AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680033930.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680033930.01.T01 MTR_6g089480 64.463 121 12 1 3 123 226 315 7.42e-43 143
MsG0680033930.01.T01 MTR_1g101950 52.632 114 23 1 3 116 255 337 6.25e-31 112
MsG0680033930.01.T01 MTR_0046s0180 44.737 114 32 1 3 116 27 109 6.66e-27 96.7
MsG0680033930.01.T01 MTR_1g069745 50.000 108 23 1 9 116 209 285 4.13e-26 99.4
MsG0680033930.01.T01 MTR_1g069490 49.123 114 27 1 3 116 316 398 5.60e-26 100
MsG0680033930.01.T01 MTR_1g057810 47.414 116 30 1 3 118 479 563 3.95e-25 99.0
MsG0680033930.01.T01 MTR_1g105150 47.414 116 30 1 3 118 465 549 5.08e-25 98.6
MsG0680033930.01.T01 MTR_1g054730 47.222 108 26 1 12 119 314 390 4.02e-23 92.4
MsG0680033930.01.T01 MTR_5g079460 44.444 117 34 2 3 119 298 383 1.05e-22 91.3
MsG0680033930.01.T01 MTR_7g075860 43.103 116 35 3 3 118 275 359 1.98e-18 79.3
MsG0680033930.01.T01 MTR_6g089480 81.818 44 8 0 3 46 226 269 3.49e-18 77.8
MsG0680033930.01.T01 MTR_6g089480 81.818 44 8 0 3 46 226 269 3.76e-18 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680033930.01.T01 AT5G51830 53.043 115 23 2 3 117 255 338 9.42e-31 112
MsG0680033930.01.T01 AT5G51830 53.043 115 23 2 3 117 255 338 9.42e-31 112
MsG0680033930.01.T01 AT1G66430 43.333 120 37 1 3 122 296 384 1.59e-23 93.6

Find 24 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATTCCTGCACAGAAATT+TGG 0.199104 6:+76734836 None:intergenic
TGTGAAACAGCTTCCTTTGT+AGG 0.304120 6:+76733534 None:intergenic
ACCTCTTTCTGTAACTGTTA+TGG 0.347968 6:+76733572 None:intergenic
GCTGGTGATGCATTTGTTAG+TGG 0.420129 6:-76734766 MsG0680033930.01.T01:CDS
GTTAAACCTGTTGACACAAC+TGG 0.432282 6:-76734790 MsG0680033930.01.T01:CDS
CTGATAGAGGCAACGGTGGC+GGG 0.436664 6:-76734542 MsG0680033930.01.T01:CDS
CCAGCACCAGTTGTGTCAAC+AGG 0.441337 6:+76734784 None:intergenic
CTGTGCAGGAATTTCGAGGC+AGG 0.465166 6:-76734828 MsG0680033930.01.T01:CDS
AACGGTGGCGGGAAGTTCTC+CGG 0.480949 6:-76734531 MsG0680033930.01.T01:intron
GAATTTCGAGGCAGGGTTGG+AGG 0.497205 6:-76734820 MsG0680033930.01.T01:CDS
CAGTATAGCTTCTGACATTG+AGG 0.499738 6:-76734734 MsG0680033930.01.T01:CDS
ACTGATAGAGGCAACGGTGG+CGG 0.506155 6:-76734543 MsG0680033930.01.T01:CDS
CCTGTTGACACAACTGGTGC+TGG 0.514806 6:-76734784 MsG0680033930.01.T01:CDS
GCTTCCTTTGTAGGAAGTGA+AGG 0.529815 6:+76733543 None:intergenic
GCCATAACAGTTACAGAAAG+AGG 0.530881 6:-76733573 MsG0680033930.01.T01:CDS
CAGGAATTTCGAGGCAGGGT+TGG 0.538929 6:-76734823 MsG0680033930.01.T01:CDS
GTGGTGCCAAATTTCTGTGC+AGG 0.549852 6:-76734842 MsG0680033930.01.T01:CDS
TGCCTCTATCAGTTTCTCAC+CGG 0.553487 6:+76734553 None:intergenic
ATTTCTGTGCAGGAATTTCG+AGG 0.557516 6:-76734832 MsG0680033930.01.T01:CDS
AATTCCTTCACTTCCTACAA+AGG 0.581630 6:-76733547 MsG0680033930.01.T01:CDS
TGTGCAGGAATTTCGAGGCA+GGG 0.593911 6:-76734827 MsG0680033930.01.T01:CDS
GTCCGGTGAGAAACTGATAG+AGG 0.604985 6:-76734555 MsG0680033930.01.T01:CDS
TGAGAAACTGATAGAGGCAA+CGG 0.621701 6:-76734549 MsG0680033930.01.T01:CDS
GAAACTGATAGAGGCAACGG+TGG 0.719932 6:-76734546 MsG0680033930.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATGAAATTTATATTTTCT+TGG - Chr6:76734703-76734722 MsG0680033930.01.T01:intron 10.0%
!!! AGTCAAAAAATATTTTTACT+GGG - Chr6:76733756-76733775 MsG0680033930.01.T01:intron 15.0%
!!! GAGATTATTTTTTTTACAAA+TGG - Chr6:76734305-76734324 MsG0680033930.01.T01:intron 15.0%
!!! GTAAAAATATTTTTTGACTA+AGG + Chr6:76733755-76733774 None:intergenic 15.0%
!!! TAGTCAAAAAATATTTTTAC+TGG - Chr6:76733755-76733774 MsG0680033930.01.T01:intron 15.0%
!! AAATTATCATTTGCTTTCAA+GGG - Chr6:76734332-76734351 MsG0680033930.01.T01:intron 20.0%
!! TAAATTATCATTTGCTTTCA+AGG - Chr6:76734331-76734350 MsG0680033930.01.T01:intron 20.0%
!!! AAAAATACTCTTTTTTTACG+AGG + Chr6:76734228-76734247 None:intergenic 20.0%
!!! AATATTCATGGTTTTAGTTT+TGG + Chr6:76734198-76734217 None:intergenic 20.0%
!!! GTCAAAAAATATTTTTACTG+GGG - Chr6:76733757-76733776 MsG0680033930.01.T01:intron 20.0%
! AAAGATAAAGGAACTGAAAT+TGG - Chr6:76734283-76734302 MsG0680033930.01.T01:intron 25.0%
! AAGCTAAGTCATCTTTATAT+AGG - Chr6:76733977-76733996 MsG0680033930.01.T01:intron 25.0%
! AATGAGCAAATACAAAGATA+AGG + Chr6:76733689-76733708 None:intergenic 25.0%
! GATGAAGGAAATAAAGATAA+AGG - Chr6:76734271-76734290 MsG0680033930.01.T01:intron 25.0%
!! GAAATTTATATTTTCTTGGC+AGG - Chr6:76734707-76734726 MsG0680033930.01.T01:intron 25.0%
!! TTGTATTTTGCTAATGTATG+TGG - Chr6:76734753-76734772 MsG0680033930.01.T01:CDS 25.0%
ATATAATCACCTCTTGATGA+AGG - Chr6:76734256-76734275 MsG0680033930.01.T01:intron 30.0%
GGATTAAAAACTAATCTGTC+CGG - Chr6:76733778-76733797 MsG0680033930.01.T01:intron 30.0%
! TCTTTATTTCCTTCATCAAG+AGG + Chr6:76734268-76734287 None:intergenic 30.0%
AACGTATGCAAGCATAAATC+AGG - Chr6:76734548-76734567 MsG0680033930.01.T01:CDS 35.0%
AATTCCTTCACTTCCTACAA+AGG - Chr6:76734803-76734822 MsG0680033930.01.T01:CDS 35.0%
ACCTCTTTCTGTAACTGTTA+TGG + Chr6:76734781-76734800 None:intergenic 35.0%
AGTCAGTATGTGAAATGAGA+TGG - Chr6:76733910-76733929 MsG0680033930.01.T01:intron 35.0%
CGAGGACAGTAAAATATTCA+TGG + Chr6:76734210-76734229 None:intergenic 35.0%
GAAATTCCTGCACAGAAATT+TGG + Chr6:76733517-76733536 None:intergenic 35.0%
GGAAAAGTGAATCATACCTT+GGG - Chr6:76733950-76733969 MsG0680033930.01.T01:intron 35.0%
! ACGAGTAAAAGCGTATCATT+TGG - Chr6:76734394-76734413 MsG0680033930.01.T01:intron 35.0%
! ATGGAATGTGTGAAAAGTGT+GGG - Chr6:76733929-76733948 MsG0680033930.01.T01:intron 35.0%
!!! TCATGGTTTTAGTTTTGGAC+TGG + Chr6:76734193-76734212 None:intergenic 35.0%
ATAACAGTCCCAATGAGATG+TGG - Chr6:76734015-76734034 MsG0680033930.01.T01:intron 40.0%
ATTTCTGTGCAGGAATTTCG+AGG - Chr6:76733518-76733537 MsG0680033930.01.T01:CDS 40.0%
CAGTATAGCTTCTGACATTG+AGG - Chr6:76733616-76733635 MsG0680033930.01.T01:CDS 40.0%
GATGGAATGTGTGAAAAGTG+TGG - Chr6:76733928-76733947 MsG0680033930.01.T01:intron 40.0%
GCATACGTTCATGTACAAGT+GGG + Chr6:76734537-76734556 None:intergenic 40.0%
GCCATAACAGTTACAGAAAG+AGG - Chr6:76734777-76734796 MsG0680033930.01.T01:CDS 40.0%
GGGAAAAGTGAATCATACCT+TGG - Chr6:76733949-76733968 MsG0680033930.01.T01:intron 40.0%
GTTAAACCTGTTGACACAAC+TGG - Chr6:76733560-76733579 MsG0680033930.01.T01:CDS 40.0%
TGAGAAACTGATAGAGGCAA+CGG - Chr6:76733801-76733820 MsG0680033930.01.T01:intron 40.0%
TGCATACGTTCATGTACAAG+TGG + Chr6:76734538-76734557 None:intergenic 40.0%
TGTGAAACAGCTTCCTTTGT+AGG + Chr6:76734819-76734838 None:intergenic 40.0%
! ATGTGTCGTTGTGCTGTATA+AGG - Chr6:76734620-76734639 MsG0680033930.01.T01:intron 40.0%
! TGTGTCGTTGTGCTGTATAA+GGG - Chr6:76734621-76734640 MsG0680033930.01.T01:intron 40.0%
!! TCACATACTGACTTGAGCAT+TGG + Chr6:76733903-76733922 None:intergenic 40.0%
ATGACTTAGCTTCACTCCCA+AGG + Chr6:76733969-76733988 None:intergenic 45.0%
ATGATGCGCCACATCTCATT+GGG + Chr6:76734026-76734045 None:intergenic 45.0%
GCTTCCTTTGTAGGAAGTGA+AGG + Chr6:76734810-76734829 None:intergenic 45.0%
TGCCTCTATCAGTTTCTCAC+CGG + Chr6:76733800-76733819 None:intergenic 45.0%
! GCTGGTGATGCATTTGTTAG+TGG - Chr6:76733584-76733603 MsG0680033930.01.T01:CDS 45.0%
!!! TTAGTTTTGGACTGGCCAGA+AGG + Chr6:76734185-76734204 None:intergenic 45.0%
AAGACTCATCGCCAACGTAC+CGG + Chr6:76733841-76733860 None:intergenic 50.0%
ATACCAAGGCACATCGTCTG+AGG + Chr6:76734136-76734155 None:intergenic 50.0%
ATGAGATGTGGCGCATCATC+AGG - Chr6:76734027-76734046 MsG0680033930.01.T01:intron 50.0%
GAAACTGATAGAGGCAACGG+TGG - Chr6:76733804-76733823 MsG0680033930.01.T01:intron 50.0%
GACACGTGGACAGAATACCA+AGG + Chr6:76734150-76734169 None:intergenic 50.0%
GATGATGCGCCACATCTCAT+TGG + Chr6:76734027-76734046 None:intergenic 50.0%
GTCCGGTGAGAAACTGATAG+AGG - Chr6:76733795-76733814 MsG0680033930.01.T01:intron 50.0%
TACCAAGGCACATCGTCTGA+GGG + Chr6:76734135-76734154 None:intergenic 50.0%
TGTGCAGGAATTTCGAGGCA+GGG - Chr6:76733523-76733542 MsG0680033930.01.T01:CDS 50.0%
! GTCAGCGTTGAATTGCCTTC+TGG - Chr6:76734167-76734186 MsG0680033930.01.T01:intron 50.0%
! GTGGTGCCAAATTTCTGTGC+AGG - Chr6:76733508-76733527 MsG0680033930.01.T01:CDS 50.0%
ACGTTGGCGATGAGTCTTCG+CGG - Chr6:76733843-76733862 MsG0680033930.01.T01:intron 55.0%
ACTGATAGAGGCAACGGTGG+CGG - Chr6:76733807-76733826 MsG0680033930.01.T01:intron 55.0%
CAGGAATTTCGAGGCAGGGT+TGG - Chr6:76733527-76733546 MsG0680033930.01.T01:CDS 55.0%
CCAGCACCAGTTGTGTCAAC+AGG + Chr6:76733569-76733588 None:intergenic 55.0%
CCTGTTGACACAACTGGTGC+TGG - Chr6:76733566-76733585 MsG0680033930.01.T01:CDS 55.0%
CTGTGCAGGAATTTCGAGGC+AGG - Chr6:76733522-76733541 MsG0680033930.01.T01:CDS 55.0%
GAATTTCGAGGCAGGGTTGG+AGG - Chr6:76733530-76733549 MsG0680033930.01.T01:CDS 55.0%
GGCAATTCAACGCTGACACG+TGG + Chr6:76734164-76734183 None:intergenic 55.0%
! TGGAGTACTATCGTGCCTGC+AGG + Chr6:76733883-76733902 None:intergenic 55.0%
ACCGCACACGTGTCCTCCAA+CGG + Chr6:76734056-76734075 None:intergenic 60.0%
AGTCTTCGCGGTGGGACGAA+AGG - Chr6:76733855-76733874 MsG0680033930.01.T01:intron 60.0%
CATCATCAGGAGCCCGTTGG+AGG - Chr6:76734040-76734059 MsG0680033930.01.T01:intron 60.0%
CGGGAAGTTCTCCGGTACGT+TGG - Chr6:76733827-76733846 MsG0680033930.01.T01:intron 60.0%
CTCCCTCAGACGATGTGCCT+TGG - Chr6:76734130-76734149 MsG0680033930.01.T01:intron 60.0%
CTGATAGAGGCAACGGTGGC+GGG - Chr6:76733808-76733827 MsG0680033930.01.T01:intron 60.0%
GAGGTGGCGTGCATTGCTGT+TGG - Chr6:76734103-76734122 MsG0680033930.01.T01:intron 60.0%
TGGCGATGAGTCTTCGCGGT+GGG - Chr6:76733847-76733866 MsG0680033930.01.T01:intron 60.0%
TTGGCGATGAGTCTTCGCGG+TGG - Chr6:76733846-76733865 MsG0680033930.01.T01:intron 60.0%
!! AACGGTGGCGGGAAGTTCTC+CGG - Chr6:76733819-76733838 MsG0680033930.01.T01:intron 60.0%
CCCGTTGGAGGACACGTGTG+CGG - Chr6:76734052-76734071 MsG0680033930.01.T01:intron 65.0%
CCGCACACGTGTCCTCCAAC+GGG + Chr6:76734055-76734074 None:intergenic 65.0%
CGTGTGCGGTGTCTGATGCG+CGG - Chr6:76734066-76734085 MsG0680033930.01.T01:intron 65.0%
GCGCATCATCAGGAGCCCGT+TGG - Chr6:76734037-76734056 MsG0680033930.01.T01:intron 65.0%
GGACGCGTGCTTCAGTGAGG+TGG - Chr6:76734087-76734106 MsG0680033930.01.T01:intron 65.0%
!! GTGGGACGAAAGGTGCCTGC+AGG - Chr6:76733865-76733884 MsG0680033930.01.T01:intron 65.0%
CGCGGACGCGTGCTTCAGTG+AGG - Chr6:76734084-76734103 MsG0680033930.01.T01:intron 70.0%
Chromosome Type Strat End Strand Name
Chr6 gene 76733506 76734866 76733506 ID=MsG0680033930.01;Name=MsG0680033930.01
Chr6 mRNA 76733506 76734866 76733506 ID=MsG0680033930.01.T01;Parent=MsG0680033930.01;Name=MsG0680033930.01.T01;_AED=0.49;_eAED=0.64;_QI=0|0|0|1|0|0.33|3|0|123
Chr6 exon 76734731 76734866 76734731 ID=MsG0680033930.01.T01:exon:2018;Parent=MsG0680033930.01.T01
Chr6 exon 76734532 76734629 76734532 ID=MsG0680033930.01.T01:exon:2019;Parent=MsG0680033930.01.T01
Chr6 exon 76733506 76733643 76733506 ID=MsG0680033930.01.T01:exon:2020;Parent=MsG0680033930.01.T01
Chr6 CDS 76734731 76734866 76734731 ID=MsG0680033930.01.T01:cds;Parent=MsG0680033930.01.T01
Chr6 CDS 76734532 76734629 76734532 ID=MsG0680033930.01.T01:cds;Parent=MsG0680033930.01.T01
Chr6 CDS 76733506 76733643 76733506 ID=MsG0680033930.01.T01:cds;Parent=MsG0680033930.01.T01
Gene Sequence

>MsG0680033930.01.T01

TTGTGGTGCCAAATTTCTGTGCAGGAATTTCGAGGCAGGGTTGGAGGTGTTAAAGTTAAACCTGTTGACACAACTGGTGCTGGTGATGCATTTGTTAGTGGATTTCTGTACAGTATAGCTTCTGACATTGAGGTTTTTGTATATACCTTAGTCAAAAAATATTTTTACTGGGGATTAAAAACTAATCTGTCCGGTGAGAAACTGATAGAGGCAACGGTGGCGGGAAGTTCTCCGGATGAGAAAAGTCTGAAGAAAGCTTTGTATTTTGCTAATGTATGTGGTGCCATAACAGTTACAGAAAGAGGTGCAATTCCTTCACTTCCTACAAAGGAAGCTGTTTCACAATTCTTACTAGAAGCAGCTGTAATATAA
Protein sequence

>MsG0680033930.01.T01

LWCQISVQEFRGRVGGVKVKPVDTTGAGDAFVSGFLYSIASDIEVFVYTLVKKYFYWGLKTNLSGEKLIEATVAGSSPDEKSLKKALYFANVCGAITVTERGAIPSLPTKEAVSQFLLEAAVI*