AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016537.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016537.01.T01 MTR_3g091700 63.603 272 58 4 1 271 30 261 1.80e-116 335
MsG0380016537.01.T01 MTR_3g435550 47.321 112 53 1 164 269 59 170 2.11e-29 110
MsG0380016537.01.T01 MTR_5g024070 37.719 114 58 1 164 264 201 314 1.04e-19 87.4
MsG0380016537.01.T01 MTR_3g091720 75.000 52 6 1 220 271 19 63 1.07e-17 75.5
MsG0380016537.01.T01 MTR_0140s0010 28.652 178 107 6 109 270 65 238 2.57e-12 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016537.01.T01 AT5G53040 52.381 105 50 0 164 268 148 252 1.11e-32 120
MsG0380016537.01.T01 AT5G66990 49.550 111 45 1 169 268 164 274 8.41e-32 119
MsG0380016537.01.T01 AT1G18790 44.094 127 54 2 149 265 120 239 2.37e-28 109
MsG0380016537.01.T01 AT1G74480 43.443 122 59 1 150 261 121 242 1.64e-27 108
MsG0380016537.01.T01 AT4G35590 33.824 136 70 2 150 265 171 306 1.52e-17 81.3
MsG0380016537.01.T01 AT4G35590 33.824 136 70 2 150 265 221 356 2.39e-17 81.3
MsG0380016537.01.T01 AT5G16100 37.113 97 53 1 152 240 342 438 1.71e-12 67.4

Find 49 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGGTAAAGCAACATTTA+AGG 0.169846 3:+84909631 None:intergenic
CATTGCAATTTGATGATATA+AGG 0.198698 3:-84909310 MsG0380016537.01.T01:CDS
TCGGTGTAATGCCCCATTTC+AGG 0.239025 3:+84909614 None:intergenic
AAATGTTGCTTTACCTGAAA+TGG 0.239415 3:-84909627 MsG0380016537.01.T01:CDS
TCTTCATTCAATTCCATTTC+AGG 0.242189 3:+84908824 None:intergenic
AACTACTTTGATCAAGGTAT+TGG 0.343714 3:+84909672 None:intergenic
TCAGGTAAAGCAACATTTAA+GGG 0.355156 3:+84909632 None:intergenic
AATGTTGCTTTACCTGAAAT+GGG 0.356567 3:-84909626 MsG0380016537.01.T01:CDS
TTGTGAACAAACAAGAGAAA+TGG 0.359147 3:-84909520 MsG0380016537.01.T01:CDS
ATGATTTCATTGAGTTTGAT+TGG 0.364629 3:-84909778 MsG0380016537.01.T01:CDS
TGACCTCTTCCTTATGATAC+TGG 0.365686 3:+84909337 None:intergenic
AGCAATACTCTTCCCTTTGT+CGG 0.387658 3:+84909595 None:intergenic
GTTGAGGCTTCCAAGAAAAC+AGG 0.393183 3:-84909560 MsG0380016537.01.T01:CDS
CCCTGCATCTATTCTTCAAA+AGG 0.394587 3:+84909231 None:intergenic
GTTAGAGAAACTTCCTGAAA+TGG 0.395826 3:-84908837 MsG0380016537.01.T01:CDS
GAGTGGATTTGTTGAAGCTT+CGG 0.430431 3:-84909456 MsG0380016537.01.T01:CDS
TGTTGTGTGATGCAGGAAAT+GGG 0.433682 3:-84908902 MsG0380016537.01.T01:intron
GGCAAACGAGGTTGCTATGA+TGG 0.435987 3:-84908876 MsG0380016537.01.T01:CDS
TGTGAACAAACAAGAGAAAT+GGG 0.437906 3:-84909519 MsG0380016537.01.T01:CDS
TGTACTCATCGACAACCTTA+AGG 0.442882 3:-84909162 MsG0380016537.01.T01:intron
AACTCAATGAAATCATCAAA+TGG 0.477184 3:+84909785 None:intergenic
CTGCTACTTGGCAATGGTAG+TGG 0.480934 3:+84909368 None:intergenic
CTGGTACTAGTACTGCTACT+TGG 0.482625 3:+84909356 None:intergenic
TGATTTCATTGAGTTTGATT+GGG 0.486276 3:-84909777 MsG0380016537.01.T01:CDS
AGGTTGAAGCTCAAGGGTTG+AGG 0.489859 3:+84908741 None:intergenic
TGTGATGCAGGAAATGGGTT+TGG 0.499818 3:-84908897 MsG0380016537.01.T01:intron
GTACTAGTACCAGTATCATA+AGG 0.506441 3:-84909346 MsG0380016537.01.T01:CDS
TTGTGAAGAAAGAGGTTGAA+GGG 0.507686 3:-84909406 MsG0380016537.01.T01:CDS
TCTCAAAACTACTTTGATCA+AGG 0.511922 3:+84909666 None:intergenic
CTATGATGGAGAAGAAGAAA+AGG 0.520048 3:-84908862 MsG0380016537.01.T01:CDS
AAGATCATTGAACCACCCAT+TGG 0.537266 3:+84909718 None:intergenic
TTTGTGAAGAAAGAGGTTGA+AGG 0.545050 3:-84909407 MsG0380016537.01.T01:CDS
GGTTGAAGCTCAAGGGTTGA+GGG 0.549829 3:+84908742 None:intergenic
TGTGAAGAAAGAGGTTGAAG+GGG 0.555743 3:-84909405 MsG0380016537.01.T01:CDS
ATGGGGCATTACACCGACAA+AGG 0.558093 3:-84909608 MsG0380016537.01.T01:CDS
TGGGGCATTACACCGACAAA+GGG 0.567564 3:-84909607 MsG0380016537.01.T01:CDS
CCTGCATCTATTCTTCAAAA+GGG 0.589493 3:+84909232 None:intergenic
ACATTGAGTGCTGCTGAGAG+TGG 0.594289 3:-84909473 MsG0380016537.01.T01:CDS
GTACCAGTATCATAAGGAAG+AGG 0.604409 3:-84909340 MsG0380016537.01.T01:CDS
GGGAAGAGTATTGCTGAGAG+TGG 0.605279 3:-84909587 MsG0380016537.01.T01:CDS
GGAAATGGGTTTGGCAAACG+AGG 0.606744 3:-84908888 MsG0380016537.01.T01:CDS
CTAGTACTGCTACTTGGCAA+TGG 0.610956 3:+84909362 None:intergenic
ATGTTGCTTTACCTGAAATG+GGG 0.616338 3:-84909625 MsG0380016537.01.T01:CDS
GCAGGGAGCTCAACATCACT+AGG 0.620032 3:-84909214 MsG0380016537.01.T01:CDS
GGTGGCCTCACAGAAAATTG+AGG 0.625800 3:-84909193 MsG0380016537.01.T01:CDS
ATGAAGAAATCAAGAAGCTG+AGG 0.626377 3:-84908808 MsG0380016537.01.T01:CDS
GCTGCTAAGAAAATGAATGT+TGG 0.631864 3:-84909260 MsG0380016537.01.T01:CDS
GCACTCAATGTCAATGACAA+TGG 0.653270 3:+84909485 None:intergenic
GGGAGCTCAACATCACTAGG+TGG 0.707852 3:-84909211 MsG0380016537.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATAATTTTTTATCAAC+TGG - Chr3:84909603-84909622 MsG0380016537.01.T01:CDS 10.0%
!! AACATAAAGAATATACCTTA+AGG + Chr3:84909404-84909423 None:intergenic 20.0%
!!! TTTTGATGTTCCTTTAAAAA+TGG - Chr3:84909266-84909285 MsG0380016537.01.T01:CDS 20.0%
! AACTCAATGAAATCATCAAA+TGG + Chr3:84908766-84908785 None:intergenic 25.0%
! ATCCAAACAAAGATAATGTT+AGG + Chr3:84909465-84909484 None:intergenic 25.0%
! ATGATTTCATTGAGTTTGAT+TGG - Chr3:84908770-84908789 MsG0380016537.01.T01:CDS 25.0%
! ATTTCAATTGTCATTCAAAG+TGG + Chr3:84909524-84909543 None:intergenic 25.0%
! TGATTTCATTGAGTTTGATT+GGG - Chr3:84908771-84908790 MsG0380016537.01.T01:CDS 25.0%
! TGGTGTAAAAATGATTACTT+TGG + Chr3:84908813-84908832 None:intergenic 25.0%
! TTCCTAACATTATCTTTGTT+TGG - Chr3:84909460-84909479 MsG0380016537.01.T01:CDS 25.0%
! TTTCAATTGTCATTCAAAGT+GGG + Chr3:84909523-84909542 None:intergenic 25.0%
!! CATTGCAATTTGATGATATA+AGG - Chr3:84909238-84909257 MsG0380016537.01.T01:CDS 25.0%
!! TTTGAAGTACTTAACAATGT+GGG + Chr3:84909439-84909458 None:intergenic 25.0%
!!! AGTAATCATTTTTACACCAA+TGG - Chr3:84908814-84908833 MsG0380016537.01.T01:CDS 25.0%
!!! ATTTTTTATCAACTGGTCAT+AGG - Chr3:84909610-84909629 MsG0380016537.01.T01:CDS 25.0%
!!! GTAATCATTTTTACACCAAT+GGG - Chr3:84908815-84908834 MsG0380016537.01.T01:CDS 25.0%
!!! TTTTGAAGTACTTAACAATG+TGG + Chr3:84909440-84909459 None:intergenic 25.0%
AACTACTTTGATCAAGGTAT+TGG + Chr3:84908879-84908898 None:intergenic 30.0%
GAAACTTGAAACTGTAGTTT+GGG - Chr3:84909551-84909570 MsG0380016537.01.T01:CDS 30.0%
TCAGGTAAAGCAACATTTAA+GGG + Chr3:84908919-84908938 None:intergenic 30.0%
TCTCAAAACTACTTTGATCA+AGG + Chr3:84908885-84908904 None:intergenic 30.0%
TCTTCATTCAATTCCATTTC+AGG + Chr3:84909727-84909746 None:intergenic 30.0%
TGAAACTTGAAACTGTAGTT+TGG - Chr3:84909550-84909569 MsG0380016537.01.T01:CDS 30.0%
TGTGAACAAACAAGAGAAAT+GGG - Chr3:84909029-84909048 MsG0380016537.01.T01:intron 30.0%
TTCAGGTAAAGCAACATTTA+AGG + Chr3:84908920-84908939 None:intergenic 30.0%
TTGTGAACAAACAAGAGAAA+TGG - Chr3:84909028-84909047 MsG0380016537.01.T01:intron 30.0%
! TTGAAGTACTTAACAATGTG+GGG + Chr3:84909438-84909457 None:intergenic 30.0%
!! AAACTGATTTCCTGTTTTCT+TGG + Chr3:84909001-84909020 None:intergenic 30.0%
!! AAATGTTGCTTTACCTGAAA+TGG - Chr3:84908921-84908940 MsG0380016537.01.T01:intron 30.0%
!! AATGTTGCTTTACCTGAAAT+GGG - Chr3:84908922-84908941 MsG0380016537.01.T01:intron 30.0%
!! ATTATTTTGTTGTGTGATGC+AGG - Chr3:84909639-84909658 MsG0380016537.01.T01:CDS 30.0%
!!! TTCTTAGCAGCCATTTTTAA+AGG + Chr3:84909279-84909298 None:intergenic 30.0%
ATGAAGAAATCAAGAAGCTG+AGG - Chr3:84909740-84909759 MsG0380016537.01.T01:CDS 35.0%
CCTGCATCTATTCTTCAAAA+GGG + Chr3:84909319-84909338 None:intergenic 35.0%
GAGCATTAGACTCAAATTGT+AGG - Chr3:84909490-84909509 MsG0380016537.01.T01:CDS 35.0%
GCTGCTAAGAAAATGAATGT+TGG - Chr3:84909288-84909307 MsG0380016537.01.T01:CDS 35.0%
GTACTAGTACCAGTATCATA+AGG - Chr3:84909202-84909221 MsG0380016537.01.T01:CDS 35.0%
GTTAGAGAAACTTCCTGAAA+TGG - Chr3:84909711-84909730 MsG0380016537.01.T01:CDS 35.0%
TTGTGAAGAAAGAGGTTGAA+GGG - Chr3:84909142-84909161 MsG0380016537.01.T01:intron 35.0%
TTTGTGAAGAAAGAGGTTGA+AGG - Chr3:84909141-84909160 MsG0380016537.01.T01:intron 35.0%
! AAAAACTGAAAGTGGGTTTG+TGG - Chr3:84909116-84909135 MsG0380016537.01.T01:intron 35.0%
! CTATGATGGAGAAGAAGAAA+AGG - Chr3:84909686-84909705 MsG0380016537.01.T01:CDS 35.0%
! TGAAGTACTTAACAATGTGG+GGG + Chr3:84909437-84909456 None:intergenic 35.0%
! TGTGGATTTTGTGAAGAAAG+AGG - Chr3:84909134-84909153 MsG0380016537.01.T01:intron 35.0%
!! ATCATTTTTACACCAATGGG+TGG - Chr3:84908818-84908837 MsG0380016537.01.T01:CDS 35.0%
!! ATGTTGCTTTACCTGAAATG+GGG - Chr3:84908923-84908942 MsG0380016537.01.T01:intron 35.0%
!! CCTTTTGAAGAATAGATGCA+GGG - Chr3:84909317-84909336 MsG0380016537.01.T01:CDS 35.0%
AAGATCATTGAACCACCCAT+TGG + Chr3:84908833-84908852 None:intergenic 40.0%
ACTTGAAACTGTAGTTTGGG+TGG - Chr3:84909554-84909573 MsG0380016537.01.T01:CDS 40.0%
AGCAATACTCTTCCCTTTGT+CGG + Chr3:84908956-84908975 None:intergenic 40.0%
CCCTGCATCTATTCTTCAAA+AGG + Chr3:84909320-84909339 None:intergenic 40.0%
CTTCGGCAAAAACTGAAAGT+GGG - Chr3:84909109-84909128 MsG0380016537.01.T01:intron 40.0%
GCACTCAATGTCAATGACAA+TGG + Chr3:84909066-84909085 None:intergenic 40.0%
GTACCAGTATCATAAGGAAG+AGG - Chr3:84909208-84909227 MsG0380016537.01.T01:CDS 40.0%
TAGACTCAAATTGTAGGACC+AGG - Chr3:84909496-84909515 MsG0380016537.01.T01:CDS 40.0%
TGACCTCTTCCTTATGATAC+TGG + Chr3:84909214-84909233 None:intergenic 40.0%
TGTACTCATCGACAACCTTA+AGG - Chr3:84909386-84909405 MsG0380016537.01.T01:CDS 40.0%
TGTGAAGAAAGAGGTTGAAG+GGG - Chr3:84909143-84909162 MsG0380016537.01.T01:intron 40.0%
TGTTGTGTGATGCAGGAAAT+GGG - Chr3:84909646-84909665 MsG0380016537.01.T01:CDS 40.0%
TTGTTGTGTGATGCAGGAAA+TGG - Chr3:84909645-84909664 MsG0380016537.01.T01:CDS 40.0%
! AAGCTCCTCAATTTTCTGTG+AGG + Chr3:84909363-84909382 None:intergenic 40.0%
! GAAGTACTTAACAATGTGGG+GGG + Chr3:84909436-84909455 None:intergenic 40.0%
!! CCCTTTTGAAGAATAGATGC+AGG - Chr3:84909316-84909335 MsG0380016537.01.T01:CDS 40.0%
!! GAGTGGATTTGTTGAAGCTT+CGG - Chr3:84909092-84909111 MsG0380016537.01.T01:intron 40.0%
!! TTTGGGTGGAGCATTTTTGT+TGG - Chr3:84909568-84909587 MsG0380016537.01.T01:CDS 40.0%
CTGGTACTAGTACTGCTACT+TGG + Chr3:84909195-84909214 None:intergenic 45.0%
GCTTCGGCAAAAACTGAAAG+TGG - Chr3:84909108-84909127 MsG0380016537.01.T01:intron 45.0%
GTTGAGGCTTCCAAGAAAAC+AGG - Chr3:84908988-84909007 MsG0380016537.01.T01:intron 45.0%
TTGTCATTCAAAGTGGGTCC+TGG + Chr3:84909517-84909536 None:intergenic 45.0%
! CTAGTACTGCTACTTGGCAA+TGG + Chr3:84909189-84909208 None:intergenic 45.0%
! TGTGATGCAGGAAATGGGTT+TGG - Chr3:84909651-84909670 MsG0380016537.01.T01:CDS 45.0%
!!! TGCTGAGAGTGGTTTTGTTG+AGG - Chr3:84908972-84908991 MsG0380016537.01.T01:intron 45.0%
GGCAAACGAGGTTGCTATGA+TGG - Chr3:84909672-84909691 MsG0380016537.01.T01:CDS 50.0%
GGTGGCCTCACAGAAAATTG+AGG - Chr3:84909355-84909374 MsG0380016537.01.T01:CDS 50.0%
TCGGTGTAATGCCCCATTTC+AGG + Chr3:84908937-84908956 None:intergenic 50.0%
! ACATTGAGTGCTGCTGAGAG+TGG - Chr3:84909075-84909094 MsG0380016537.01.T01:intron 50.0%
! ATGGGGCATTACACCGACAA+AGG - Chr3:84908940-84908959 MsG0380016537.01.T01:intron 50.0%
! CTGCTACTTGGCAATGGTAG+TGG + Chr3:84909183-84909202 None:intergenic 50.0%
! GGAAATGGGTTTGGCAAACG+AGG - Chr3:84909660-84909679 MsG0380016537.01.T01:CDS 50.0%
! TGGGGCATTACACCGACAAA+GGG - Chr3:84908941-84908960 MsG0380016537.01.T01:intron 50.0%
!! GGGAAGAGTATTGCTGAGAG+TGG - Chr3:84908961-84908980 MsG0380016537.01.T01:intron 50.0%
GCAGGGAGCTCAACATCACT+AGG - Chr3:84909334-84909353 MsG0380016537.01.T01:CDS 55.0%
GGGAGCTCAACATCACTAGG+TGG - Chr3:84909337-84909356 MsG0380016537.01.T01:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr3 gene 84908751 84909819 84908751 ID=MsG0380016537.01;Name=MsG0380016537.01
Chr3 mRNA 84908751 84909819 84908751 ID=MsG0380016537.01.T01;Parent=MsG0380016537.01;Name=MsG0380016537.01.T01;_AED=0.28;_eAED=0.28;_QI=0|0|0|1|1|0.5|2|0|271
Chr3 exon 84909163 84909819 84909163 ID=MsG0380016537.01.T01:exon:14389;Parent=MsG0380016537.01.T01
Chr3 exon 84908751 84908909 84908751 ID=MsG0380016537.01.T01:exon:14388;Parent=MsG0380016537.01.T01
Chr3 CDS 84909163 84909819 84909163 ID=MsG0380016537.01.T01:cds;Parent=MsG0380016537.01.T01
Chr3 CDS 84908751 84908909 84908751 ID=MsG0380016537.01.T01:cds;Parent=MsG0380016537.01.T01
Gene Sequence

>MsG0380016537.01.T01

ATGGATATTTCACCATTTGATGATTTCATTGAGTTTGATTGGGCAACTCAGTTTTCATACCAAAGTAATCATTTTTACACCAATGGGTGGTTCAATGATCTTGAAAACTTCAACTTTGATTTCAACCAATACCTTGATCAAAGTAGTTTTGAGATCGATCAAAAGCCCTTAAATGTTGCTTTACCTGAAATGGGGCATTACACCGACAAAGGGAAGAGTATTGCTGAGAGTGGTTTTGTTGAGGCTTCCAAGAAAACAGGAAATCAGTTTGTGAGTTTTGTGAACAAACAAGAGAAATGGGAGAATCAAGAGCCATTGTCATTGACATTGAGTGCTGCTGAGAGTGGATTTGTTGAAGCTTCGGCAAAAACTGAAAGTGGGTTTGTGGATTTTGTGAAGAAAGAGGTTGAAGGGGAAAATCAAAAATTGCCACTACCATTGCCAAGTAGCAGTACTAGTACCAGTATCATAAGGAAGAGGTCAATTTCATTGCAATTTGATGATATAAGGAAACATTTTGATGTTCCTTTAAAAATGGCTGCTAAGAAAATGAATGTTGGTGTGACCCTTTTGAAGAATAGATGCAGGGAGCTCAACATCACTAGGTGGCCTCACAGAAAATTGAGGAGCTTGACTGTACTCATCGACAACCTTAAGGAAATGGGTTTGGCAAACGAGGTTGCTATGATGGAGAAGAAGAAAAGGATGTTAGAGAAACTTCCTGAAATGGAATTGAATGAAGAAATCAAGAAGCTGAGGCAAGCATGCTTTAAAGCTAAATACAAGAAGAGAAGATTAATTGCCCTCAACCCTTGA
Protein sequence

>MsG0380016537.01.T01

MDISPFDDFIEFDWATQFSYQSNHFYTNGWFNDLENFNFDFNQYLDQSSFEIDQKPLNVALPEMGHYTDKGKSIAESGFVEASKKTGNQFVSFVNKQEKWENQEPLSLTLSAAESGFVEASAKTESGFVDFVKKEVEGENQKLPLPLPSSSTSTSIIRKRSISLQFDDIRKHFDVPLKMAAKKMNVGVTLLKNRCRELNITRWPHRKLRSLTVLIDNLKEMGLANEVAMMEKKKRMLEKLPEMELNEEIKKLRQACFKAKYKKRRLIALNP*