AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280011299.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280011299.01.T01 MTR_2g101770 65.812 117 37 2 1 115 1 116 4.70e-44 142
MsG0280011299.01.T02 MTR_2g101770 76.119 67 16 0 1 67 50 116 2.43e-30 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280011299.01.T01 AT1G79850 50.000 108 49 3 10 115 15 119 7.20e-25 94.0
MsG0280011299.01.T02 AT1G79850 59.701 67 27 0 1 67 53 119 3.72e-22 85.1

Find 39 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAATACGTTTCTTGTATTT+AGG 0.176759 2:+82136442 None:intergenic
CCTGTTCCTGCTAGGAATTC+TGG 0.226525 2:-82136308 MsG0280011299.01.T01:CDS
TGTTTCATAGCTTTGATTGA+TGG 0.340078 2:+82136537 None:intergenic
GGTAAGGCTGATAATTCTTC+TGG 0.342682 2:-82136287 MsG0280011299.01.T01:CDS
AAAAGTTTATTCTTACTAAT+AGG 0.349225 2:+82136340 None:intergenic
CTAAATACAAGAAACGTATT+AGG 0.362043 2:-82136441 MsG0280011299.01.T01:CDS
TTTGATTGATGGAAGGGATT+GGG 0.366091 2:+82136548 None:intergenic
TTGATGGAAGGGATTGGGGC+TGG 0.379607 2:+82136553 None:intergenic
TGATGGAAGGGATTGGGGCT+GGG 0.417770 2:+82136554 None:intergenic
CGCCATTGTCCGTTGAGAAA+TGG 0.423739 2:+82136622 None:intergenic
TTGCTGTTCCTGTTCCTGCT+AGG 0.444869 2:-82136316 MsG0280011299.01.T01:CDS
CTTTGATTGATGGAAGGGAT+TGG 0.447339 2:+82136547 None:intergenic
AGAAGAACAGCCTCGGACTC+AGG 0.451888 2:-82136234 MsG0280011299.01.T01:CDS
CCAGAATTCCTAGCAGGAAC+AGG 0.463154 2:+82136308 None:intergenic
TAGGATGAAGAAGAAGTATC+AGG 0.470403 2:-82136422 MsG0280011299.01.T01:CDS
CGTTTCTTGTATTTAGGATG+AGG 0.484431 2:+82136448 None:intergenic
TTGATTGATGGAAGGGATTG+GGG 0.489144 2:+82136549 None:intergenic
GGATAGAGAGAGTGTGGATG+TGG 0.489261 2:+82136575 None:intergenic
CATAGCTTTGATTGATGGAA+GGG 0.496999 2:+82136542 None:intergenic
CCTCGACATTCCGCTTCAAT+CGG 0.508100 2:-82136261 MsG0280011299.01.T01:CDS
TCCTGCTAGGAATTCTGGTA+AGG 0.524466 2:-82136303 MsG0280011299.01.T01:CDS
TCTTCTTGCTCCGATTGAAG+CGG 0.531289 2:+82136251 None:intergenic
TCATAGCTTTGATTGATGGA+AGG 0.545842 2:+82136541 None:intergenic
GGGCTGGGATAGAGAGAGTG+TGG 0.548257 2:+82136569 None:intergenic
GCCTTACCAGAATTCCTAGC+AGG 0.562008 2:+82136302 None:intergenic
AAATGGTGTTGAGAGCGTGC+TGG 0.564865 2:+82136639 None:intergenic
CACCATTTCTCAACGGACAA+TGG 0.572277 2:-82136624 MsG0280011299.01.T01:CDS
AATGGTGTTGAGAGCGTGCT+GGG 0.576801 2:+82136640 None:intergenic
CAACGACAAAACCGTGTCTG+TGG 0.577696 2:-82136487 MsG0280011299.01.T01:CDS
CGGAGCAAGAAGAACAGCCT+CGG 0.582708 2:-82136241 MsG0280011299.01.T01:CDS
ACGAGTTACTTCCACAGACA+CGG 0.591262 2:+82136476 None:intergenic
CAATCAAAGCTATGAAACAA+TGG 0.598950 2:-82136533 MsG0280011299.01.T01:CDS
CTCTCAACACCATTTCTCAA+CGG 0.607510 2:-82136631 MsG0280011299.01.T01:CDS
CAAAACTAAGCCTGAGTCCG+AGG 0.612564 2:+82136224 None:intergenic
CAAAGCTATGAAACAATGGA+AGG 0.617092 2:-82136529 MsG0280011299.01.T01:CDS
GGGCTTTGAGAGACGAGTGA+GGG 0.632183 2:+82136596 None:intergenic
TGGGCTTTGAGAGACGAGTG+AGG 0.637946 2:+82136595 None:intergenic
CCGATTGAAGCGGAATGTCG+AGG 0.647031 2:+82136261 None:intergenic
GATAGAGAGAGTGTGGATGT+GGG 0.697666 2:+82136576 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGTTTATTCTTACTAAT+AGG + Chr2:82136525-82136544 None:intergenic 15.0%
! CTAAATACAAGAAACGTATT+AGG - Chr2:82136421-82136440 MsG0280011299.01.T01:CDS 25.0%
! CTAATACGTTTCTTGTATTT+AGG + Chr2:82136423-82136442 None:intergenic 25.0%
CAATCAAAGCTATGAAACAA+TGG - Chr2:82136329-82136348 MsG0280011299.01.T01:CDS 30.0%
!! TGTTTCATAGCTTTGATTGA+TGG + Chr2:82136328-82136347 None:intergenic 30.0%
CAAAGCTATGAAACAATGGA+AGG - Chr2:82136333-82136352 MsG0280011299.01.T01:CDS 35.0%
TTTGATTGATGGAAGGGATT+GGG + Chr2:82136317-82136336 None:intergenic 35.0%
! CCTGAAAACGTTTTCAAAGT+TGG - Chr2:82136471-82136490 MsG0280011299.01.T01:CDS 35.0%
! CGTTTCTTGTATTTAGGATG+AGG + Chr2:82136417-82136436 None:intergenic 35.0%
!! CATAGCTTTGATTGATGGAA+GGG + Chr2:82136323-82136342 None:intergenic 35.0%
!! CCAACTTTGAAAACGTTTTC+AGG + Chr2:82136474-82136493 None:intergenic 35.0%
!! TAGGATGAAGAAGAAGTATC+AGG - Chr2:82136440-82136459 MsG0280011299.01.T01:CDS 35.0%
!! TCATAGCTTTGATTGATGGA+AGG + Chr2:82136324-82136343 None:intergenic 35.0%
CTCTCAACACCATTTCTCAA+CGG - Chr2:82136231-82136250 MsG0280011299.01.T01:CDS 40.0%
CTTTGATTGATGGAAGGGAT+TGG + Chr2:82136318-82136337 None:intergenic 40.0%
GGTAAGGCTGATAATTCTTC+TGG - Chr2:82136575-82136594 MsG0280011299.01.T01:CDS 40.0%
TTGATTGATGGAAGGGATTG+GGG + Chr2:82136316-82136335 None:intergenic 40.0%
ACGAGTTACTTCCACAGACA+CGG + Chr2:82136389-82136408 None:intergenic 45.0%
CACCATTTCTCAACGGACAA+TGG - Chr2:82136238-82136257 MsG0280011299.01.T01:CDS 45.0%
TCCTGCTAGGAATTCTGGTA+AGG - Chr2:82136559-82136578 MsG0280011299.01.T01:CDS 45.0%
TCTTCTTGCTCCGATTGAAG+CGG + Chr2:82136614-82136633 None:intergenic 45.0%
! GATAGAGAGAGTGTGGATGT+GGG + Chr2:82136289-82136308 None:intergenic 45.0%
!! AGACACGGTTTTGTCGTTGT+GGG + Chr2:82136374-82136393 None:intergenic 45.0%
CAAAACTAAGCCTGAGTCCG+AGG + Chr2:82136641-82136660 None:intergenic 50.0%
CAACGACAAAACCGTGTCTG+TGG - Chr2:82136375-82136394 MsG0280011299.01.T01:CDS 50.0%
CCAGAATTCCTAGCAGGAAC+AGG + Chr2:82136557-82136576 None:intergenic 50.0%
CCTCGACATTCCGCTTCAAT+CGG - Chr2:82136601-82136620 MsG0280011299.01.T01:CDS 50.0%
CCTGTTCCTGCTAGGAATTC+TGG - Chr2:82136554-82136573 MsG0280011299.01.T01:CDS 50.0%
CGCCATTGTCCGTTGAGAAA+TGG + Chr2:82136243-82136262 None:intergenic 50.0%
GCCTTACCAGAATTCCTAGC+AGG + Chr2:82136563-82136582 None:intergenic 50.0%
! AAATGGTGTTGAGAGCGTGC+TGG + Chr2:82136226-82136245 None:intergenic 50.0%
! AATGGTGTTGAGAGCGTGCT+GGG + Chr2:82136225-82136244 None:intergenic 50.0%
! GGATAGAGAGAGTGTGGATG+TGG + Chr2:82136290-82136309 None:intergenic 50.0%
! TTGCTGTTCCTGTTCCTGCT+AGG - Chr2:82136546-82136565 MsG0280011299.01.T01:CDS 50.0%
!! CAGACACGGTTTTGTCGTTG+TGG + Chr2:82136375-82136394 None:intergenic 50.0%
AGAAGAACAGCCTCGGACTC+AGG - Chr2:82136628-82136647 MsG0280011299.01.T01:CDS 55.0%
CCGATTGAAGCGGAATGTCG+AGG + Chr2:82136604-82136623 None:intergenic 55.0%
CGGAGCAAGAAGAACAGCCT+CGG - Chr2:82136621-82136640 MsG0280011299.01.T01:CDS 55.0%
TGATGGAAGGGATTGGGGCT+GGG + Chr2:82136311-82136330 None:intergenic 55.0%
TTGATGGAAGGGATTGGGGC+TGG + Chr2:82136312-82136331 None:intergenic 55.0%
!! GGGCTTTGAGAGACGAGTGA+GGG + Chr2:82136269-82136288 None:intergenic 55.0%
!! TGGGCTTTGAGAGACGAGTG+AGG + Chr2:82136270-82136289 None:intergenic 55.0%
GGGCTGGGATAGAGAGAGTG+TGG + Chr2:82136296-82136315 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 82136204 82136680 82136204 ID=MsG0280011299.01;Name=MsG0280011299.01
Chr2 mRNA 82136204 82136680 82136204 ID=MsG0280011299.01.T01;Parent=MsG0280011299.01;Name=MsG0280011299.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|158
Chr2 exon 82136204 82136680 82136204 ID=MsG0280011299.01.T01:exon:12403;Parent=MsG0280011299.01.T01
Chr2 CDS 82136204 82136680 82136204 ID=MsG0280011299.01.T01:cds;Parent=MsG0280011299.01.T01
Chr2 mRNA 82136204 82136536 82136204 ID=MsG0280011299.01.T02;Parent=MsG0280011299.01;Name=MsG0280011299.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|110
Chr2 exon 82136204 82136536 82136204 ID=MsG0280011299.01.T02:exon:12404;Parent=MsG0280011299.01.T02
Chr2 CDS 82136204 82136536 82136204 ID=MsG0280011299.01.T02:cds;Parent=MsG0280011299.01.T02
Chr2 mRNA 82136317 82136388 82136317 ID=MsG0280011299.01.T03;Parent=MsG0280011299.01;Name=MsG0280011299.01.T03;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|23
Chr2 exon 82136317 82136388 82136317 ID=MsG0280011299.01.T03:exon:12405;Parent=MsG0280011299.01.T03
Chr2 CDS 82136317 82136388 82136317 ID=MsG0280011299.01.T03:cds;Parent=MsG0280011299.01.T03
Gene Sequence

>MsG0280011299.01.T01

ATGTGGCTTCTGCAACTTCCCAGCACGCTCTCAACACCATTTCTCAACGGACAATGGCGTCGCCCTCACTCGTCTCTCAAAGCCCACATCCACACTCTCTCTATCCCAGCCCCAATCCCTTCCATCAATCAAAGCTATGAAACAATGGAAGGAAAAGTTTGTGTGTGCCCACAACGACAAAACCGTGTCTGTGGAAGTAACTCGTTAGCACCTCATCCTAAATACAAGAAACGTATTAGGATGAAGAAGAAGTATCAGGCTCATGATCCTGAAAACGTTTTCAAAGTTGGTGATGTTGTTCAGCTTTGTAAAATTAGACCTATTAGTAAGAATAAACTTTTCTTGCTGTTCCTGTTCCTGCTAGGAATTCTGGTAAGGCTGATAATTCTTCTGGTGACCTCGACATTCCGCTTCAATCGGAGCAAGAAGAACAGCCTCGGACTCAGGCTTAGTTTTGCAGTCTCTCTTACTCTTTAA

>MsG0280011299.01.T02

ATGGAAGGAAAAGTTTGTGTGTGCCCACAACGACAAAACCGTGTCTGTGGAAGTAACTCGTTAGCACCTCATCCTAAATACAAGAAACGTATTAGGATGAAGAAGAAGTATCAGGCTCATGATCCTGAAAACGTTTTCAAAGTTGGTGATGTTGTTCAGCTTTGTAAAATTAGACCTATTAGTAAGAATAAACTTTTCTTGCTGTTCCTGTTCCTGCTAGGAATTCTGGTAAGGCTGATAATTCTTCTGGTGACCTCGACATTCCGCTTCAATCGGAGCAAGAAGAACAGCCTCGGACTCAGGCTTAGTTTTGCAGTCTCTCTTACTCTTTAA

>MsG0280011299.01.T03

ATGTTGTTCAGCTTTGTAAAATTAGACCTATTAGTAAGAATAAACTTTTCTTGCTGTTCCTGTTCCTGCTAG

Protein sequence

>MsG0280011299.01.T01

MWLLQLPSTLSTPFLNGQWRRPHSSLKAHIHTLSIPAPIPSINQSYETMEGKVCVCPQRQNRVCGSNSLAPHPKYKKRIRMKKKYQAHDPENVFKVGDVVQLCKIRPISKNKLFLLFLFLLGILVRLIILLVTSTFRFNRSKKNSLGLRLSFAVSLTL*

>MsG0280011299.01.T02

MEGKVCVCPQRQNRVCGSNSLAPHPKYKKRIRMKKKYQAHDPENVFKVGDVVQLCKIRPISKNKLFLLFLFLLGILVRLIILLVTSTFRFNRSKKNSLGLRLSFAVSLTL*

>MsG0280011299.01.T03

MLFSFVKLDLLVRINFSCCSCSC*