AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080048186.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048186.01.T01 MTR_4g097220 95.588 136 6 0 1 136 1 136 1.13e-94 271
MsG0080048186.01.T01 MTR_4g097220 96.825 126 4 0 1 126 1 126 1.15e-88 257
MsG0080048186.01.T01 MTR_4g106790 39.869 153 72 3 1 133 1 153 5.27e-28 103
MsG0080048186.01.T01 MTR_4g106790 42.105 133 58 2 1 114 1 133 1.66e-27 102
MsG0080048186.01.T01 MTR_3g078300 44.643 112 47 2 1 97 1 112 2.63e-25 96.7
MsG0080048186.01.T01 MTR_3g078300 44.643 112 47 2 1 97 1 112 9.92e-25 95.1
MsG0080048186.01.T01 MTR_5g035430 47.525 101 48 1 1 96 1 101 1.22e-24 94.7
MsG0080048186.01.T01 MTR_8g063200 48.421 95 41 2 1 87 1 95 6.53e-24 92.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048186.01.T01 AT5G67620 76.415 106 24 1 1 105 1 106 2.81e-55 173
MsG0080048186.01.T01 AT5G62900 51.456 103 49 1 1 103 1 102 8.42e-28 102
MsG0080048186.01.T01 AT5G50090 49.550 111 51 2 1 106 1 111 7.54e-25 94.4
MsG0080048186.01.T01 AT5G50090 49.550 111 51 2 1 106 1 111 7.61e-25 95.1
MsG0080048186.01.T01 AT5G50090 49.550 111 51 2 1 106 1 111 7.66e-25 94.7
MsG0080048186.01.T01 AT1G60010 38.793 116 59 2 1 104 1 116 6.51e-21 85.1
MsG0080048186.01.T01 AT1G10530 32.692 156 86 3 1 139 1 154 4.95e-20 82.8

Find 38 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTGATGACACTTTGCTTAT+TGG 0.123509 contig240end:-45132 MsG0080048186.01.T01:CDS
TTACAAAGCATTGCAGAATT+TGG 0.165154 contig240end:-43401 MsG0080048186.01.T01:CDS
TGAAACTTAATTACCTTAAC+TGG 0.236093 contig240end:+44722 None:intergenic
GCAAGATTGAGAGGATTTAT+TGG 0.272858 contig240end:-45275 MsG0080048186.01.T01:CDS
TTAATGTTATAGTTTCAAAT+TGG 0.378436 contig240end:-44697 MsG0080048186.01.T01:intron
AAATTCTGCAATGCTTTGTA+AGG 0.387024 contig240end:+43403 None:intergenic
TGACACTTTGCTTATTGGTC+AGG 0.391638 contig240end:-45127 MsG0080048186.01.T01:CDS
GAATTGTCAAGCTGCAGAAT+TGG 0.405080 contig240end:-45325 MsG0080048186.01.T01:CDS
TCGAAGAAATGTGGTAAACT+TGG 0.433100 contig240end:-44818 MsG0080048186.01.T01:CDS
ACCTTAACTGGACTAGGATT+CGG 0.447919 contig240end:+44734 None:intergenic
GTGGGTTGTAGATGTATTGA+AGG 0.454729 contig240end:-44849 MsG0080048186.01.T01:intron
TCCGAATCCTAGTCCAGTTA+AGG 0.460882 contig240end:-44735 MsG0080048186.01.T01:CDS
TGTGTTGTGTCAGGTGGAAC+AGG 0.461365 contig240end:-43516 MsG0080048186.01.T01:intron
TCTGCAATGCTTTGTAAGGC+TGG 0.461811 contig240end:+43407 None:intergenic
TTTGTAAGGCTGGCCTCCAT+TGG 0.463118 contig240end:+43417 None:intergenic
AGAAGCAATAACAGAAGTGT+TGG 0.498291 contig240end:-43464 MsG0080048186.01.T01:CDS
TTGAAGGAGAGTGGTAATCA+TGG 0.498388 contig240end:-44788 MsG0080048186.01.T01:CDS
TAAACTTGGGAAATTGTTGA+AGG 0.502500 contig240end:-44804 MsG0080048186.01.T01:CDS
CCAATAAGCAAAGTGTCATC+AGG 0.507918 contig240end:+45132 None:intergenic
GGGAAATTGTTGAAGGAGAG+TGG 0.509749 contig240end:-44797 MsG0080048186.01.T01:CDS
ATCCTCTCAATCTTGCTCCC+TGG 0.517252 contig240end:+45282 None:intergenic
TTGGTCTGTTAGTGCTCATG+AGG 0.527619 contig240end:-45256 MsG0080048186.01.T01:CDS
CGAAGAAATGTGGTAAACTT+GGG 0.529302 contig240end:-44817 MsG0080048186.01.T01:CDS
TGAAGGAGAGTGGTAATCAT+GGG 0.531959 contig240end:-44787 MsG0080048186.01.T01:CDS
CCATTCTCAGATTTAAGAGT+AGG 0.536503 contig240end:+45186 None:intergenic
TTGTTGGTGGTAGTGGCCAA+TGG 0.537451 contig240end:-43433 MsG0080048186.01.T01:CDS
GAGGTTATGAATTCAAATCC+TGG 0.537803 contig240end:-45237 MsG0080048186.01.T01:CDS
CCTACTCTTAAATCTGAGAA+TGG 0.540696 contig240end:-45186 MsG0080048186.01.T01:CDS
AGAAGCTTGAGATGTTTCAA+TGG 0.541690 contig240end:+45159 None:intergenic
TTAATTACCTTAACTGGACT+AGG 0.548847 contig240end:+44728 None:intergenic
ACAGTTGTGATACATCATCC+AGG 0.558304 contig240end:-45300 MsG0080048186.01.T01:CDS
ATCCAGGGAGCAAGATTGAG+AGG 0.609389 contig240end:-45284 MsG0080048186.01.T01:CDS
GAGTTTGCTTCGAAGAAATG+TGG 0.621219 contig240end:-44827 MsG0080048186.01.T01:CDS
ACTCAACGAACGGAGAGCAA+TGG 0.634599 contig240end:-43491 MsG0080048186.01.T01:CDS
TTGGTGGTAGTGGCCAATGG+AGG 0.645219 contig240end:-43430 MsG0080048186.01.T01:CDS
GGAACAGGCGACTCAACGAA+CGG 0.652981 contig240end:-43501 MsG0080048186.01.T01:CDS
ACAAGAGCAACATAGTGACC+AGG 0.657647 contig240end:+45219 None:intergenic
CAGTTGTGATACATCATCCA+GGG 0.658613 contig240end:-45299 MsG0080048186.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACTATGTTATATTATTATT+TGG + contig240end:43640-43659 None:intergenic 10.0%
!! CAAAAATAAAAGATGAATAA+AGG + contig240end:45180-45199 None:intergenic 15.0%
!! CGATAATTATAAAAATGTAA+AGG - contig240end:44913-44932 MsG0080048186.01.T01:intron 15.0%
!! TAAATTTACCAAAAAAATTG+TGG - contig240end:43830-43849 MsG0080048186.01.T01:intron 15.0%
!! TTAATGTTATAGTTTCAAAT+TGG - contig240end:44017-44036 MsG0080048186.01.T01:intron 15.0%
!!! TTACTTTTAACAAATTTTAG+AGG - contig240end:44189-44208 MsG0080048186.01.T01:intron 15.0%
!! ACAAAAAAAAATGTATCGTT+TGG - contig240end:45055-45074 MsG0080048186.01.T01:intron 20.0%
!! CGATTGAAAAATAATAATTC+AGG + contig240end:44441-44460 None:intergenic 20.0%
!! TACTATGATTTCTAATACAA+TGG + contig240end:45096-45115 None:intergenic 20.0%
!! TTAGAAATCATAGTATGATT+TGG - contig240end:45101-45120 MsG0080048186.01.T01:intron 20.0%
!!! TTTGTTTAGATTTGATGATT+TGG + contig240end:44825-44844 None:intergenic 20.0%
! CTTATTCATAAGAGACATTT+AGG + contig240end:43755-43774 None:intergenic 25.0%
! TAATTCAGGTGTTAATGATT+TGG + contig240end:44427-44446 None:intergenic 25.0%
! TAGATTATCATCGTGAATTT+AGG + contig240end:44660-44679 None:intergenic 25.0%
! TCAACAAAAGTTAATACATG+CGG + contig240end:43732-43751 None:intergenic 25.0%
! TGAAACTTAATTACCTTAAC+TGG + contig240end:43995-44014 None:intergenic 25.0%
! TGTTGTTAAATAAGACTAGA+AGG + contig240end:43665-43684 None:intergenic 25.0%
!! AAAATTGTGGACATGAATTT+TGG - contig240end:43843-43862 MsG0080048186.01.T01:intron 25.0%
!!! ATTCATGTCCACAATTTTTT+TGG + contig240end:43841-43860 None:intergenic 25.0%
!!! TTTTATTTTTGTGTTGTGTC+AGG - contig240end:45189-45208 MsG0080048186.01.T01:CDS 25.0%
AAACAAAAAGTTAGTACCAC+TGG - contig240end:44838-44857 MsG0080048186.01.T01:CDS 30.0%
AAATTCTGCAATGCTTTGTA+AGG + contig240end:45314-45333 None:intergenic 30.0%
ACTGGTAATCTAACAATCAT+AGG - contig240end:44856-44875 MsG0080048186.01.T01:intron 30.0%
AGCAAAGTCAATTGCAAAAA+AGG + contig240end:44085-44104 None:intergenic 30.0%
ATGTCTCTTATGAATAAGAC+CGG - contig240end:43757-43776 MsG0080048186.01.T01:intron 30.0%
ATTTATCAATCTCGAGTACT+CGG + contig240end:44390-44409 None:intergenic 30.0%
CTCTTGTTAGACATAGATTA+AGG - contig240end:44048-44067 MsG0080048186.01.T01:intron 30.0%
GATTTCTAATACAATGGTCA+TGG + contig240end:45090-45109 None:intergenic 30.0%
GGAACAAAAAGTGATAAAAG+TGG + contig240end:44774-44793 None:intergenic 30.0%
GTAATCTAACAATCATAGGA+CGG - contig240end:44860-44879 MsG0080048186.01.T01:intron 30.0%
TAAACTTGGGAAATTGTTGA+AGG - contig240end:43910-43929 MsG0080048186.01.T01:intron 30.0%
TATGATTGTTAGATTACCAG+TGG + contig240end:44857-44876 None:intergenic 30.0%
TTAATTACCTTAACTGGACT+AGG + contig240end:43989-44008 None:intergenic 30.0%
TTCTTGTAAACCTCTTAGTT+AGG + contig240end:44542-44561 None:intergenic 30.0%
TTTATGAAATGGAAACGTGA+AGG + contig240end:44795-44814 None:intergenic 30.0%
! ACATCTAGTTCAACAAAAGT+TGG - contig240end:43684-43703 MsG0080048186.01.T01:intron 30.0%
! CATGCCAAAAAACTATTTTG+CGG + contig240end:44566-44585 None:intergenic 30.0%
! GTGAATTTAGGATAACTAAG+TGG + contig240end:44648-44667 None:intergenic 30.0%
!! TTACAAAGCATTGCAGAATT+TGG - contig240end:45313-45332 MsG0080048186.01.T01:CDS 30.0%
!!! AAAATAGTTTTTTGGCATGC+AGG - contig240end:44567-44586 MsG0080048186.01.T01:intron 30.0%
!!! AAATAGTTTTTTGGCATGCA+GGG - contig240end:44568-44587 MsG0080048186.01.T01:intron 30.0%
!!! GAAACCGCAAAATAGTTTTT+TGG - contig240end:44559-44578 MsG0080048186.01.T01:intron 30.0%
!!! TTGGTAGTGCTTTTATGAAA+TGG + contig240end:44806-44825 None:intergenic 30.0%
ACTGTTACTACCTAACTAAG+AGG - contig240end:44529-44548 MsG0080048186.01.T01:intron 35.0%
AGAAGCTTGAGATGTTTCAA+TGG + contig240end:43558-43577 None:intergenic 35.0%
ATCATAGCAACCAAAAGGTT+TGG + contig240end:44498-44517 None:intergenic 35.0%
ATCCATCATTGTTTGGATTG+TGG + contig240end:44739-44758 None:intergenic 35.0%
CCATTCTCAGATTTAAGAGT+AGG + contig240end:43531-43550 None:intergenic 35.0%
CCTACTCTTAAATCTGAGAA+TGG - contig240end:43528-43547 MsG0080048186.01.T01:intron 35.0%
CGAAGAAATGTGGTAAACTT+GGG - contig240end:43897-43916 MsG0080048186.01.T01:intron 35.0%
GAGGTTATGAATTCAAATCC+TGG - contig240end:43477-43496 MsG0080048186.01.T01:CDS 35.0%
GATAAAAGTGGCAGAACAAA+GGG + contig240end:44762-44781 None:intergenic 35.0%
GCAAGATTGAGAGGATTTAT+TGG - contig240end:43439-43458 MsG0080048186.01.T01:CDS 35.0%
TCGAAGAAATGTGGTAAACT+TGG - contig240end:43896-43915 MsG0080048186.01.T01:intron 35.0%
TCTAATACAATGGTCATGGA+TGG + contig240end:45086-45105 None:intergenic 35.0%
TCTTAGTTAGGTAGTAACAG+TGG + contig240end:44530-44549 None:intergenic 35.0%
TGACTATGCAACGGAATATT+AGG - contig240end:44689-44708 MsG0080048186.01.T01:intron 35.0%
TGATAAAAGTGGCAGAACAA+AGG + contig240end:44763-44782 None:intergenic 35.0%
TTGAAAATTGACACTCTCTC+CGG + contig240end:43779-43798 None:intergenic 35.0%
! AGAAGCAATAACAGAAGTGT+TGG - contig240end:45250-45269 MsG0080048186.01.T01:CDS 35.0%
! ATTGTGGACATGAATTTTGG+TGG - contig240end:43846-43865 MsG0080048186.01.T01:intron 35.0%
! GCATTTTTCCCTTTATCTCT+TGG - contig240end:45123-45142 MsG0080048186.01.T01:CDS 35.0%
!! AGTGTTGGAAGACATTTTGT+TGG - contig240end:45265-45284 MsG0080048186.01.T01:CDS 35.0%
!! TATCGCTTGATCAGTTTTGA+AGG - contig240end:43612-43631 MsG0080048186.01.T01:intron 35.0%
!! TATTTTTGTGTTGTGTCAGG+TGG - contig240end:45192-45211 MsG0080048186.01.T01:CDS 35.0%
!! TTGTGGACATGAATTTTGGT+GGG - contig240end:43847-43866 MsG0080048186.01.T01:intron 35.0%
!!! AATAGTTTTTTGGCATGCAG+GGG - contig240end:44569-44588 MsG0080048186.01.T01:intron 35.0%
AAACGCATCGTTATACCCTA+CGG - contig240end:44304-44323 MsG0080048186.01.T01:intron 40.0%
ACAGTTGTGATACATCATCC+AGG - contig240end:43414-43433 MsG0080048186.01.T01:CDS 40.0%
ATCGTTATACCCTACGGAAA+CGG - contig240end:44310-44329 MsG0080048186.01.T01:intron 40.0%
ATTACAAACCCGTTTCCGTA+GGG + contig240end:44322-44341 None:intergenic 40.0%
CAAAGGGATCCATCATTGTT+TGG + contig240end:44746-44765 None:intergenic 40.0%
CACACACACCAAGAGATAAA+GGG + contig240end:45134-45153 None:intergenic 40.0%
CAGTTGTGATACATCATCCA+GGG - contig240end:43415-43434 MsG0080048186.01.T01:CDS 40.0%
CCAACATCATAGCAACCAAA+AGG + contig240end:44503-44522 None:intergenic 40.0%
CCTGATGACACTTTGCTTAT+TGG - contig240end:43582-43601 MsG0080048186.01.T01:intron 40.0%
CTAACAATCATAGGACGGTA+TGG - contig240end:44865-44884 MsG0080048186.01.T01:intron 40.0%
CTCCACAATCCAAACAATGA+TGG - contig240end:44734-44753 MsG0080048186.01.T01:CDS 40.0%
GAATTGTCAAGCTGCAGAAT+TGG - contig240end:43389-43408 MsG0080048186.01.T01:CDS 40.0%
GCATCTAGTTGACTATGCAA+CGG - contig240end:44680-44699 MsG0080048186.01.T01:intron 40.0%
GGTATGCCTTAGTCGAAATT+TGG - contig240end:43705-43724 MsG0080048186.01.T01:intron 40.0%
TATAACGATGCGTTTCAACG+TGG + contig240end:44299-44318 None:intergenic 40.0%
TGAAGGAGAGTGGTAATCAT+GGG - contig240end:43927-43946 MsG0080048186.01.T01:intron 40.0%
TGACACTTTGCTTATTGGTC+AGG - contig240end:43587-43606 MsG0080048186.01.T01:intron 40.0%
TTGAAGGAGAGTGGTAATCA+TGG - contig240end:43926-43945 MsG0080048186.01.T01:intron 40.0%
! ACCTTAACTGGACTAGGATT+CGG + contig240end:43983-44002 None:intergenic 40.0%
! CCAATAAGCAAAGTGTCATC+AGG + contig240end:43585-43604 None:intergenic 40.0%
! GAGTTTGCTTCGAAGAAATG+TGG - contig240end:43887-43906 MsG0080048186.01.T01:intron 40.0%
! GTGGGTTGTAGATGTATTGA+AGG - contig240end:43865-43884 MsG0080048186.01.T01:intron 40.0%
! GTTGGAAGACATTTTGTTGG+TGG - contig240end:45268-45287 MsG0080048186.01.T01:CDS 40.0%
! TAGCAACCAAAAGGTTTGGT+AGG + contig240end:44494-44513 None:intergenic 40.0%
!! ATAAAGGCACTGCATAGGAT+AGG + contig240end:45164-45183 None:intergenic 40.0%
!! CCTTTTGGTTGCTATGATGT+TGG - contig240end:44500-44519 MsG0080048186.01.T01:intron 40.0%
!! GATGAATAAAGGCACTGCAT+AGG + contig240end:45169-45188 None:intergenic 40.0%
!!! AGACATTTTGTTGGTGGTAG+TGG - contig240end:45274-45293 MsG0080048186.01.T01:CDS 40.0%
ACAAGAGCAACATAGTGACC+AGG + contig240end:43498-43517 None:intergenic 45.0%
ATCAATCTCGAGTACTCGGA+AGG + contig240end:44386-44405 None:intergenic 45.0%
CACTGCATAGGATAGGCATT+AGG + contig240end:45157-45176 None:intergenic 45.0%
CATTACAAACCCGTTTCCGT+AGG + contig240end:44323-44342 None:intergenic 45.0%
GCACACACACCAAGAGATAA+AGG + contig240end:45135-45154 None:intergenic 45.0%
GGGAAATTGTTGAAGGAGAG+TGG - contig240end:43917-43936 MsG0080048186.01.T01:intron 45.0%
TCCGAATCCTAGTCCAGTTA+AGG - contig240end:43979-43998 MsG0080048186.01.T01:intron 45.0%
TCGTTATACCCTACGGAAAC+GGG - contig240end:44311-44330 MsG0080048186.01.T01:intron 45.0%
TCTGCAATGCTTTGTAAGGC+TGG + contig240end:45310-45329 None:intergenic 45.0%
TGCGGTCCAAATTTCGACTA+AGG + contig240end:43714-43733 None:intergenic 45.0%
TTGGTCTGTTAGTGCTCATG+AGG - contig240end:43458-43477 MsG0080048186.01.T01:CDS 45.0%
! TTGCGTCCTACCAAACCTTT+TGG - contig240end:44485-44504 MsG0080048186.01.T01:intron 45.0%
ACTCAACGAACGGAGAGCAA+TGG - contig240end:45223-45242 MsG0080048186.01.T01:CDS 50.0%
ATCCAGGGAGCAAGATTGAG+AGG - contig240end:43430-43449 MsG0080048186.01.T01:CDS 50.0%
ATCCTCTCAATCTTGCTCCC+TGG + contig240end:43435-43454 None:intergenic 50.0%
TGTGTTGTGTCAGGTGGAAC+AGG - contig240end:45198-45217 MsG0080048186.01.T01:CDS 50.0%
!! TTGTTGGTGGTAGTGGCCAA+TGG - contig240end:45281-45300 MsG0080048186.01.T01:CDS 50.0%
!! TTTGTAAGGCTGGCCTCCAT+TGG + contig240end:45300-45319 None:intergenic 50.0%
GGAACAGGCGACTCAACGAA+CGG - contig240end:45213-45232 MsG0080048186.01.T01:CDS 55.0%
! TTTGGCATGCAGGGGCACAT+AGG - contig240end:44577-44596 MsG0080048186.01.T01:intron 55.0%
!! TTGGTGGTAGTGGCCAATGG+AGG - contig240end:45284-45303 MsG0080048186.01.T01:CDS 55.0%
Chromosome Type Strat End Strand Name
contig240end gene 43384 45352 43384 ID=MsG0080048186.01;Name=MsG0080048186.01
contig240end mRNA 43384 45352 43384 ID=MsG0080048186.01.T01;Parent=MsG0080048186.01;Name=MsG0080048186.01.T01;_AED=0.43;_eAED=0.59;_QI=0|0|0|1|1|1|3|0|184
contig240end exon 45103 45352 45103 ID=MsG0080048186.01.T01:exon:8524;Parent=MsG0080048186.01.T01
contig240end exon 44698 44860 44698 ID=MsG0080048186.01.T01:exon:8523;Parent=MsG0080048186.01.T01
contig240end exon 43384 43525 43384 ID=MsG0080048186.01.T01:exon:8522;Parent=MsG0080048186.01.T01
contig240end CDS 45103 45352 45103 ID=MsG0080048186.01.T01:cds;Parent=MsG0080048186.01.T01
contig240end CDS 44698 44860 44698 ID=MsG0080048186.01.T01:cds;Parent=MsG0080048186.01.T01
contig240end CDS 43384 43525 43384 ID=MsG0080048186.01.T01:cds;Parent=MsG0080048186.01.T01
Gene Sequence

>MsG0080048186.01.T01

ATGGGGAATTGTCAAGCTGCAGAATTGGCAACAGTTGTGATACATCATCCAGGGAGCAAGATTGAGAGGATTTATTGGTCTGTTAGTGCTCATGAGGTTATGAATTCAAATCCTGGTCACTATGTTGCTCTTGTTGTTTCATCACCTACTCTTAAATCTGAGAATGGTATGCCATTGAAACATCTCAAGCTTCTTCGACCTGATGACACTTTGCTTATTGGTCAGGTTTATCGCTTGATCAGTTTTGAAGATGTATTGAAGGAGTTTGCTTCGAAGAAATGTGGTAAACTTGGGAAATTGTTGAAGGAGAGTGGTAATCATGGGATTCAGATGAAACATAGAGACTTCAGAGCTCCGAATCCTAGTCCAGTTAAGGTAATTAAGTTTCATGTTAATGTTATAGTTTCAAATTGGTGGAACAGGCGACTCAACGAACGGAGAGCAATGGCAGCAGAAGCAATAACAGAAGTGTTGGAAGACATTTTGTTGGTGGTAGTGGCCAATGGAGGCCAGCCTTACAAAGCATTGCAGAATTTGGAACTTGAACTCACTTAA
Protein sequence

>MsG0080048186.01.T01

MGNCQAAELATVVIHHPGSKIERIYWSVSAHEVMNSNPGHYVALVVSSPTLKSENGMPLKHLKLLRPDDTLLIGQVYRLISFEDVLKEFASKKCGKLGKLLKESGNHGIQMKHRDFRAPNPSPVKVIKFHVNVIVSNWWNRRLNERRAMAAEAITEVLEDILLVVVANGGQPYKALQNLELELT*