AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0099690

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0099690 MtrunA17_Chr1g0150751 95.853 217 7 2 1 216 24 239 3.52e-132 371
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 68 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCGCCTTCTTCGGGTTC+AGG 0.278379 1_3:+5905315 Msa0099690:CDS
TGAGGCATAATAATAGTAAT+AGG 0.283637 1_3:-5905388 None:intergenic
TTTGAAATCTTCGCCTTCTT+CGG 0.306660 1_3:+5905308 Msa0099690:CDS
CAAGGACAACCTAAAGTAAT+TGG 0.337399 1_3:+5905339 Msa0099690:CDS
TTGAAATCTTCGCCTTCTTC+GGG 0.338296 1_3:+5905309 Msa0099690:CDS
GAATTTGATGAAGCAAGTTT+AGG 0.338870 1_3:-5904967 None:intergenic
AGTCCTTCGTCACATTCTTC+CGG 0.348481 1_3:+5905267 Msa0099690:CDS
GTCCTTCGTCACATTCTTCC+GGG 0.349605 1_3:+5905268 Msa0099690:CDS
GGCGGTCCACCAATTACTTT+AGG 0.371369 1_3:-5905348 None:intergenic
TTTAGAAGTGGAGGAGGAGG+AGG 0.374484 1_3:-5905177 None:intergenic
TTTGATGATGTGAGTGGAAA+TGG 0.378894 1_3:-5905150 None:intergenic
TTCATCAGATATTCTTTGCT+TGG 0.384427 1_3:+5905466 Msa0099690:CDS
TAATAATAGTAATAGGGATA+TGG 0.384788 1_3:-5905381 None:intergenic
TGTGTTAGGAGTGGAGTAGA+TGG 0.387212 1_3:-5905087 None:intergenic
GTTAATAGTGGAGGAGGTGG+AGG 0.430557 1_3:-5905114 None:intergenic
TGGGGTGTTATTAGTGGAAA+AGG 0.432885 1_3:-5905060 None:intergenic
TTGATGATGTGAGTGGAAAT+GGG 0.439050 1_3:-5905149 None:intergenic
CCTTCTTCGGGTTCAGGTCA+AGG 0.439335 1_3:+5905321 Msa0099690:CDS
GGTGAATATGATGTTAATAG+TGG 0.445887 1_3:-5905126 None:intergenic
GAGGCATAATAATAGTAATA+GGG 0.446723 1_3:-5905387 None:intergenic
AGTGGAGTAGATGGAGGGTG+GGG 0.452281 1_3:-5905078 None:intergenic
GGAGGGTGGGGTGTTATTAG+TGG 0.452753 1_3:-5905066 None:intergenic
ATGCATAATAAACCACTTGA+AGG 0.460999 1_3:-5904901 None:intergenic
GGGGTGTTATTAGTGGAAAA+GGG 0.461571 1_3:-5905059 None:intergenic
GATGTTAATAGTGGAGGAGG+TGG 0.484497 1_3:-5905117 None:intergenic
AAAGAGAACATTGGAGATTG+AGG 0.496507 1_3:+5904861 Msa0099690:CDS
GGGTGTTATTAGTGGAAAAG+GGG 0.496788 1_3:-5905058 None:intergenic
GAGTGGAGTAGATGGAGGGT+GGG 0.505478 1_3:-5905079 None:intergenic
GAAGAATGTGACGAAGGACT+TGG 0.508990 1_3:-5905264 None:intergenic
GGCGAAGATTTCAAAGGTGG+TGG 0.511485 1_3:-5905300 None:intergenic
GGAGTGGAGTAGATGGAGGG+TGG 0.519473 1_3:-5905080 None:intergenic
TTTGTTTGCAAAGAGAACAT+TGG 0.519949 1_3:+5904852 Msa0099690:CDS
GGTGGTGGTGAACAAATTGT+AGG 0.526245 1_3:-5904943 None:intergenic
GTCAACAAAGGAGGAGGTGA+AGG 0.526752 1_3:-5905024 None:intergenic
TTTGATGAAGCAAGTTTAGG+AGG 0.539473 1_3:-5904964 None:intergenic
GATGAAGCAAGTTTAGGAGG+TGG 0.545014 1_3:-5904961 None:intergenic
GAAGATTTCAAAGGTGGTGG+AGG 0.554576 1_3:-5905297 None:intergenic
GAATGTGACGAAGGACTTGG+TGG 0.555897 1_3:-5905261 None:intergenic
CCTTGACCTGAACCCGAAGA+AGG 0.567300 1_3:-5905321 None:intergenic
TATGATGTTAATAGTGGAGG+AGG 0.568744 1_3:-5905120 None:intergenic
GGACAACCTAAAGTAATTGG+TGG 0.583322 1_3:+5905342 Msa0099690:CDS
GAAGCAAGTTTAGGAGGTGG+TGG 0.584772 1_3:-5904958 None:intergenic
TGATGATGTGAGTGGAAATG+GGG 0.585770 1_3:-5905148 None:intergenic
AAAGTTGAAGAGCCTTCAAG+TGG 0.589794 1_3:+5904889 Msa0099690:CDS
AGGTGGTGGAGGAGTTTCCC+CGG 0.592101 1_3:-5905286 None:intergenic
GTGGTGGAAGACTTAGTGAT+GGG 0.594811 1_3:-5905212 None:intergenic
GTTAGGAGTGGAGTAGATGG+AGG 0.597422 1_3:-5905084 None:intergenic
TTAGGAGTGGAGTAGATGGA+GGG 0.598597 1_3:-5905083 None:intergenic
TTTGGTGTCAACAAAGGAGG+AGG 0.602071 1_3:-5905030 None:intergenic
GGTGCATTTGGTGTCAACAA+AGG 0.602133 1_3:-5905036 None:intergenic
GAAGGACTTGGTGGAGATGG+TGG 0.605778 1_3:-5905252 None:intergenic
GGTGGAAGACTTAGTGATGG+GGG 0.608316 1_3:-5905210 None:intergenic
GACGAAGGACTTGGTGGAGA+TGG 0.610720 1_3:-5905255 None:intergenic
GAATATGATGTTAATAGTGG+AGG 0.611804 1_3:-5905123 None:intergenic
GGTAGAGTCAACAATGGTGG+TGG 0.613265 1_3:-5905228 None:intergenic
GGACTTGGTGGAGATGGTGG+CGG 0.623426 1_3:-5905249 None:intergenic
GGAGAATTTGATGATGTGAG+TGG 0.631413 1_3:-5905156 None:intergenic
GCATTTGGTGTCAACAAAGG+AGG 0.639121 1_3:-5905033 None:intergenic
TCCTTCGTCACATTCTTCCG+GGG 0.641768 1_3:+5905269 Msa0099690:CDS
TGGTGGAAGACTTAGTGATG+GGG 0.649103 1_3:-5905211 None:intergenic
GAAGAAGGCGAAGATTTCAA+AGG 0.649156 1_3:-5905306 None:intergenic
GAAGGCGAAGATTTCAAAGG+TGG 0.657373 1_3:-5905303 None:intergenic
GGCGGTAGAGTCAACAATGG+TGG 0.660549 1_3:-5905231 None:intergenic
GGTGGTGGAAGACTTAGTGA+TGG 0.666350 1_3:-5905213 None:intergenic
GGTGTTATTAGTGGAAAAGG+GGG 0.675151 1_3:-5905057 None:intergenic
TCCCCGGAAGAATGTGACGA+AGG 0.679405 1_3:-5905270 None:intergenic
GATGATGTGAGTGGAAATGG+GGG 0.687997 1_3:-5905147 None:intergenic
GGTGGCGGTAGAGTCAACAA+TGG 0.730976 1_3:-5905234 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATAATAGTAATAGGGATA+TGG - chr1_3:5905384-5905403 None:intergenic 20.0%
! GAGGCATAATAATAGTAATA+GGG - chr1_3:5905390-5905409 None:intergenic 25.0%
! TGAGGCATAATAATAGTAAT+AGG - chr1_3:5905391-5905410 None:intergenic 25.0%
TTTGTTTGCAAAGAGAACAT+TGG + chr1_3:5904852-5904871 Msa0099690:CDS 30.0%
ATGCATAATAAACCACTTGA+AGG - chr1_3:5904904-5904923 None:intergenic 30.0%
GAATTTGATGAAGCAAGTTT+AGG - chr1_3:5904970-5904989 None:intergenic 30.0%
GAATATGATGTTAATAGTGG+AGG - chr1_3:5905126-5905145 None:intergenic 30.0%
GGTGAATATGATGTTAATAG+TGG - chr1_3:5905129-5905148 None:intergenic 30.0%
TTCATCAGATATTCTTTGCT+TGG + chr1_3:5905466-5905485 Msa0099690:CDS 30.0%
AAAGAGAACATTGGAGATTG+AGG + chr1_3:5904861-5904880 Msa0099690:CDS 35.0%
TTTGATGAAGCAAGTTTAGG+AGG - chr1_3:5904967-5904986 None:intergenic 35.0%
! TATGATGTTAATAGTGGAGG+AGG - chr1_3:5905123-5905142 None:intergenic 35.0%
!! TTGATGATGTGAGTGGAAAT+GGG - chr1_3:5905152-5905171 None:intergenic 35.0%
!! TTTGATGATGTGAGTGGAAA+TGG - chr1_3:5905153-5905172 None:intergenic 35.0%
!! TATGATTTTAGAAGTGGAGG+AGG - chr1_3:5905186-5905205 None:intergenic 35.0%
!! GGATATGATTTTAGAAGTGG+AGG - chr1_3:5905189-5905208 None:intergenic 35.0%
!! GGAGGATATGATTTTAGAAG+TGG - chr1_3:5905192-5905211 None:intergenic 35.0%
! TTTGAAATCTTCGCCTTCTT+CGG + chr1_3:5905308-5905327 Msa0099690:CDS 35.0%
CAAGGACAACCTAAAGTAAT+TGG + chr1_3:5905339-5905358 Msa0099690:CDS 35.0%
!! TAGGGATATGGATAGTTTTG+TGG - chr1_3:5905372-5905391 None:intergenic 35.0%
AGAAAAATGAGATGCACTTG+AGG - chr1_3:5905409-5905428 None:intergenic 35.0%
AAAGTTGAAGAGCCTTCAAG+TGG + chr1_3:5904889-5904908 Msa0099690:CDS 40.0%
! AGGTGAAGGATTTTGTGTTG+GGG - chr1_3:5905013-5905032 None:intergenic 40.0%
! GAGGTGAAGGATTTTGTGTT+GGG - chr1_3:5905014-5905033 None:intergenic 40.0%
!! GGTGTTATTAGTGGAAAAGG+GGG - chr1_3:5905060-5905079 None:intergenic 40.0%
!! GGGTGTTATTAGTGGAAAAG+GGG - chr1_3:5905061-5905080 None:intergenic 40.0%
!! GGGGTGTTATTAGTGGAAAA+GGG - chr1_3:5905062-5905081 None:intergenic 40.0%
!! TGGGGTGTTATTAGTGGAAA+AGG - chr1_3:5905063-5905082 None:intergenic 40.0%
! TGATGATGTGAGTGGAAATG+GGG - chr1_3:5905151-5905170 None:intergenic 40.0%
!! GGAGAATTTGATGATGTGAG+TGG - chr1_3:5905159-5905178 None:intergenic 40.0%
GAAGAAGGCGAAGATTTCAA+AGG - chr1_3:5905309-5905328 None:intergenic 40.0%
TTGAAATCTTCGCCTTCTTC+GGG + chr1_3:5905309-5905328 Msa0099690:CDS 40.0%
GGACAACCTAAAGTAATTGG+TGG + chr1_3:5905342-5905361 Msa0099690:CDS 40.0%
!!! GGATATGGATAGTTTTGTGG+CGG - chr1_3:5905369-5905388 None:intergenic 40.0%
! GGTGGTGGTGAACAAATTGT+AGG - chr1_3:5904946-5904965 None:intergenic 45.0%
GATGAAGCAAGTTTAGGAGG+TGG - chr1_3:5904964-5904983 None:intergenic 45.0%
! GGTGAAGGATTTTGTGTTGG+GGG - chr1_3:5905012-5905031 None:intergenic 45.0%
! GGAGGTGAAGGATTTTGTGT+TGG - chr1_3:5905015-5905034 None:intergenic 45.0%
!! TTTGGTGTCAACAAAGGAGG+AGG - chr1_3:5905033-5905052 None:intergenic 45.0%
!! GCATTTGGTGTCAACAAAGG+AGG - chr1_3:5905036-5905055 None:intergenic 45.0%
!! GGTGCATTTGGTGTCAACAA+AGG - chr1_3:5905039-5905058 None:intergenic 45.0%
TTAGGAGTGGAGTAGATGGA+GGG - chr1_3:5905086-5905105 None:intergenic 45.0%
TGTGTTAGGAGTGGAGTAGA+TGG - chr1_3:5905090-5905109 None:intergenic 45.0%
! GGAGGATTTTGTGTTAGGAG+TGG - chr1_3:5905099-5905118 None:intergenic 45.0%
! GAGGTGGAGGATTTTGTGTT+AGG - chr1_3:5905104-5905123 None:intergenic 45.0%
! GATGTTAATAGTGGAGGAGG+TGG - chr1_3:5905120-5905139 None:intergenic 45.0%
GATGATGTGAGTGGAAATGG+GGG - chr1_3:5905150-5905169 None:intergenic 45.0%
!! GATTTTAGAAGTGGAGGAGG+AGG - chr1_3:5905183-5905202 None:intergenic 45.0%
TGGTGGAAGACTTAGTGATG+GGG - chr1_3:5905214-5905233 None:intergenic 45.0%
! GTGGTGGAAGACTTAGTGAT+GGG - chr1_3:5905215-5905234 None:intergenic 45.0%
GAAGAATGTGACGAAGGACT+TGG - chr1_3:5905267-5905286 None:intergenic 45.0%
AGTCCTTCGTCACATTCTTC+CGG + chr1_3:5905267-5905286 Msa0099690:CDS 45.0%
! GAAGATTTCAAAGGTGGTGG+AGG - chr1_3:5905300-5905319 None:intergenic 45.0%
GAAGGCGAAGATTTCAAAGG+TGG - chr1_3:5905306-5905325 None:intergenic 45.0%
GAAGCAAGTTTAGGAGGTGG+TGG - chr1_3:5904961-5904980 None:intergenic 50.0%
! TTTTGTGTTGGGGGTGAAGG+AGG - chr1_3:5905003-5905022 None:intergenic 50.0%
! GGATTTTGTGTTGGGGGTGA+AGG - chr1_3:5905006-5905025 None:intergenic 50.0%
GTCAACAAAGGAGGAGGTGA+AGG - chr1_3:5905027-5905046 None:intergenic 50.0%
! AGTGGAAAAGGGGGTGCATT+TGG - chr1_3:5905051-5905070 None:intergenic 50.0%
GTTAGGAGTGGAGTAGATGG+AGG - chr1_3:5905087-5905106 None:intergenic 50.0%
! GTTAATAGTGGAGGAGGTGG+AGG - chr1_3:5905117-5905136 None:intergenic 50.0%
TTTAGAAGTGGAGGAGGAGG+AGG - chr1_3:5905180-5905199 None:intergenic 50.0%
GGTGGAAGACTTAGTGATGG+GGG - chr1_3:5905213-5905232 None:intergenic 50.0%
!! GGTGGTGGAAGACTTAGTGA+TGG - chr1_3:5905216-5905235 None:intergenic 50.0%
GGTAGAGTCAACAATGGTGG+TGG - chr1_3:5905231-5905250 None:intergenic 50.0%
GAATGTGACGAAGGACTTGG+TGG - chr1_3:5905264-5905283 None:intergenic 50.0%
GTCCTTCGTCACATTCTTCC+GGG + chr1_3:5905268-5905287 Msa0099690:CDS 50.0%
TCCTTCGTCACATTCTTCCG+GGG + chr1_3:5905269-5905288 Msa0099690:CDS 50.0%
GGCGAAGATTTCAAAGGTGG+TGG - chr1_3:5905303-5905322 None:intergenic 50.0%
GGCGGTCCACCAATTACTTT+AGG - chr1_3:5905351-5905370 None:intergenic 50.0%
!! GGAGGGTGGGGTGTTATTAG+TGG - chr1_3:5905069-5905088 None:intergenic 55.0%
AGTGGAGTAGATGGAGGGTG+GGG - chr1_3:5905081-5905100 None:intergenic 55.0%
GAGTGGAGTAGATGGAGGGT+GGG - chr1_3:5905082-5905101 None:intergenic 55.0%
! GGAAGACTTAGTGATGGGGG+AGG - chr1_3:5905210-5905229 None:intergenic 55.0%
GGCGGTAGAGTCAACAATGG+TGG - chr1_3:5905234-5905253 None:intergenic 55.0%
! GGTGGCGGTAGAGTCAACAA+TGG - chr1_3:5905237-5905256 None:intergenic 55.0%
!! GAAGGACTTGGTGGAGATGG+TGG - chr1_3:5905255-5905274 None:intergenic 55.0%
!! GACGAAGGACTTGGTGGAGA+TGG - chr1_3:5905258-5905277 None:intergenic 55.0%
TCCCCGGAAGAATGTGACGA+AGG - chr1_3:5905273-5905292 None:intergenic 55.0%
! TCTTCGCCTTCTTCGGGTTC+AGG + chr1_3:5905315-5905334 Msa0099690:CDS 55.0%
CCTTGACCTGAACCCGAAGA+AGG - chr1_3:5905324-5905343 None:intergenic 55.0%
! CCTTCTTCGGGTTCAGGTCA+AGG + chr1_3:5905321-5905340 Msa0099690:CDS 55.0%
GTGTTGGGGGTGAAGGAGGA+GGG - chr1_3:5904999-5905018 None:intergenic 60.0%
TGTGTTGGGGGTGAAGGAGG+AGG - chr1_3:5905000-5905019 None:intergenic 60.0%
GGAGTGGAGTAGATGGAGGG+TGG - chr1_3:5905083-5905102 None:intergenic 60.0%
!! GGACTTGGTGGAGATGGTGG+CGG - chr1_3:5905252-5905271 None:intergenic 60.0%
!! AGGTGGTGGAGGAGTTTCCC+CGG - chr1_3:5905289-5905308 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 5904841 5905491 5904841 ID=Msa0099690;Name=Msa0099690
chr1_3 mRNA 5904841 5905491 5904841 ID=Msa0099690-mRNA-1;Parent=Msa0099690;Name=Msa0099690-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|-1|0|1|-1|1|1|0|216
chr1_3 exon 5904841 5905491 5904841 ID=Msa0099690-mRNA-1:exon:2261;Parent=Msa0099690-mRNA-1
chr1_3 CDS 5904841 5905491 5904841 ID=Msa0099690-mRNA-1:cds;Parent=Msa0099690-mRNA-1
Gene Sequence

>Msa0099690

ATGTTGTTGGTTTTGTTTGCAAAGAGAACATTGGAGATTGAGGACAACAAAGTTGAAGAGCCTTCAAGTGGTTTATTATGCATTAGTGAATGTGTCACATGTCCTACAATTTGTTCACCACCACCTCCTAAACTTGCTTCATCAAATTCAAATCACCCTCCTCCTTCACCCCCAACACAAAATCCTTCACCTCCTCCTTTGTTGACACCAAATGCACCCCCTTTTCCACTAATAACACCCCACCCTCCATCTACTCCACTCCTAACACAAAATCCTCCACCTCCTCCACTATTAACATCATATTCACCCCCATTTCCACTCACATCATCAAATTCTCCTCCTCCTCCTCCACTTCTAAAATCATATCCTCCCCCATCACTAAGTCTTCCACCACCATTGTTGACTCTACCGCCACCATCTCCACCAAGTCCTTCGTCACATTCTTCCGGGGAAACTCCTCCACCACCTTTGAAATCTTCGCCTTCTTCGGGTTCAGGTCAAGGACAACCTAAAGTAATTGGTGGACCGCCACAAAACTATCCATATCCCTATTACTATTATTATGCCTCAAGTGCATCTCATTTTTCTAATCATGTTGTACTCTTCTTTATTGTACTTTTGTTCATTCATCAGATATTCTTTGCTTGGTAA
Protein sequence

>Msa0099690

MLLVLFAKRTLEIEDNKVEEPSSGLLCISECVTCPTICSPPPPKLASSNSNHPPPSPPTQNPSPPPLLTPNAPPFPLITPHPPSTPLLTQNPPPPPLLTSYSPPFPLTSSNSPPPPPLLKSYPPPSLSLPPPLLTLPPPSPPSPSSHSSGETPPPPLKSSPSSGSGQGQPKVIGGPPQNYPYPYYYYYASSASHFSNHVVLFFIVLLFIHQIFFAW*