAGTATGAGCAAG+AGG + chr7_1:80689877-80689896 None:intergenic 50.0%
CAGGATGATAGGGTGGATAG+GGG + chr7_1:80689920-80689939 None:intergenic 50.0%
CCAGGATGATAGGGTGGATA+GGG + chr7_1:80689921-80689940 None:intergenic 50.0%
TCCAGGATGATAGGGTGGAT+AGG + chr7_1:80689922-80689941 None:intergenic 50.0%
TCTCATCCAGGATGATAGGG+TGG + chr7_1:80689927-80689946 None:intergenic 50.0%
TTGCAGGAGTGATCTCATCC+AGG + chr7_1:80689939-80689958 None:intergenic 50.0%
TGATGGCAGCAGGGGTAAGT+TGG + chr7_1:80689852-80689871 None:intergenic 55.0%
! AAGAGGTGTGATGGCAGCAG+GGG + chr7_1:80689860-80689879 None:intergenic 55.0%
! CAAGAGGTGTGATGGCAGCA+GGG + chr7_1:80689861-80689880 None:intergenic 55.0%
CCCTATCCACCCTATCATCC+TGG - chr7_1:80689918-80689937 Msa1042690:five_prime_UTR 55.0%
TGATGGCAGCAGGGGTAAGT+TGG + chr7_1:80689852-80689871 None:intergenic 55.0%
! AAGAGGTGTGATGGCAGCAG+GGG + chr7_1:80689860-80689879 None:intergenic 55.0%
! CAAGAGGTGTGATGGCAGCA+GGG + chr7_1:80689861-80689880 None:intergenic 55.0%
CCCTATCCACCCTATCATCC+TGG - chr7_1:80689918-80689937 Msa1042690:five_prime_UTR 55.0%
! GCAAGAGGTGTGATGGCAGC+AGG + chr7_1:80689862-80689881 None:intergenic 60.0%
! GCAAGAGGTGTGATGGCAGC+AGG + chr7_1:80689862-80689881 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 80689056 80689978 80689056 ID=Msa1042690;Name=Msa1042690
chr7_1 mRNA 80689056 80689978 80689056 ID=Msa1042690-mRNA-1;Parent=Msa1042690;Name=Msa1042690-mRNA-1;_AED=0.29;_eAED=0.46;_QI=565|0|0.5|1|1|0.5|2|0|74
chr7_1 exon 80689056 80689247 80689056 ID=Msa1042690-mRNA-1:exon:22050;Parent=Msa1042690-mRNA-1
chr7_1 exon 80689384 80689978 80689384 ID=Msa1042690-mRNA-1:exon:22049;Parent=Msa1042690-mRNA-1
chr7_1 five_prime_UTR 80689414 80689978 80689414 ID=Msa1042690-mRNA-1:five_prime_utr;Parent=Msa1042690-mRNA-1
chr7_1 CDS 80689384 80689413 80689384 ID=Msa1042690-mRNA-1:cds;Parent=Msa1042690-mRNA-1
chr7_1 CDS 80689056 80689247 80689056 ID=Msa1042690-mRNA-1:cds;Parent=Msa1042690-mRNA-1
Gene Sequence

>Msa1042690

ATGGAGAGTGATGATGTTACTATCTCAGTTATGCAAACCCCTTCCACCATGTTGCAGAATGTTGAAGGAGGCAAGAACTGGGACTCACTCAGCCAACTTACCCCTGCTGCCATCACACCTCTTGCTCATACTACCTCTGCTAAGATTGGTTCAAGTGCTACCCCTATCCACCCTATCATCCTGGATGAGATCACTCCTGCAAAAAACTCTTACTCTAAGATG
Protein sequence

>Msa1042690

MESDDVTISVMQTPSTMLQNVEGGKNWDSLSQLTPAAITPLAHTTSAKIGSSATPIHPIILDEITPAKNSYSKM