AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014053.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014053.01.T01 MTR_4g050863 60.891 202 37 5 1 163 38 236 3.47e-54 179
MsG0380014053.01.T01 MTR_4g034770 83.333 66 7 1 223 284 1 66 2.47e-29 116
MsG0380014053.01.T01 MTR_3g080300 93.333 45 3 0 223 267 1 45 4.09e-24 92.8
MsG0380014053.01.T01 MTR_4g071480 78.462 65 8 1 38 102 1 59 6.32e-23 94.0
MsG0380014053.01.T01 MTR_3g077610 91.111 45 4 0 1 45 38 82 2.31e-21 87.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014053.01.T01 ATCG00500 36.607 336 119 8 1 282 8 303 7.57e-47 164

Find 41 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCGATTTCACTACTATTT+TGG 0.110779 3:+48740196 None:intergenic
TCAATTCAATGATGTTTAAT+AGG 0.172116 3:-48740740 None:intergenic
ATCATTGCTATCATCGAAAA+TGG 0.246021 3:+48740401 None:intergenic
CTAAAATGTAACTAGCCTTT+TGG 0.259078 3:+48740292 None:intergenic
GATATTATTCCAATTATATA+TGG 0.263222 3:+48740476 None:intergenic
TCCATATCAGTTAAAATAGA+TGG 0.266329 3:+48740639 None:intergenic
ATAGTTATTCCATATATAAT+TGG 0.282228 3:-48740485 MsG0380014053.01.T01:CDS
CAATTCAATGATGTTTAATA+GGG 0.284928 3:-48740739 None:intergenic
TCGATTATCAAAGATGGAAT+AGG 0.335262 3:-48739860 None:intergenic
ATCATTAATAGTTGTATTGA+AGG 0.345443 3:-48740456 MsG0380014053.01.T01:CDS
AGTAAATCAATAGACAGTTT+TGG 0.359068 3:-48740693 MsG0380014053.01.T01:CDS
GTCTTCCGAATTAAATTCAA+TGG 0.370040 3:+48739948 None:intergenic
ATGATTATTTAGTAGATGTC+AGG 0.378156 3:-48740596 MsG0380014053.01.T01:CDS
GGTTATCTTCGTTCTGAAAT+CGG 0.381009 3:-48740435 MsG0380014053.01.T01:CDS
TTAATAGGGGTTTAGAATAC+AGG 0.397527 3:-48740725 MsG0380014053.01.T01:CDS
GGATCCCATTGAATTTAATT+CGG 0.414293 3:-48739953 MsG0380014053.01.T01:CDS
ACAAATACAATGATAGTGAT+TGG 0.419651 3:-48740356 MsG0380014053.01.T01:CDS
TAGGAAATTCCGTATGTTCA+TGG 0.422353 3:+48740539 None:intergenic
GTTGCCTGCGACAATTGTTA+TGG 0.448985 3:-48740120 MsG0380014053.01.T01:CDS
TCTTCCGAATTAAATTCAAT+GGG 0.472920 3:+48739949 None:intergenic
TATTTAGTAGATGTCAGGGT+TGG 0.484894 3:-48740591 MsG0380014053.01.T01:CDS
TCCAGGTACTTGGAATCCTA+TGG 0.498677 3:-48739995 MsG0380014053.01.T01:CDS
CAAATACAATGATAGTGATT+GGG 0.514193 3:-48740355 MsG0380014053.01.T01:CDS
TCCATAGGATTCCAAGTACC+TGG 0.523036 3:+48739994 None:intergenic
TAGTTATAGCCATGAACATA+CGG 0.548429 3:-48740548 MsG0380014053.01.T01:CDS
TAGTGGCAATGATAGTGATA+AGG 0.552635 3:-48740220 MsG0380014053.01.T01:CDS
TGATTATTTAGTAGATGTCA+GGG 0.554876 3:-48740595 MsG0380014053.01.T01:CDS
CCATATCAGTTAAAATAGAT+GGG 0.566449 3:+48740640 None:intergenic
GAGACCATGTCTTCATCCAT+AGG 0.580226 3:+48739979 None:intergenic
TGATTATGATAAGCTCCAAA+AGG 0.584378 3:-48740307 MsG0380014053.01.T01:CDS
TCGAAAAGAGTCGTTACAAG+AGG 0.588356 3:+48739879 None:intergenic
AATTCAATGATGTTTAATAG+GGG 0.588438 3:-48740738 None:intergenic
GATGATAGTGGCAATGATAG+TGG 0.588786 3:-48740237 MsG0380014053.01.T01:CDS
GTTTCCATAACAATTGTCGC+AGG 0.592295 3:+48740116 None:intergenic
GAATCCTATGGATGAAGACA+TGG 0.596325 3:-48739983 MsG0380014053.01.T01:CDS
AGTGATTGGGACAATGATAG+TGG 0.597015 3:-48740342 MsG0380014053.01.T01:CDS
ATGAATATTTGTGAATACTG+TGG 0.601177 3:-48740066 MsG0380014053.01.T01:CDS
GGATGAAGACATGGTCTCTG+TGG 0.626356 3:-48739974 MsG0380014053.01.T01:CDS
AGGGGTTTAGAATACAGGTG+TGG 0.652609 3:-48740720 MsG0380014053.01.T01:CDS
ACTGATAGTGATGATGATAG+TGG 0.658064 3:-48740249 MsG0380014053.01.T01:CDS
TAGTATAATAACTATCACAA+AGG 0.691526 3:-48740169 MsG0380014053.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTATTCCATATATAAT+TGG - Chr3:48740108-48740127 MsG0380014053.01.T01:CDS 15.0%
!! GATATTATTCCAATTATATA+TGG + Chr3:48740120-48740139 None:intergenic 15.0%
!!! TGATAAAACTTTTTTAGTTA+GGG - Chr3:48740079-48740098 MsG0380014053.01.T01:CDS 15.0%
!! ATCATTAATAGTTGTATTGA+AGG - Chr3:48740137-48740156 MsG0380014053.01.T01:CDS 20.0%
!! TAGTATAATAACTATCACAA+AGG - Chr3:48740424-48740443 MsG0380014053.01.T01:CDS 20.0%
!!! CTAAAAAAGTTTTATCAGAT+AGG + Chr3:48740076-48740095 None:intergenic 20.0%
!!! CTGATAAAACTTTTTTAGTT+AGG - Chr3:48740078-48740097 MsG0380014053.01.T01:CDS 20.0%
!!! TTTACACTGTTATTTTCAAT+AGG + Chr3:48739927-48739946 None:intergenic 20.0%
! ATGAATATTTGTGAATACTG+TGG - Chr3:48740527-48740546 MsG0380014053.01.T01:CDS 25.0%
! ATGATTATTTAGTAGATGTC+AGG - Chr3:48739997-48740016 MsG0380014053.01.T01:CDS 25.0%
! CCATATCAGTTAAAATAGAT+GGG + Chr3:48739956-48739975 None:intergenic 25.0%
! TCCATATCAGTTAAAATAGA+TGG + Chr3:48739957-48739976 None:intergenic 25.0%
! TCTTCCGAATTAAATTCAAT+GGG + Chr3:48740647-48740666 None:intergenic 25.0%
! TGATTATTTAGTAGATGTCA+GGG - Chr3:48739998-48740017 MsG0380014053.01.T01:CDS 25.0%
!! AAATGATTTTTCGCATTTGT+GGG - Chr3:48740451-48740470 MsG0380014053.01.T01:CDS 25.0%
!! ACAAATACAATGATAGTGAT+TGG - Chr3:48740237-48740256 MsG0380014053.01.T01:CDS 25.0%
!! AGTAAATCAATAGACAGTTT+TGG - Chr3:48739900-48739919 MsG0380014053.01.T01:CDS 25.0%
!! CAAATACAATGATAGTGATT+GGG - Chr3:48740238-48740257 MsG0380014053.01.T01:CDS 25.0%
ATCATTGCTATCATCGAAAA+TGG + Chr3:48740195-48740214 None:intergenic 30.0%
GGATCCCATTGAATTTAATT+CGG - Chr3:48740640-48740659 MsG0380014053.01.T01:CDS 30.0%
GTCTTCCGAATTAAATTCAA+TGG + Chr3:48740648-48740667 None:intergenic 30.0%
TAGTTATAGCCATGAACATA+CGG - Chr3:48740045-48740064 MsG0380014053.01.T01:CDS 30.0%
TGATTATGATAAGCTCCAAA+AGG - Chr3:48740286-48740305 MsG0380014053.01.T01:CDS 30.0%
! CAAATGATTTTTCGCATTTG+TGG - Chr3:48740450-48740469 MsG0380014053.01.T01:CDS 30.0%
! CTCTTTTCGATTATCAAAGA+TGG - Chr3:48740727-48740746 MsG0380014053.01.T01:CDS 30.0%
! GAATCAAGACTATTTTCAGA+AGG + Chr3:48740674-48740693 None:intergenic 30.0%
! TCTCGATTTCACTACTATTT+TGG + Chr3:48740400-48740419 None:intergenic 30.0%
! TTAATAGGGGTTTAGAATAC+AGG - Chr3:48739868-48739887 MsG0380014053.01.T01:CDS 30.0%
!!! CCCATCTATTTTAACTGATA+TGG - Chr3:48739953-48739972 MsG0380014053.01.T01:CDS 30.0%
!!! CTAAAATGTAACTAGCCTTT+TGG + Chr3:48740304-48740323 None:intergenic 30.0%
TAGGAAATTCCGTATGTTCA+TGG + Chr3:48740057-48740076 None:intergenic 35.0%
TATTTAGTAGATGTCAGGGT+TGG - Chr3:48740002-48740021 MsG0380014053.01.T01:CDS 35.0%
! ACTGATAGTGATGATGATAG+TGG - Chr3:48740344-48740363 MsG0380014053.01.T01:CDS 35.0%
! TAGTGGCAATGATAGTGATA+AGG - Chr3:48740373-48740392 MsG0380014053.01.T01:CDS 35.0%
!! ATCGAACTTTTGATTGATCC+AGG - Chr3:48740581-48740600 MsG0380014053.01.T01:CDS 35.0%
!! GGTTATCTTCGTTCTGAAAT+CGG - Chr3:48740158-48740177 MsG0380014053.01.T01:CDS 35.0%
!! TCAGTGTCACTATCATTTTC+CGG + Chr3:48740329-48740348 None:intergenic 35.0%
!! TTTTGATTGATCCAGGTACT+TGG - Chr3:48740588-48740607 MsG0380014053.01.T01:CDS 35.0%
!!! GGCTAGTTACATTTTAGAAC+CGG - Chr3:48740307-48740326 MsG0380014053.01.T01:CDS 35.0%
AGTGATTGGGACAATGATAG+TGG - Chr3:48740251-48740270 MsG0380014053.01.T01:CDS 40.0%
GAATCCTATGGATGAAGACA+TGG - Chr3:48740610-48740629 MsG0380014053.01.T01:CDS 40.0%
GTTTCCATAACAATTGTCGC+AGG + Chr3:48740480-48740499 None:intergenic 40.0%
TCGAAAAGAGTCGTTACAAG+AGG + Chr3:48740717-48740736 None:intergenic 40.0%
!! GATGATAGTGGCAATGATAG+TGG - Chr3:48740356-48740375 MsG0380014053.01.T01:CDS 40.0%
GAGACCATGTCTTCATCCAT+AGG + Chr3:48740617-48740636 None:intergenic 45.0%
GTTGCCTGCGACAATTGTTA+TGG - Chr3:48740473-48740492 MsG0380014053.01.T01:CDS 45.0%
TCCAGGTACTTGGAATCCTA+TGG - Chr3:48740598-48740617 MsG0380014053.01.T01:CDS 45.0%
TCCATAGGATTCCAAGTACC+TGG + Chr3:48740602-48740621 None:intergenic 45.0%
! AGGGGTTTAGAATACAGGTG+TGG - Chr3:48739873-48739892 MsG0380014053.01.T01:CDS 45.0%
GGATGAAGACATGGTCTCTG+TGG - Chr3:48740619-48740638 MsG0380014053.01.T01:CDS 50.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48739861 48740754 48739861 ID=MsG0380014053.01;Name=MsG0380014053.01
Chr3 mRNA 48739861 48740754 48739861 ID=MsG0380014053.01.T01;Parent=MsG0380014053.01;Name=MsG0380014053.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|1|1|0|297
Chr3 exon 48739861 48740754 48739861 ID=MsG0380014053.01.T01:exon:9272;Parent=MsG0380014053.01.T01
Chr3 CDS 48739861 48740754 48739861 ID=MsG0380014053.01.T01:cds;Parent=MsG0380014053.01.T01
Gene Sequence

>MsG0380014053.01.T01

ATGATGTTTAATAGGGGTTTAGAATACAGGTGTGGTTTAAGTAAATCAATAGACAGTTTTGGTCCTATTGAAAATAACAGTGTAAACGAAGACCCATCTATTTTAACTGATATGGATAATACTATTCATAGTGATTATGATTATTTAGTAGATGTCAGGGTTGGAAAAACAATAGTGAGAATTCTAGTTATAGCCATGAACATACGGAATTTCCTATCTGATAAAACTTTTTTAGTTAGGGATAGTAATAGTTATTCCATATATAATTGGAATAATATCATTAATAGTTGTATTGAAGGTTATCTTCGTTCTGAAATCGGTATTGATAATTCCATTTTCGATGATAGCAATGATAGTGACAGTGACAATGACAGTGACAAATACAATGATAGTGATTGGGACAATGATAGTGGCAATGATAGTGATGATTATGATAAGCTCCAAAAGGCTAGTTACATTTTAGAACCGGAAAATGATAGTGACACTGATAGTGATGATGATAGTGGCAATGATAGTGGCAATGATAGTGATAAGGTCCAAAATAGTAGTGAAATCGAGAGTACTAGTATAATAACTATCACAAAGGATACAAATGATTTTTCGCATTTGTGGGTTGCCTGCGACAATTGTTATGGAAACAATTATAAGAGATTTTTTAAATCAAAAATGAATATTTGTGAATACTGTGGATGTCATTTGAAAATGAGCAGTTCAGATCGAATCGAACTTTTGATTGATCCAGGTACTTGGAATCCTATGGATGAAGACATGGTCTCTGTGGATCCCATTGAATTTAATTCGGAAGACGAACCTTCTGAAAATAGTCTTGATTCTTCTGAAAATAGTCTTGATTCCTCTTGTAACGACTCTTTTCGATTATCAAAGATGGAATAG

Protein sequence

>MsG0380014053.01.T01

MMFNRGLEYRCGLSKSIDSFGPIENNSVNEDPSILTDMDNTIHSDYDYLVDVRVGKTIVRILVIAMNIRNFLSDKTFLVRDSNSYSIYNWNNIINSCIEGYLRSEIGIDNSIFDDSNDSDSDNDSDKYNDSDWDNDSGNDSDDYDKLQKASYILEPENDSDTDSDDDSGNDSGNDSDKVQNSSEIESTSIITITKDTNDFSHLWVACDNCYGNNYKRFFKSKMNICEYCGCHLKMSSSDRIELLIDPGTWNPMDEDMVSVDPIEFNSEDEPSENSLDSSENSLDSSCNDSFRLSKME*