AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014023.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014023.01.T01 MTR_0187s0090 74.286 105 27 0 35 139 17 121 2.30e-52 164
MsG0380014023.01.T01 MTR_1g084890 92.593 81 6 0 59 139 63 143 3.34e-51 162
MsG0380014023.01.T01 MTR_3g035600 95.062 81 4 0 59 139 1281 1361 2.95e-48 167
MsG0380014023.01.T01 MTR_3g035600 58.537 82 34 0 58 139 549 630 1.36e-28 111
MsG0380014023.01.T01 MTR_0002s0580 95.062 81 4 0 59 139 1216 1296 3.75e-48 167
MsG0380014023.01.T01 MTR_0002s0580 58.537 82 34 0 58 139 525 606 2.99e-28 110
MsG0380014023.01.T01 MTR_4g010980 96.667 60 2 0 1 60 37 96 5.82e-35 119
MsG0380014023.01.T01 MTR_6g055020 96.667 60 2 0 1 60 40 99 1.77e-33 119
MsG0380014023.01.T01 MTR_7g117920 96.667 60 2 0 1 60 40 99 3.14e-33 120
MsG0380014023.01.T01 MTR_7g033765 96.667 60 2 0 1 60 40 99 7.20e-33 122
MsG0380014023.01.T01 MTR_4g451275 96.667 60 2 0 1 60 40 99 2.08e-32 120
MsG0380014023.01.T01 MTR_7g021780 96.667 60 2 0 1 60 40 99 4.38e-32 120
MsG0380014023.01.T01 MTR_7g033755 93.333 60 4 0 1 60 1 60 4.45e-32 119
MsG0380014023.01.T01 MTR_3g035730 95.000 60 3 0 1 60 40 99 7.55e-32 119
MsG0380014023.01.T01 MTR_7g051470 94.000 50 3 0 59 108 24 73 1.65e-27 98.6
MsG0380014023.01.T01 MTR_0002s0650 83.333 60 10 0 1 60 40 99 3.15e-27 107
MsG0380014023.01.T01 MTR_8g020540 80.000 55 11 0 74 128 17 71 2.67e-26 95.5
MsG0380014023.01.T01 MTR_7g070670 95.556 45 2 0 1 45 85 129 1.66e-23 90.1
MsG0380014023.01.T01 MTR_4g051177 48.611 72 32 2 58 129 533 599 1.37e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014023.01.T01 ATCG00340 95.062 81 4 0 59 139 512 592 1.41e-48 167
MsG0380014023.01.T01 ATCG00480 88.333 60 7 0 1 60 40 99 8.32e-31 116
MsG0380014023.01.T01 ATCG00350 58.537 82 34 0 58 139 525 606 1.93e-28 110

Find 34 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGAAGTACAGCAATTATT+AGG 0.280859 3:-48675700 MsG0380014023.01.T01:CDS
CAAGTTAATGCCGGATAAAA+AGG 0.286351 3:-48675098 MsG0380014023.01.T01:CDS
AATAGGCCCTGGAGACTTCT+TGG 0.291103 3:-48675197 MsG0380014023.01.T01:intron
ACTACATTGATCTTAGTAAA+AGG 0.318422 3:-48675142 MsG0380014023.01.T01:CDS
AGGTGGTACTTGTGATATTT+CGG 0.337233 3:-48675038 MsG0380014023.01.T01:CDS
GTTCATCATGCTATTGCTCT+TGG 0.356168 3:-48675175 MsG0380014023.01.T01:CDS
ATTGGAAGCACATTACATTA+TGG 0.362426 3:-48674947 MsG0380014023.01.T01:CDS
GATCTTAGTAAAAGGTGCTT+TGG 0.374490 3:-48675134 MsG0380014023.01.T01:CDS
TACTTGTGATATTTCGGCTT+GGG 0.388402 3:-48675032 MsG0380014023.01.T01:CDS
TTCTGGATGTTAAATACCAT+TGG 0.434396 3:-48674989 MsG0380014023.01.T01:CDS
CCTTGCGATGGTCCGGGACG+AGG 0.437446 3:-48675058 MsG0380014023.01.T01:CDS
TACAACGCTCTGATAGTTCA+AGG 0.440441 3:-48675757 MsG0380014023.01.T01:CDS
ATCAGAGCGTTGTAAATATT+AGG 0.471609 3:+48675766 None:intergenic
GAAGCACATTACATTATGGC+AGG 0.483523 3:-48674943 MsG0380014023.01.T01:CDS
TGATGAACCAAGAAGTCTCC+AGG 0.488702 3:+48675190 None:intergenic
GTACTTGTGATATTTCGGCT+TGG 0.507122 3:-48675033 MsG0380014023.01.T01:CDS
GGATGTTAAATACCATTGGA+TGG 0.537926 3:-48674985 MsG0380014023.01.T01:CDS
AGATGGTCTAAAGAGAGGAA+TGG 0.562943 3:-48675641 MsG0380014023.01.T01:CDS
ATTGATCGAAACTTTAGCAT+GGG 0.580772 3:-48674713 MsG0380014023.01.T01:CDS
AATTGATCGAAACTTTAGCA+TGG 0.602118 3:-48674714 MsG0380014023.01.T01:CDS
GTTCAAGGTCGAGATACTGT+TGG 0.608652 3:-48675742 MsG0380014023.01.T01:CDS
TCACAAGTACCACCTCGTCC+CGG 0.616107 3:+48675046 None:intergenic
CCTCGTCCCGGACCATCGCA+AGG 0.619085 3:+48675058 None:intergenic
ACGCGGTTCCAAGTTAATGC+CGG 0.621292 3:-48675107 MsG0380014023.01.T01:CDS
TGCGATGGTCCGGGACGAGG+TGG 0.624370 3:-48675055 MsG0380014023.01.T01:CDS
GGAATGGATGTGATTGACAC+GGG 0.632746 3:-48675625 MsG0380014023.01.T01:CDS
AGGAATGGATGTGATTGACA+CGG 0.636823 3:-48675626 MsG0380014023.01.T01:CDS
CCATCGAATCAAATTCGCCA+TGG 0.637092 3:+48674676 None:intergenic
GGGCTCATGAACGCACACCA+TGG 0.639994 3:-48674693 MsG0380014023.01.T01:CDS
GCTACAGATGGTCTAAAGAG+AGG 0.640370 3:-48675646 MsG0380014023.01.T01:CDS
AAGCACATTACATTATGGCA+GGG 0.643333 3:-48674942 MsG0380014023.01.T01:intron
GTAGCTATGAGTGCTACAGA+TGG 0.664604 3:-48675658 MsG0380014023.01.T01:CDS
GATGAACCAAGAAGTCTCCA+GGG 0.675300 3:+48675191 None:intergenic
AAAGGTGCTTTGGATGCACG+CGG 0.702966 3:-48675124 MsG0380014023.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAGGTTCTTAATTAAAA+CGG + Chr3:48675079-48675098 None:intergenic 15.0%
!! AATTCTCTATTCTTAACAAT+AGG - Chr3:48675239-48675258 MsG0380014023.01.T01:intron 20.0%
!! ATAAACTATTCATACCAAAA+GGG + Chr3:48675633-48675652 None:intergenic 20.0%
!! ATTTGTATCTAACTGTATAA+AGG + Chr3:48674981-48675000 None:intergenic 20.0%
!! CTTTAATTCTGTTTCAAAAA+TGG + Chr3:48675007-48675026 None:intergenic 20.0%
! AATAAAAAGTAACCATCCAA+TGG + Chr3:48675483-48675502 None:intergenic 25.0%
! AATTCTTCACAACTTATCAA+CGG - Chr3:48675601-48675620 MsG0380014023.01.T01:intron 25.0%
! ACTACATTGATCTTAGTAAA+AGG - Chr3:48675311-48675330 MsG0380014023.01.T01:intron 25.0%
! GATAAACTATTCATACCAAA+AGG + Chr3:48675634-48675653 None:intergenic 25.0%
! GATTTATGTTCTTAATCTCA+TGG - Chr3:48675700-48675719 MsG0380014023.01.T01:CDS 25.0%
! TATGAATAGTTTATCAGTCT+GGG - Chr3:48675639-48675658 MsG0380014023.01.T01:CDS 25.0%
!! TAACCAAAATCCTTTTTATC+CGG + Chr3:48675368-48675387 None:intergenic 25.0%
!! TTCTTATTTGACATCTTGTT+GGG - Chr3:48675670-48675689 MsG0380014023.01.T01:CDS 25.0%
!!! ATTGGATGGTTACTTTTTAT+TGG - Chr3:48675482-48675501 MsG0380014023.01.T01:intron 25.0%
AATTGATCGAAACTTTAGCA+TGG - Chr3:48675739-48675758 MsG0380014023.01.T01:CDS 30.0%
ATTGATCGAAACTTTAGCAT+GGG - Chr3:48675740-48675759 MsG0380014023.01.T01:CDS 30.0%
CTACAGGACCTAAAATTAAT+AGG + Chr3:48674918-48674937 None:intergenic 30.0%
CTCATGGTAAAACTTCATAT+GGG - Chr3:48675120-48675139 MsG0380014023.01.T01:CDS 30.0%
GAATCTTCTACCTATTTGAT+GGG - Chr3:48675553-48675572 MsG0380014023.01.T01:intron 30.0%
GATGGTTAAGAGATTATCTA+TGG - Chr3:48675575-48675594 MsG0380014023.01.T01:intron 30.0%
GTATGAATAGTTTATCAGTC+TGG - Chr3:48675638-48675657 MsG0380014023.01.T01:CDS 30.0%
TGAATCTTCTACCTATTTGA+TGG - Chr3:48675552-48675571 MsG0380014023.01.T01:intron 30.0%
TGTGAAGTACAGCAATTATT+AGG - Chr3:48674753-48674772 MsG0380014023.01.T01:intron 30.0%
TTAATAGCATTTAACCAACC+AGG + Chr3:48675209-48675228 None:intergenic 30.0%
TTCTGGATGTTAAATACCAT+TGG - Chr3:48675464-48675483 MsG0380014023.01.T01:intron 30.0%
TTTATCTTCAACGAATAGTC+CGG - Chr3:48675154-48675173 MsG0380014023.01.T01:CDS 30.0%
! ATTGGAAGCACATTACATTA+TGG - Chr3:48675506-48675525 MsG0380014023.01.T01:intron 30.0%
! GTTCTTATTTGACATCTTGT+TGG - Chr3:48675669-48675688 MsG0380014023.01.T01:CDS 30.0%
! TCTTATTTGACATCTTGTTG+GGG - Chr3:48675671-48675690 MsG0380014023.01.T01:CDS 30.0%
! TTGGAGAGCCTATTAATTTT+AGG - Chr3:48674907-48674926 MsG0380014023.01.T01:intron 30.0%
!! AAGCGTTTTATTCGTATCAA+AGG - Chr3:48675035-48675054 MsG0380014023.01.T01:CDS 30.0%
!! AGCGTTTTATTCGTATCAAA+GGG - Chr3:48675036-48675055 MsG0380014023.01.T01:CDS 30.0%
!! ATCAGAGCGTTGTAAATATT+AGG + Chr3:48674690-48674709 None:intergenic 30.0%
!! CATTTTATTTGGCAGTTTTC+TGG - Chr3:48675447-48675466 MsG0380014023.01.T01:intron 30.0%
!!! TGGTTACTTTTTATTGGCAT+TGG - Chr3:48675488-48675507 MsG0380014023.01.T01:intron 30.0%
AAGAACCTATATTTGCCCAA+TGG - Chr3:48675087-48675106 MsG0380014023.01.T01:CDS 35.0%
AAGCACATTACATTATGGCA+GGG - Chr3:48675511-48675530 MsG0380014023.01.T01:intron 35.0%
AGGTGGTACTTGTGATATTT+CGG - Chr3:48675415-48675434 MsG0380014023.01.T01:intron 35.0%
ATGAGCAGATTGTATCCATT+GGG + Chr3:48675105-48675124 None:intergenic 35.0%
CAAGTTAATGCCGGATAAAA+AGG - Chr3:48675355-48675374 MsG0380014023.01.T01:intron 35.0%
GCTCATGGTAAAACTTCATA+TGG - Chr3:48675119-48675138 MsG0380014023.01.T01:CDS 35.0%
GGATGTTAAATACCATTGGA+TGG - Chr3:48675468-48675487 MsG0380014023.01.T01:intron 35.0%
GTATCTAACTGTATAAAGGC+AGG + Chr3:48674977-48674996 None:intergenic 35.0%
TACTTGTGATATTTCGGCTT+GGG - Chr3:48675421-48675440 MsG0380014023.01.T01:intron 35.0%
TCTTAACCATCCCATCAAAT+AGG + Chr3:48675566-48675585 None:intergenic 35.0%
TGTATCCATTGGGCAAATAT+AGG + Chr3:48675095-48675114 None:intergenic 35.0%
! ATCAACGGATATAACCCTTT+TGG - Chr3:48675616-48675635 MsG0380014023.01.T01:CDS 35.0%
! ATGCCGGATAAAAAGGATTT+TGG - Chr3:48675362-48675381 MsG0380014023.01.T01:intron 35.0%
! CTTTTTATCCGGCATTAACT+TGG + Chr3:48675357-48675376 None:intergenic 35.0%
!! ATTTTAGGTCCTGTAGATAC+TGG - Chr3:48674922-48674941 MsG0380014023.01.T01:intron 35.0%
!! GATCTTAGTAAAAGGTGCTT+TGG - Chr3:48675319-48675338 MsG0380014023.01.T01:intron 35.0%
!! GCGTTTTATTCGTATCAAAG+GGG - Chr3:48675037-48675056 MsG0380014023.01.T01:CDS 35.0%
!! TTTTAGGTCCTGTAGATACT+GGG - Chr3:48674923-48674942 MsG0380014023.01.T01:intron 35.0%
AGATGGTCTAAAGAGAGGAA+TGG - Chr3:48674812-48674831 MsG0380014023.01.T01:intron 40.0%
AGGAATGGATGTGATTGACA+CGG - Chr3:48674827-48674846 MsG0380014023.01.T01:intron 40.0%
ATGTTCTTAATCTCATGGCG+CGG - Chr3:48675705-48675724 MsG0380014023.01.T01:CDS 40.0%
CAATGGATACAATCTGCTCA+TGG - Chr3:48675104-48675123 MsG0380014023.01.T01:CDS 40.0%
CACGTTGAAAATTCGACCTA+GGG + Chr3:48674886-48674905 None:intergenic 40.0%
CATGAGCAGATTGTATCCAT+TGG + Chr3:48675106-48675125 None:intergenic 40.0%
CTATTCTTAACAATAGGCCC+TGG - Chr3:48675245-48675264 MsG0380014023.01.T01:intron 40.0%
CTTCTACCTATTTGATGGGA+TGG - Chr3:48675557-48675576 MsG0380014023.01.T01:intron 40.0%
GAAGCACATTACATTATGGC+AGG - Chr3:48675510-48675529 MsG0380014023.01.T01:intron 40.0%
GTACTTGTGATATTTCGGCT+TGG - Chr3:48675420-48675439 MsG0380014023.01.T01:intron 40.0%
GTTCATCATGCTATTGCTCT+TGG - Chr3:48675278-48675297 MsG0380014023.01.T01:intron 40.0%
TACAACGCTCTGATAGTTCA+AGG - Chr3:48674696-48674715 MsG0380014023.01.T01:CDS 40.0%
! GGTTATAGTTTTCCTTGCGA+TGG - Chr3:48675383-48675402 MsG0380014023.01.T01:intron 40.0%
ATAGTTTATCAGTCTGGGCG+TGG - Chr3:48675644-48675663 MsG0380014023.01.T01:CDS 45.0%
ATGTTGTGCCCAGTATCTAC+AGG + Chr3:48674934-48674953 None:intergenic 45.0%
GATGAACCAAGAAGTCTCCA+GGG + Chr3:48675265-48675284 None:intergenic 45.0%
GCACGTTGAAAATTCGACCT+AGG + Chr3:48674887-48674906 None:intergenic 45.0%
GCTACAGATGGTCTAAAGAG+AGG - Chr3:48674807-48674826 MsG0380014023.01.T01:intron 45.0%
GGAATGGATGTGATTGACAC+GGG - Chr3:48674828-48674847 MsG0380014023.01.T01:intron 45.0%
GTAGCTATGAGTGCTACAGA+TGG - Chr3:48674795-48674814 MsG0380014023.01.T01:intron 45.0%
GTTCAAGGTCGAGATACTGT+TGG - Chr3:48674711-48674730 MsG0380014023.01.T01:CDS 45.0%
TAACTGTATAAAGGCAGGCG+CGG + Chr3:48674972-48674991 None:intergenic 45.0%
TAATCTCATGGCGCGGATAT+TGG - Chr3:48675712-48675731 MsG0380014023.01.T01:CDS 45.0%
TGATGAACCAAGAAGTCTCC+AGG + Chr3:48675266-48675285 None:intergenic 45.0%
! GGCTTGGGACGCATTTTATT+TGG - Chr3:48675436-48675455 MsG0380014023.01.T01:intron 45.0%
! GGTCGAATTTTCAACGTGCT+TGG - Chr3:48674888-48674907 MsG0380014023.01.T01:intron 45.0%
! TAGTTTTCCTTGCGATGGTC+CGG - Chr3:48675388-48675407 MsG0380014023.01.T01:intron 45.0%
AATAGGCCCTGGAGACTTCT+TGG - Chr3:48675256-48675275 MsG0380014023.01.T01:intron 50.0%
ACGCGGTTCCAAGTTAATGC+CGG - Chr3:48675346-48675365 MsG0380014023.01.T01:intron 50.0%
GAAGCATATGGTTGCCTGGT+TGG - Chr3:48675192-48675211 MsG0380014023.01.T01:CDS 50.0%
TGACATCTTGTTGGGGCTAC+TGG - Chr3:48675678-48675697 MsG0380014023.01.T01:CDS 50.0%
! AGTTTTCCTTGCGATGGTCC+GGG - Chr3:48675389-48675408 MsG0380014023.01.T01:intron 50.0%
!! AAAGGTGCTTTGGATGCACG+CGG - Chr3:48675329-48675348 MsG0380014023.01.T01:intron 50.0%
GCAGGCGCGGATCTATGAAT+AGG + Chr3:48674959-48674978 None:intergenic 55.0%
GCTCCCCTAAGTGTTCCAGT+CGG - Chr3:48674852-48674871 MsG0380014023.01.T01:intron 55.0%
TCACAAGTACCACCTCGTCC+CGG + Chr3:48675410-48675429 None:intergenic 55.0%
! TCCGCCGACTGGAACACTTA+GGG + Chr3:48674859-48674878 None:intergenic 55.0%
AATAGTCCGGCGCTCAGTGC+GGG - Chr3:48675167-48675186 MsG0380014023.01.T01:CDS 60.0%
CCCCTAAGTGTTCCAGTCGG+CGG - Chr3:48674855-48674874 MsG0380014023.01.T01:intron 60.0%
CTCATGGCGCGGATATTGGC+AGG - Chr3:48675716-48675735 MsG0380014023.01.T01:CDS 60.0%
GAATAGTCCGGCGCTCAGTG+CGG - Chr3:48675166-48675185 MsG0380014023.01.T01:CDS 60.0%
GGGCGAAGCATATGGTTGCC+TGG - Chr3:48675188-48675207 MsG0380014023.01.T01:CDS 60.0%
GGGCTCATGAACGCACACCA+TGG - Chr3:48675760-48675779 MsG0380014023.01.T01:CDS 60.0%
TCAGTGCGGGGCGAAGCATA+TGG - Chr3:48675180-48675199 MsG0380014023.01.T01:CDS 60.0%
! CCGCCGACTGGAACACTTAG+GGG + Chr3:48674858-48674877 None:intergenic 60.0%
! CTCCGCCGACTGGAACACTT+AGG + Chr3:48674860-48674879 None:intergenic 60.0%
ATAGTCCGGCGCTCAGTGCG+GGG - Chr3:48675168-48675187 MsG0380014023.01.T01:CDS 65.0%
CCAGTCGGCGGAGCAACCCT+AGG - Chr3:48674867-48674886 MsG0380014023.01.T01:intron 70.0%
CCTAGGGTTGCTCCGCCGAC+TGG + Chr3:48674870-48674889 None:intergenic 70.0%
CCTCGTCCCGGACCATCGCA+AGG + Chr3:48675398-48675417 None:intergenic 70.0%
CCTTGCGATGGTCCGGGACG+AGG - Chr3:48675395-48675414 MsG0380014023.01.T01:intron 70.0%
TGCGATGGTCCGGGACGAGG+TGG - Chr3:48675398-48675417 MsG0380014023.01.T01:intron 70.0%
CTTCGCCCCGCACTGAGCGC+CGG + Chr3:48675176-48675195 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48674684 48675791 48674684 ID=MsG0380014023.01;Name=MsG0380014023.01
Chr3 mRNA 48674684 48675791 48674684 ID=MsG0380014023.01.T01;Parent=MsG0380014023.01;Name=MsG0380014023.01.T01;_AED=0.50;_eAED=0.68;_QI=0|0|0|1|0.5|0.33|3|0|167
Chr3 exon 48675614 48675791 48675614 ID=MsG0380014023.01.T01:exon:9257;Parent=MsG0380014023.01.T01
Chr3 exon 48674943 48675214 48674943 ID=MsG0380014023.01.T01:exon:9256;Parent=MsG0380014023.01.T01
Chr3 exon 48674684 48674737 48674684 ID=MsG0380014023.01.T01:exon:9255;Parent=MsG0380014023.01.T01
Chr3 CDS 48675614 48675791 48675614 ID=MsG0380014023.01.T01:cds;Parent=MsG0380014023.01.T01
Chr3 CDS 48674943 48675214 48674943 ID=MsG0380014023.01.T01:cds;Parent=MsG0380014023.01.T01
Chr3 CDS 48674684 48674737 48674684 ID=MsG0380014023.01.T01:cds;Parent=MsG0380014023.01.T01
Gene Sequence

>MsG0380014023.01.T01

ATGCCTAATATTTACAACGCTCTGATAGTTCAAGGTCGAGATACTGTTGGACAAGAAATTAACGTAACTTGTGAAGTACAGCAATTATTAGGAAATAATAGAGTTAGAGCTGTAGCTATGAGTGCTACAGATGGTCTAAAGAGAGGAATGGATGTGATTGACACGGGAGCTCCCCTAAGCCCTGGAGACTTCTTGGTTCATCATGCTATTGCTCTTGGTTTACATACAACTACATTGATCTTAGTAAAAGGTGCTTTGGATGCACGCGGTTCCAAGTTAATGCCGGATAAAAAGGATTTTGGTTATAGTTTTCCTTGCGATGGTCCGGGACGAGGTGGTACTTGTGATATTTCGGCTTGGGACGCATTTTATTTGGCAGTTTTCTGGATGTTAAATACCATTGGATGGTTACTTTTTATTGGCATTGGAAGCACATTACATTATGGCAGGGAATTGATCGAAACTTTAGCATGGGCTCATGAACGCACACCATGGCGAATTTGA

Protein sequence

>MsG0380014023.01.T01

MPNIYNALIVQGRDTVGQEINVTCEVQQLLGNNRVRAVAMSATDGLKRGMDVIDTGAPLSPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWLLFIGIGSTLHYGRELIETLAWAHERTPWRI*