AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1000060


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1000060 MtrunA17_Chr6g0486171 79.151 259 53 1 10 268 4 261 1.35e-148 416
Msa1000060 MtrunA17_Chr6g0486181 34.529 223 135 6 1 215 1 220 3.06e-27 106
Msa1000060 MtrunA17_Chr6g0486131 44.526 137 50 4 70 192 1 125 1.19e-24 98.6
Msa1000060 MtrunA17_Chr6g0486151 36.517 178 97 7 101 268 124 295 5.93e-21 90.1
Msa1000060 MtrunA17_Chr6g0486141 35.115 131 83 2 103 232 109 238 2.25e-16 78.2
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 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGAGTGTTAAACAATGATT+TGG 0.292646 6_4:+82776851 Msa1000060:CDS
TCCTTATGAACACCCTTCTT+TGG 0.298019 6_4:+82776890 Msa1000060:CDS
TTAAAATTTGTTTCATAAAG+TGG 0.347789 6_4:-82776612 None:intergenic
TGAGAATAATGGTGAAGAAA+TGG 0.366292 6_4:+82777013 Msa1000060:CDS
TCCTATAGTCACACCTTGAT+TGG 0.369054 6_4:-82777069 None:intergenic
TCACGAAGATGGTCTCATTA+AGG 0.371609 6_4:+82776482 Msa1000060:CDS
CAATTTGAGATTGAGAATAA+TGG 0.399801 6_4:+82777002 Msa1000060:CDS
TGATTTGGATGTTTCAATGA+AGG 0.418905 6_4:+82776866 Msa1000060:CDS
TGAGGTTGGACTTTCAATAA+TGG 0.420134 6_4:+82776821 Msa1000060:CDS
ACCAAAGAAGGGTGTTCATA+AGG 0.427204 6_4:-82776891 None:intergenic
AAGTATCTACAACATGGATT+TGG 0.430508 6_4:+82776934 Msa1000060:CDS
TCCAATCAAGGTGTGACTAT+AGG 0.442635 6_4:+82777068 Msa1000060:CDS
ATATGGACATCCTAGTTTGT+TGG 0.452148 6_4:-82777146 None:intergenic
GTTCCCACGCTCTTCTCTGA+TGG 0.459245 6_4:-82776348 None:intergenic
ATTTGAAGCAATACCAAAGA+AGG 0.460237 6_4:-82776903 None:intergenic
TAATGAGACTAAGAACCATT+GGG 0.460274 6_4:+82776635 Msa1000060:CDS
TAATAATATGCCAACAAACT+AGG 0.470313 6_4:+82777136 Msa1000060:CDS
TATAATGAAGAATGTAAATA+CGG 0.476092 6_4:-82776538 None:intergenic
GGAAATAGTATTTCCAATCA+AGG 0.493381 6_4:+82777056 Msa1000060:CDS
ACACTACGTAGATGGTAAAT+CGG 0.499784 6_4:+82776431 Msa1000060:CDS
ACAGTGTCACACTACGTAGA+TGG 0.500726 6_4:+82776423 Msa1000060:CDS
ATAATGAGACTAAGAACCAT+TGG 0.500792 6_4:+82776634 Msa1000060:CDS
TTGGGGAGGGATTACGAAAA+CGG 0.508005 6_4:+82776653 Msa1000060:CDS
GTGACTATAGGAGATTATAA+TGG 0.514750 6_4:+82777080 Msa1000060:CDS
CGCAGTTTCAGTAGAGAGGA+AGG 0.521608 6_4:+82776395 Msa1000060:CDS
GTTTCATAAAGTGGATCGAT+GGG 0.528809 6_4:-82776603 None:intergenic
TTGATAATATATCACGAAGA+TGG 0.534894 6_4:+82776471 Msa1000060:CDS
GTGCAGCAGAAGAGAAAGAA+GGG 0.548287 6_4:+82776720 Msa1000060:CDS
CTACAACATGGATTTGGAAG+TGG 0.549890 6_4:+82776940 Msa1000060:CDS
GTGAAGAAATGGAACAGTCT+AGG 0.551780 6_4:+82777024 Msa1000060:CDS
TGTTTCATAAAGTGGATCGA+TGG 0.554991 6_4:-82776604 None:intergenic
AACACGCAGTTTCAGTAGAG+AGG 0.566105 6_4:+82776391 Msa1000060:CDS
GGTGCAGCAGAAGAGAAAGA+AGG 0.574995 6_4:+82776719 Msa1000060:CDS
AATGTAAATACGGATCCAGT+AGG 0.609266 6_4:-82776528 None:intergenic
AGACTAAGAACCATTGGGGA+GGG 0.620733 6_4:+82776640 Msa1000060:CDS
TTTGAAGCAATACCAAAGAA+GGG 0.625309 6_4:-82776902 None:intergenic
TTTCCATCAGAGAAGAGCGT+GGG 0.629126 6_4:+82776345 Msa1000060:CDS
AAAACGGATGTTGCATACCG+TGG 0.641753 6_4:+82776669 Msa1000060:CDS
GAGACTAAGAACCATTGGGG+AGG 0.649630 6_4:+82776639 Msa1000060:CDS
GAACAGTCTAGGCAAATCAG+AGG 0.652405 6_4:+82777035 Msa1000060:CDS
TTCAACAAGTATCTACAACA+TGG 0.659448 6_4:+82776928 Msa1000060:CDS
AAATGATGGGAATCTTCTTG+TGG 0.669532 6_4:+82776698 Msa1000060:CDS
AACATGGATTTGGAAGTGGA+CGG 0.683514 6_4:+82776944 Msa1000060:CDS
AATGAGACTAAGAACCATTG+GGG 0.684064 6_4:+82776636 Msa1000060:CDS
TGTGCCACTCTGATTGCACA+AGG 0.692862 6_4:-82776753 None:intergenic
AAAGCCTTGTGCAATCAGAG+TGG 0.727260 6_4:+82776749 Msa1000060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAATGAAGAATGTAAATA+CGG - chr6_4:82776541-82776560 None:intergenic 15.0%
!!! TTAAAATTTGTTTCATAAAG+TGG - chr6_4:82776615-82776634 None:intergenic 15.0%
!! TATAATGAAGAATGTAAATA+CGG - chr6_4:82776541-82776560 None:intergenic 15.0%
!!! TTAAAATTTGTTTCATAAAG+TGG - chr6_4:82776615-82776634 None:intergenic 15.0%
!! TTGATAATATATCACGAAGA+TGG + chr6_4:82776471-82776490 Msa1000060:CDS 25.0%
!! GACTTAAATTTCGTTTTCTA+CGG + chr6_4:82776504-82776523 Msa1000060:CDS 25.0%
! TTTAAGTCGAAAAAATAGTG+AGG + chr6_4:82776803-82776822 Msa1000060:CDS 25.0%
!! TAGAGTGTTAAACAATGATT+TGG + chr6_4:82776851-82776870 Msa1000060:CDS 25.0%
!! CAATTTGAGATTGAGAATAA+TGG + chr6_4:82777002-82777021 Msa1000060:CDS 25.0%
!! TTGATAATATATCACGAAGA+TGG + chr6_4:82776471-82776490 Msa1000060:CDS 25.0%
!! GACTTAAATTTCGTTTTCTA+CGG + chr6_4:82776504-82776523 Msa1000060:CDS 25.0%
! TTTAAGTCGAAAAAATAGTG+AGG + chr6_4:82776803-82776822 Msa1000060:CDS 25.0%
!! TAGAGTGTTAAACAATGATT+TGG + chr6_4:82776851-82776870 Msa1000060:CDS 25.0%
!! CAATTTGAGATTGAGAATAA+TGG + chr6_4:82777002-82777021 Msa1000060:CDS 25.0%
ATAATGAGACTAAGAACCAT+TGG + chr6_4:82776634-82776653 Msa1000060:CDS 30.0%
TAATGAGACTAAGAACCATT+GGG + chr6_4:82776635-82776654 Msa1000060:CDS 30.0%
! TGATTTGGATGTTTCAATGA+AGG + chr6_4:82776866-82776885 Msa1000060:CDS 30.0%
! TTTGAAGCAATACCAAAGAA+GGG - chr6_4:82776905-82776924 None:intergenic 30.0%
! ATTTGAAGCAATACCAAAGA+AGG - chr6_4:82776906-82776925 None:intergenic 30.0%
TTCAACAAGTATCTACAACA+TGG + chr6_4:82776928-82776947 Msa1000060:CDS 30.0%
AAGTATCTACAACATGGATT+TGG + chr6_4:82776934-82776953 Msa1000060:CDS 30.0%
TGAGAATAATGGTGAAGAAA+TGG + chr6_4:82777013-82777032 Msa1000060:CDS 30.0%
GGAAATAGTATTTCCAATCA+AGG + chr6_4:82777056-82777075 Msa1000060:CDS 30.0%
GTGACTATAGGAGATTATAA+TGG + chr6_4:82777080-82777099 Msa1000060:CDS 30.0%
ATAATGAGACTAAGAACCAT+TGG + chr6_4:82776634-82776653 Msa1000060:CDS 30.0%
TAATGAGACTAAGAACCATT+GGG + chr6_4:82776635-82776654 Msa1000060:CDS 30.0%
! TGATTTGGATGTTTCAATGA+AGG + chr6_4:82776866-82776885 Msa1000060:CDS 30.0%
! TTTGAAGCAATACCAAAGAA+GGG - chr6_4:82776905-82776924 None:intergenic 30.0%
! ATTTGAAGCAATACCAAAGA+AGG - chr6_4:82776906-82776925 None:intergenic 30.0%
TTCAACAAGTATCTACAACA+TGG + chr6_4:82776928-82776947 Msa1000060:CDS 30.0%
AAGTATCTACAACATGGATT+TGG + chr6_4:82776934-82776953 Msa1000060:CDS 30.0%
TGAGAATAATGGTGAAGAAA+TGG + chr6_4:82777013-82777032 Msa1000060:CDS 30.0%
GGAAATAGTATTTCCAATCA+AGG + chr6_4:82777056-82777075 Msa1000060:CDS 30.0%
GTGACTATAGGAGATTATAA+TGG + chr6_4:82777080-82777099 Msa1000060:CDS 30.0%
ACACTACGTAGATGGTAAAT+CGG + chr6_4:82776431-82776450 Msa1000060:CDS 35.0%
AATGTAAATACGGATCCAGT+AGG - chr6_4:82776531-82776550 None:intergenic 35.0%
GTTTCATAAAGTGGATCGAT+GGG - chr6_4:82776606-82776625 None:intergenic 35.0%
TGTTTCATAAAGTGGATCGA+TGG - chr6_4:82776607-82776626 None:intergenic 35.0%
AATGAGACTAAGAACCATTG+GGG + chr6_4:82776636-82776655 Msa1000060:CDS 35.0%
TACCGTGGAGATAAAAATGA+TGG + chr6_4:82776684-82776703 Msa1000060:CDS 35.0%
ACCGTGGAGATAAAAATGAT+GGG + chr6_4:82776685-82776704 Msa1000060:CDS 35.0%
!! TCCCATCATTTTTATCTCCA+CGG - chr6_4:82776689-82776708 None:intergenic 35.0%
! AAATGATGGGAATCTTCTTG+TGG + chr6_4:82776698-82776717 Msa1000060:CDS 35.0%
AGTCGAAAAAATAGTGAGGT+TGG + chr6_4:82776807-82776826 Msa1000060:CDS 35.0%
TGAGGTTGGACTTTCAATAA+TGG + chr6_4:82776821-82776840 Msa1000060:CDS 35.0%
ACACTACGTAGATGGTAAAT+CGG + chr6_4:82776431-82776450 Msa1000060:CDS 35.0%
AATGTAAATACGGATCCAGT+AGG - chr6_4:82776531-82776550 None:intergenic 35.0%
GTTTCATAAAGTGGATCGAT+GGG - chr6_4:82776606-82776625 None:intergenic 35.0%
TGTTTCATAAAGTGGATCGA+TGG - chr6_4:82776607-82776626 None:intergenic 35.0%
AATGAGACTAAGAACCATTG+GGG + chr6_4:82776636-82776655 Msa1000060:CDS 35.0%
TACCGTGGAGATAAAAATGA+TGG + chr6_4:82776684-82776703 Msa1000060:CDS 35.0%
ACCGTGGAGATAAAAATGAT+GGG + chr6_4:82776685-82776704 Msa1000060:CDS 35.0%
!! TCCCATCATTTTTATCTCCA+CGG - chr6_4:82776689-82776708 None:intergenic 35.0%
! AAATGATGGGAATCTTCTTG+TGG + chr6_4:82776698-82776717 Msa1000060:CDS 35.0%
AGTCGAAAAAATAGTGAGGT+TGG + chr6_4:82776807-82776826 Msa1000060:CDS 35.0%
TGAGGTTGGACTTTCAATAA+TGG + chr6_4:82776821-82776840 Msa1000060:CDS 35.0%
TCACGAAGATGGTCTCATTA+AGG + chr6_4:82776482-82776501 Msa1000060:CDS 40.0%
TCCTTATGAACACCCTTCTT+TGG + chr6_4:82776890-82776909 Msa1000060:CDS 40.0%
!! ACCAAAGAAGGGTGTTCATA+AGG - chr6_4:82776894-82776913 None:intergenic 40.0%
CTACAACATGGATTTGGAAG+TGG + chr6_4:82776940-82776959 Msa1000060:CDS 40.0%
AACATGGATTTGGAAGTGGA+CGG + chr6_4:82776944-82776963 Msa1000060:CDS 40.0%
GTGAAGAAATGGAACAGTCT+AGG + chr6_4:82777024-82777043 Msa1000060:CDS 40.0%
TCCAATCAAGGTGTGACTAT+AGG + chr6_4:82777068-82777087 Msa1000060:CDS 40.0%
TCCTATAGTCACACCTTGAT+TGG - chr6_4:82777072-82777091 None:intergenic 40.0%
TCACGAAGATGGTCTCATTA+AGG + chr6_4:82776482-82776501 Msa1000060:CDS 40.0%
TCCTTATGAACACCCTTCTT+TGG + chr6_4:82776890-82776909 Msa1000060:CDS 40.0%
!! ACCAAAGAAGGGTGTTCATA+AGG - chr6_4:82776894-82776913 None:intergenic 40.0%
CTACAACATGGATTTGGAAG+TGG + chr6_4:82776940-82776959 Msa1000060:CDS 40.0%
AACATGGATTTGGAAGTGGA+CGG + chr6_4:82776944-82776963 Msa1000060:CDS 40.0%
GTGAAGAAATGGAACAGTCT+AGG + chr6_4:82777024-82777043 Msa1000060:CDS 40.0%
TCCAATCAAGGTGTGACTAT+AGG + chr6_4:82777068-82777087 Msa1000060:CDS 40.0%
TCCTATAGTCACACCTTGAT+TGG - chr6_4:82777072-82777091 None:intergenic 40.0%
! TTTTCCATCAGAGAAGAGCG+TGG + chr6_4:82776344-82776363 Msa1000060:CDS 45.0%
! TTTCCATCAGAGAAGAGCGT+GGG + chr6_4:82776345-82776364 Msa1000060:CDS 45.0%
AACACGCAGTTTCAGTAGAG+AGG + chr6_4:82776391-82776410 Msa1000060:CDS 45.0%
ACAGTGTCACACTACGTAGA+TGG + chr6_4:82776423-82776442 Msa1000060:CDS 45.0%
! TTCGTTTTCTACGGACCTAC+TGG + chr6_4:82776513-82776532 Msa1000060:CDS 45.0%
AGACTAAGAACCATTGGGGA+GGG + chr6_4:82776640-82776659 Msa1000060:CDS 45.0%
! TTTTCGTAATCCCTCCCCAA+TGG - chr6_4:82776653-82776672 None:intergenic 45.0%
TTGGGGAGGGATTACGAAAA+CGG + chr6_4:82776653-82776672 Msa1000060:CDS 45.0%
AAAACGGATGTTGCATACCG+TGG + chr6_4:82776669-82776688 Msa1000060:CDS 45.0%
GTGCAGCAGAAGAGAAAGAA+GGG + chr6_4:82776720-82776739 Msa1000060:CDS 45.0%
! AAAGCCTTGTGCAATCAGAG+TGG + chr6_4:82776749-82776768 Msa1000060:CDS 45.0%
GAACAGTCTAGGCAAATCAG+AGG + chr6_4:82777035-82777054 Msa1000060:CDS 45.0%
! TTTTCCATCAGAGAAGAGCG+TGG + chr6_4:82776344-82776363 Msa1000060:CDS 45.0%
! TTTCCATCAGAGAAGAGCGT+GGG + chr6_4:82776345-82776364 Msa1000060:CDS 45.0%
AACACGCAGTTTCAGTAGAG+AGG + chr6_4:82776391-82776410 Msa1000060:CDS 45.0%
ACAGTGTCACACTACGTAGA+TGG + chr6_4:82776423-82776442 Msa1000060:CDS 45.0%
! TTCGTTTTCTACGGACCTAC+TGG + chr6_4:82776513-82776532 Msa1000060:CDS 45.0%
AGACTAAGAACCATTGGGGA+GGG + chr6_4:82776640-82776659 Msa1000060:CDS 45.0%
! TTTTCGTAATCCCTCCCCAA+TGG - chr6_4:82776653-82776672 None:intergenic 45.0%
TTGGGGAGGGATTACGAAAA+CGG + chr6_4:82776653-82776672 Msa1000060:CDS 45.0%
AAAACGGATGTTGCATACCG+TGG + chr6_4:82776669-82776688 Msa1000060:CDS 45.0%
GTGCAGCAGAAGAGAAAGAA+GGG + chr6_4:82776720-82776739 Msa1000060:CDS 45.0%
! AAAGCCTTGTGCAATCAGAG+TGG + chr6_4:82776749-82776768 Msa1000060:CDS 45.0%
GAACAGTCTAGGCAAATCAG+AGG + chr6_4:82777035-82777054 Msa1000060:CDS 45.0%
CGCAGTTTCAGTAGAGAGGA+AGG + chr6_4:82776395-82776414 Msa1000060:CDS 50.0%
GAGACTAAGAACCATTGGGG+AGG + chr6_4:82776639-82776658 Msa1000060:CDS 50.0%
GGTGCAGCAGAAGAGAAAGA+AGG + chr6_4:82776719-82776738 Msa1000060:CDS 50.0%
! TGTGCCACTCTGATTGCACA+AGG - chr6_4:82776756-82776775 None:intergenic 50.0%
CGCAGTTTCAGTAGAGAGGA+AGG + chr6_4:82776395-82776414 Msa1000060:CDS 50.0%
GAGACTAAGAACCATTGGGG+AGG + chr6_4:82776639-82776658 Msa1000060:CDS 50.0%
GGTGCAGCAGAAGAGAAAGA+AGG + chr6_4:82776719-82776738 Msa1000060:CDS 50.0%
! TGTGCCACTCTGATTGCACA+AGG - chr6_4:82776756-82776775 None:intergenic 50.0%
GTTCCCACGCTCTTCTCTGA+TGG - chr6_4:82776351-82776370 None:intergenic 55.0%
GTTCCCACGCTCTTCTCTGA+TGG - chr6_4:82776351-82776370 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 82776333 82777157 82776333 ID=Msa1000060;Name=Msa1000060
chr6_4 mRNA 82776333 82777157 82776333 ID=Msa1000060-mRNA-1;Parent=Msa1000060;Name=Msa1000060-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|274
chr6_4 exon 82776333 82777157 82776333 ID=Msa1000060-mRNA-1:exon:15939;Parent=Msa1000060-mRNA-1
chr6_4 CDS 82776333 82777157 82776333 ID=Msa1000060-mRNA-1:cds;Parent=Msa1000060-mRNA-1
Gene Sequence

>Msa1000060

ATGGGAAATAGTTTTCCATCAGAGAAGAGCGTGGGAACGAATGCAAGCATCAAACTTGAACACGCAGTTTCAGTAGAGAGGAAGGCATATACAGTGTCACACTACGTAGATGGTAAATCGGTTGTTATACTCTACTTATTGATAATATATCACGAAGATGGTCTCATTAAGGACTTAAATTTCGTTTTCTACGGACCTACTGGATCCGTATTTACATTCTTCATTATAAATAAAGCTGAAAACAATCTTCTTAATTGCTGTCATACTAATCCCATCGATCCACTTTATGAAACAAATTTTAATAATGAGACTAAGAACCATTGGGGAGGGATTACGAAAACGGATGTTGCATACCGTGGAGATAAAAATGATGGGAATCTTCTTGTGGTGCAGCAGAAGAGAAAGAAGGGAGTTGAAAAGCCTTGTGCAATCAGAGTGGCACACTATTATGCTTATAGTAAACAATGCTTTTTAAGTCGAAAAAATAGTGAGGTTGGACTTTCAATAATGGTAGATATTAGAGTGTTAAACAATGATTTGGATGTTTCAATGAAGGATCCTTATGAACACCCTTCTTTGGTATTGCTTCAAATGTTTCAACAAGTATCTACAACATGGATTTGGAAGTGGACGGCATGCTCTCATTGTGCTGCACAAACTCATATGCAGCAATTTGAGATTGAGAATAATGGTGAAGAAATGGAACAGTCTAGGCAAATCAGAGGAAATAGTATTTCCAATCAAGGTGTGACTATAGGAGATTATAATGGTAATTTAGTTGTATCTGCTTCACGTATATATGTTAATAATATGCCAACAAACTAG

Protein sequence

>Msa1000060

MGNSFPSEKSVGTNASIKLEHAVSVERKAYTVSHYVDGKSVVILYLLIIYHEDGLIKDLNFVFYGPTGSVFTFFIINKAENNLLNCCHTNPIDPLYETNFNNETKNHWGGITKTDVAYRGDKNDGNLLVVQQKRKKGVEKPCAIRVAHYYAYSKQCFLSRKNSEVGLSIMVDIRVLNNDLDVSMKDPYEHPSLVLLQMFQQVSTTWIWKWTACSHCAAQTHMQQFEIENNGEEMEQSRQIRGNSISNQGVTIGDYNGNLVVSASRIYVNNMPTN*