AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480023093.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023093.01.T01 MTR_8g086330 100.000 81 0 0 1 81 1 81 2.15e-53 160
MsG0480023093.01.T01 MTR_4g028080 92.405 79 6 0 1 79 1 79 6.65e-40 126
MsG0480023093.01.T01 MTR_1g082400 60.000 80 24 1 5 76 21 100 9.16e-25 89.4
MsG0480023093.01.T01 MTR_2g093770 60.976 82 26 1 4 79 21 102 4.70e-24 87.4
MsG0480023093.01.T01 MTR_5g066500 66.071 56 16 1 9 64 56 108 8.66e-16 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023093.01.T01 AT3G60540 80.769 78 14 1 4 80 3 80 3.44e-34 112
MsG0480023093.01.T01 AT3G60540 80.769 78 14 1 4 80 3 80 3.44e-34 112
MsG0480023093.01.T01 AT3G60540 80.769 78 14 1 4 80 3 80 3.44e-34 112
MsG0480023093.01.T01 AT2G45070 82.500 80 10 1 4 79 3 82 3.54e-32 107
MsG0480023093.01.T01 AT2G45070 82.500 80 10 1 4 79 3 82 3.54e-32 107
MsG0480023093.01.T01 AT2G45070 82.500 80 10 1 4 79 3 82 3.54e-32 107
MsG0480023093.01.T01 AT2G45070 82.500 80 10 1 4 79 3 82 3.54e-32 107
MsG0480023093.01.T01 AT5G60460 58.621 87 28 1 2 80 19 105 3.36e-23 85.5
MsG0480023093.01.T01 AT5G60460 58.621 87 28 1 2 80 19 105 3.36e-23 85.5

Find 49 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTGCTGCACTTCCTCTTT+GGG 0.153735 4:+80747011 None:intergenic
TCGCTGCTGCACTTCCTCTT+TGG 0.195557 4:+80747010 None:intergenic
AATTAATATAGCCTCAAAAT+TGG 0.203104 4:-80746546 MsG0480023093.01.T01:three_prime_UTR
ACACCCGGTGGTGGGGCATC+TGG 0.275877 4:-80746964 MsG0480023093.01.T01:CDS
GGGGCATCTGGAGGAGCTGC+AGG 0.292492 4:-80746952 MsG0480023093.01.T01:CDS
ACTTGATACAATCATCCTTT+TGG 0.324642 4:-80746685 MsG0480023093.01.T01:three_prime_UTR
AGAGAATACAATATGAAGTT+AGG 0.340470 4:-80746789 MsG0480023093.01.T01:three_prime_UTR
CTCATCACAAGAACCACATT+TGG 0.388681 4:+80746880 None:intergenic
TATGAAGTTAGGTTCGTTAT+GGG 0.391775 4:-80746778 MsG0480023093.01.T01:three_prime_UTR
TCATCACAAGAACCACATTT+GGG 0.392066 4:+80746881 None:intergenic
GTGTTTCAGAAAATGGCTTC+AGG 0.402843 4:-80747045 MsG0480023093.01.T01:intron
ATATGAAGTTAGGTTCGTTA+TGG 0.404423 4:-80746779 MsG0480023093.01.T01:three_prime_UTR
GTTGCCATCCTTCATGTGAT+TGG 0.409593 4:-80746838 MsG0480023093.01.T01:CDS
TCCTCCAGATGCCCCACCAC+CGG 0.423552 4:+80746960 None:intergenic
ATTAATATAGCCTCAAAATT+GGG 0.451198 4:-80746545 MsG0480023093.01.T01:three_prime_UTR
TGAACTAGCAGCGACGTGTT+TGG 0.454587 4:-80746616 MsG0480023093.01.T01:three_prime_UTR
CTGGTACAATGTTATGGCCA+AGG 0.478673 4:-80746642 MsG0480023093.01.T01:three_prime_UTR
AGAAGAAATAAATGACCAAA+AGG 0.479134 4:+80746670 None:intergenic
GGGCATCTGGAGGAGCTGCA+GGG 0.495153 4:-80746951 MsG0480023093.01.T01:CDS
TGTTACCTCTGCTGTGGAAA+CGG 0.501593 4:+80747957 None:intergenic
CGACTGCAAGCATGAGAAGA+AGG 0.502053 4:-80746990 MsG0480023093.01.T01:CDS
AGAAGGAAGACACCCGGTGG+TGG 0.513757 4:-80746973 MsG0480023093.01.T01:CDS
TTTGGGGAGATCTTGAGTCC+AGG 0.515537 4:+80746898 None:intergenic
CCCGGTGGTGGGGCATCTGG+AGG 0.518412 4:-80746961 MsG0480023093.01.T01:CDS
CCTCCAGATGCCCCACCACC+GGG 0.523682 4:+80746961 None:intergenic
GCTGCTGCACTTCCTCTTTG+GGG 0.527227 4:+80747012 None:intergenic
GTGGTTCTTGTGATGAGCAT+TGG 0.535637 4:-80746874 MsG0480023093.01.T01:CDS
GAAGGAAGACACCCGGTGGT+GGG 0.541352 4:-80746972 MsG0480023093.01.T01:CDS
TTGGGGAGATCTTGAGTCCA+GGG 0.546700 4:+80746899 None:intergenic
TGGCAAGTTGTACTTGCGTA+AGG 0.559707 4:-80746818 MsG0480023093.01.T01:CDS
TATAGCCTCAAAATTGGGTG+TGG 0.577770 4:-80746540 None:intergenic
GGTGGAGCAGCTCCCCAAAG+AGG 0.584751 4:-80747024 MsG0480023093.01.T01:CDS
CAAGTTGTACTTGCGTAAGG+AGG 0.591387 4:-80746815 MsG0480023093.01.T01:CDS
AAGGAAGACACCCGGTGGTG+GGG 0.594885 4:-80746971 MsG0480023093.01.T01:CDS
ATGAAGTTAGGTTCGTTATG+GGG 0.606908 4:-80746777 MsG0480023093.01.T01:three_prime_UTR
TTTCAGAAAATGGCTTCAGG+TGG 0.611619 4:-80747042 MsG0480023093.01.T01:intron
GAGTGTTGTTACCTCTGCTG+TGG 0.615767 4:+80747951 None:intergenic
ACAACTTGCCAATCACATGA+AGG 0.616873 4:+80746830 None:intergenic
TCGCTGCTAGTTCAAAACCT+TGG 0.619534 4:+80746625 None:intergenic
CTTGCCAATCACATGAAGGA+TGG 0.620482 4:+80746834 None:intergenic
ACTCAAGATCTCCCCAAATG+TGG 0.630953 4:-80746893 MsG0480023093.01.T01:CDS
TCAACTGCAAAGATAAATCG+AGG 0.641925 4:+80747991 None:intergenic
TGGGGAGATCTTGAGTCCAG+GGG 0.642908 4:+80746900 None:intergenic
AAAGATAAATCGAGGGACAG+AGG 0.653147 4:+80747999 None:intergenic
GAACTCCGTTTCCACAGCAG+AGG 0.662903 4:-80747962 MsG0480023093.01.T01:intron
ATGAGAAGAAGGAAGACACC+CGG 0.674561 4:-80746979 MsG0480023093.01.T01:CDS
CATCACAAGAACCACATTTG+GGG 0.690194 4:+80746882 None:intergenic
CAACTGCAAAGATAAATCGA+GGG 0.696467 4:+80747992 None:intergenic
AGAAGAAGGAAGACACCCGG+TGG 0.765392 4:-80746976 MsG0480023093.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACCATAAAATTTTAATTAAT+CGG + Chr4:80747254-80747273 None:intergenic 10.0%
!!! AATTGTTAGAAATTTTGTTT+TGG - Chr4:80746980-80746999 MsG0480023093.01.T01:CDS 15.0%
!!! ACCGATTAATTAAAATTTTA+TGG - Chr4:80747250-80747269 MsG0480023093.01.T01:intron 15.0%
!!! TAATTAACTATGATTTTGTT+TGG - Chr4:80747967-80747986 MsG0480023093.01.T01:five_prime_UTR 15.0%
!!! TTATTGAATGATCATTTTTA+GGG - Chr4:80747184-80747203 MsG0480023093.01.T01:intron 15.0%
!!! TTTTTTAACAATATGTTTTG+AGG - Chr4:80747810-80747829 MsG0480023093.01.T01:intron 15.0%
!! AATTAATATAGCCTCAAAAT+TGG - Chr4:80748014-80748033 MsG0480023093.01.T01:five_prime_UTR 20.0%
!! ATTAATATAGCCTCAAAATT+GGG - Chr4:80748015-80748034 MsG0480023093.01.T01:five_prime_UTR 20.0%
!! ATTATTTATGCTCATCTATT+TGG - Chr4:80746923-80746942 MsG0480023093.01.T01:CDS 20.0%
!!! ATGGTTTGTTTGTTTATTTT+CGG - Chr4:80747269-80747288 MsG0480023093.01.T01:intron 20.0%
!!! ATGTTTTAGTTGTGTAATTA+TGG - Chr4:80746875-80746894 MsG0480023093.01.T01:CDS 20.0%
!!! CATTTATTTCTTCTTTTATC+TGG - Chr4:80747899-80747918 MsG0480023093.01.T01:intron 20.0%
!!! CTTATTGAATGATCATTTTT+AGG - Chr4:80747183-80747202 MsG0480023093.01.T01:intron 20.0%
!!! TTTATTTTCGGATATTGTTA+GGG - Chr4:80747281-80747300 MsG0480023093.01.T01:intron 20.0%
! AACGAAATAAATCCACAAAT+CGG + Chr4:80746767-80746786 None:intergenic 25.0%
! AATACATGTGTTTCAGAAAA+TGG - Chr4:80747508-80747527 MsG0480023093.01.T01:intron 25.0%
! AGAAGAAATAAATGACCAAA+AGG + Chr4:80747893-80747912 None:intergenic 25.0%
! AGAGAATACAATATGAAGTT+AGG - Chr4:80747771-80747790 MsG0480023093.01.T01:intron 25.0%
! ATTGAATAAAAGAGACAAAG+TGG + Chr4:80746637-80746656 None:intergenic 25.0%
!! AACCGAACAGTTTTTAATAT+CGG + Chr4:80747343-80747362 None:intergenic 25.0%
!! TTTTATCTGGTACAATGTTA+TGG - Chr4:80747912-80747931 MsG0480023093.01.T01:intron 25.0%
!!! GTTTATTTTCGGATATTGTT+AGG - Chr4:80747280-80747299 MsG0480023093.01.T01:intron 25.0%
ACATGGTCATTCATGAAAAT+TGG + Chr4:80747093-80747112 None:intergenic 30.0%
AGGGTTTGTAATTGTTTAGT+TGG - Chr4:80747203-80747222 MsG0480023093.01.T01:intron 30.0%
ATATGAAGTTAGGTTCGTTA+TGG - Chr4:80747781-80747800 MsG0480023093.01.T01:intron 30.0%
GGGTTTGTAATTGTTTAGTT+GGG - Chr4:80747204-80747223 MsG0480023093.01.T01:intron 30.0%
TATGAAGTTAGGTTCGTTAT+GGG - Chr4:80747782-80747801 MsG0480023093.01.T01:intron 30.0%
TGCCGATATTAAAAACTGTT+CGG - Chr4:80747338-80747357 MsG0480023093.01.T01:intron 30.0%
! AATCTAAAATCACCAGATCT+AGG + Chr4:80746816-80746835 None:intergenic 30.0%
! ACTTGATACAATCATCCTTT+TGG - Chr4:80747875-80747894 MsG0480023093.01.T01:intron 30.0%
! ATGCTCATCTATTTGGTTTA+AGG - Chr4:80746930-80746949 MsG0480023093.01.T01:CDS 30.0%
! GTTGTGCATTACATTTTCAT+TGG - Chr4:80747466-80747485 MsG0480023093.01.T01:intron 30.0%
! TATCAACACAAAAGCATACA+TGG + Chr4:80747110-80747129 None:intergenic 30.0%
! TGCTCATCTATTTGGTTTAA+GGG - Chr4:80746931-80746950 MsG0480023093.01.T01:CDS 30.0%
!! TGTTTTGAATTGCTTTCGAT+CGG - Chr4:80746731-80746750 MsG0480023093.01.T01:three_prime_UTR 30.0%
AAAAGCCGAAGAAACATCAT+CGG + Chr4:80746686-80746705 None:intergenic 35.0%
AAGTCAAAGCACGAAGATTA+AGG + Chr4:80746712-80746731 None:intergenic 35.0%
ATGAAGTTAGGTTCGTTATG+GGG - Chr4:80747783-80747802 MsG0480023093.01.T01:intron 35.0%
CAACTGCAAAGATAAATCGA+GGG + Chr4:80746571-80746590 None:intergenic 35.0%
GTTATCCGATGATGTTTCTT+CGG - Chr4:80746678-80746697 MsG0480023093.01.T01:three_prime_UTR 35.0%
TCAACTGCAAAGATAAATCG+AGG + Chr4:80746572-80746591 None:intergenic 35.0%
TCATATGAGCAACAGATGAT+AGG + Chr4:80747442-80747461 None:intergenic 35.0%
TCATCACAAGAACCACATTT+GGG + Chr4:80747682-80747701 None:intergenic 35.0%
TCTTGATACATTCCTAGATC+TGG - Chr4:80746801-80746820 MsG0480023093.01.T01:exon 35.0%
TTCGGATATTGTTAGGGTTA+GGG - Chr4:80747287-80747306 MsG0480023093.01.T01:intron 35.0%
TTGTAATTGTTTAGTTGGGC+AGG - Chr4:80747208-80747227 MsG0480023093.01.T01:intron 35.0%
TTTCGGATATTGTTAGGGTT+AGG - Chr4:80747286-80747305 MsG0480023093.01.T01:intron 35.0%
! CAGATGATAGGTAGTAGTTT+TGG + Chr4:80747430-80747449 None:intergenic 35.0%
AAAGATAAATCGAGGGACAG+AGG + Chr4:80746564-80746583 None:intergenic 40.0%
ACAACTTGCCAATCACATGA+AGG + Chr4:80747733-80747752 None:intergenic 40.0%
CATCACAAGAACCACATTTG+GGG + Chr4:80747681-80747700 None:intergenic 40.0%
CCAACATAACGATCAATCTC+AGG + Chr4:80747372-80747391 None:intergenic 40.0%
CCTGAGATTGATCGTTATGT+TGG - Chr4:80747369-80747388 MsG0480023093.01.T01:intron 40.0%
CCTTATCCTATCTACTGCAA+AGG + Chr4:80747315-80747334 None:intergenic 40.0%
CCTTTGCAGTAGATAGGATA+AGG - Chr4:80747312-80747331 MsG0480023093.01.T01:intron 40.0%
CTCATCACAAGAACCACATT+TGG + Chr4:80747683-80747702 None:intergenic 40.0%
GAGATTGATCGTTATGTTGG+AGG - Chr4:80747372-80747391 MsG0480023093.01.T01:intron 40.0%
GTGTTTCAGAAAATGGCTTC+AGG - Chr4:80747515-80747534 MsG0480023093.01.T01:intron 40.0%
TTGATCGTTATGTTGGAGGA+AGG - Chr4:80747376-80747395 MsG0480023093.01.T01:intron 40.0%
TTTCAGAAAATGGCTTCAGG+TGG - Chr4:80747518-80747537 MsG0480023093.01.T01:intron 40.0%
! GGGTTGTGATTTTGTGTCAT+AGG - Chr4:80746951-80746970 MsG0480023093.01.T01:CDS 40.0%
!!! TGATAGGTAGTAGTTTTGGC+AGG + Chr4:80747426-80747445 None:intergenic 40.0%
ACTCAAGATCTCCCCAAATG+TGG - Chr4:80747667-80747686 MsG0480023093.01.T01:intron 45.0%
ATGAGAAGAAGGAAGACACC+CGG - Chr4:80747581-80747600 MsG0480023093.01.T01:intron 45.0%
CAAGTTGTACTTGCGTAAGG+AGG - Chr4:80747745-80747764 MsG0480023093.01.T01:intron 45.0%
CTGGTACAATGTTATGGCCA+AGG - Chr4:80747918-80747937 MsG0480023093.01.T01:intron 45.0%
CTTGCCAATCACATGAAGGA+TGG + Chr4:80747729-80747748 None:intergenic 45.0%
GTGGTTCTTGTGATGAGCAT+TGG - Chr4:80747686-80747705 MsG0480023093.01.T01:intron 45.0%
GTTGCCATCCTTCATGTGAT+TGG - Chr4:80747722-80747741 MsG0480023093.01.T01:intron 45.0%
TCGCTGCTAGTTCAAAACCT+TGG + Chr4:80747938-80747957 None:intergenic 45.0%
TGGCAAGTTGTACTTGCGTA+AGG - Chr4:80747742-80747761 MsG0480023093.01.T01:intron 45.0%
TGTTACCTCTGCTGTGGAAA+CGG + Chr4:80746606-80746625 None:intergenic 45.0%
!! TTTTACACTGATGATGCCCC+TGG - Chr4:80747644-80747663 MsG0480023093.01.T01:intron 45.0%
AGGGCTCCTTTGCAGTAGAT+AGG - Chr4:80747306-80747325 MsG0480023093.01.T01:intron 50.0%
CGACTGCAAGCATGAGAAGA+AGG - Chr4:80747570-80747589 MsG0480023093.01.T01:intron 50.0%
GGGCAGGAGAAAAAACAGAG+TGG - Chr4:80747224-80747243 MsG0480023093.01.T01:intron 50.0%
TGAACTAGCAGCGACGTGTT+TGG - Chr4:80747944-80747963 MsG0480023093.01.T01:intron 50.0%
TTGGGGAGATCTTGAGTCCA+GGG + Chr4:80747664-80747683 None:intergenic 50.0%
TTTGGGGAGATCTTGAGTCC+AGG + Chr4:80747665-80747684 None:intergenic 50.0%
! GAGTGTTGTTACCTCTGCTG+TGG + Chr4:80746612-80746631 None:intergenic 50.0%
! GGTGATTGCGATCCGATTTG+TGG - Chr4:80746752-80746771 MsG0480023093.01.T01:three_prime_UTR 50.0%
AGAAGAAGGAAGACACCCGG+TGG - Chr4:80747584-80747603 MsG0480023093.01.T01:intron 55.0%
CGCTGCTGCACTTCCTCTTT+GGG + Chr4:80747552-80747571 None:intergenic 55.0%
GAACTCCGTTTCCACAGCAG+AGG - Chr4:80746598-80746617 MsG0480023093.01.T01:three_prime_UTR 55.0%
GCTGCTGCACTTCCTCTTTG+GGG + Chr4:80747551-80747570 None:intergenic 55.0%
TCGCTGCTGCACTTCCTCTT+TGG + Chr4:80747553-80747572 None:intergenic 55.0%
TGGGGAGATCTTGAGTCCAG+GGG + Chr4:80747663-80747682 None:intergenic 55.0%
AAGGAAGACACCCGGTGGTG+GGG - Chr4:80747589-80747608 MsG0480023093.01.T01:intron 60.0%
AGAAGGAAGACACCCGGTGG+TGG - Chr4:80747587-80747606 MsG0480023093.01.T01:intron 60.0%
GAAGGAAGACACCCGGTGGT+GGG - Chr4:80747588-80747607 MsG0480023093.01.T01:intron 60.0%
GGGCATCTGGAGGAGCTGCA+GGG - Chr4:80747609-80747628 MsG0480023093.01.T01:intron 65.0%
GGTGGAGCAGCTCCCCAAAG+AGG - Chr4:80747536-80747555 MsG0480023093.01.T01:intron 65.0%
TCCTCCAGATGCCCCACCAC+CGG + Chr4:80747603-80747622 None:intergenic 65.0%
CCTCCAGATGCCCCACCACC+GGG + Chr4:80747602-80747621 None:intergenic 70.0%
! GGGGCATCTGGAGGAGCTGC+AGG - Chr4:80747608-80747627 MsG0480023093.01.T01:intron 70.0%
!! ACACCCGGTGGTGGGGCATC+TGG - Chr4:80747596-80747615 MsG0480023093.01.T01:intron 70.0%
!! CCCGGTGGTGGGGCATCTGG+AGG - Chr4:80747599-80747618 MsG0480023093.01.T01:intron 75.0%
Chromosome Type Strat End Strand Name
Chr4 gene 80746542 80748040 80746542 ID=MsG0480023093.01;Name=MsG0480023093.01
Chr4 mRNA 80746542 80748040 80746542 ID=MsG0480023093.01.T01;Parent=MsG0480023093.01;Name=MsG0480023093.01.T01;_AED=0.49;_eAED=0.49;_QI=78|0|0.5|1|0|0.5|2|268|81
Chr4 exon 80746542 80747055 80746542 ID=MsG0480023093.01.T01:exon:23743;Parent=MsG0480023093.01.T01
Chr4 exon 80747963 80748040 80747963 ID=MsG0480023093.01.T01:exon:23742;Parent=MsG0480023093.01.T01
Chr4 five_prime_UTR 80747963 80748040 80747963 ID=MsG0480023093.01.T01:five_prime_utr;Parent=MsG0480023093.01.T01
Chr4 CDS 80746810 80747055 80746810 ID=MsG0480023093.01.T01:cds;Parent=MsG0480023093.01.T01
Chr4 three_prime_UTR 80746542 80746809 80746542 ID=MsG0480023093.01.T01:three_prime_utr;Parent=MsG0480023093.01.T01
Gene Sequence

>MsG0480023093.01.T01

ATGGCTTCAGGTGGAGCAGCTCCCCAAAGAGGAAGTGCAGCAGCGACTGCAAGCATGAGAAGAAGGAAGACACCCGGTGGTGGGGCATCTGGAGGAGCTGCAGGGACTATGCTTCAGTTTTACACTGATGATGCCCCTGGACTCAAGATCTCCCCAAATGTGGTTCTTGTGATGAGCATTGGCTTTATAGCATTTGTTGCCATCCTTCATGTGATTGGCAAGTTGTACTTGCGTAAGGAGGCTTAG
Protein sequence

>MsG0480023093.01.T01

MASGGAAPQRGSAAATASMRRRKTPGGGASGGAAGTMLQFYTDDAPGLKISPNVVLVMSIGFIAFVAILHVIGKLYLRKEA*