AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580028142.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580028142.01.T01 MTR_4g123470 35.385 195 122 3 16 209 19 210 2.86e-30 112
MsG0580028142.01.T01 MTR_5g053510 57.647 85 34 1 144 226 25 109 1.36e-27 101
MsG0580028142.01.T01 MTR_1g054495 26.009 223 160 4 1 222 1 219 1.84e-24 97.1
MsG0580028142.01.T01 MTR_7g025150 30.303 231 140 8 1 222 1 219 2.69e-22 91.3
MsG0580028142.01.T01 MTR_4g085790 30.088 226 147 8 1 222 1 219 5.04e-22 90.5
MsG0580028142.01.T01 MTR_0014s0220 25.121 207 135 4 5 210 623 810 7.80e-19 85.1
MsG0580028142.01.T01 MTR_4g053550 49.296 71 35 1 24 93 47 117 1.50e-18 79.0
MsG0580028142.01.T01 MTR_1g054485 27.419 186 131 3 1 185 1 183 5.25e-17 76.3
MsG0580028142.01.T01 MTR_1g090753 34.906 106 68 1 26 130 43 148 1.38e-12 63.9
MsG0580028142.01.T01 MTR_1g041870 28.481 158 98 3 65 222 29 171 1.32e-11 61.6
MsG0580028142.01.T01 MTR_5g074790 29.464 112 77 2 8 117 154 265 1.41e-11 62.8
MsG0580028142.01.T01 MTR_7g039210 21.397 229 152 4 1 201 1 229 6.85e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 69 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCAAATTCATCAGTGAATT+TGG 0.125206 5:+75383139 None:intergenic
ACAATGTGTCTTTAGGAATT+TGG 0.142567 5:-75383173 MsG0580028142.01.T01:intron
AGTCTTGAAGAGGCCGATTT+TGG 0.199679 5:-75383404 MsG0580028142.01.T01:CDS
CTGATTTCAATGATTTCTTA+TGG 0.239474 5:-75382682 MsG0580028142.01.T01:CDS
TCAAATTCATCAGTGAATTT+GGG 0.278770 5:+75383140 None:intergenic
CCAACCCTTCGTTAGCTTGC+TGG 0.293858 5:+75382571 None:intergenic
GCACATCTCCAGCCTGATAT+TGG 0.349705 5:+75382528 None:intergenic
TTAAGCAACAGGTGAGAGTT+AGG 0.354686 5:+75383448 None:intergenic
CACATTGACCCCTTTGCAAA+TGG 0.355395 5:-75382841 MsG0580028142.01.T01:CDS
CTGCGTTTCAAGTTCTTTGA+TGG 0.370866 5:-75382506 MsG0580028142.01.T01:CDS
CTGCACGACCAGCCAATATC+AGG 0.371998 5:-75382540 MsG0580028142.01.T01:CDS
CGTGGATTACATCACTTGAT+TGG 0.380696 5:+75382329 None:intergenic
CTGATTCTGTTTAGCTATGT+TGG 0.402336 5:-75382978 MsG0580028142.01.T01:CDS
GATTATTTGACCATTGTCAT+TGG 0.404983 5:+75382631 None:intergenic
GTTGCAAAGCCTCCCAAAAT+CGG 0.416978 5:+75383391 None:intergenic
AGACGAACACACAACTTGAT+TGG 0.422524 5:+75382431 None:intergenic
CATAAGAAATCATTGAAATC+AGG 0.427387 5:+75382683 None:intergenic
CAGCCATGGTGTTAAGCAAC+AGG 0.434230 5:+75383437 None:intergenic
AAACAAAGGATTCATAATAC+AGG 0.435820 5:+75382379 None:intergenic
TTGACGACGTGGGTCCAGTC+TGG 0.447707 5:-75383121 MsG0580028142.01.T01:CDS
TATGGATTGCAGGAAACAAA+AGG 0.462520 5:+75382273 None:intergenic
AATACAGGGGCGCCTAATAC+AGG 0.467954 5:+75382394 None:intergenic
GAAGTCTTGTGCTTCTGCTA+TGG 0.476473 5:+75382892 None:intergenic
TCAGCTTCATGCCTTCAAAC+TGG 0.481449 5:+75382997 None:intergenic
AGTAGATTTGTTATCACACT+TGG 0.481808 5:-75382951 MsG0580028142.01.T01:CDS
ACTCTGCCACGGTTAACTAA+TGG 0.484622 5:-75383044 MsG0580028142.01.T01:CDS
AATTCGCATCCATTTGCAAA+GGG 0.485601 5:+75382832 None:intergenic
CAGCAAGCTAACGAAGGGTT+GGG 0.497952 5:-75382570 MsG0580028142.01.T01:CDS
CACACTTGGGAATACAATTG+AGG 0.504352 5:-75382937 MsG0580028142.01.T01:CDS
ATCTCCAGCCTGATATTGGC+TGG 0.512753 5:+75382532 None:intergenic
CCAGCAAGCTAACGAAGGGT+TGG 0.517788 5:-75382571 MsG0580028142.01.T01:CDS
CTGTTGCTTAACACCATGGC+TGG 0.520138 5:-75383436 MsG0580028142.01.T01:exon
TGCGTTTCAAGTTCTTTGAT+GGG 0.523138 5:-75382505 MsG0580028142.01.T01:CDS
AACTGTTCATTTACCACACA+AGG 0.524327 5:-75383371 MsG0580028142.01.T01:intron
TTCAATGATTTCTTATGGAA+TGG 0.526065 5:-75382677 MsG0580028142.01.T01:CDS
AATGGATGCGAATTCTGAAC+TGG 0.528366 5:-75382823 MsG0580028142.01.T01:intron
TGCCACGGTTAACTAATGGC+TGG 0.531042 5:-75383040 MsG0580028142.01.T01:CDS
CAAATTCATCAGTGAATTTG+GGG 0.542034 5:+75383141 None:intergenic
ACTGCTATTCATTACCAAGT+TGG 0.542667 5:-75382605 MsG0580028142.01.T01:CDS
ATGGATTGCAGGAAACAAAA+GGG 0.547596 5:+75382274 None:intergenic
CACTGATGAATTTGACGACG+TGG 0.552994 5:-75383132 MsG0580028142.01.T01:CDS
CATAAAGACACTTGAAACAA+AGG 0.569967 5:+75382365 None:intergenic
TGGAATTTAATTGACGCTGA+AGG 0.570875 5:-75383101 MsG0580028142.01.T01:CDS
GAATTCGCATCCATTTGCAA+AGG 0.571229 5:+75382831 None:intergenic
AAGAAATCATTGAAATCAGG+TGG 0.573987 5:+75382686 None:intergenic
GCGTCAATTAAATTCCAGAC+TGG 0.579334 5:+75383107 None:intergenic
AACAAAGGATTCATAATACA+GGG 0.582164 5:+75382380 None:intergenic
AATCATTGAAATCAGGTGGA+AGG 0.583795 5:+75382690 None:intergenic
GTAGATTTGTTATCACACTT+GGG 0.584740 5:-75382950 MsG0580028142.01.T01:CDS
TTGTTCCTCTCCAATGACAA+TGG 0.585814 5:-75382641 MsG0580028142.01.T01:CDS
GAACACACAACTTGATTGGA+AGG 0.585955 5:+75382435 None:intergenic
TTTGACCATTGTCATTGGAG+AGG 0.597349 5:+75382636 None:intergenic
ACAATTCAGCTACTCTGCCA+CGG 0.617034 5:-75383055 MsG0580028142.01.T01:CDS
ACTCACCAGCAAGCTAACGA+AGG 0.624585 5:-75382576 MsG0580028142.01.T01:CDS
CGCTGAAGGAAATTCTCATG+AGG 0.625269 5:-75383087 MsG0580028142.01.T01:CDS
GATATCGCGCAGTCTTGAAG+AGG 0.633574 5:-75383414 MsG0580028142.01.T01:CDS
GTGCTTCTGCTATGGTACGT+AGG 0.636405 5:+75382900 None:intergenic
TGAAATTACGAAACCTTGTG+TGG 0.636743 5:+75383358 None:intergenic
CAAGCTAACGAAGGGTTGGG+AGG 0.643100 5:-75382567 MsG0580028142.01.T01:CDS
ACGACCAGCCAATATCAGGC+TGG 0.644275 5:-75382536 MsG0580028142.01.T01:CDS
CTCACCAGCAAGCTAACGAA+GGG 0.650798 5:-75382575 MsG0580028142.01.T01:CDS
GACTGCGCGATATCCAGCCA+TGG 0.651701 5:+75383423 None:intergenic
ATTCGCATCCATTTGCAAAG+GGG 0.653436 5:+75382833 None:intergenic
TCACCTGTTGCTTAACACCA+TGG 0.660351 5:-75383440 MsG0580028142.01.T01:exon
ACTGATGAATTTGACGACGT+GGG 0.661784 5:-75383131 MsG0580028142.01.T01:CDS
TGGTGAGTGAGTCACCAACT+TGG 0.680717 5:+75382591 None:intergenic
AACAAAATATAAGTTCATCG+TGG 0.683011 5:+75382311 None:intergenic
GTCCAGCCATTAGTTAACCG+TGG 0.698189 5:+75383038 None:intergenic
ACAAAGGATTCATAATACAG+GGG 0.723022 5:+75382381 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTGTATTATTTAGAGAA+TGG + Chr5:75382295-75382314 None:intergenic 15.0%
!!! GTAAATTTTCTTTGTAATTA+AGG + Chr5:75382570-75382589 None:intergenic 15.0%
!! CAACAATGAAAATTAAGATT+AGG + Chr5:75383053-75383072 None:intergenic 20.0%
!! TGTTTATTAAAATCTGCAAA+TGG - Chr5:75383003-75383022 MsG0580028142.01.T01:CDS 20.0%
! AAACAAAGGATTCATAATAC+AGG + Chr5:75383400-75383419 None:intergenic 25.0%
! AACAAAATATAAGTTCATCG+TGG + Chr5:75383468-75383487 None:intergenic 25.0%
! AACAAAGGATTCATAATACA+GGG + Chr5:75383399-75383418 None:intergenic 25.0%
! AAGGTTTCGTAATTTCATTT+CGG - Chr5:75382424-75382443 MsG0580028142.01.T01:three_prime_UTR 25.0%
! AGATATATACTTTGCAATAG+AGG + Chr5:75382483-75382502 None:intergenic 25.0%
! CATAAGAAATCATTGAAATC+AGG + Chr5:75383096-75383115 None:intergenic 25.0%
! CTGATTTCAATGATTTCTTA+TGG - Chr5:75383094-75383113 MsG0580028142.01.T01:CDS 25.0%
! TCAAATTCATCAGTGAATTT+GGG + Chr5:75382639-75382658 None:intergenic 25.0%
! TTCAATGATTTCTTATGGAA+TGG - Chr5:75383099-75383118 MsG0580028142.01.T01:CDS 25.0%
!!! TGCAGATTTTAATAAACACA+TGG + Chr5:75383001-75383020 None:intergenic 25.0%
AAGAAATCATTGAAATCAGG+TGG + Chr5:75383093-75383112 None:intergenic 30.0%
ACAAAGGATTCATAATACAG+GGG + Chr5:75383398-75383417 None:intergenic 30.0%
CAAATTCATCAGTGAATTTG+GGG + Chr5:75382638-75382657 None:intergenic 30.0%
CATAAAGACACTTGAAACAA+AGG + Chr5:75383414-75383433 None:intergenic 30.0%
GATTATTTGACCATTGTCAT+TGG + Chr5:75383148-75383167 None:intergenic 30.0%
GTCAAATTCATCAGTGAATT+TGG + Chr5:75382640-75382659 None:intergenic 30.0%
TTTCATTGTTGTCTAAATGC+AGG - Chr5:75383062-75383081 MsG0580028142.01.T01:CDS 30.0%
! ACAATGTGTCTTTAGGAATT+TGG - Chr5:75382603-75382622 MsG0580028142.01.T01:CDS 30.0%
! AGACAATTTTACCAGTTTGA+AGG - Chr5:75382768-75382787 MsG0580028142.01.T01:intron 30.0%
! CTGTTTTATGTACCTGTATT+AGG - Chr5:75383370-75383389 MsG0580028142.01.T01:intron 30.0%
!! AGTAGATTTGTTATCACACT+TGG - Chr5:75382825-75382844 MsG0580028142.01.T01:CDS 30.0%
!! GTAGATTTGTTATCACACTT+GGG - Chr5:75382826-75382845 MsG0580028142.01.T01:CDS 30.0%
AACTGTTCATTTACCACACA+AGG - Chr5:75382405-75382424 MsG0580028142.01.T01:three_prime_UTR 35.0%
AATCATTGAAATCAGGTGGA+AGG + Chr5:75383089-75383108 None:intergenic 35.0%
AATTCGCATCCATTTGCAAA+GGG + Chr5:75382947-75382966 None:intergenic 35.0%
ACTGCTATTCATTACCAAGT+TGG - Chr5:75383171-75383190 MsG0580028142.01.T01:intron 35.0%
CAACTCAACAATGTGTCTTT+AGG - Chr5:75382596-75382615 MsG0580028142.01.T01:CDS 35.0%
CTGATTCTGTTTAGCTATGT+TGG - Chr5:75382798-75382817 MsG0580028142.01.T01:intron 35.0%
TGAAATTACGAAACCTTGTG+TGG + Chr5:75382421-75382440 None:intergenic 35.0%
TGGAATTTAATTGACGCTGA+AGG - Chr5:75382675-75382694 MsG0580028142.01.T01:CDS 35.0%
!! TGCGTTTCAAGTTCTTTGAT+GGG - Chr5:75383271-75383290 MsG0580028142.01.T01:intron 35.0%
AATGGATGCGAATTCTGAAC+TGG - Chr5:75382953-75382972 MsG0580028142.01.T01:CDS 40.0%
ACTGATGAATTTGACGACGT+GGG - Chr5:75382645-75382664 MsG0580028142.01.T01:CDS 40.0%
AGACGAACACACAACTTGAT+TGG + Chr5:75383348-75383367 None:intergenic 40.0%
ATTCGCATCCATTTGCAAAG+GGG + Chr5:75382946-75382965 None:intergenic 40.0%
CACACTTGGGAATACAATTG+AGG - Chr5:75382839-75382858 MsG0580028142.01.T01:CDS 40.0%
GAACACACAACTTGATTGGA+AGG + Chr5:75383344-75383363 None:intergenic 40.0%
GAATTCGCATCCATTTGCAA+AGG + Chr5:75382948-75382967 None:intergenic 40.0%
GCGTCAATTAAATTCCAGAC+TGG + Chr5:75382672-75382691 None:intergenic 40.0%
TTAAGCAACAGGTGAGAGTT+AGG + Chr5:75382331-75382350 None:intergenic 40.0%
TTGTTCCTCTCCAATGACAA+TGG - Chr5:75383135-75383154 MsG0580028142.01.T01:CDS 40.0%
TTTGACCATTGTCATTGGAG+AGG + Chr5:75383143-75383162 None:intergenic 40.0%
! CGTGGATTACATCACTTGAT+TGG + Chr5:75383450-75383469 None:intergenic 40.0%
!! CTGCGTTTCAAGTTCTTTGA+TGG - Chr5:75383270-75383289 MsG0580028142.01.T01:intron 40.0%
ACAATTCAGCTACTCTGCCA+CGG - Chr5:75382721-75382740 MsG0580028142.01.T01:intron 45.0%
ACTCTGCCACGGTTAACTAA+TGG - Chr5:75382732-75382751 MsG0580028142.01.T01:intron 45.0%
CACATTGACCCCTTTGCAAA+TGG - Chr5:75382935-75382954 MsG0580028142.01.T01:CDS 45.0%
CACTGATGAATTTGACGACG+TGG - Chr5:75382644-75382663 MsG0580028142.01.T01:CDS 45.0%
CGCTGAAGGAAATTCTCATG+AGG - Chr5:75382689-75382708 MsG0580028142.01.T01:CDS 45.0%
GTTGCAAAGCCTCCCAAAAT+CGG + Chr5:75382388-75382407 None:intergenic 45.0%
TCAGCTTCATGCCTTCAAAC+TGG + Chr5:75382782-75382801 None:intergenic 45.0%
! GAAGTCTTGTGCTTCTGCTA+TGG + Chr5:75382887-75382906 None:intergenic 45.0%
! TCACCTGTTGCTTAACACCA+TGG - Chr5:75382336-75382355 MsG0580028142.01.T01:three_prime_UTR 45.0%
!! AGTCTTGAAGAGGCCGATTT+TGG - Chr5:75382372-75382391 MsG0580028142.01.T01:three_prime_UTR 45.0%
!! GTCTTGAAGAGGCCGATTTT+GGG - Chr5:75382373-75382392 MsG0580028142.01.T01:three_prime_UTR 45.0%
ACTCACCAGCAAGCTAACGA+AGG - Chr5:75383200-75383219 MsG0580028142.01.T01:intron 50.0%
ATCTCCAGCCTGATATTGGC+TGG + Chr5:75383247-75383266 None:intergenic 50.0%
CAGCAAGCTAACGAAGGGTT+GGG - Chr5:75383206-75383225 MsG0580028142.01.T01:intron 50.0%
CTCACCAGCAAGCTAACGAA+GGG - Chr5:75383201-75383220 MsG0580028142.01.T01:intron 50.0%
GATATCGCGCAGTCTTGAAG+AGG - Chr5:75382362-75382381 MsG0580028142.01.T01:three_prime_UTR 50.0%
GCACATCTCCAGCCTGATAT+TGG + Chr5:75383251-75383270 None:intergenic 50.0%
GTCCAGCCATTAGTTAACCG+TGG + Chr5:75382741-75382760 None:intergenic 50.0%
GTGCTTCTGCTATGGTACGT+AGG + Chr5:75382879-75382898 None:intergenic 50.0%
TGCCACGGTTAACTAATGGC+TGG - Chr5:75382736-75382755 MsG0580028142.01.T01:intron 50.0%
TGGTGAGTGAGTCACCAACT+TGG + Chr5:75383188-75383207 None:intergenic 50.0%
! CAGCCATGGTGTTAAGCAAC+AGG + Chr5:75382342-75382361 None:intergenic 50.0%
! CTGTTGCTTAACACCATGGC+TGG - Chr5:75382340-75382359 MsG0580028142.01.T01:three_prime_UTR 50.0%
!! AATACAGGGGCGCCTAATAC+AGG + Chr5:75383385-75383404 None:intergenic 50.0%
!! TTGAAGAGGCCGATTTTGGG+AGG - Chr5:75382376-75382395 MsG0580028142.01.T01:three_prime_UTR 50.0%
ACGACCAGCCAATATCAGGC+TGG - Chr5:75383240-75383259 MsG0580028142.01.T01:intron 55.0%
CAAGCTAACGAAGGGTTGGG+AGG - Chr5:75383209-75383228 MsG0580028142.01.T01:intron 55.0%
CCAGCAAGCTAACGAAGGGT+TGG - Chr5:75383205-75383224 MsG0580028142.01.T01:intron 55.0%
CTGCACGACCAGCCAATATC+AGG - Chr5:75383236-75383255 MsG0580028142.01.T01:intron 55.0%
!! CCAACCCTTCGTTAGCTTGC+TGG + Chr5:75383208-75383227 None:intergenic 55.0%
GACTGCGCGATATCCAGCCA+TGG + Chr5:75382356-75382375 None:intergenic 60.0%
TTGACGACGTGGGTCCAGTC+TGG - Chr5:75382655-75382674 MsG0580028142.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr5 gene 75382286 75383512 75382286 ID=MsG0580028142.01;Name=MsG0580028142.01
Chr5 mRNA 75382286 75383512 75382286 ID=MsG0580028142.01.T01;Parent=MsG0580028142.01;Name=MsG0580028142.01.T01;_AED=0.44;_eAED=0.44;_QI=69|1|1|1|1|1|3|177|226
Chr5 exon 75382286 75382714 75382286 ID=MsG0580028142.01.T01:exon:45822;Parent=MsG0580028142.01.T01
Chr5 exon 75382824 75383180 75382824 ID=MsG0580028142.01.T01:exon:45821;Parent=MsG0580028142.01.T01
Chr5 exon 75383372 75383512 75383372 ID=MsG0580028142.01.T01:exon:45820;Parent=MsG0580028142.01.T01
Chr5 five_prime_UTR 75383444 75383512 75383444 ID=MsG0580028142.01.T01:five_prime_utr;Parent=MsG0580028142.01.T01
Chr5 CDS 75383372 75383443 75383372 ID=MsG0580028142.01.T01:cds;Parent=MsG0580028142.01.T01
Chr5 CDS 75382824 75383180 75382824 ID=MsG0580028142.01.T01:cds;Parent=MsG0580028142.01.T01
Chr5 CDS 75382463 75382714 75382463 ID=MsG0580028142.01.T01:cds;Parent=MsG0580028142.01.T01
Chr5 three_prime_UTR 75382286 75382462 75382286 ID=MsG0580028142.01.T01:three_prime_utr;Parent=MsG0580028142.01.T01
Gene Sequence

>MsG0580028142.01.T01

ATGGCTGGATATCGCGCAGTCTTGAAGAGGCCGATTTTGGGAGGCTTTGCAACTGTTCATTTACCACACAAGGAATTTGGAGAAATAAACCCCAAATTCACTGATGAATTTGACGACGTGGGTCCAGTCTGGAATTTAATTGACGCTGAAGGAAATTCTCATGAGGTTACATTCAACAATTCAGCTACTCTGCCACGGTTAACTAATGGCTGGACAGACTTGAGACAATTTTACCAGTTTGAAGGCATGAAGCTGATTCTGTTTAGCTATGTTGGTCAAAGTAGATTTGTTATCACACTTGGGAATACAATTGAGGACACTAATGATATACCTACGTACCATAGCAGAAGCACAAGACTTCAGAATAACAAGTCTTTCTTTTTTGACATCACATTGACCCCTTTGCAAATGGATGCGAATTCTGAACTGGTCCTTCCACCTGATTTCAATGATTTCTTATGGAATGGTGACTTTGATTATTTGTTCCTCTCCAATGACAATGGTCAAATAATCAAGACTGCTATTCATTACCAAGTTGGTGACTCACTCACCAGCAAGCTAACGAAGGGTTGGGAGGAATTCTGCACGACCAGCCAATATCAGGCTGGAGATGTGCTGCGTTTCAAGTTCTTTGATGGGAAACTGAAGAATTTTGTTCATGTCTTTATAAACAATGCTTAG
Protein sequence

>MsG0580028142.01.T01

MAGYRAVLKRPILGGFATVHLPHKEFGEINPKFTDEFDDVGPVWNLIDAEGNSHEVTFNNSATLPRLTNGWTDLRQFYQFEGMKLILFSYVGQSRFVITLGNTIEDTNDIPTYHSRSTRLQNNKSFFFDITLTPLQMDANSELVLPPDFNDFLWNGDFDYLFLSNDNGQIIKTAIHYQVGDSLTSKLTKGWEEFCTTSQYQAGDVLRFKFFDGKLKNFVHVFINNA*