AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1043870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1043870 MtrunA17_Chr1g0153661 79.461 297 15 3 1 293 1 255 2.36e-155 434
Msa1043870 MtrunA17_Chr3g0133811 46.739 276 108 11 31 291 43 294 4.16e-32 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1043870 AT5G42750.1 37.261 314 153 12 10 284 17 325 8.28e-20 88.2

Find 40 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGACTTATTGTTATTATT+AGG 0.149195 7_2:+2016835 None:intergenic
TCTGAGAATAATTCTCTTAT+AGG 0.206112 7_2:+2016658 None:intergenic
GGATTTATGTGAAGATAATT+TGG 0.218251 7_2:+2016816 None:intergenic
TGGACTTATTGTTATTATTA+GGG 0.253926 7_2:+2016836 None:intergenic
GGGAAGAGGATTGTGAATTT+TGG 0.259584 7_2:+2016911 None:intergenic
TCTTGTTTATTTCTAGTTCT+AGG 0.261211 7_2:+2016322 None:intergenic
AAGGGAAGTGTGAGAAGATT+TGG 0.268332 7_2:+2016731 None:intergenic
TTATCATTAAGTTCAAATAA+AGG 0.298290 7_2:-2016520 Msa1043870:CDS
CTGAGAATAATTCTCTTATA+GGG 0.331590 7_2:+2016659 None:intergenic
TATCATTAAGTTCAAATAAA+GGG 0.343051 7_2:-2016519 Msa1043870:CDS
TCCTCCTAGTGATAGTAGTA+TGG 0.363665 7_2:-2016191 Msa1043870:CDS
ATTAGGGAATGTTGTGTTGA+AGG 0.417429 7_2:+2016852 None:intergenic
AGTTCAAATAAAGGGACAAA+AGG 0.423209 7_2:-2016511 Msa1043870:CDS
AAAAGAACACCACTGTTTGA+TGG 0.436121 7_2:+2016232 None:intergenic
AACAAGAATTGATGAAAGGT+TGG 0.450874 7_2:-2016306 Msa1043870:CDS
TGAAGGAAAATTCATGAGAA+GGG 0.465614 7_2:+2016890 None:intergenic
TGGTGTGAACATGGTTGTGA+TGG 0.479025 7_2:+2016931 None:intergenic
AAATTCATGAGAAGGGGAAG+AGG 0.485413 7_2:+2016897 None:intergenic
GTTCAAATAAAGGGACAAAA+GGG 0.497754 7_2:-2016510 Msa1043870:CDS
CTATCACTAGGAGGAGTAAG+AGG 0.500454 7_2:+2016199 None:intergenic
GAACGAGGCGATATCGATGA+AGG 0.509000 7_2:+2016712 None:intergenic
GTGAAGGAAAATTCATGAGA+AGG 0.523242 7_2:+2016889 None:intergenic
TCGTTCTTCGACAAATTCCA+TGG 0.546869 7_2:-2016695 Msa1043870:CDS
TGGAAGAAAATATCATCAGC+TGG 0.551272 7_2:+2016772 None:intergenic
GGAGAAGTTCTCATTGATGC+TGG 0.584601 7_2:+2016253 None:intergenic
AATAAACAAGAATTGATGAA+AGG 0.588793 7_2:-2016310 Msa1043870:CDS
AGGGAGGGTGAAACTATCCA+TGG 0.597551 7_2:+2016678 None:intergenic
AAGTGTGAGAAGATTTGGAG+AGG 0.598817 7_2:+2016736 None:intergenic
AAAGGTTGGAGTATGAAACT+AGG 0.604735 7_2:-2016292 Msa1043870:CDS
TGATAAATCAAGTGCTGTGA+AGG 0.608117 7_2:+2016795 None:intergenic
AGAATAATTCTCTTATAGGG+AGG 0.614827 7_2:+2016662 None:intergenic
ATGGAATTTGTCGAAGAACG+AGG 0.618111 7_2:+2016697 None:intergenic
GAATAATTCTCTTATAGGGA+GGG 0.624482 7_2:+2016663 None:intergenic
GAAGGAAAATTCATGAGAAG+GGG 0.624850 7_2:+2016891 None:intergenic
AACGAGGCGATATCGATGAA+GGG 0.633590 7_2:+2016713 None:intergenic
TCTTCCATACTACTATCACT+AGG 0.641134 7_2:+2016187 None:intergenic
GGAGAGGAAGTAAATGACCA+TGG 0.661995 7_2:+2016752 None:intergenic
TCCATACTACTATCACTAGG+AGG 0.675840 7_2:+2016190 None:intergenic
GGAATTGTGTGAGATTGTGA+AGG 0.688265 7_2:+2016873 None:intergenic
AGAACTTCTCCATCAAACAG+TGG 0.700411 7_2:-2016241 Msa1043870:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATAGAATCATCAAAAA+AGG - chr7_2:2016512-2016531 Msa1043870:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG + chr7_2:2016550-2016569 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG - chr7_2:2016561-2016580 Msa1043870:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG - chr7_2:2016562-2016581 Msa1043870:CDS 15.0%
!!! ATTTTCTCTATTTTGAAAAA+TGG + chr7_2:2016696-2016715 None:intergenic 15.0%
!! AAATATAGAATCATCAAAAA+AGG - chr7_2:2016512-2016531 Msa1043870:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG + chr7_2:2016550-2016569 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG - chr7_2:2016561-2016580 Msa1043870:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG - chr7_2:2016562-2016581 Msa1043870:CDS 15.0%
!!! ATTTTCTCTATTTTGAAAAA+TGG + chr7_2:2016696-2016715 None:intergenic 15.0%
!!! TGGACTTATTGTTATTATTA+GGG + chr7_2:2016248-2016267 None:intergenic 20.0%
!!! TTGGACTTATTGTTATTATT+AGG + chr7_2:2016249-2016268 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG - chr7_2:2016726-2016745 Msa1043870:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG - chr7_2:2016771-2016790 Msa1043870:CDS 20.0%
!!! TGGACTTATTGTTATTATTA+GGG + chr7_2:2016248-2016267 None:intergenic 20.0%
!!! TTGGACTTATTGTTATTATT+AGG + chr7_2:2016249-2016268 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG - chr7_2:2016726-2016745 Msa1043870:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG - chr7_2:2016771-2016790 Msa1043870:CDS 20.0%
! GGATTTATGTGAAGATAATT+TGG + chr7_2:2016268-2016287 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG + chr7_2:2016425-2016444 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG + chr7_2:2016426-2016445 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG - chr7_2:2016665-2016684 Msa1043870:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG + chr7_2:2016762-2016781 None:intergenic 25.0%
! GGATTTATGTGAAGATAATT+TGG + chr7_2:2016268-2016287 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG + chr7_2:2016425-2016444 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG + chr7_2:2016426-2016445 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG - chr7_2:2016665-2016684 Msa1043870:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG + chr7_2:2016762-2016781 None:intergenic 25.0%
TGAAGGAAAATTCATGAGAA+GGG + chr7_2:2016194-2016213 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG + chr7_2:2016421-2016440 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG + chr7_2:2016422-2016441 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG - chr7_2:2016518-2016537 Msa1043870:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG - chr7_2:2016519-2016538 Msa1043870:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG - chr7_2:2016570-2016589 Msa1043870:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG - chr7_2:2016571-2016590 Msa1043870:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG - chr7_2:2016775-2016794 Msa1043870:CDS 30.0%
TGAAGGAAAATTCATGAGAA+GGG + chr7_2:2016194-2016213 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG + chr7_2:2016421-2016440 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG + chr7_2:2016422-2016441 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG - chr7_2:2016518-2016537 Msa1043870:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG - chr7_2:2016519-2016538 Msa1043870:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG - chr7_2:2016570-2016589 Msa1043870:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG - chr7_2:2016571-2016590 Msa1043870:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG - chr7_2:2016775-2016794 Msa1043870:CDS 30.0%
!! TGTGAATTTTGGTGTGAACA+TGG + chr7_2:2016162-2016181 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG + chr7_2:2016193-2016212 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG + chr7_2:2016195-2016214 None:intergenic 35.0%
ATTAGGGAATGTTGTGTTGA+AGG + chr7_2:2016232-2016251 None:intergenic 35.0%
! TGATAAATCAAGTGCTGTGA+AGG + chr7_2:2016289-2016308 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+TGG + chr7_2:2016312-2016331 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG - chr7_2:2016312-2016331 Msa1043870:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG - chr7_2:2016789-2016808 Msa1043870:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG + chr7_2:2016852-2016871 None:intergenic 35.0%
TCTTCCATACTACTATCACT+AGG + chr7_2:2016897-2016916 None:intergenic 35.0%
!! TGTGAATTTTGGTGTGAACA+TGG + chr7_2:2016162-2016181 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG + chr7_2:2016193-2016212 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG + chr7_2:2016195-2016214 None:intergenic 35.0%
ATTAGGGAATGTTGTGTTGA+AGG + chr7_2:2016232-2016251 None:intergenic 35.0%
! TGATAAATCAAGTGCTGTGA+AGG + chr7_2:2016289-2016308 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+TGG + chr7_2:2016312-2016331 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG - chr7_2:2016312-2016331 Msa1043870:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG - chr7_2:2016789-2016808 Msa1043870:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG + chr7_2:2016852-2016871 None:intergenic 35.0%
TCTTCCATACTACTATCACT+AGG + chr7_2:2016897-2016916 None:intergenic 35.0%
! GGGAAGAGGATTGTGAATTT+TGG + chr7_2:2016173-2016192 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG + chr7_2:2016187-2016206 None:intergenic 40.0%
GGAATTGTGTGAGATTGTGA+AGG + chr7_2:2016211-2016230 None:intergenic 40.0%
AAGTGTGAGAAGATTTGGAG+AGG + chr7_2:2016348-2016367 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG + chr7_2:2016353-2016372 None:intergenic 40.0%
ATGGAATTTGTCGAAGAACG+AGG + chr7_2:2016387-2016406 None:intergenic 40.0%
TCGTTCTTCGACAAATTCCA+TGG - chr7_2:2016386-2016405 Msa1043870:CDS 40.0%
AGAACTTCTCCATCAAACAG+TGG - chr7_2:2016840-2016859 Msa1043870:CDS 40.0%
TCCTCCTAGTGATAGTAGTA+TGG - chr7_2:2016890-2016909 Msa1043870:CDS 40.0%
TCCATACTACTATCACTAGG+AGG + chr7_2:2016894-2016913 None:intergenic 40.0%
! GGGAAGAGGATTGTGAATTT+TGG + chr7_2:2016173-2016192 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG + chr7_2:2016187-2016206 None:intergenic 40.0%
GGAATTGTGTGAGATTGTGA+AGG + chr7_2:2016211-2016230 None:intergenic 40.0%
AAGTGTGAGAAGATTTGGAG+AGG + chr7_2:2016348-2016367 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG + chr7_2:2016353-2016372 None:intergenic 40.0%
ATGGAATTTGTCGAAGAACG+AGG + chr7_2:2016387-2016406 None:intergenic 40.0%
TCGTTCTTCGACAAATTCCA+TGG - chr7_2:2016386-2016405 Msa1043870:CDS 40.0%
AGAACTTCTCCATCAAACAG+TGG - chr7_2:2016840-2016859 Msa1043870:CDS 40.0%
TCCTCCTAGTGATAGTAGTA+TGG - chr7_2:2016890-2016909 Msa1043870:CDS 40.0%
TCCATACTACTATCACTAGG+AGG + chr7_2:2016894-2016913 None:intergenic 40.0%
TGGTGTGAACATGGTTGTGA+TGG + chr7_2:2016153-2016172 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG + chr7_2:2016332-2016351 None:intergenic 45.0%
AACGAGGCGATATCGATGAA+GGG + chr7_2:2016371-2016390 None:intergenic 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG + chr7_2:2016467-2016486 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG + chr7_2:2016468-2016487 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG + chr7_2:2016831-2016850 None:intergenic 45.0%
CTATCACTAGGAGGAGTAAG+AGG + chr7_2:2016885-2016904 None:intergenic 45.0%
TGGTGTGAACATGGTTGTGA+TGG + chr7_2:2016153-2016172 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG + chr7_2:2016332-2016351 None:intergenic 45.0%
AACGAGGCGATATCGATGAA+GGG + chr7_2:2016371-2016390 None:intergenic 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG + chr7_2:2016467-2016486 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG + chr7_2:2016468-2016487 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG + chr7_2:2016831-2016850 None:intergenic 45.0%
CTATCACTAGGAGGAGTAAG+AGG + chr7_2:2016885-2016904 None:intergenic 45.0%
GAACGAGGCGATATCGATGA+AGG + chr7_2:2016372-2016391 None:intergenic 50.0%
AGGGAGGGTGAAACTATCCA+TGG + chr7_2:2016406-2016425 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG + chr7_2:2016469-2016488 None:intergenic 50.0%
GAACGAGGCGATATCGATGA+AGG + chr7_2:2016372-2016391 None:intergenic 50.0%
AGGGAGGGTGAAACTATCCA+TGG + chr7_2:2016406-2016425 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG + chr7_2:2016469-2016488 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 2016111 2016992 2016111 ID=Msa1043870;Name=Msa1043870
chr7_2 mRNA 2016111 2016992 2016111 ID=Msa1043870-mRNA-1;Parent=Msa1043870;Name=Msa1043870-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|293
chr7_2 exon 2016111 2016992 2016111 ID=Msa1043870-mRNA-1:exon:445;Parent=Msa1043870-mRNA-1
chr7_2 CDS 2016111 2016992 2016111 ID=Msa1043870-mRNA-1:cds;Parent=Msa1043870-mRNA-1
Gene Sequence

>Msa1043870

ATGGAAAAACAAATTGAAGTAGAAAATCAACAACAAAAACCATCACAACCATGTTCACACCAAAATTCACAATCCTCTTCCCCTTCTCATGAATTTTCCTTCACAATCTCACACAATTCCTTCAACACAACATTCCCTAATAATAACAATAAGTCCAAATTATCTTCACATAAATCCTTCACAGCACTTGATTTATCACCAGCTGATGATATTTTCTTCCATGGTCATTTACTTCCTCTCCAAATCTTCTCACACTTCCCTTCATCGATATCGCCTCGTTCTTCGACAAATTCCATGGATAGTTTCACCCTCCCTATAAGAGAATTATTCTCAGAAGATGATGATGAAAATCTCCCCACAAAAGACAGTAGCAGCAGCAGCAACAGCAACAATAGCAGCAAAAATATAGAATCATCAAAAAAGGTAGAGGGTAAGTCCAAGTTTTCATTTTTATCATTAAGTTCAAATAAAGGGACAAAAGGGTGTATTAAAGAGAAAGAAGATAAAGTGAAGAATAAGAAGAAGCTGAGATTTGATTTTGATGTGTTACATGCAGTGAAAAAGTACTTAAGAAAGGTGAAGCCATTTTTCAAAATAGAGAAAATTAGAGAACATAAAAAGTCTTATTCTTATTCAGGAAATGTAACACCTAGAACTAGAAATAAACAAGAATTGATGAAAGGTTGGAGTATGAAACTAGGACAATATTATTCAGCACCAGCATCAATGAGAACTTCTCCATCAAACAGTGGTGTTCTTTTTGCTACTGCACCTCTTACTCCTCCTAGTGATAGTAGTATGGAAGAGTTACAAGCTGCTATTCAATCTGCAATTGCTCATTGCAAAAATTCATATTCAAAAGAAGAGAAACTCAATTGCTGA

Protein sequence

>Msa1043870

MEKQIEVENQQQKPSQPCSHQNSQSSSPSHEFSFTISHNSFNTTFPNNNNKSKLSSHKSFTALDLSPADDIFFHGHLLPLQIFSHFPSSISPRSSTNSMDSFTLPIRELFSEDDDENLPTKDSSSSSNSNNSSKNIESSKKVEGKSKFSFLSLSSNKGTKGCIKEKEDKVKNKKKLRFDFDVLHAVKKYLRKVKPFFKIEKIREHKKSYSYSGNVTPRTRNKQELMKGWSMKLGQYYSAPASMRTSPSNSGVLFATAPLTPPSDSSMEELQAAIQSAIAHCKNSYSKEEKLNC*