AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0100250


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0100250 MtrunA17_Chr1g0153661 79.461 297 15 3 1 293 1 255 1.10e-155 434
Msa0100250 MtrunA17_Chr3g0133811 46.377 276 109 11 31 291 43 294 1.65e-31 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0100250 AT5G42750.1 36.943 314 154 12 10 284 17 325 4.05e-19 86.3

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 1_3:+6780954 None:intergenic
GGAATTATGTGAAGATAATT+TGG 0.179633 1_3:+6780935 None:intergenic
TCTGAGAATAATTCTCTTAT+AGG 0.206112 1_3:+6780777 None:intergenic
TGGACTTATTGTTATTATTA+GGG 0.253926 1_3:+6780955 None:intergenic
GGGAAGAGGATTGTGAATTT+TGG 0.259584 1_3:+6781030 None:intergenic
TCTTGTTTATTTCTAGTTCT+AGG 0.261211 1_3:+6780441 None:intergenic
AAGGGAAGTGTGAGAAGATT+TGG 0.268332 1_3:+6780850 None:intergenic
TTATCATTAAGTTCAAATAA+AGG 0.298290 1_3:-6780639 Msa0100250:CDS
CTGAGAATAATTCTCTTATA+GGG 0.331590 1_3:+6780778 None:intergenic
TATCATTAAGTTCAAATAAA+GGG 0.343051 1_3:-6780638 Msa0100250:CDS
TCCTCCTAGTGATAGTAGTA+TGG 0.363665 1_3:-6780310 Msa0100250:CDS
ATTAGGGAATGTTGTGTTGA+AGG 0.417429 1_3:+6780971 None:intergenic
AGTTCAAATAAAGGGACAAA+AGG 0.423209 1_3:-6780630 Msa0100250:CDS
AAAAGAACACCACTGTTTGA+TGG 0.436121 1_3:+6780351 None:intergenic
AACAAGAATTGATGAAAGGT+TGG 0.450874 1_3:-6780425 Msa0100250:CDS
TGAAGGAAAATTCATGAGAA+GGG 0.465614 1_3:+6781009 None:intergenic
AAATTCATGAGAAGGGGAAG+AGG 0.485413 1_3:+6781016 None:intergenic
AGATAAATCAAGTGCTGTAA+AGG 0.490240 1_3:+6780914 None:intergenic
GTTCAAATAAAGGGACAAAA+GGG 0.497754 1_3:-6780629 Msa0100250:CDS
CTATCACTAGGAGGAGTAAG+AGG 0.500454 1_3:+6780318 None:intergenic
GAGCGAGGCGATATCGATGA+AGG 0.509000 1_3:+6780831 None:intergenic
TGGTGTGAACATGGTTGTGA+TGG 0.517409 1_3:+6781050 None:intergenic
GTGAAGGAAAATTCATGAGA+AGG 0.523242 1_3:+6781008 None:intergenic
TGGAAGAAAATATCATCAGC+TGG 0.534065 1_3:+6780891 None:intergenic
AGGGAGGGTGAAACTTTCCA+TGG 0.557155 1_3:+6780797 None:intergenic
TCGCTCTTCGACAAATTCCA+TGG 0.560768 1_3:-6780814 Msa0100250:CDS
ATGGAATTTGTCGAAGAGCG+AGG 0.564320 1_3:+6780816 None:intergenic
GGAGAAGTTCTCATTGATGC+TGG 0.584601 1_3:+6780372 None:intergenic
AATAAACAAGAATTGATGAA+AGG 0.588793 1_3:-6780429 Msa0100250:CDS
AAGTGTGAGAAGATTTGGAG+AGG 0.598817 1_3:+6780855 None:intergenic
AAAGGTTGGAGTATGAAACT+AGG 0.604735 1_3:-6780411 Msa0100250:CDS
AGAATAATTCTCTTATAGGG+AGG 0.614827 1_3:+6780781 None:intergenic
GAATAATTCTCTTATAGGGA+GGG 0.624482 1_3:+6780782 None:intergenic
GAAGGAAAATTCATGAGAAG+GGG 0.624850 1_3:+6781010 None:intergenic
AGCGAGGCGATATCGATGAA+GGG 0.633590 1_3:+6780832 None:intergenic
TCTTCCATACTACTATCACT+AGG 0.641134 1_3:+6780306 None:intergenic
GGAGAGGAAGTAAATGACCA+TGG 0.661995 1_3:+6780871 None:intergenic
GGAGTTGTGTGAGATTGTGA+AGG 0.675634 1_3:+6780992 None:intergenic
TCCATACTACTATCACTAGG+AGG 0.675840 1_3:+6780309 None:intergenic
AGAACTTCTCCATCAAACAG+TGG 0.700411 1_3:-6780360 Msa0100250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATAGAATCATCAAAAA+AGG - chr1_3:6780631-6780650 Msa0100250:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG + chr1_3:6780669-6780688 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG - chr1_3:6780680-6780699 Msa0100250:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG - chr1_3:6780681-6780700 Msa0100250:CDS 15.0%
!!! ATTTTCTCTATTTTGAAAAA+TGG + chr1_3:6780815-6780834 None:intergenic 15.0%
!! AAATATAGAATCATCAAAAA+AGG - chr1_3:6780631-6780650 Msa0100250:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG + chr1_3:6780669-6780688 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG - chr1_3:6780680-6780699 Msa0100250:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG - chr1_3:6780681-6780700 Msa0100250:CDS 15.0%
!!! ATTTTCTCTATTTTGAAAAA+TGG + chr1_3:6780815-6780834 None:intergenic 15.0%
!!! TGGACTTATTGTTATTATTA+GGG + chr1_3:6780367-6780386 None:intergenic 20.0%
!!! TTGGACTTATTGTTATTATT+AGG + chr1_3:6780368-6780387 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG - chr1_3:6780845-6780864 Msa0100250:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG - chr1_3:6780890-6780909 Msa0100250:CDS 20.0%
!!! TGGACTTATTGTTATTATTA+GGG + chr1_3:6780367-6780386 None:intergenic 20.0%
!!! TTGGACTTATTGTTATTATT+AGG + chr1_3:6780368-6780387 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG - chr1_3:6780845-6780864 Msa0100250:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG - chr1_3:6780890-6780909 Msa0100250:CDS 20.0%
! GGAATTATGTGAAGATAATT+TGG + chr1_3:6780387-6780406 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG + chr1_3:6780544-6780563 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG + chr1_3:6780545-6780564 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG - chr1_3:6780784-6780803 Msa0100250:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG + chr1_3:6780881-6780900 None:intergenic 25.0%
! GGAATTATGTGAAGATAATT+TGG + chr1_3:6780387-6780406 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG + chr1_3:6780544-6780563 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG + chr1_3:6780545-6780564 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG - chr1_3:6780784-6780803 Msa0100250:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG + chr1_3:6780881-6780900 None:intergenic 25.0%
TGAAGGAAAATTCATGAGAA+GGG + chr1_3:6780313-6780332 None:intergenic 30.0%
! AGATAAATCAAGTGCTGTAA+AGG + chr1_3:6780408-6780427 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG + chr1_3:6780540-6780559 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG + chr1_3:6780541-6780560 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG - chr1_3:6780637-6780656 Msa0100250:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG - chr1_3:6780638-6780657 Msa0100250:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG - chr1_3:6780689-6780708 Msa0100250:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG - chr1_3:6780690-6780709 Msa0100250:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG - chr1_3:6780894-6780913 Msa0100250:CDS 30.0%
TGAAGGAAAATTCATGAGAA+GGG + chr1_3:6780313-6780332 None:intergenic 30.0%
! AGATAAATCAAGTGCTGTAA+AGG + chr1_3:6780408-6780427 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG + chr1_3:6780540-6780559 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG + chr1_3:6780541-6780560 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG - chr1_3:6780637-6780656 Msa0100250:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG - chr1_3:6780638-6780657 Msa0100250:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG - chr1_3:6780689-6780708 Msa0100250:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG - chr1_3:6780690-6780709 Msa0100250:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG - chr1_3:6780894-6780913 Msa0100250:CDS 30.0%
!! TGTGAATTTTGGTGTGAACA+TGG + chr1_3:6780281-6780300 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG + chr1_3:6780312-6780331 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG + chr1_3:6780314-6780333 None:intergenic 35.0%
ATTAGGGAATGTTGTGTTGA+AGG + chr1_3:6780351-6780370 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+TGG + chr1_3:6780431-6780450 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG - chr1_3:6780431-6780450 Msa0100250:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG - chr1_3:6780908-6780927 Msa0100250:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG + chr1_3:6780971-6780990 None:intergenic 35.0%
TCTTCCATACTACTATCACT+AGG + chr1_3:6781016-6781035 None:intergenic 35.0%
!! TGTGAATTTTGGTGTGAACA+TGG + chr1_3:6780281-6780300 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG + chr1_3:6780312-6780331 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG + chr1_3:6780314-6780333 None:intergenic 35.0%
ATTAGGGAATGTTGTGTTGA+AGG + chr1_3:6780351-6780370 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+TGG + chr1_3:6780431-6780450 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG - chr1_3:6780431-6780450 Msa0100250:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG - chr1_3:6780908-6780927 Msa0100250:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG + chr1_3:6780971-6780990 None:intergenic 35.0%
TCTTCCATACTACTATCACT+AGG + chr1_3:6781016-6781035 None:intergenic 35.0%
! GGGAAGAGGATTGTGAATTT+TGG + chr1_3:6780292-6780311 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG + chr1_3:6780306-6780325 None:intergenic 40.0%
AAGTGTGAGAAGATTTGGAG+AGG + chr1_3:6780467-6780486 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG + chr1_3:6780472-6780491 None:intergenic 40.0%
AGAACTTCTCCATCAAACAG+TGG - chr1_3:6780959-6780978 Msa0100250:CDS 40.0%
TCCTCCTAGTGATAGTAGTA+TGG - chr1_3:6781009-6781028 Msa0100250:CDS 40.0%
TCCATACTACTATCACTAGG+AGG + chr1_3:6781013-6781032 None:intergenic 40.0%
! GGGAAGAGGATTGTGAATTT+TGG + chr1_3:6780292-6780311 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG + chr1_3:6780306-6780325 None:intergenic 40.0%
AAGTGTGAGAAGATTTGGAG+AGG + chr1_3:6780467-6780486 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG + chr1_3:6780472-6780491 None:intergenic 40.0%
AGAACTTCTCCATCAAACAG+TGG - chr1_3:6780959-6780978 Msa0100250:CDS 40.0%
TCCTCCTAGTGATAGTAGTA+TGG - chr1_3:6781009-6781028 Msa0100250:CDS 40.0%
TCCATACTACTATCACTAGG+AGG + chr1_3:6781013-6781032 None:intergenic 40.0%
TGGTGTGAACATGGTTGTGA+TGG + chr1_3:6780272-6780291 None:intergenic 45.0%
GGAGTTGTGTGAGATTGTGA+AGG + chr1_3:6780330-6780349 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG + chr1_3:6780451-6780470 None:intergenic 45.0%
ATGGAATTTGTCGAAGAGCG+AGG + chr1_3:6780506-6780525 None:intergenic 45.0%
TCGCTCTTCGACAAATTCCA+TGG - chr1_3:6780505-6780524 Msa0100250:CDS 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG + chr1_3:6780586-6780605 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG + chr1_3:6780587-6780606 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG + chr1_3:6780950-6780969 None:intergenic 45.0%
CTATCACTAGGAGGAGTAAG+AGG + chr1_3:6781004-6781023 None:intergenic 45.0%
TGGTGTGAACATGGTTGTGA+TGG + chr1_3:6780272-6780291 None:intergenic 45.0%
GGAGTTGTGTGAGATTGTGA+AGG + chr1_3:6780330-6780349 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG + chr1_3:6780451-6780470 None:intergenic 45.0%
ATGGAATTTGTCGAAGAGCG+AGG + chr1_3:6780506-6780525 None:intergenic 45.0%
TCGCTCTTCGACAAATTCCA+TGG - chr1_3:6780505-6780524 Msa0100250:CDS 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG + chr1_3:6780586-6780605 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG + chr1_3:6780587-6780606 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG + chr1_3:6780950-6780969 None:intergenic 45.0%
CTATCACTAGGAGGAGTAAG+AGG + chr1_3:6781004-6781023 None:intergenic 45.0%
AGCGAGGCGATATCGATGAA+GGG + chr1_3:6780490-6780509 None:intergenic 50.0%
AGGGAGGGTGAAACTTTCCA+TGG + chr1_3:6780525-6780544 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG + chr1_3:6780588-6780607 None:intergenic 50.0%
AGCGAGGCGATATCGATGAA+GGG + chr1_3:6780490-6780509 None:intergenic 50.0%
AGGGAGGGTGAAACTTTCCA+TGG + chr1_3:6780525-6780544 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG + chr1_3:6780588-6780607 None:intergenic 50.0%
GAGCGAGGCGATATCGATGA+AGG + chr1_3:6780491-6780510 None:intergenic 55.0%
GAGCGAGGCGATATCGATGA+AGG + chr1_3:6780491-6780510 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 6780230 6781111 6780230 ID=Msa0100250;Name=Msa0100250
chr1_3 mRNA 6780230 6781111 6780230 ID=Msa0100250-mRNA-1;Parent=Msa0100250;Name=Msa0100250-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|293
chr1_3 exon 6780230 6781111 6780230 ID=Msa0100250-mRNA-1:exon:2526;Parent=Msa0100250-mRNA-1
chr1_3 CDS 6780230 6781111 6780230 ID=Msa0100250-mRNA-1:cds;Parent=Msa0100250-mRNA-1
Gene Sequence

>Msa0100250

ATGGAAAAACAAATTGAAGTAGAAAATCAACAACAAAAGCCATCACAACCATGTTCACACCAAAATTCACAATCCTCTTCCCCTTCTCATGAATTTTCCTTCACAATCTCACACAACTCCTTCAACACAACATTCCCTAATAATAACAATAAGTCCAAATTATCTTCACATAATTCCTTTACAGCACTTGATTTATCTCCAGCTGATGATATTTTCTTCCATGGTCATTTACTTCCTCTCCAAATCTTCTCACACTTCCCTTCATCGATATCGCCTCGCTCTTCGACAAATTCCATGGAAAGTTTCACCCTCCCTATAAGAGAATTATTCTCAGAAGATGATGATGAAAATCTCCCCACAAAAGACAGTAGCAGCAGCAGCAACAGCAACAATAGCAGCAAAAATATAGAATCATCAAAAAAGGTAGAGGGTAAGTCCAAGTTTTCATTTTTATCATTAAGTTCAAATAAAGGGACAAAAGGGTGTATTAAAGAGAAAGAAGATAAAGTGAAGAATAAGAAGAAGCTGAGATTTGATTTTGATGTGTTACATGCAGTGAAAAAGTACTTAAGAAAGGTGAAGCCATTTTTCAAAATAGAGAAAATTAGAGAACATAAAAAGTCTTATTCTTATTCAGGAAATGTAACACCTAGAACTAGAAATAAACAAGAATTGATGAAAGGTTGGAGTATGAAACTAGGACAATATTATTCAGCACCAGCATCAATGAGAACTTCTCCATCAAACAGTGGTGTTCTTTTTGCTACTGCACCTCTTACTCCTCCTAGTGATAGTAGTATGGAAGAGTTACAAGCTGCTATTCAATCTGCAATTGCTCATTGCAAAAATTCATATTCAAAAGAAGAGAAACTCAATTGCTGA

Protein sequence

>Msa0100250

MEKQIEVENQQQKPSQPCSHQNSQSSSPSHEFSFTISHNSFNTTFPNNNNKSKLSSHNSFTALDLSPADDIFFHGHLLPLQIFSHFPSSISPRSSTNSMESFTLPIRELFSEDDDENLPTKDSSSSSNSNNSSKNIESSKKVEGKSKFSFLSLSSNKGTKGCIKEKEDKVKNKKKLRFDFDVLHAVKKYLRKVKPFFKIEKIREHKKSYSYSGNVTPRTRNKQELMKGWSMKLGQYYSAPASMRTSPSNSGVLFATAPLTPPSDSSMEELQAAIQSAIAHCKNSYSKEEKLNC*