AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1162250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1162250 MtrunA17_Chr5g0393501 30.303 165 110 2 3 162 77 241 9.55e-22 88.2
Msa1162250 MtrunA17_Chr4g0044671 30.000 150 95 5 5 148 62 207 2.98e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATACACTGTTTGACTTCT+AGG 0.109128 7_4:+52804093 Msa1162250:five_prime_UTR
CCCATACCAATTGTGATGTT+TGG 0.340839 7_4:+52804671 Msa1162250:CDS
AGGAATTTGCCAAAAGTATC+AGG 0.344083 7_4:-52804566 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 7_4:+52804557 Msa1162250:intron
AGTCGTGATGTTTCACTCTA+AGG 0.360647 7_4:-52804586 None:intergenic
CGATTATTCAATGAATTTAG+TGG 0.362359 7_4:+52804267 Msa1162250:CDS
ACCTTTGAAATTCCTATCGC+TGG 0.400328 7_4:+52804417 Msa1162250:CDS
TCCAAACATCACAATTGGTA+TGG 0.411232 7_4:-52804672 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 7_4:-52804308 None:intergenic
CCAAACATCACAATTGGTAT+GGG 0.452680 7_4:-52804671 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 7_4:+52804712 Msa1162250:CDS
TCAATATTTGTACGAGCTAC+CGG 0.465762 7_4:+52804147 Msa1162250:five_prime_UTR
GAGCAATGTCACTTGCTAGA+TGG 0.472188 7_4:+52804169 Msa1162250:five_prime_UTR
GGCCGTTGTTGACAGATGGT+TGG 0.487397 7_4:+52804235 Msa1162250:CDS
TGTGCTGCCAATGGTATTGA+GGG 0.501205 7_4:+52804713 Msa1162250:CDS
CTGTTTGACTTCTAGGATGT+TGG 0.502336 7_4:+52804100 Msa1162250:five_prime_UTR
ATTATTGCTTTCCAGTACCT+TGG 0.503165 7_4:+52804297 Msa1162250:CDS
ACAGGAATGACATAGTCATA+TGG 0.506205 7_4:-52804626 None:intergenic
CCAATTGTGATGTTTGGAAA+AGG 0.511741 7_4:+52804677 Msa1162250:CDS
AAATATTGAGCAACGAAGAA+TGG 0.514560 7_4:-52804133 None:intergenic
ACACGATGCTACCGTACTCA+TGG 0.523476 7_4:-52804388 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 7_4:+52804231 Msa1162250:CDS
AAGGGAAAACAACTGCAAGC+TGG 0.535824 7_4:-52804066 None:intergenic
TGGTACGGTGGATAATCAGC+TGG 0.535891 7_4:-52804363 None:intergenic
TTGTGATGTTTGGAAAAGGC+TGG 0.536068 7_4:+52804681 Msa1162250:CDS
TTTCAAGTGCAAGTGTGTCA+TGG 0.544420 7_4:+52804751 Msa1162250:CDS
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 7_4:+52804300 Msa1162250:CDS
TCTGTATATTTGAGTCTCAC+AGG 0.555272 7_4:-52804644 None:intergenic
ACCGTACCATTCCATGAGTA+CGG 0.577505 7_4:+52804377 Msa1162250:CDS
ATGCTACCGTACTCATGGAA+TGG 0.577726 7_4:-52804383 None:intergenic
GTCTCCGCCCTCAATACCAT+TGG 0.581950 7_4:-52804720 None:intergenic
TCTAGCAAGTGACATTGCTC+CGG 0.590324 7_4:-52804166 None:intergenic
ACCGTACTCATGGAATGGTA+CGG 0.605102 7_4:-52804378 None:intergenic
TGTCACTTGCTAGATGGTGA+TGG 0.612054 7_4:+52804175 Msa1162250:five_prime_UTR
TGTTAAACAAATCAGTTAGT+CGG 0.616534 7_4:+52804214 Msa1162250:CDS
TCCAGCGATAGGAATTTCAA+AGG 0.627051 7_4:-52804418 None:intergenic
CAAACATCACAATTGGTATG+GGG 0.630299 7_4:-52804670 None:intergenic
GATTTCGTATATCCAGCGAT+AGG 0.640357 7_4:-52804429 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 7_4:-52804237 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 7_4:-52804314 None:intergenic
TGGATATACGAAATCACCGA+AGG 0.681793 7_4:+52804437 Msa1162250:CDS
GTACTCATGGAATGGTACGG+TGG 0.720319 7_4:-52804375 None:intergenic
GCTGCCAATGGTATTGAGGG+CGG 0.739556 7_4:+52804716 Msa1162250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATATATGCTATTTTAATA+CGG + chr7_4:52804497-52804516 Msa1162250:intron 10.0%
!!! TTATATATGCTATTTTAATA+CGG + chr7_4:52804497-52804516 Msa1162250:intron 10.0%
!!! ATGAAAATTAAATCCTTTTT+TGG + chr7_4:52804012-52804031 Msa1162250:five_prime_UTR 15.0%
!!! TCTGAATTTTTTGTTTTTTT+AGG + chr7_4:52804538-52804557 Msa1162250:intron 15.0%
!!! ATGAAAATTAAATCCTTTTT+TGG + chr7_4:52804012-52804031 Msa1162250:five_prime_UTR 15.0%
!!! TCTGAATTTTTTGTTTTTTT+AGG + chr7_4:52804538-52804557 Msa1162250:intron 15.0%
!!! AAATTAAATCCTTTTTTGGT+TGG + chr7_4:52804016-52804035 Msa1162250:five_prime_UTR 20.0%
!! ATATTAAATCCAACCAAAAA+AGG - chr7_4:52804028-52804047 None:intergenic 20.0%
!!! TTTTTATGCTATTCAATTAG+AGG + chr7_4:52804473-52804492 Msa1162250:intron 20.0%
!!! AAATTAAATCCTTTTTTGGT+TGG + chr7_4:52804016-52804035 Msa1162250:five_prime_UTR 20.0%
!! ATATTAAATCCAACCAAAAA+AGG - chr7_4:52804028-52804047 None:intergenic 20.0%
!!! TTTTTATGCTATTCAATTAG+AGG + chr7_4:52804473-52804492 Msa1162250:intron 20.0%
! CAAACAGTGTATCAAAAAAA+GGG - chr7_4:52804087-52804106 None:intergenic 25.0%
! TCAAACAGTGTATCAAAAAA+AGG - chr7_4:52804088-52804107 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG + chr7_4:52804214-52804233 Msa1162250:CDS 25.0%
! CGATTATTCAATGAATTTAG+TGG + chr7_4:52804267-52804286 Msa1162250:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG - chr7_4:52804456-52804475 None:intergenic 25.0%
! CAAACAGTGTATCAAAAAAA+GGG - chr7_4:52804087-52804106 None:intergenic 25.0%
! TCAAACAGTGTATCAAAAAA+AGG - chr7_4:52804088-52804107 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG + chr7_4:52804214-52804233 Msa1162250:CDS 25.0%
! CGATTATTCAATGAATTTAG+TGG + chr7_4:52804267-52804286 Msa1162250:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG - chr7_4:52804456-52804475 None:intergenic 25.0%
AAATATTGAGCAACGAAGAA+TGG - chr7_4:52804136-52804155 None:intergenic 30.0%
AAATATTGAGCAACGAAGAA+TGG - chr7_4:52804136-52804155 None:intergenic 30.0%
! TGATACACTGTTTGACTTCT+AGG + chr7_4:52804093-52804112 Msa1162250:five_prime_UTR 35.0%
TCAATATTTGTACGAGCTAC+CGG + chr7_4:52804147-52804166 Msa1162250:five_prime_UTR 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr7_4:52804297-52804316 Msa1162250:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr7_4:52804317-52804336 None:intergenic 35.0%
! TAGGAACTACCTGATACTTT+TGG + chr7_4:52804557-52804576 Msa1162250:intron 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG - chr7_4:52804569-52804588 None:intergenic 35.0%
ACAGGAATGACATAGTCATA+TGG - chr7_4:52804629-52804648 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr7_4:52804647-52804666 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG - chr7_4:52804673-52804692 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG - chr7_4:52804674-52804693 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG - chr7_4:52804675-52804694 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG - chr7_4:52804680-52804699 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG + chr7_4:52804677-52804696 Msa1162250:CDS 35.0%
! TGATACACTGTTTGACTTCT+AGG + chr7_4:52804093-52804112 Msa1162250:five_prime_UTR 35.0%
TCAATATTTGTACGAGCTAC+CGG + chr7_4:52804147-52804166 Msa1162250:five_prime_UTR 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr7_4:52804297-52804316 Msa1162250:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr7_4:52804317-52804336 None:intergenic 35.0%
! TAGGAACTACCTGATACTTT+TGG + chr7_4:52804557-52804576 Msa1162250:intron 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG - chr7_4:52804569-52804588 None:intergenic 35.0%
ACAGGAATGACATAGTCATA+TGG - chr7_4:52804629-52804648 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr7_4:52804647-52804666 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG - chr7_4:52804673-52804692 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG - chr7_4:52804674-52804693 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG - chr7_4:52804675-52804694 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG - chr7_4:52804680-52804699 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG + chr7_4:52804677-52804696 Msa1162250:CDS 35.0%
!! CTGTTTGACTTCTAGGATGT+TGG + chr7_4:52804100-52804119 Msa1162250:five_prime_UTR 40.0%
!! ACCTTTGAAATTCCTATCGC+TGG + chr7_4:52804417-52804436 Msa1162250:CDS 40.0%
TCCAGCGATAGGAATTTCAA+AGG - chr7_4:52804421-52804440 None:intergenic 40.0%
GATTTCGTATATCCAGCGAT+AGG - chr7_4:52804432-52804451 None:intergenic 40.0%
TGGATATACGAAATCACCGA+AGG + chr7_4:52804437-52804456 Msa1162250:CDS 40.0%
AGTCGTGATGTTTCACTCTA+AGG - chr7_4:52804589-52804608 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG + chr7_4:52804671-52804690 Msa1162250:CDS 40.0%
TTGTGATGTTTGGAAAAGGC+TGG + chr7_4:52804681-52804700 Msa1162250:CDS 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG + chr7_4:52804751-52804770 Msa1162250:CDS 40.0%
!! CTGTTTGACTTCTAGGATGT+TGG + chr7_4:52804100-52804119 Msa1162250:five_prime_UTR 40.0%
!! ACCTTTGAAATTCCTATCGC+TGG + chr7_4:52804417-52804436 Msa1162250:CDS 40.0%
TCCAGCGATAGGAATTTCAA+AGG - chr7_4:52804421-52804440 None:intergenic 40.0%
GATTTCGTATATCCAGCGAT+AGG - chr7_4:52804432-52804451 None:intergenic 40.0%
TGGATATACGAAATCACCGA+AGG + chr7_4:52804437-52804456 Msa1162250:CDS 40.0%
AGTCGTGATGTTTCACTCTA+AGG - chr7_4:52804589-52804608 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG + chr7_4:52804671-52804690 Msa1162250:CDS 40.0%
TTGTGATGTTTGGAAAAGGC+TGG + chr7_4:52804681-52804700 Msa1162250:CDS 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG + chr7_4:52804751-52804770 Msa1162250:CDS 40.0%
AAGGGAAAACAACTGCAAGC+TGG - chr7_4:52804069-52804088 None:intergenic 45.0%
TCTAGCAAGTGACATTGCTC+CGG - chr7_4:52804169-52804188 None:intergenic 45.0%
! GAGCAATGTCACTTGCTAGA+TGG + chr7_4:52804169-52804188 Msa1162250:five_prime_UTR 45.0%
! TGTCACTTGCTAGATGGTGA+TGG + chr7_4:52804175-52804194 Msa1162250:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr7_4:52804240-52804259 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr7_4:52804300-52804319 Msa1162250:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr7_4:52804311-52804330 None:intergenic 45.0%
ACCGTACCATTCCATGAGTA+CGG + chr7_4:52804377-52804396 Msa1162250:CDS 45.0%
ACCGTACTCATGGAATGGTA+CGG - chr7_4:52804381-52804400 None:intergenic 45.0%
ATGCTACCGTACTCATGGAA+TGG - chr7_4:52804386-52804405 None:intergenic 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr7_4:52804704-52804723 Msa1162250:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr7_4:52804712-52804731 Msa1162250:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr7_4:52804713-52804732 Msa1162250:CDS 45.0%
AAGGGAAAACAACTGCAAGC+TGG - chr7_4:52804069-52804088 None:intergenic 45.0%
TCTAGCAAGTGACATTGCTC+CGG - chr7_4:52804169-52804188 None:intergenic 45.0%
! GAGCAATGTCACTTGCTAGA+TGG + chr7_4:52804169-52804188 Msa1162250:five_prime_UTR 45.0%
! TGTCACTTGCTAGATGGTGA+TGG + chr7_4:52804175-52804194 Msa1162250:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr7_4:52804240-52804259 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr7_4:52804300-52804319 Msa1162250:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr7_4:52804311-52804330 None:intergenic 45.0%
ACCGTACCATTCCATGAGTA+CGG + chr7_4:52804377-52804396 Msa1162250:CDS 45.0%
ACCGTACTCATGGAATGGTA+CGG - chr7_4:52804381-52804400 None:intergenic 45.0%
ATGCTACCGTACTCATGGAA+TGG - chr7_4:52804386-52804405 None:intergenic 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr7_4:52804704-52804723 Msa1162250:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr7_4:52804712-52804731 Msa1162250:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr7_4:52804713-52804732 Msa1162250:CDS 45.0%
TGGTACGGTGGATAATCAGC+TGG - chr7_4:52804366-52804385 None:intergenic 50.0%
GTACTCATGGAATGGTACGG+TGG - chr7_4:52804378-52804397 None:intergenic 50.0%
ACACGATGCTACCGTACTCA+TGG - chr7_4:52804391-52804410 None:intergenic 50.0%
TGGTACGGTGGATAATCAGC+TGG - chr7_4:52804366-52804385 None:intergenic 50.0%
GTACTCATGGAATGGTACGG+TGG - chr7_4:52804378-52804397 None:intergenic 50.0%
ACACGATGCTACCGTACTCA+TGG - chr7_4:52804391-52804410 None:intergenic 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr7_4:52804231-52804250 Msa1162250:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr7_4:52804235-52804254 Msa1162250:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr7_4:52804716-52804735 Msa1162250:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr7_4:52804723-52804742 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr7_4:52804231-52804250 Msa1162250:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr7_4:52804235-52804254 Msa1162250:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr7_4:52804716-52804735 Msa1162250:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr7_4:52804723-52804742 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 52804000 52804805 52804000 ID=Msa1162250;Name=Msa1162250
chr7_4 mRNA 52804000 52804805 52804000 ID=Msa1162250-mRNA-1;Parent=Msa1162250;Name=Msa1162250-mRNA-1;_AED=0.05;_eAED=0.05;_QI=213|1|0.5|1|1|1|2|0|163
chr7_4 exon 52804000 52804458 52804000 ID=Msa1162250-mRNA-1:exon:15213;Parent=Msa1162250-mRNA-1
chr7_4 exon 52804560 52804805 52804560 ID=Msa1162250-mRNA-1:exon:15214;Parent=Msa1162250-mRNA-1
chr7_4 five_prime_UTR 52804000 52804212 52804000 ID=Msa1162250-mRNA-1:five_prime_utr;Parent=Msa1162250-mRNA-1
chr7_4 CDS 52804213 52804458 52804213 ID=Msa1162250-mRNA-1:cds;Parent=Msa1162250-mRNA-1
chr7_4 CDS 52804560 52804805 52804560 ID=Msa1162250-mRNA-1:cds;Parent=Msa1162250-mRNA-1
Gene Sequence

>Msa1162250

ATGTTAAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTGCGATTATTCAATGAATTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCCAGCTGATTATCCACCGTACCATTCCATGAGTACGGTAGCATCGTGTTATTGTACCTTTGAAATTCCTATCGCTGGATATACGAAATCACCGAAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGACTACGTCATGTTGTGCGCTCCATATGACTATGTCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAATTGTGATGTTTGGAAAAGGCTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTAATTTTCAAGTGCAAGTGTGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa1162250

MLNKSVSRPLLTDGWSALRLFNEFSGSKIIAFQYLGGSRFQIFVFAHNITPADYPPYHSMSTVASCYCTFEIPIAGYTKSPKELPDTFGKFLRVKHHDYVMLCAPYDYVIPVRLKYTDDPIPIVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*