AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480023489.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023489.01.T01 MTR_8g094180 95.745 141 1 1 2 137 228 368 1.05e-95 280
MsG0480023489.01.T01 MTR_8g094180 96.591 88 3 0 2 89 228 315 4.47e-58 183
MsG0480023489.01.T01 MTR_2g024120 56.034 116 50 1 21 136 253 367 1.46e-40 139
MsG0480023489.01.T01 MTR_4g127550 34.821 112 59 5 24 130 285 387 5.95e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023489.01.T01 AT5G14550 76.378 127 30 0 2 128 210 336 1.16e-68 211
MsG0480023489.01.T01 AT5G14550 73.485 132 35 0 2 133 237 368 2.87e-68 211
MsG0480023489.01.T01 AT5G14550 75.591 127 31 0 2 128 237 363 1.58e-67 208
MsG0480023489.01.T01 AT1G62305 54.054 111 50 1 23 133 236 345 4.21e-39 135
MsG0480023489.01.T01 AT1G62305 54.054 111 50 1 23 133 260 369 7.40e-39 134
MsG0480023489.01.T01 AT1G11940 52.174 115 54 1 21 135 264 377 1.45e-38 134
MsG0480023489.01.T01 AT5G14550 72.222 72 20 0 16 87 238 309 5.41e-32 116

Find 30 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTGTTGGACAGTCTGTTT+TGG 0.165391 4:+85900973 MsG0480023489.01.T01:intron
AAAAGCCGCTACCCGAATTT+TGG 0.189280 4:+85899268 MsG0480023489.01.T01:CDS
GATGCTTATTAAATTTATAA+AGG 0.310256 4:+85899948 MsG0480023489.01.T01:CDS
GACTTGATCCCTCCAAAATT+CGG 0.318399 4:-85899280 None:intergenic
TAGTAAACTTTCTTGCAAAA+AGG 0.331608 4:-85900548 None:intergenic
TCCACGGCGCTCACGATCTC+TGG 0.364508 4:-85899887 None:intergenic
GTTTGAACATAGTGTTCATC+TGG 0.409473 4:-85899566 None:intergenic
TGCTTGTACACCATTCTCTT+CGG 0.432521 4:-85900503 None:intergenic
TGGTATACAGTTGTGGATCT+TGG 0.438795 4:-85899546 None:intergenic
ACTTGATCCCTCCAAAATTC+GGG 0.445648 4:-85899279 None:intergenic
TTACTAGGACTGCTGCTTTG+AGG 0.451390 4:+85900565 MsG0480023489.01.T01:CDS
CTAAATGTACAATACAATAT+CGG 0.452590 4:-85901130 None:intergenic
ACACTATGTTCAAACATTGC+TGG 0.459415 4:+85899574 MsG0480023489.01.T01:CDS
TGCTTTGAGGCTTCTTAACA+TGG 0.485012 4:+85900578 MsG0480023489.01.T01:CDS
TTTATAAATTTAATAAGCAT+CGG 0.496105 4:-85899946 None:intergenic
TGGATCTTGGACGTGTCAGC+AGG 0.503820 4:-85899533 None:intergenic
GCGCTCACGATCTCTGGAGT+TGG 0.504969 4:-85899881 None:intergenic
TCCCTCCAAAATTCGGGTAG+CGG 0.515418 4:-85899273 None:intergenic
TCTGAGAACTTATAAGTCAC+TGG 0.518003 4:-85899916 None:intergenic
AAGAGAATGGTGTACAAGCA+AGG 0.546374 4:+85900506 MsG0480023489.01.T01:CDS
ACTCTGCTTGTATCAGCCAC+TGG 0.557794 4:-85901029 None:intergenic
GTTCATCTGGTATACAGTTG+TGG 0.575948 4:-85899553 None:intergenic
AACAAAATGCTTATTGCCAG+TGG 0.587980 4:+85901013 MsG0480023489.01.T01:three_prime_UTR
GATCAGTGACACATACTGCA+TGG 0.596005 4:+85899851 MsG0480023489.01.T01:CDS
ATCAGTGACACATACTGCAT+GGG 0.597196 4:+85899852 MsG0480023489.01.T01:CDS
AGAGAATGGTGTACAAGCAA+GGG 0.597758 4:+85900507 MsG0480023489.01.T01:CDS
GAGATCGTGAGCGCCGTGGA+TGG 0.599731 4:+85899890 MsG0480023489.01.T01:CDS
AGACTGAATACCGAAGAGAA+TGG 0.627600 4:+85900493 MsG0480023489.01.T01:CDS
AAGTCACTGGATGCCATCCA+CGG 0.632825 4:-85899903 None:intergenic
TCCAGAGATCGTGAGCGCCG+TGG 0.637645 4:+85899886 MsG0480023489.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATAAATTTAATAAGCAT+CGG - Chr4:85899949-85899968 None:intergenic 10.0%
!!! TAATTAATATTTTGTTAGAA+TGG + Chr4:85900084-85900103 MsG0480023489.01.T01:intron 10.0%
!!! TGATTTATTTTTTTTTTTGT+AGG + Chr4:85900449-85900468 MsG0480023489.01.T01:intron 10.0%
!! AGAAAAAAAAAAAAAAAGCA+AGG + Chr4:85900180-85900199 MsG0480023489.01.T01:intron 15.0%
!! ATTAAGATTCAGAATTTATT+AGG - Chr4:85900252-85900271 None:intergenic 15.0%
!! GATGCTTATTAAATTTATAA+AGG + Chr4:85899948-85899967 MsG0480023489.01.T01:CDS 15.0%
!! TATATAAACTAATAAAAGCA+AGG + Chr4:85900142-85900161 MsG0480023489.01.T01:intron 15.0%
!! AAAAATATTAAAGCAAAACC+AGG - Chr4:85899768-85899787 None:intergenic 20.0%
!! AAAATATTAAAGCAAAACCA+GGG - Chr4:85899767-85899786 None:intergenic 20.0%
!! CTAAATGTACAATACAATAT+CGG - Chr4:85901133-85901152 None:intergenic 20.0%
!! TTCAATATTTCATTCTGAAT+TGG + Chr4:85899428-85899447 MsG0480023489.01.T01:intron 20.0%
!! TTCATTCTGTGATAATAATA+GGG + Chr4:85900020-85900039 MsG0480023489.01.T01:intron 20.0%
!! TTGAGTTATTTATCTAAACA+AGG + Chr4:85900916-85900935 MsG0480023489.01.T01:intron 20.0%
!! TTTCATTCTGTGATAATAAT+AGG + Chr4:85900019-85900038 MsG0480023489.01.T01:intron 20.0%
! AAAGTCAAACTATGTTTCAT+AGG - Chr4:85900822-85900841 None:intergenic 25.0%
! AATAATAGGGTTATCATACT+AGG + Chr4:85900033-85900052 MsG0480023489.01.T01:intron 25.0%
! ATAAGTGCTTATCATATTAG+TGG - Chr4:85900881-85900900 None:intergenic 25.0%
! ATGGTAAGTTCATATATCAT+AGG + Chr4:85900597-85900616 MsG0480023489.01.T01:intron 25.0%
! CAGAAAATAAGTAACAATCT+CGG - Chr4:85900950-85900969 None:intergenic 25.0%
! TAGTAAACTTTCTTGCAAAA+AGG - Chr4:85900551-85900570 None:intergenic 25.0%
! TGGTAAGTTCATATATCATA+GGG + Chr4:85900598-85900617 MsG0480023489.01.T01:intron 25.0%
!! TTTAGTTTCTTCGATTTGAT+TGG + Chr4:85900677-85900696 MsG0480023489.01.T01:intron 25.0%
!! TTTTTGCAAGAAAGTTTACT+AGG + Chr4:85900550-85900569 MsG0480023489.01.T01:CDS 25.0%
!!! TTCTAAGTCTTGTTAAATAG+CGG + Chr4:85900372-85900391 MsG0480023489.01.T01:intron 25.0%
ATCTTTCATTAGTTGACTGA+CGG - Chr4:85900283-85900302 None:intergenic 30.0%
ATTCAGAATTTATTAGGAGC+AGG - Chr4:85900246-85900265 None:intergenic 30.0%
ATTGGTACATGATGTCAATT+AGG + Chr4:85899446-85899465 MsG0480023489.01.T01:intron 30.0%
!! CTTATTTTCTGATTCTCTGT+TGG + Chr4:85900959-85900978 MsG0480023489.01.T01:intron 30.0%
!! GAATGGTACTTGATAATGAT+AGG + Chr4:85900101-85900120 MsG0480023489.01.T01:intron 30.0%
AACAAAATGCTTATTGCCAG+TGG + Chr4:85901013-85901032 MsG0480023489.01.T01:three_prime_UTR 35.0%
ACACTATGTTCAAACATTGC+TGG + Chr4:85899574-85899593 MsG0480023489.01.T01:CDS 35.0%
ACTATGTTTCATAGGCTACT+TGG - Chr4:85900814-85900833 None:intergenic 35.0%
AGCTCTTTCAAACAGTCTAA+AGG - Chr4:85900733-85900752 None:intergenic 35.0%
ATGATGTCAATTAGGTTCGT+AGG + Chr4:85899454-85899473 MsG0480023489.01.T01:intron 35.0%
ATTTATTAGGAGCAGGATCA+AGG - Chr4:85900239-85900258 None:intergenic 35.0%
GTTTGAACATAGTGTTCATC+TGG - Chr4:85899569-85899588 None:intergenic 35.0%
TCTGAGAACTTATAAGTCAC+TGG - Chr4:85899919-85899938 None:intergenic 35.0%
! AAAAGCAAGGTGTGAGATTT+TGG + Chr4:85900193-85900212 MsG0480023489.01.T01:intron 35.0%
! GAGGTCTTTTTGCTAGATTT+GGG - Chr4:85899812-85899831 None:intergenic 35.0%
! TCAAGAAAGTGATTTTGCAG+TGG - Chr4:85899993-85900012 None:intergenic 35.0%
!! CAGTCTAAAGGTGTTTATGT+CGG - Chr4:85900721-85900740 None:intergenic 35.0%
!! TTCGTGTTAGTTCTTTTTCG+AGG - Chr4:85899831-85899850 None:intergenic 35.0%
AAGAGAATGGTGTACAAGCA+AGG + Chr4:85900506-85900525 MsG0480023489.01.T01:CDS 40.0%
ACTTGATCCCTCCAAAATTC+GGG - Chr4:85899282-85899301 None:intergenic 40.0%
AGACTGAATACCGAAGAGAA+TGG + Chr4:85900493-85900512 MsG0480023489.01.T01:CDS 40.0%
AGAGAATGGTGTACAAGCAA+GGG + Chr4:85900507-85900526 MsG0480023489.01.T01:CDS 40.0%
ATCAGTGACACATACTGCAT+GGG + Chr4:85899852-85899871 MsG0480023489.01.T01:CDS 40.0%
ATGCAACAGTGTTCACAGAA+AGG - Chr4:85899616-85899635 None:intergenic 40.0%
GACTTGATCCCTCCAAAATT+CGG - Chr4:85899283-85899302 None:intergenic 40.0%
GTTCATCTGGTATACAGTTG+TGG - Chr4:85899556-85899575 None:intergenic 40.0%
TCTTGCAAAAAGGAAGCAAG+TGG - Chr4:85900541-85900560 None:intergenic 40.0%
TGCTTGTACACCATTCTCTT+CGG - Chr4:85900506-85900525 None:intergenic 40.0%
TGGTATACAGTTGTGGATCT+TGG - Chr4:85899549-85899568 None:intergenic 40.0%
! CGAGGTCTTTTTGCTAGATT+TGG - Chr4:85899813-85899832 None:intergenic 40.0%
! TCTGTTGGACAGTCTGTTTT+GGG + Chr4:85900974-85900993 MsG0480023489.01.T01:intron 40.0%
!! ATATTTTTACGCGATCACCC+TGG + Chr4:85899747-85899766 MsG0480023489.01.T01:intron 40.0%
!! TGCTTTGAGGCTTCTTAACA+TGG + Chr4:85900578-85900597 MsG0480023489.01.T01:CDS 40.0%
GATCAGTGACACATACTGCA+TGG + Chr4:85899851-85899870 MsG0480023489.01.T01:CDS 45.0%
GCAAAAAGGAAGCAAGTGGA+CGG - Chr4:85900537-85900556 None:intergenic 45.0%
GGGTTATCATACTAGGAAGC+TGG + Chr4:85900040-85900059 MsG0480023489.01.T01:intron 45.0%
! AAAAGCCGCTACCCGAATTT+TGG + Chr4:85899268-85899287 MsG0480023489.01.T01:CDS 45.0%
! CTCTGTTGGACAGTCTGTTT+TGG + Chr4:85900973-85900992 MsG0480023489.01.T01:intron 45.0%
!! TTACTAGGACTGCTGCTTTG+AGG + Chr4:85900565-85900584 MsG0480023489.01.T01:CDS 45.0%
AAGTCACTGGATGCCATCCA+CGG - Chr4:85899906-85899925 None:intergenic 50.0%
ACTCTGCTTGTATCAGCCAC+TGG - Chr4:85901032-85901051 None:intergenic 50.0%
TCCCTCCAAAATTCGGGTAG+CGG - Chr4:85899276-85899295 None:intergenic 50.0%
TCAGCAGGCTGCGCAAAGAA+AGG - Chr4:85899521-85899540 None:intergenic 55.0%
TGGATCTTGGACGTGTCAGC+AGG - Chr4:85899536-85899555 None:intergenic 55.0%
! AGCCGCTACCCGAATTTTGG+AGG + Chr4:85899271-85899290 MsG0480023489.01.T01:CDS 55.0%
! GCCGCTACCCGAATTTTGGA+GGG + Chr4:85899272-85899291 MsG0480023489.01.T01:CDS 55.0%
!! GCGCTCACGATCTCTGGAGT+TGG - Chr4:85899884-85899903 None:intergenic 60.0%
TCCACGGCGCTCACGATCTC+TGG - Chr4:85899890-85899909 None:intergenic 65.0%
! GAGATCGTGAGCGCCGTGGA+TGG + Chr4:85899890-85899909 MsG0480023489.01.T01:CDS 65.0%
! TCCAGAGATCGTGAGCGCCG+TGG + Chr4:85899886-85899905 MsG0480023489.01.T01:CDS 65.0%
Chromosome Type Strat End Strand Name
Chr4 gene 85899261 85901255 85899261 ID=MsG0480023489.01;Name=MsG0480023489.01
Chr4 mRNA 85899261 85901255 85899261 ID=MsG0480023489.01.T01;Parent=MsG0480023489.01;Name=MsG0480023489.01.T01;_AED=0.47;_eAED=0.48;_QI=0|1|0.8|1|0.5|0.6|5|246|137
Chr4 exon 85899261 85899305 85899261 ID=MsG0480023489.01.T01:exon:6359;Parent=MsG0480023489.01.T01
Chr4 exon 85899533 85899598 85899533 ID=MsG0480023489.01.T01:exon:6360;Parent=MsG0480023489.01.T01
Chr4 exon 85899820 85899969 85899820 ID=MsG0480023489.01.T01:exon:6361;Parent=MsG0480023489.01.T01
Chr4 exon 85900471 85900599 85900471 ID=MsG0480023489.01.T01:exon:6362;Parent=MsG0480023489.01.T01
Chr4 exon 85900986 85901255 85900986 ID=MsG0480023489.01.T01:exon:6363;Parent=MsG0480023489.01.T01
Chr4 CDS 85899261 85899305 85899261 ID=MsG0480023489.01.T01:cds;Parent=MsG0480023489.01.T01
Chr4 CDS 85899533 85899598 85899533 ID=MsG0480023489.01.T01:cds;Parent=MsG0480023489.01.T01
Chr4 CDS 85899820 85899969 85899820 ID=MsG0480023489.01.T01:cds;Parent=MsG0480023489.01.T01
Chr4 CDS 85900471 85900599 85900471 ID=MsG0480023489.01.T01:cds;Parent=MsG0480023489.01.T01
Chr4 CDS 85900986 85901009 85900986 ID=MsG0480023489.01.T01:cds;Parent=MsG0480023489.01.T01
Chr4 three_prime_UTR 85901010 85901255 85901010 ID=MsG0480023489.01.T01:three_prime_utr;Parent=MsG0480023489.01.T01
Gene Sequence

>MsG0480023489.01.T01

ATGCAGAAAAAGCCGCTACCCGAATTTTGGAGGGATCAAGTCATTCCTGCTGACACGTCCAAGATCCACAACTGTATACCAGATGAACACTATGTTCAAACATTGCTGGCTCAAAAAGACCTCGAAAAAGAACTAACACGAAGATCAGTGACACATACTGCATGGGATATTTCCAACTCCAGAGATCGTGAGCGCCGTGGATGGCATCCAGTGACTTATAAGTTCTCAGATGCTACTCCGATGCTTATTAAATTTATAAAGGAAATAGATAATATTTATTACGAGACTGAATACCGAAGAGAATGGTGTACAAGCAAGGGTAAACCGTCCACTTGCTTCCTTTTTGCAAGAAAGTTTACTAGGACTGCTGCTTTGAGGCTTCTTAACATGTCTGTTTTGGGAGATTTCAGTTAA

Protein sequence

>MsG0480023489.01.T01

MQKKPLPEFWRDQVIPADTSKIHNCIPDEHYVQTLLAQKDLEKELTRRSVTHTAWDISNSRDRERRGWHPVTYKFSDATPMLIKFIKEIDNIYYETEYRREWCTSKGKPSTCFLFARKFTRTAALRLLNMSVLGDFS*