AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480020187.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020187.01.T01 MTR_0008s0390 94.444 90 5 0 52 141 183 272 1.38e-56 177
MsG0480020187.01.T01 MTR_0008s0390 96.970 33 1 0 1 33 1 33 1.11e-15 71.6
MsG0480020187.01.T01 MTR_0008s0470 64.220 109 22 1 50 141 183 291 3.49e-40 136
MsG0480020187.01.T01 MTR_0008s0470 100.000 33 0 0 1 33 1 33 1.60e-16 74.3
MsG0480020187.01.T01 MTR_0251s0050 55.340 103 39 2 39 141 177 272 9.03e-28 103
MsG0480020187.01.T01 MTR_0251s0050 96.970 33 1 0 1 33 1 33 1.34e-15 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACAAAACTTTCGGTAGTA+TGG 0.284671 4:+36001619 None:intergenic
TAGTATATGACAAGGATATT+TGG 0.309668 4:-36001452 MsG0480020187.01.T01:CDS
TTTGTCATGGATAATGATTT+TGG 0.329855 4:-36001603 MsG0480020187.01.T01:CDS
CGACAACTCCCTAAGTTTGC+AGG 0.342502 4:-36002254 MsG0480020187.01.T01:CDS
CTATATTTACCTGCAAACTT+AGG 0.368822 4:+36002245 None:intergenic
CCTTCATGTGACAAAATTAG+TGG 0.383309 4:-36002355 MsG0480020187.01.T01:CDS
ACTAGATATGTTGCTGGAAT+TGG 0.387649 4:-36002277 MsG0480020187.01.T01:CDS
ATTATCCATGACAAAACTTT+CGG 0.398726 4:+36001611 None:intergenic
CATGGACTGCTGAAGAAGAT+AGG 0.410291 4:-36002318 MsG0480020187.01.T01:CDS
CACTGTTCCACTTGGTGTGT+TGG 0.421769 4:+36001647 None:intergenic
TATATTTACCTGCAAACTTA+GGG 0.430529 4:+36002246 None:intergenic
TATGTCACTAGATATGTTGC+TGG 0.502652 4:-36002283 MsG0480020187.01.T01:CDS
TGGGACATGTCAACTTCATA+TGG 0.510490 4:+36001528 None:intergenic
AGATTCATTTATAGAAGATG+TGG 0.523349 4:-36001697 MsG0480020187.01.T01:CDS
CAGGTAAATATAGAACTTTG+CGG 0.530496 4:-36002235 MsG0480020187.01.T01:intron
GTGACAAAATTAGTGGAATG+AGG 0.554265 4:-36002348 MsG0480020187.01.T01:CDS
AAAGGTATCAGTAGTTCAGT+TGG 0.561036 4:+36001501 None:intergenic
AAAATTAGTGGAATGAGGAA+AGG 0.574126 4:-36002343 MsG0480020187.01.T01:CDS
AATCTTTCCAACACACCAAG+TGG 0.595510 4:-36001654 MsG0480020187.01.T01:CDS
GTGGAATGAGGAAAGGAACA+TGG 0.603385 4:-36002336 MsG0480020187.01.T01:CDS
ACTACTGATACCTTTGTCGA+TGG 0.606426 4:-36001493 MsG0480020187.01.T01:CDS
TCAGTAGTTCAGTTGGAACG+TGG 0.618063 4:+36001508 None:intergenic
CAGTAGTTCAGTTGGAACGT+GGG 0.647890 4:+36001509 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTCTATAGTATATGACA+AGG - Chr4:36002353-36002372 MsG0480020187.01.T01:CDS 20.0%
! AAAGTTTCCTCTTTGATATT+AGG + Chr4:36001750-36001769 None:intergenic 25.0%
! AGATTCATTTATAGAAGATG+TGG - Chr4:36002116-36002135 MsG0480020187.01.T01:intron 25.0%
! ATTATCCATGACAAAACTTT+CGG + Chr4:36002205-36002224 None:intergenic 25.0%
! ATTTCACTAGATGATGAAAA+TGG + Chr4:36002042-36002061 None:intergenic 25.0%
! TAGTATATGACAAGGATATT+TGG - Chr4:36002361-36002380 MsG0480020187.01.T01:CDS 25.0%
! TATATTTACCTGCAAACTTA+GGG + Chr4:36001570-36001589 None:intergenic 25.0%
! TTTCACTAGATGATGAAAAT+GGG + Chr4:36002041-36002060 None:intergenic 25.0%
!! TGACCATAAATTTTATCTCA+AGG + Chr4:36001634-36001653 None:intergenic 25.0%
!! TTTGTCATGGATAATGATTT+TGG - Chr4:36002210-36002229 MsG0480020187.01.T01:intron 25.0%
!!! CTATTGCATTTTTTTGATTC+AGG - Chr4:36001672-36001691 MsG0480020187.01.T01:CDS 25.0%
AAAATTAGTGGAATGAGGAA+AGG - Chr4:36001470-36001489 MsG0480020187.01.T01:CDS 30.0%
AAACTTTACTCAACAAGAAG+AGG - Chr4:36001763-36001782 MsG0480020187.01.T01:intron 30.0%
AGACATAATTGAATCCACAA+AGG - Chr4:36001944-36001963 MsG0480020187.01.T01:intron 30.0%
ATAAAAAGCTTGGGAATAGA+TGG - Chr4:36001804-36001823 MsG0480020187.01.T01:intron 30.0%
ATAATGAAGTGAAGAACCAT+TGG - Chr4:36001860-36001879 MsG0480020187.01.T01:intron 30.0%
ATCAGAATGCATAAAAAGCT+TGG - Chr4:36001794-36001813 MsG0480020187.01.T01:intron 30.0%
ATGATGAAAATGGGGATAAA+GGG + Chr4:36002032-36002051 None:intergenic 30.0%
CAGGTAAATATAGAACTTTG+CGG - Chr4:36001578-36001597 MsG0480020187.01.T01:CDS 30.0%
CCTCCTTGAGATAAAATTTA+TGG - Chr4:36001628-36001647 MsG0480020187.01.T01:CDS 30.0%
CTATATTTACCTGCAAACTT+AGG + Chr4:36001571-36001590 None:intergenic 30.0%
TCAGAATGCATAAAAAGCTT+GGG - Chr4:36001795-36001814 MsG0480020187.01.T01:intron 30.0%
TTCACTAGATGATGAAAATG+GGG + Chr4:36002040-36002059 None:intergenic 30.0%
! AAGATGTGGATGAAAGTTTT+TGG - Chr4:36002130-36002149 MsG0480020187.01.T01:intron 30.0%
! AAGCTTTTTAGATGCTTACA+AGG - Chr4:36002233-36002252 MsG0480020187.01.T01:intron 30.0%
! CCATAAATTTTATCTCAAGG+AGG + Chr4:36001631-36001650 None:intergenic 30.0%
! TTGAGGAGTAATTTGGTAAT+TGG + Chr4:36001980-36001999 None:intergenic 30.0%
!! TTTTTGATTCAGGTCTTTCA+AGG - Chr4:36001682-36001701 MsG0480020187.01.T01:CDS 30.0%
!!! TGTCAACAGTTGATAGTTTT+TGG - Chr4:36002256-36002275 MsG0480020187.01.T01:CDS 30.0%
AACTGGATTGAGGAGTAATT+TGG + Chr4:36001987-36002006 None:intergenic 35.0%
ACCAAAATCATCCAAAGAAG+TGG + Chr4:36002091-36002110 None:intergenic 35.0%
ACTAGATATGTTGCTGGAAT+TGG - Chr4:36001536-36001555 MsG0480020187.01.T01:CDS 35.0%
AGATCACAATTCCACTTCTT+TGG - Chr4:36002077-36002096 MsG0480020187.01.T01:intron 35.0%
CACTTCATTATCTGTTCTTC+CGG + Chr4:36001851-36001870 None:intergenic 35.0%
CCTTCATGTGACAAAATTAG+TGG - Chr4:36001458-36001477 MsG0480020187.01.T01:CDS 35.0%
GATGATGAAAATGGGGATAA+AGG + Chr4:36002033-36002052 None:intergenic 35.0%
GGAATTGTGATCTAAAGATG+TGG + Chr4:36002070-36002089 None:intergenic 35.0%
GTGACAAAATTAGTGGAATG+AGG - Chr4:36001465-36001484 MsG0480020187.01.T01:CDS 35.0%
TATGTCACTAGATATGTTGC+TGG - Chr4:36001530-36001549 MsG0480020187.01.T01:CDS 35.0%
TCTTAGGCCTAATATCAAAG+AGG - Chr4:36001740-36001759 MsG0480020187.01.T01:intron 35.0%
TGACAAAACTTTCGGTAGTA+TGG + Chr4:36002197-36002216 None:intergenic 35.0%
TTAGGTGGCTGAATTATCTT+AGG - Chr4:36001724-36001743 MsG0480020187.01.T01:intron 35.0%
TTGGATATATCTCTCCTTTG+TGG + Chr4:36001961-36001980 None:intergenic 35.0%
! CCACTAATTTTGTCACATGA+AGG + Chr4:36001461-36001480 None:intergenic 35.0%
! TCCACTTCTTTGGATGATTT+TGG - Chr4:36002087-36002106 MsG0480020187.01.T01:intron 35.0%
! TTTTCAGATTCCATCGACAA+AGG + Chr4:36002333-36002352 None:intergenic 35.0%
!! AAAGGTATCAGTAGTTCAGT+TGG + Chr4:36002315-36002334 None:intergenic 35.0%
!! TACTACCGAAAGTTTTGTCA+TGG - Chr4:36002197-36002216 MsG0480020187.01.T01:intron 35.0%
AATCTTTCCAACACACCAAG+TGG - Chr4:36002159-36002178 MsG0480020187.01.T01:intron 40.0%
ACTACTGATACCTTTGTCGA+TGG - Chr4:36002320-36002339 MsG0480020187.01.T01:CDS 40.0%
ATTCAGGTCTTTCAAGGTGT+GGG - Chr4:36001688-36001707 MsG0480020187.01.T01:CDS 40.0%
GAATAGATGGTCAACCATTG+CGG - Chr4:36001817-36001836 MsG0480020187.01.T01:intron 40.0%
TGGGACATGTCAACTTCATA+TGG + Chr4:36002288-36002307 None:intergenic 40.0%
!! AGAACTTTGCGGTATTGACT+TGG - Chr4:36001589-36001608 MsG0480020187.01.T01:CDS 40.0%
!! GAACTTTGCGGTATTGACTT+GGG - Chr4:36001590-36001609 MsG0480020187.01.T01:CDS 40.0%
AAATGGGGATAAAGGGCCAT+TGG + Chr4:36002025-36002044 None:intergenic 45.0%
CAGTAGTTCAGTTGGAACGT+GGG + Chr4:36002307-36002326 None:intergenic 45.0%
GAGATTTGGGAACTGGATTG+AGG + Chr4:36001997-36002016 None:intergenic 45.0%
GATTCAGGTCTTTCAAGGTG+TGG - Chr4:36001687-36001706 MsG0480020187.01.T01:CDS 45.0%
GGAAGAGTTGTAGACTTAGG+TGG - Chr4:36001709-36001728 MsG0480020187.01.T01:intron 45.0%
GTGGAATGAGGAAAGGAACA+TGG - Chr4:36001477-36001496 MsG0480020187.01.T01:CDS 45.0%
GTGGGAAGAGTTGTAGACTT+AGG - Chr4:36001706-36001725 MsG0480020187.01.T01:intron 45.0%
TCAGTAGTTCAGTTGGAACG+TGG + Chr4:36002308-36002327 None:intergenic 45.0%
TCCCAAATCTCAGACACCAA+TGG - Chr4:36002006-36002025 MsG0480020187.01.T01:intron 45.0%
! CATGGACTGCTGAAGAAGAT+AGG - Chr4:36001495-36001514 MsG0480020187.01.T01:CDS 45.0%
! GCCATTGGTGTCTGAGATTT+GGG + Chr4:36002010-36002029 None:intergenic 45.0%
! TCTTGAGAGAAGTGTGCCAA+TGG + Chr4:36001879-36001898 None:intergenic 45.0%
!! TGGTTTTGCACTGTTCCACT+TGG + Chr4:36002177-36002196 None:intergenic 45.0%
AACCATTGCGGCTGAGTTAC+CGG - Chr4:36001829-36001848 MsG0480020187.01.T01:intron 50.0%
CGACAACTCCCTAAGTTTGC+AGG - Chr4:36001559-36001578 MsG0480020187.01.T01:CDS 50.0%
! GGCCATTGGTGTCTGAGATT+TGG + Chr4:36002011-36002030 None:intergenic 50.0%
! GGTGTCTGAGATTTGGGAAC+TGG + Chr4:36002004-36002023 None:intergenic 50.0%
!! CACTGTTCCACTTGGTGTGT+TGG + Chr4:36002169-36002188 None:intergenic 50.0%
TTCCGGTAACTCAGCCGCAA+TGG + Chr4:36001834-36001853 None:intergenic 55.0%
!! GCGGTATTGACTTGGGACCT+GGG - Chr4:36001597-36001616 MsG0480020187.01.T01:CDS 55.0%
!! TGCGGTATTGACTTGGGACC+TGG - Chr4:36001596-36001615 MsG0480020187.01.T01:CDS 55.0%
! TCAAGGAGGAGCACACTCCC+AGG + Chr4:36001617-36001636 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr4 gene 36001446 36002389 36001446 ID=MsG0480020187.01;Name=MsG0480020187.01
Chr4 mRNA 36001446 36002389 36001446 ID=MsG0480020187.01.T01;Parent=MsG0480020187.01;Name=MsG0480020187.01.T01;_AED=0.34;_eAED=0.37;_QI=0|0|0|1|1|1|2|0|141
Chr4 exon 36002236 36002389 36002236 ID=MsG0480020187.01.T01:exon:39203;Parent=MsG0480020187.01.T01
Chr4 exon 36001446 36001717 36001446 ID=MsG0480020187.01.T01:exon:39204;Parent=MsG0480020187.01.T01
Chr4 CDS 36002236 36002389 36002236 ID=MsG0480020187.01.T01:cds;Parent=MsG0480020187.01.T01
Chr4 CDS 36001446 36001717 36001446 ID=MsG0480020187.01.T01:cds;Parent=MsG0480020187.01.T01
Gene Sequence

>MsG0480020187.01.T01

ATGGCTAGAACTCCTTCATGTGACAAAATTAGTGGAATGAGGAAAGGAACATGGACTGCTGAAGAAGATAGGAAATTAATTGCTTATGTCACTAGATATGTTGCTGGAATTGGCGACAACTCCCTAAGTTTGCAGGTAAATATAGAACTTTGCGATTCATTTATAGAAGATGTGGATGAAAGTTTTTGGCTTCATAATCTTTCCAACACACCAAGTGGAACAGTGCAAAACCATACTACCGAAAGTTTTGTCATGGATAATGATTTTGGAAGCTTTTTAGATGCTTACAAGGTGTCAACAGTTGATAGTTTTTGGACACAACCATATGAAGTTGACATGTCCCACGTTCCAACTGAACTACTGATACCTTTGTCGATGGAATCTGAAAAATTTTCTATAGTATATGACAAGGATATTTGGAGTTGA
Protein sequence

>MsG0480020187.01.T01

MARTPSCDKISGMRKGTWTAEEDRKLIAYVTRYVAGIGDNSLSLQVNIELCDSFIEDVDESFWLHNLSNTPSGTVQNHTTESFVMDNDFGSFLDAYKVSTVDSFWTQPYEVDMSHVPTELLIPLSMESEKFSIVYDKDIWS*