AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0880046291.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880046291.01.T01 MTR_4g104990 92.667 150 11 0 9 158 24 173 1.45e-81 238
MsG0880046291.01.T01 MTR_4g104900 68.966 87 26 1 1 86 1 87 5.15e-34 117
MsG0880046291.01.T01 MTR_4g104890 52.903 155 50 5 1 143 25 168 1.15e-33 117
MsG0880046291.01.T01 MTR_4g104940 43.448 145 65 4 1 132 1 141 3.01e-31 110
MsG0880046291.01.T01 MTR_4g104960 41.727 139 66 4 5 132 16 150 1.97e-27 100
MsG0880046291.01.T01 MTR_4g104880 66.316 95 31 1 1 94 1 95 1.52e-24 99.0
MsG0880046291.01.T01 MTR_4g104880 66.316 95 31 1 1 94 1 95 1.61e-24 99.0
MsG0880046291.01.T01 MTR_4g104980 46.763 139 55 4 1 127 21 152 3.16e-23 90.9
MsG0880046291.01.T01 MTR_4g104950 75.362 69 16 1 18 85 3 71 5.71e-16 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880046291.01.T01 AT4G24690 53.488 86 39 1 2 86 5 90 1.73e-23 96.3

Find 24 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCATGAGTAAAATTGAAAA+TGG 0.223897 8:+71605961 None:intergenic
GATTAGAGGGTCTTTAGTTT+TGG 0.253834 8:-71605663 MsG0880046291.01.T01:CDS
AACTCTCTATAGGTGAAATA+TGG 0.273632 8:-71606070 MsG0880046291.01.T01:intron
ACGAACCTGCTGAAACAAAA+TGG 0.310642 8:-71605685 MsG0880046291.01.T01:CDS
TTCTCAAGAATTGTAATTGC+TGG 0.315294 8:+71605858 None:intergenic
GGGTTCTGCTCTGGTGATAA+AGG 0.375199 8:-71607049 MsG0880046291.01.T01:intron
TATATCTATGGGTTCTGCTC+TGG 0.398091 8:-71607058 None:intergenic
GCTGAAACAAAATGGATTAG+AGG 0.399211 8:-71605677 MsG0880046291.01.T01:CDS
GTTTCAGCAGGTTCGTCATC+TGG 0.412295 8:+71605692 None:intergenic
TCTTAACATGGTTAGTTTGA+AGG 0.424365 8:-71605996 MsG0880046291.01.T01:CDS
GTACACATGATCCATAATCT+TGG 0.483593 8:-71605830 MsG0880046291.01.T01:CDS
TGTTGATGAAGAGGGTGACT+TGG 0.514717 8:-71605921 MsG0880046291.01.T01:CDS
AGAGGATGATAGACTTGAGA+AGG 0.524450 8:+71605630 None:intergenic
CAGACGTTTCAGTGTTCCTG+TGG 0.559522 8:-71606038 MsG0880046291.01.T01:CDS
CTGAAACAAAATGGATTAGA+GGG 0.559986 8:-71605676 MsG0880046291.01.T01:CDS
ACTTGATTATTCTCATCCAC+AGG 0.562935 8:+71606022 None:intergenic
TTGAGATATGTTGATGAAGA+GGG 0.581333 8:-71605929 MsG0880046291.01.T01:CDS
TTAGTTTGAAGGCTAAGATA+CGG 0.582738 8:-71605985 MsG0880046291.01.T01:CDS
GAGGATGATAGACTTGAGAA+GGG 0.599879 8:+71605631 None:intergenic
GGGTGACTTGGTGAATCTTG+TGG 0.610599 8:-71605909 MsG0880046291.01.T01:CDS
TTTGAGATATGTTGATGAAG+AGG 0.627843 8:-71605930 MsG0880046291.01.T01:CDS
TAATCAAGTGGATCTTAACA+TGG 0.654514 8:-71606008 MsG0880046291.01.T01:CDS
TGTGGATGAGAATAATCAAG+TGG 0.662046 8:-71606020 MsG0880046291.01.T01:CDS
AGGAACACTGAAACGTCTGA+AGG 0.667617 8:+71606042 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGATTCTATATTAATAAAAA+TGG + Chr8:71606066-71606085 None:intergenic 10.0%
!! AACTAAAACATAAATTAGAA+AGG + Chr8:71605863-71605882 None:intergenic 15.0%
!! ACTAAAACATAAATTAGAAA+GGG + Chr8:71605862-71605881 None:intergenic 15.0%
!! AAAAAAAATAAACAAAGGCA+GGG + Chr8:71606246-71606265 None:intergenic 20.0%
!! AGTATATAAATTTCTTAAGC+AGG - Chr8:71606484-71606503 MsG0880046291.01.T01:intron 20.0%
!! TAAAAAAAATAAACAAAGGC+AGG + Chr8:71606247-71606266 None:intergenic 20.0%
!!! AACAAAGTTGAAATTTTAGA+AGG - Chr8:71606126-71606145 MsG0880046291.01.T01:intron 20.0%
!!! AACTTTTGACATTTTTATAG+AGG + Chr8:71606034-71606053 None:intergenic 20.0%
!!! AGTTTAATTGTTTTGATGAT+AGG - Chr8:71605879-71605898 MsG0880046291.01.T01:CDS 20.0%
!!! ATGATTTGTTTGTTCTTTTT+TGG - Chr8:71605997-71606016 MsG0880046291.01.T01:CDS 20.0%
!!! ATGTGATGTGTTTTAAAAAA+GGG + Chr8:71606436-71606455 None:intergenic 20.0%
!!! TGATTTGTTTGTTCTTTTTT+GGG - Chr8:71605998-71606017 MsG0880046291.01.T01:CDS 20.0%
!!! TTTAAAATGTTACCATGTTT+AGG - Chr8:71606390-71606409 MsG0880046291.01.T01:intron 20.0%
!!! TTTGGTTCATCATATTAATT+AGG - Chr8:71605963-71605982 MsG0880046291.01.T01:CDS 20.0%
! AAAAACAACATGATATTGAG+AGG + Chr8:71606550-71606569 None:intergenic 25.0%
! AACAAAAAATAGAGAGAAAG+AGG + Chr8:71605671-71605690 None:intergenic 25.0%
! ACAAAAAATAGAGAGAAAGA+GGG + Chr8:71605670-71605689 None:intergenic 25.0%
! ATAATCTTGGCAAAAAGATA+TGG - Chr8:71606862-71606881 MsG0880046291.01.T01:intron 25.0%
! TAAAAAAGGGAAATGTTAAC+TGG + Chr8:71606423-71606442 None:intergenic 25.0%
! TGCATGAGTAAAATTGAAAA+TGG + Chr8:71606721-71606740 None:intergenic 25.0%
! TTCAGACTTAATTGTAGATT+TGG + Chr8:71606513-71606532 None:intergenic 25.0%
!! ATATCTTTTTGCCAAGATTA+TGG + Chr8:71606863-71606882 None:intergenic 25.0%
!!! ATTGCATGTCATGTTTTTAT+TGG - Chr8:71606306-71606325 MsG0880046291.01.T01:intron 25.0%
!!! GATGTGATGTGTTTTAAAAA+AGG + Chr8:71606437-71606456 None:intergenic 25.0%
!!! TGTTTATGTTTTTGTTGTTG+TGG - Chr8:71606926-71606945 MsG0880046291.01.T01:intron 25.0%
!!! TTGCATGTCATGTTTTTATT+GGG - Chr8:71606307-71606326 MsG0880046291.01.T01:intron 25.0%
AACTCTCTATAGGTGAAATA+TGG - Chr8:71606609-71606628 MsG0880046291.01.T01:intron 30.0%
GAAAATCTTCTTAACATCCA+TGG + Chr8:71606167-71606186 None:intergenic 30.0%
GAACAAACAAATCATTCGTA+TGG + Chr8:71605992-71606011 None:intergenic 30.0%
TAATCAAGTGGATCTTAACA+TGG - Chr8:71606671-71606690 MsG0880046291.01.T01:intron 30.0%
TTCTCAAGAATTGTAATTGC+TGG + Chr8:71606824-71606843 None:intergenic 30.0%
! TTAGTTTGAAGGCTAAGATA+CGG - Chr8:71606694-71606713 MsG0880046291.01.T01:intron 30.0%
! TTGAGATATGTTGATGAAGA+GGG - Chr8:71606750-71606769 MsG0880046291.01.T01:intron 30.0%
! TTTGAGATATGTTGATGAAG+AGG - Chr8:71606749-71606768 MsG0880046291.01.T01:intron 30.0%
!! CTGAAACAAAATGGATTAGA+GGG - Chr8:71607003-71607022 MsG0880046291.01.T01:intron 30.0%
!! TCTTAACATGGTTAGTTTGA+AGG - Chr8:71606683-71606702 MsG0880046291.01.T01:intron 30.0%
!! TGCACTCATTTTAGTCAATT+AGG - Chr8:71605751-71605770 MsG0880046291.01.T01:CDS 30.0%
!! TGCATGTCATGTTTTTATTG+GGG - Chr8:71606308-71606327 MsG0880046291.01.T01:intron 30.0%
!!! ATTAGAGGGTCTTTAGTTTT+GGG - Chr8:71607017-71607036 MsG0880046291.01.T01:intron 30.0%
!!! GTTTTTGTTGTTGTGGTTTT+GGG - Chr8:71606933-71606952 MsG0880046291.01.T01:intron 30.0%
!!! TGTTTTTGTTGTTGTGGTTT+TGG - Chr8:71606932-71606951 MsG0880046291.01.T01:intron 30.0%
AAATAAACAAAGGCAGGGTA+TGG + Chr8:71606241-71606260 None:intergenic 35.0%
AATAAACAAAGGCAGGGTAT+GGG + Chr8:71606240-71606259 None:intergenic 35.0%
ACTTGATTATTCTCATCCAC+AGG + Chr8:71606660-71606679 None:intergenic 35.0%
AGGAACATGTTGAAATTGCA+AGG - Chr8:71605899-71605918 MsG0880046291.01.T01:CDS 35.0%
AGGGAAATGTTAACTGGTTA+AGG + Chr8:71606417-71606436 None:intergenic 35.0%
CAAATCATGATCCTAGTAAC+GGG + Chr8:71605947-71605966 None:intergenic 35.0%
CCAAATCATGATCCTAGTAA+CGG + Chr8:71605948-71605967 None:intergenic 35.0%
GGAACATGTTGAAATTGCAA+GGG - Chr8:71605900-71605919 MsG0880046291.01.T01:CDS 35.0%
GTACACATGATCCATAATCT+TGG - Chr8:71606849-71606868 MsG0880046291.01.T01:intron 35.0%
TAGAAAGGGATGCACAAAAA+CGG + Chr8:71605848-71605867 None:intergenic 35.0%
TCTTGGCAAAAAGATATGGA+AGG - Chr8:71606866-71606885 MsG0880046291.01.T01:intron 35.0%
TGTGGATGAGAATAATCAAG+TGG - Chr8:71606659-71606678 MsG0880046291.01.T01:intron 35.0%
TTCACTTGTGAACTCTCTAT+AGG - Chr8:71606599-71606618 MsG0880046291.01.T01:intron 35.0%
! GGTTTTCTTGTCATATTCCA+TGG - Chr8:71606147-71606166 MsG0880046291.01.T01:intron 35.0%
!! ATCATTTGGTGTATTGCAAG+CGG + Chr8:71606207-71606226 None:intergenic 35.0%
!! CTAATCCATTTTGTTTCAGC+AGG + Chr8:71607002-71607021 None:intergenic 35.0%
!! GATTAGAGGGTCTTTAGTTT+TGG - Chr8:71607016-71607035 MsG0880046291.01.T01:intron 35.0%
!! GCTGAAACAAAATGGATTAG+AGG - Chr8:71607002-71607021 MsG0880046291.01.T01:intron 35.0%
ACGAACCTGCTGAAACAAAA+TGG - Chr8:71606994-71607013 MsG0880046291.01.T01:intron 40.0%
ACTGGTTAAGGACCTAAACA+TGG + Chr8:71606405-71606424 None:intergenic 40.0%
AGAAAGGGATGCACAAAAAC+GGG + Chr8:71605847-71605866 None:intergenic 40.0%
AGAGGATGATAGACTTGAGA+AGG + Chr8:71607052-71607071 None:intergenic 40.0%
CCGTTACTAGGATCATGATT+TGG - Chr8:71605945-71605964 MsG0880046291.01.T01:CDS 40.0%
GAGGATGATAGACTTGAGAA+GGG + Chr8:71607051-71607070 None:intergenic 40.0%
TCTTCTTAACGAGTGTCTCT+GGG - Chr8:71606331-71606350 MsG0880046291.01.T01:intron 40.0%
!!! TGTTCTTTTTTGGGTGCATG+TGG - Chr8:71606007-71606026 MsG0880046291.01.T01:CDS 40.0%
ACCATCATGATCCCGTTACT+AGG - Chr8:71605933-71605952 MsG0880046291.01.T01:CDS 45.0%
AGGAACACTGAAACGTCTGA+AGG + Chr8:71606640-71606659 None:intergenic 45.0%
CTTCTTAACGAGTGTCTCTG+GGG - Chr8:71606332-71606351 MsG0880046291.01.T01:intron 45.0%
GTCTTCTTAACGAGTGTCTC+TGG - Chr8:71606330-71606349 MsG0880046291.01.T01:intron 45.0%
TGGGAAGGGTCATCATCATT+TGG + Chr8:71606221-71606240 None:intergenic 45.0%
! TCCTAGTAACGGGATCATGA+TGG + Chr8:71605937-71605956 None:intergenic 45.0%
! TGTTGATGAAGAGGGTGACT+TGG - Chr8:71606758-71606777 MsG0880046291.01.T01:intron 45.0%
!! AAAATAAAAAAAATAAACAA+AGG + Chr8:71606251-71606270 None:intergenic 5.0%
!!! TTTTTTTATTTTTTATTCTA+TGG - Chr8:71606259-71606278 MsG0880046291.01.T01:intron 5.0%
AACAAAGGCAGGGTATGGGA+AGG + Chr8:71606236-71606255 None:intergenic 50.0%
ACAAAGGCAGGGTATGGGAA+GGG + Chr8:71606235-71606254 None:intergenic 50.0%
CAGACGTTTCAGTGTTCCTG+TGG - Chr8:71606641-71606660 MsG0880046291.01.T01:intron 50.0%
GGGTTCTGCTCTGGTGATAA+AGG - Chr8:71605630-71605649 MsG0880046291.01.T01:CDS 50.0%
GTTTCAGCAGGTTCGTCATC+TGG + Chr8:71606990-71607009 None:intergenic 50.0%
!! GGGTGACTTGGTGAATCTTG+TGG - Chr8:71606770-71606789 MsG0880046291.01.T01:intron 50.0%
Chromosome Type Strat End Strand Name
Chr8 gene 71605628 71607073 71605628 ID=MsG0880046291.01;Name=MsG0880046291.01
Chr8 mRNA 71605628 71607073 71605628 ID=MsG0880046291.01.T01;Parent=MsG0880046291.01;Name=MsG0880046291.01.T01;_AED=0.53;_eAED=0.53;_QI=0|0|0|1|1|1|2|0|158
Chr8 exon 71607050 71607073 71607050 ID=MsG0880046291.01.T01:exon:15546;Parent=MsG0880046291.01.T01
Chr8 exon 71605628 71606080 71605628 ID=MsG0880046291.01.T01:exon:15545;Parent=MsG0880046291.01.T01
Chr8 CDS 71607050 71607073 71607050 ID=MsG0880046291.01.T01:cds;Parent=MsG0880046291.01.T01
Chr8 CDS 71605628 71606080 71605628 ID=MsG0880046291.01.T01:cds;Parent=MsG0880046291.01.T01
Gene Sequence

>MsG0880046291.01.T01

ATGGGTTCTGCTCTGGTGATAAAGGTGAAATATGGAAATACCTTCAGACGTTTCAGTGTTCCTGTGGATGAGAATAATCAAGTGGATCTTAACATGGTTAGTTTGAAGGCTAAGATACGGTCCATTTTCAATTTTACTCATGCAAATTTCAGTTTGAGATATGTTGATGAAGAGGGTGACTTGGTGAATCTTGTGGATGATGATGATTTGCATGACATGATGAGCCAGCAATTACAATTCTTGAGAATTGAAGTACACATGATCCATAATCTTGGCAAAAAGATATGGAAGGAAATAATATTTAACGAAGAAAAATTATTTTACAGTCTTGTTTATGTTTTTGTTGTTGTGGTTTTGGGTGTGTTGTGTTTAGCGATTGTTTTCAATCTACCAGATGACGAACCTGCTGAAACAAAATGGATTAGAGGGTCTTTAGTTTTGGGTCTTTTGACCCTTCTCAAGTCTATCATCCTCTAA
Protein sequence

>MsG0880046291.01.T01

MGSALVIKVKYGNTFRRFSVPVDENNQVDLNMVSLKAKIRSIFNFTHANFSLRYVDEEGDLVNLVDDDDLHDMMSQQLQFLRIEVHMIHNLGKKIWKEIIFNEEKLFYSLVYVFVVVVLGVLCLAIVFNLPDDEPAETKWIRGSLVLGLLTLLKSIIL*