AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080047812.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080047812.01.T01 MTR_2g105430 100.000 57 0 0 1 57 68 124 1.20e-38 125
MsG0080047812.01.T01 MTR_6g008680 46.552 58 29 1 1 58 10 65 4.47e-15 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080047812.01.T01 AT5G43150 41.818 55 30 1 4 58 10 62 3.53e-12 55.8

Find 45 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACAAATTTATGCATATT+TGG 0.139534 contig110end:+6344 MsG0080047811.01.T01:CDS
AGCGCAAGCAACTGCCTTTC+TGG 0.183427 contig110end:+7499 MsG0080047812.01.T01:three_prime_UTR
TAATACTTTACAAATAAAAT+TGG 0.235179 contig110end:+7604 MsG0080047812.01.T01:three_prime_UTR
CGCATTGCAGTGCTAGTTCT+TGG 0.250346 contig110end:+7647 MsG0080047812.01.T01:three_prime_UTR
GCAGTAACTATTCCTCAAAA+TGG 0.310904 contig110end:-7784 None:intergenic
AAGGGCAAGGGCAAGGGCAG+GGG 0.349176 contig110end:+6246 MsG0080047812.01.T01:five_prime_UTR
CAAGGGCAAGGGCAGGGGCA+TGG 0.366059 contig110end:+6251 MsG0080047812.01.T01:five_prime_UTR
TAAAGTATTAAATTTGTGTT+TGG 0.378924 contig110end:-7591 None:intergenic
ATTGCGAGGAAGCTTTAGTA+TGG 0.392622 contig110end:-7548 None:intergenic
GCAAGGGCAAGGGCAAGGGC+AGG 0.392948 contig110end:+6244 MsG0080047812.01.T01:five_prime_UTR
TGCTACTAGCGGCACTGGCC+TGG 0.402795 contig110end:+6195 MsG0080047812.01.T01:five_prime_UTR
GTACATGTGAGAAAGATAAA+AGG 0.406565 contig110end:-6109 None:intergenic
TATATTAACAAAATCATATG+AGG 0.406749 contig110end:+7688 MsG0080047812.01.T01:three_prime_UTR
TGCCCTTGCCCTTGCCTATG+TGG 0.413272 contig110end:-6236 None:intergenic
CGAGGAAGCTTTAGTATGGT+TGG 0.440416 contig110end:-7544 None:intergenic
CATAGGCAAGGGCAAGGGCA+AGG 0.444965 contig110end:+6239 MsG0080047812.01.T01:five_prime_UTR
TGAGGTTTATCTCGTACAAC+TGG 0.447023 contig110end:+7706 MsG0080047812.01.T01:three_prime_UTR
CAAGGGCAAGGGCAAGGGCA+GGG 0.452394 contig110end:+6245 MsG0080047812.01.T01:five_prime_UTR
AGCTTTAGTATGGTTGGAGT+TGG 0.457080 contig110end:-7538 None:intergenic
TTGATTGCTACTAGCGGCAC+TGG 0.496670 contig110end:+6190 MsG0080047812.01.T01:five_prime_UTR
AGAGAATAGTGTTGCCACAT+AGG 0.505315 contig110end:+6222 MsG0080047812.01.T01:five_prime_UTR
GCAAGGCATAGACGCCTGAC+AGG 0.537537 contig110end:-6382 None:intergenic
GGGCATGGAAAGAACAAGAA+TGG 0.538380 contig110end:+6266 MsG0080047811.01.T01:CDS
ATAGGCAAGGGCAAGGGCAA+GGG 0.539153 contig110end:+6240 MsG0080047812.01.T01:five_prime_UTR
ATATAGAAACAGAAAGAGAA+AGG 0.547565 contig110end:-6065 None:intergenic
GGCAGTTGCTTGCGCTATGG+TGG 0.552699 contig110end:-7492 None:intergenic
CAAGATGATGTACAAACTTG+TGG 0.560224 contig110end:+7407 MsG0080047811.01.T01:CDS
AGTAGTAGTGGAATTGAGAG+AGG 0.562231 contig110end:+6002 None:intergenic
AAAGGCAGTTGCTTGCGCTA+TGG 0.565751 contig110end:-7495 None:intergenic
TTGCCACATAGGCAAGGGCA+AGG 0.566012 contig110end:+6233 MsG0080047812.01.T01:five_prime_UTR
TGAAGATGTACAAGTGATGT+GGG 0.568556 contig110end:+7433 MsG0080047811.01.T01:CDS
CAACACTATTCTCTTTGACC+AGG 0.569671 contig110end:-6213 None:intergenic
CATACAAAGACTCTCCAGAA+AGG 0.593758 contig110end:-7513 None:intergenic
ATAGTGTTGCCACATAGGCA+AGG 0.603679 contig110end:+6227 MsG0080047812.01.T01:five_prime_UTR
ATGAAGATGTACAAGTGATG+TGG 0.606676 contig110end:+7432 MsG0080047811.01.T01:CDS
TGGTACAGGAGGAGCAGGAT+TGG 0.606763 contig110end:+7376 MsG0080047811.01.T01:intron
TAGTGTTGCCACATAGGCAA+GGG 0.614827 contig110end:+6228 MsG0080047812.01.T01:five_prime_UTR
ATTGATTTGATTGCTACTAG+CGG 0.638632 contig110end:+6184 MsG0080047812.01.T01:five_prime_UTR
AAGACAGTAGTAGTATCATG+TGG 0.645963 contig110end:+6304 MsG0080047811.01.T01:CDS
TGATACGGGTAGATAGAGCA+AGG 0.670563 contig110end:-6399 None:intergenic
TGCCACATAGGCAAGGGCAA+GGG 0.671240 contig110end:+6234 MsG0080047812.01.T01:five_prime_UTR
AGTCTGATTTGAAGATTGCG+AGG 0.677820 contig110end:-7562 None:intergenic
ACAGTAGTAGTATCATGTGG+AGG 0.690266 contig110end:+6307 MsG0080047811.01.T01:CDS
GTGAGAAAGATAAAAGGACA+AGG 0.702650 contig110end:-6103 None:intergenic
CAAGAACTAGCACTGCAATG+CGG 0.764502 contig110end:-7646 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAAATAATAATTATAA+TGG - contig110end:6825-6844 None:intergenic 0.0%
!! AAATATGTTGTTAATTAAAT+TGG - contig110end:6868-6887 None:intergenic 10.0%
!! TAATACTTTACAAATAAAAT+TGG + contig110end:7604-7623 MsG0080047812.01.T01:three_prime_UTR 10.0%
!! TATAGTACAATATTTATTTA+AGG - contig110end:6923-6942 None:intergenic 10.0%
!!! CTTCTTAATTTTATTATTTT+TGG + contig110end:6615-6634 MsG0080047811.01.T01:intron 10.0%
!!! TTATTTTATTTTATACCTTT+CGG + contig110end:6834-6853 MsG0080047811.01.T01:intron 10.0%
!! GTATATAATTATAATTTCCA+TGG - contig110end:6505-6524 None:intergenic 15.0%
!! TATATTAACAAAATCATATG+AGG + contig110end:7688-7707 MsG0080047812.01.T01:three_prime_UTR 15.0%
!! TTACATCATATTAATATTGA+TGG + contig110end:7202-7221 MsG0080047811.01.T01:intron 15.0%
!! TTATTTAAGGAAAAAAACTT+AGG - contig110end:6910-6929 None:intergenic 15.0%
!!! TAAAGTATTAAATTTGTGTT+TGG - contig110end:7594-7613 None:intergenic 15.0%
!! ACAACAAATTTATGCATATT+TGG + contig110end:6344-6363 MsG0080047811.01.T01:CDS 20.0%
!! ATAATTATAATTTCCATGGA+TGG - contig110end:6501-6520 None:intergenic 20.0%
!! ATGTAAGAATTACACAAAAA+GGG - contig110end:7188-7207 None:intergenic 20.0%
!! TTTCTAAGTATATAGTTGAA+TGG + contig110end:6659-6678 MsG0080047811.01.T01:intron 20.0%
! ATACTTTAGGTAAATGGAAA+GGG + contig110end:7233-7252 MsG0080047811.01.T01:intron 25.0%
! ATATAGAAACAGAAAGAGAA+AGG - contig110end:6068-6087 None:intergenic 25.0%
! CTATACTATACTAGTATACA+CGG + contig110end:7117-7136 MsG0080047811.01.T01:intron 25.0%
! GATATGATACTTTAGGTAAA+TGG + contig110end:7227-7246 MsG0080047811.01.T01:intron 25.0%
! GATGTAAGAATTACACAAAA+AGG - contig110end:7189-7208 None:intergenic 25.0%
! GTGTATACTAGTATAGTATA+GGG - contig110end:7118-7137 None:intergenic 25.0%
! TAAGTATATAGTTGAATGGA+TGG + contig110end:6663-6682 MsG0080047811.01.T01:intron 25.0%
! TACAAAATACATGATACAAG+TGG + contig110end:6948-6967 MsG0080047811.01.T01:intron 25.0%
! TCGTACAATTATATATGTTG+CGG - contig110end:6589-6608 None:intergenic 25.0%
! TTAATATTACATAAGCACAC+AGG + contig110end:6757-6776 MsG0080047811.01.T01:intron 25.0%
! TTTAAGGAAAAAAACTTAGG+TGG - contig110end:6907-6926 None:intergenic 25.0%
!!! AATAAATAGTACCGTTTTTG+CGG - contig110end:6429-6448 None:intergenic 25.0%
AAAATACATGATACAAGTGG+TGG + contig110end:6951-6970 MsG0080047811.01.T01:intron 30.0%
ACATGCATGATTTGAATGTA+AGG - contig110end:7333-7352 None:intergenic 30.0%
ATACAATTACAAACCATCCA+TGG + contig110end:6485-6504 MsG0080047811.01.T01:intron 30.0%
ATTAACAACATATTTCAGCC+AGG + contig110end:6873-6892 MsG0080047811.01.T01:intron 30.0%
ATTATAATGGCATTAGACGT+AGG - contig110end:6812-6831 None:intergenic 30.0%
ATTCTCTACAGATACTTCTT+GGG - contig110end:7271-7290 None:intergenic 30.0%
ATTGACACTGATCATCATAA+TGG - contig110end:6722-6741 None:intergenic 30.0%
CGTGTATACTAGTATAGTAT+AGG - contig110end:7119-7138 None:intergenic 30.0%
GATACTTTAGGTAAATGGAA+AGG + contig110end:7232-7251 MsG0080047811.01.T01:intron 30.0%
GATGGATGATATGATACTTT+AGG + contig110end:7220-7239 MsG0080047811.01.T01:intron 30.0%
GTACATGTGAGAAAGATAAA+AGG - contig110end:6112-6131 None:intergenic 30.0%
TACTTTAGGTAAATGGAAAG+GGG + contig110end:7234-7253 MsG0080047811.01.T01:intron 30.0%
TATTCTCTACAGATACTTCT+TGG - contig110end:7272-7291 None:intergenic 30.0%
TCAGTGTCAATATTTGCTTT+CGG + contig110end:6731-6750 MsG0080047811.01.T01:intron 30.0%
! AAACTATGATTTTTCCTGTC+AGG + contig110end:6368-6387 MsG0080047811.01.T01:CDS 30.0%
! TACTCAATAACTCCATTTTG+AGG + contig110end:7772-7791 MsG0080047812.01.T01:three_prime_UTR 30.0%
!! ATTGATTTGATTGCTACTAG+CGG + contig110end:6184-6203 MsG0080047812.01.T01:five_prime_UTR 30.0%
AAACTTTGACGTAGCTTTCA+GGG - contig110end:7079-7098 None:intergenic 35.0%
AAGACAGTAGTAGTATCATG+TGG + contig110end:6304-6323 MsG0080047811.01.T01:CDS 35.0%
AAGTTGCACTGAAAAAGATG+TGG - contig110end:7034-7053 None:intergenic 35.0%
ACAAACTTGATCTTGCTTTC+AGG + contig110end:6554-6573 MsG0080047811.01.T01:intron 35.0%
ACACTGATCATCATAATGGT+TGG - contig110end:6718-6737 None:intergenic 35.0%
ATGAAGATGTACAAGTGATG+TGG + contig110end:7432-7451 MsG0080047811.01.T01:CDS 35.0%
CAAGATGATGTACAAACTTG+TGG + contig110end:7407-7426 MsG0080047811.01.T01:CDS 35.0%
CATATTTCAGCCAGGATATA+CGG + contig110end:6881-6900 MsG0080047811.01.T01:intron 35.0%
GAAGAAGAAGAAGAAGAAAG+TGG + contig110end:6154-6173 MsG0080047812.01.T01:five_prime_UTR 35.0%
GAATTGTCATGAACTTGAAG+TGG - contig110end:6783-6802 None:intergenic 35.0%
GCAGTAACTATTCCTCAAAA+TGG - contig110end:7787-7806 None:intergenic 35.0%
GTGAGAAAGATAAAAGGACA+AGG - contig110end:6106-6125 None:intergenic 35.0%
TAAACTTTGACGTAGCTTTC+AGG - contig110end:7080-7099 None:intergenic 35.0%
TGAAGATGTACAAGTGATGT+GGG + contig110end:7433-7452 MsG0080047811.01.T01:CDS 35.0%
TGATCATCATAATGGTTGGT+TGG - contig110end:6714-6733 None:intergenic 35.0%
!! ATGCTTCAAAAAGTGTCCTA+TGG + contig110end:7145-7164 MsG0080047811.01.T01:intron 35.0%
AAATTGGTTGTGATGCCGAA+AGG - contig110end:6852-6871 None:intergenic 40.0%
ACAGTAGTAGTATCATGTGG+AGG + contig110end:6307-6326 MsG0080047811.01.T01:CDS 40.0%
AGAGAATAGTGTTGCCACAT+AGG + contig110end:6222-6241 MsG0080047812.01.T01:five_prime_UTR 40.0%
AGTACATGTTTGTGTGGTAC+AGG + contig110end:7362-7381 MsG0080047811.01.T01:intron 40.0%
CAACACTATTCTCTTTGACC+AGG - contig110end:6216-6235 None:intergenic 40.0%
CATACAAAGACTCTCCAGAA+AGG - contig110end:7516-7535 None:intergenic 40.0%
CCTATGGTTTAATGACAGAC+AGG + contig110end:7161-7180 MsG0080047811.01.T01:intron 40.0%
CCTGTCTGTCATTAAACCAT+AGG - contig110end:7164-7183 None:intergenic 40.0%
CTTATACCACTTTCATCGTG+CGG + contig110end:7051-7070 MsG0080047811.01.T01:intron 40.0%
TACCACACAAACATGTACTC+AGG - contig110end:7361-7380 None:intergenic 40.0%
TCTACAGATACTTCTTGGGA+GGG - contig110end:7267-7286 None:intergenic 40.0%
TGAGGTTTATCTCGTACAAC+TGG + contig110end:7706-7725 MsG0080047812.01.T01:three_prime_UTR 40.0%
! AGCTTTAGTATGGTTGGAGT+TGG - contig110end:7541-7560 None:intergenic 40.0%
! AGTCTGATTTGAAGATTGCG+AGG - contig110end:7565-7584 None:intergenic 40.0%
! ATTGCGAGGAAGCTTTAGTA+TGG - contig110end:7551-7570 None:intergenic 40.0%
!! AAATAGTACCGTTTTTGCGG+TGG - contig110end:6426-6445 None:intergenic 40.0%
ACATGTTTGTGTGGTACAGG+AGG + contig110end:7365-7384 MsG0080047811.01.T01:intron 45.0%
ATAGTGTTGCCACATAGGCA+AGG + contig110end:6227-6246 MsG0080047812.01.T01:five_prime_UTR 45.0%
CAAGAACTAGCACTGCAATG+CGG - contig110end:7649-7668 None:intergenic 45.0%
CGTATCAACCACCGCAAAAA+CGG + contig110end:6415-6434 MsG0080047811.01.T01:CDS 45.0%
CTCTACAGATACTTCTTGGG+AGG - contig110end:7268-7287 None:intergenic 45.0%
GACCTGAGTACATGTTTGTG+TGG + contig110end:7356-7375 MsG0080047811.01.T01:intron 45.0%
GGGCATGGAAAGAACAAGAA+TGG + contig110end:6266-6285 MsG0080047811.01.T01:CDS 45.0%
TAGTGTTGCCACATAGGCAA+GGG + contig110end:6228-6247 MsG0080047812.01.T01:five_prime_UTR 45.0%
TGATACGGGTAGATAGAGCA+AGG - contig110end:6402-6421 None:intergenic 45.0%
! CGAGGAAGCTTTAGTATGGT+TGG - contig110end:7547-7566 None:intergenic 45.0%
!! CGTTTTTGCGGTGGTTGATA+CGG - contig110end:6417-6436 None:intergenic 45.0%
!! GTTTTTGCGGTGGTTGATAC+GGG - contig110end:6416-6435 None:intergenic 45.0%
AAAGGCAGTTGCTTGCGCTA+TGG - contig110end:7498-7517 None:intergenic 50.0%
ACTTAGGTGGCCGTATATCC+TGG - contig110end:6894-6913 None:intergenic 50.0%
AGATACTTCTTGGGAGGGTC+AGG - contig110end:7262-7281 None:intergenic 50.0%
ATCCTTTGATCAGTGCCCTG+CGG + contig110end:6990-7009 MsG0080047811.01.T01:intron 50.0%
CTACCTCTATTGTTGCCGCA+GGG - contig110end:7008-7027 None:intergenic 50.0%
GATACTTCTTGGGAGGGTCA+GGG - contig110end:7261-7280 None:intergenic 50.0%
TTGATTGCTACTAGCGGCAC+TGG + contig110end:6190-6209 MsG0080047812.01.T01:five_prime_UTR 50.0%
! CGCATTGCAGTGCTAGTTCT+TGG + contig110end:7647-7666 MsG0080047812.01.T01:three_prime_UTR 50.0%
AGCGCAAGCAACTGCCTTTC+TGG + contig110end:7499-7518 MsG0080047812.01.T01:three_prime_UTR 55.0%
ATAGGCAAGGGCAAGGGCAA+GGG + contig110end:6240-6259 MsG0080047812.01.T01:five_prime_UTR 55.0%
CCTACCTCTATTGTTGCCGC+AGG - contig110end:7009-7028 None:intergenic 55.0%
CCTGCGGCAACAATAGAGGT+AGG + contig110end:7006-7025 MsG0080047811.01.T01:intron 55.0%
TGCCACATAGGCAAGGGCAA+GGG + contig110end:6234-6253 MsG0080047812.01.T01:five_prime_UTR 55.0%
TGGTACAGGAGGAGCAGGAT+TGG + contig110end:7376-7395 MsG0080047811.01.T01:intron 55.0%
TTGCCACATAGGCAAGGGCA+AGG + contig110end:6233-6252 MsG0080047812.01.T01:five_prime_UTR 55.0%
TTGTGTGGTACAGGAGGAGC+AGG + contig110end:7371-7390 MsG0080047811.01.T01:intron 55.0%
CATAGGCAAGGGCAAGGGCA+AGG + contig110end:6239-6258 MsG0080047812.01.T01:five_prime_UTR 60.0%
GCAAGGCATAGACGCCTGAC+AGG - contig110end:6385-6404 None:intergenic 60.0%
GGCAGTTGCTTGCGCTATGG+TGG - contig110end:7495-7514 None:intergenic 60.0%
GTGCCCTGCGGCAACAATAG+AGG + contig110end:7002-7021 MsG0080047811.01.T01:intron 60.0%
TGCCCTTGCCCTTGCCTATG+TGG - contig110end:6239-6258 None:intergenic 60.0%
!! AGGGCACCGCACGATGAAAG+TGG - contig110end:7060-7079 None:intergenic 60.0%
!! TGCCGCAGGGCACTGATCAA+AGG - contig110end:6995-7014 None:intergenic 60.0%
AAGGGCAAGGGCAAGGGCAG+GGG + contig110end:6246-6265 MsG0080047812.01.T01:five_prime_UTR 65.0%
CAAGGGCAAGGGCAAGGGCA+GGG + contig110end:6245-6264 MsG0080047812.01.T01:five_prime_UTR 65.0%
!! TGCTACTAGCGGCACTGGCC+TGG + contig110end:6195-6214 MsG0080047812.01.T01:five_prime_UTR 65.0%
CAAGGGCAAGGGCAGGGGCA+TGG + contig110end:6251-6270 MsG0080047812.01.T01:five_prime_UTR 70.0%
GCAAGGGCAAGGGCAAGGGC+AGG + contig110end:6244-6263 MsG0080047812.01.T01:five_prime_UTR 70.0%
Chromosome Type Strat End Strand Name
contig110end gene 6008 7818 6008 ID=MsG0080047812.01;Name=MsG0080047812.01
contig110end mRNA 6008 7818 6008 ID=MsG0080047812.01.T01;Parent=MsG0080047812.01;Name=MsG0080047812.01.T01;_AED=0.26;_eAED=0.26;_QI=347|0|0.5|1|0|0|2|337|58
contig110end exon 7387 7818 7387 ID=MsG0080047812.01.T01:exon:18662;Parent=MsG0080047812.01.T01
contig110end exon 6008 6436 6008 ID=MsG0080047812.01.T01:exon:18661;Parent=MsG0080047812.01.T01
contig110end five_prime_UTR 6008 6354 6008 ID=MsG0080047812.01.T01:five_prime_utr;Parent=MsG0080047812.01.T01
contig110end CDS 6355 6436 6355 ID=MsG0080047812.01.T01:cds;Parent=MsG0080047812.01.T01
contig110end CDS 7387 7481 7387 ID=MsG0080047812.01.T01:cds;Parent=MsG0080047812.01.T01
contig110end three_prime_UTR 7482 7818 7482 ID=MsG0080047812.01.T01:three_prime_utr;Parent=MsG0080047812.01.T01
Gene Sequence

>MsG0080047812.01.T01

ATGCATATTTGGCAAACTATGATTTTTCCTGTCAGGCGTCTATGCCTTGCTCTATCTACCCGTATCAACCACCGCAAAAACGGAGCAGGATTGGTGAAGCTTCAAGATGATGTACAAACTTGTGGATATGAAGATGTACAAGTGATGTGGGAAATGTTACAGAAAACTGAAAACTGA
Protein sequence

>MsG0080047812.01.T01

MHIWQTMIFPVRRLCLALSTRINHRKNGAGLVKLQDDVQTCGYEDVQVMWEMLQKTEN*