AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0235890


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0235890 MtrunA17_Chr2g0284471 86.555 357 12 4 1 352 1 326 0.0 539
Msa0235890 MtrunA17_Chr8g0379681 41.161 379 157 14 2 354 1 339 4.97e-62 201
Msa0235890 MtrunA17_Chr7g0244571 38.217 157 88 3 186 338 195 346 6.93e-27 108
Msa0235890 MtrunA17_Chr4g0013081 40.559 143 78 2 201 341 245 382 2.26e-25 105
Msa0235890 MtrunA17_Chr5g0432531 33.929 168 83 5 182 339 103 252 1.65e-24 100
Msa0235890 MtrunA17_Chr8g0390531 51.613 62 30 0 273 334 258 319 3.84e-16 78.2
Msa0235890 MtrunA17_Chr1g0177881 39.744 78 43 1 276 353 105 178 7.54e-13 66.2
Msa0235890 MtrunA17_Chr4g0075391 39.683 63 38 0 275 337 83 145 1.10e-11 62.4
Msa0235890 MtrunA17_Chr4g0025901 26.923 130 86 1 214 334 31 160 1.31e-11 62.8
Msa0235890 MtrunA17_Chr7g0267111 42.857 63 36 0 276 338 113 175 1.80e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0235890 AT4G18830.1 33.422 374 186 15 1 338 1 347 3.79e-33 126
Msa0235890 AT1G06920.1 65.152 66 23 0 272 337 242 307 6.53e-24 100
Msa0235890 AT2G30400.1 61.765 68 26 0 272 339 251 318 2.76e-23 99.0
Msa0235890 AT5G58360.1 44.444 90 49 1 255 344 206 294 1.65e-20 90.9
Msa0235890 AT5G01840.1 56.452 62 27 0 277 338 202 263 1.28e-19 87.8
Msa0235890 AT5G19650.1 46.774 62 33 0 273 334 154 215 1.08e-14 72.8
Msa0235890 AT2G18500.1 40.909 66 39 0 272 337 225 290 4.73e-13 69.7
Msa0235890 AT3G52525.1 46.032 63 34 0 274 336 67 129 2.01e-12 65.1
Msa0235890 AT4G04025.1 41.176 68 40 0 266 333 106 173 8.05e-11 60.8

Find 43 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTTCTTCTACTTCTTC+TGG 0.241554 2_2:+8754522 Msa0235890:CDS
TTAAAAGAGGAGGATATTAT+TGG 0.262522 2_2:+8754708 Msa0235890:CDS
GAGGAAAGCACAACAGGTTT+TGG 0.290055 2_2:+8754839 Msa0235890:CDS
TGGTTTGATATGAGTCAATA+TGG 0.296873 2_2:+8755473 Msa0235890:CDS
TTCACCCTTGAAACTTTCTT+TGG 0.300747 2_2:-8755134 None:intergenic
TTTGATATTGGTGGAAAATA+TGG 0.307283 2_2:+8754651 Msa0235890:CDS
AACTTAGAAAGCCAAGAAAA+AGG 0.308204 2_2:-8754546 None:intergenic
AAAAGGAATATGAAAATATA+AGG 0.317179 2_2:+8754805 Msa0235890:CDS
GATATGAGTCAATATGGTTT+AGG 0.337600 2_2:+8755479 Msa0235890:CDS
GAAAATATATTCACCAAGAT+TGG 0.341908 2_2:+8755154 Msa0235890:CDS
ACAGCAAAACTATCTAATTC+TGG 0.358668 2_2:-8755281 None:intergenic
GCAAAAGAATGTGTTGTTCT+TGG 0.370662 2_2:-8754948 None:intergenic
GATTAGTAAGGCAGAAGAAA+TGG 0.373351 2_2:+8755373 Msa0235890:CDS
CTTGGTGTACAAATTGTTCT+TGG 0.377176 2_2:-8754930 None:intergenic
ATCTCATAATCAAAGTATTT+AGG 0.389618 2_2:+8755444 Msa0235890:CDS
TCAACCTTTGAAACCAATCT+TGG 0.392383 2_2:-8755167 None:intergenic
GAATCTCTAAAATCCTGCTT+TGG 0.398970 2_2:-8755323 None:intergenic
ATTTGAGAGGAAAGCACAAC+AGG 0.409645 2_2:+8754833 Msa0235890:CDS
GGAAAATATGGTAACAAAAG+TGG 0.450154 2_2:+8754663 Msa0235890:CDS
TCAAAGTATTTAGGCAGGTA+TGG 0.455774 2_2:+8755453 Msa0235890:CDS
AGAAGAAATGGAAGAGTTGT+TGG 0.458484 2_2:+8755385 Msa0235890:CDS
AAAGATGAAGAAAGAAATTG+TGG 0.494347 2_2:+8755238 Msa0235890:CDS
TGAAGAGAAACAGATTAGTA+AGG 0.497006 2_2:+8755361 Msa0235890:CDS
GGAAACCAAAGAAAGTTTCA+AGG 0.508120 2_2:+8755129 Msa0235890:CDS
TTCACCAAGATTGGTTTCAA+AGG 0.510346 2_2:+8755163 Msa0235890:CDS
ACAACAAAATAATGATGAAG+TGG 0.525694 2_2:+8754463 None:intergenic
CAACAAAATAATGATGAAGT+GGG 0.537547 2_2:+8754464 None:intergenic
GTATGAATATGATAGAGAAA+AGG 0.539540 2_2:+8754788 Msa0235890:CDS
CATAATCAAAGTATTTAGGC+AGG 0.542446 2_2:+8755448 Msa0235890:CDS
CCACCAATATCAAAACATGA+AGG 0.542576 2_2:-8754642 None:intergenic
ATGTTCATCAAATCCAAAGC+AGG 0.550210 2_2:+8755310 Msa0235890:CDS
TAAAAGCATTAGAAGAAATG+AGG 0.552124 2_2:+8755201 Msa0235890:CDS
TATAGTCAAGTTAAAAGAGG+AGG 0.552468 2_2:+8754698 Msa0235890:CDS
AGGTATAGTCAAGTTAAAAG+AGG 0.552785 2_2:+8754695 Msa0235890:CDS
AAAACGGTGAATGATAAGAA+GGG 0.585607 2_2:+8754747 Msa0235890:CDS
GAAACCAAAGAAAGTTTCAA+GGG 0.604643 2_2:+8755130 Msa0235890:CDS
GATGAAGAAAGAAATTGTGG+AGG 0.614642 2_2:+8755241 Msa0235890:CDS
GATGATGCTGATGAAGAAGA+AGG 0.614756 2_2:-8754498 None:intergenic
CCAATATCAAAACATGAAGG+TGG 0.616765 2_2:-8754639 None:intergenic
ATATAAGGAGAAGATTTGAG+AGG 0.626627 2_2:+8754820 Msa0235890:CDS
AACAAAAGTGGAAGAAAACA+AGG 0.640173 2_2:+8754675 Msa0235890:CDS
AACAAAATAATGATGAAGTG+GGG 0.664450 2_2:+8754465 None:intergenic
GTTAGATCAGAAATGCAATG+CGG 0.769031 2_2:+8755503 Msa0235890:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGGAATATGAAAATATA+AGG + chr2_2:8754805-8754824 Msa0235890:CDS 15.0%
!! AAAAGGAATATGAAAATATA+AGG + chr2_2:8754805-8754824 Msa0235890:CDS 15.0%
!!! ATCTCATAATCAAAGTATTT+AGG + chr2_2:8755444-8755463 Msa0235890:CDS 20.0%
!!! ATCTCATAATCAAAGTATTT+AGG + chr2_2:8755444-8755463 Msa0235890:CDS 20.0%
! TTTGATATTGGTGGAAAATA+TGG + chr2_2:8754651-8754670 Msa0235890:CDS 25.0%
! TTAAAAGAGGAGGATATTAT+TGG + chr2_2:8754708-8754727 Msa0235890:CDS 25.0%
! CTTAGAAGATCAAAGAAAAA+CGG + chr2_2:8754731-8754750 Msa0235890:CDS 25.0%
! GTATGAATATGATAGAGAAA+AGG + chr2_2:8754788-8754807 Msa0235890:CDS 25.0%
! TAAAGACTCAAGAAAAACAA+AGG + chr2_2:8755105-8755124 Msa0235890:CDS 25.0%
! GAAAATATATTCACCAAGAT+TGG + chr2_2:8755154-8755173 Msa0235890:CDS 25.0%
!!! TAAAAGCATTAGAAGAAATG+AGG + chr2_2:8755201-8755220 Msa0235890:CDS 25.0%
! AAAGATGAAGAAAGAAATTG+TGG + chr2_2:8755238-8755257 Msa0235890:CDS 25.0%
! TTTGATATTGGTGGAAAATA+TGG + chr2_2:8754651-8754670 Msa0235890:CDS 25.0%
! TTAAAAGAGGAGGATATTAT+TGG + chr2_2:8754708-8754727 Msa0235890:CDS 25.0%
! CTTAGAAGATCAAAGAAAAA+CGG + chr2_2:8754731-8754750 Msa0235890:CDS 25.0%
! GTATGAATATGATAGAGAAA+AGG + chr2_2:8754788-8754807 Msa0235890:CDS 25.0%
! TAAAGACTCAAGAAAAACAA+AGG + chr2_2:8755105-8755124 Msa0235890:CDS 25.0%
! GAAAATATATTCACCAAGAT+TGG + chr2_2:8755154-8755173 Msa0235890:CDS 25.0%
!!! TAAAAGCATTAGAAGAAATG+AGG + chr2_2:8755201-8755220 Msa0235890:CDS 25.0%
! AAAGATGAAGAAAGAAATTG+TGG + chr2_2:8755238-8755257 Msa0235890:CDS 25.0%
AACTTAGAAAGCCAAGAAAA+AGG - chr2_2:8754549-8754568 None:intergenic 30.0%
GGAAAATATGGTAACAAAAG+TGG + chr2_2:8754663-8754682 Msa0235890:CDS 30.0%
AACAAAAGTGGAAGAAAACA+AGG + chr2_2:8754675-8754694 Msa0235890:CDS 30.0%
AGGTATAGTCAAGTTAAAAG+AGG + chr2_2:8754695-8754714 Msa0235890:CDS 30.0%
TATAGTCAAGTTAAAAGAGG+AGG + chr2_2:8754698-8754717 Msa0235890:CDS 30.0%
AAAAACGGTGAATGATAAGA+AGG + chr2_2:8754746-8754765 Msa0235890:CDS 30.0%
AAAACGGTGAATGATAAGAA+GGG + chr2_2:8754747-8754766 Msa0235890:CDS 30.0%
ATATAAGGAGAAGATTTGAG+AGG + chr2_2:8754820-8754839 Msa0235890:CDS 30.0%
GAAAAAACATGAAGAGTTGA+AGG + chr2_2:8755082-8755101 Msa0235890:CDS 30.0%
GAAACCAAAGAAAGTTTCAA+GGG + chr2_2:8755130-8755149 Msa0235890:CDS 30.0%
ACAGCAAAACTATCTAATTC+TGG - chr2_2:8755284-8755303 None:intergenic 30.0%
TGAAGAGAAACAGATTAGTA+AGG + chr2_2:8755361-8755380 Msa0235890:CDS 30.0%
! CATAATCAAAGTATTTAGGC+AGG + chr2_2:8755448-8755467 Msa0235890:CDS 30.0%
TGGTTTGATATGAGTCAATA+TGG + chr2_2:8755473-8755492 Msa0235890:CDS 30.0%
GATATGAGTCAATATGGTTT+AGG + chr2_2:8755479-8755498 Msa0235890:CDS 30.0%
AACTTAGAAAGCCAAGAAAA+AGG - chr2_2:8754549-8754568 None:intergenic 30.0%
GGAAAATATGGTAACAAAAG+TGG + chr2_2:8754663-8754682 Msa0235890:CDS 30.0%
AACAAAAGTGGAAGAAAACA+AGG + chr2_2:8754675-8754694 Msa0235890:CDS 30.0%
AGGTATAGTCAAGTTAAAAG+AGG + chr2_2:8754695-8754714 Msa0235890:CDS 30.0%
TATAGTCAAGTTAAAAGAGG+AGG + chr2_2:8754698-8754717 Msa0235890:CDS 30.0%
AAAAACGGTGAATGATAAGA+AGG + chr2_2:8754746-8754765 Msa0235890:CDS 30.0%
AAAACGGTGAATGATAAGAA+GGG + chr2_2:8754747-8754766 Msa0235890:CDS 30.0%
ATATAAGGAGAAGATTTGAG+AGG + chr2_2:8754820-8754839 Msa0235890:CDS 30.0%
GAAAAAACATGAAGAGTTGA+AGG + chr2_2:8755082-8755101 Msa0235890:CDS 30.0%
GAAACCAAAGAAAGTTTCAA+GGG + chr2_2:8755130-8755149 Msa0235890:CDS 30.0%
ACAGCAAAACTATCTAATTC+TGG - chr2_2:8755284-8755303 None:intergenic 30.0%
TGAAGAGAAACAGATTAGTA+AGG + chr2_2:8755361-8755380 Msa0235890:CDS 30.0%
! CATAATCAAAGTATTTAGGC+AGG + chr2_2:8755448-8755467 Msa0235890:CDS 30.0%
TGGTTTGATATGAGTCAATA+TGG + chr2_2:8755473-8755492 Msa0235890:CDS 30.0%
GATATGAGTCAATATGGTTT+AGG + chr2_2:8755479-8755498 Msa0235890:CDS 30.0%
TCTTCTTCTTCTACTTCTTC+TGG + chr2_2:8754522-8754541 Msa0235890:CDS 35.0%
CCAATATCAAAACATGAAGG+TGG - chr2_2:8754642-8754661 None:intergenic 35.0%
!!! CCACCTTCATGTTTTGATAT+TGG + chr2_2:8754639-8754658 Msa0235890:CDS 35.0%
CCACCAATATCAAAACATGA+AGG - chr2_2:8754645-8754664 None:intergenic 35.0%
!!! CCTTCATGTTTTGATATTGG+TGG + chr2_2:8754642-8754661 Msa0235890:CDS 35.0%
! CTTGGTGTACAAATTGTTCT+TGG - chr2_2:8754933-8754952 None:intergenic 35.0%
! GCAAAAGAATGTGTTGTTCT+TGG - chr2_2:8754951-8754970 None:intergenic 35.0%
AGACTCAAGAAAAACAAAGG+AGG + chr2_2:8755108-8755127 Msa0235890:CDS 35.0%
GGAAACCAAAGAAAGTTTCA+AGG + chr2_2:8755129-8755148 Msa0235890:CDS 35.0%
TTCACCCTTGAAACTTTCTT+TGG - chr2_2:8755137-8755156 None:intergenic 35.0%
!! TTCACCAAGATTGGTTTCAA+AGG + chr2_2:8755163-8755182 Msa0235890:CDS 35.0%
!! TCAACCTTTGAAACCAATCT+TGG - chr2_2:8755170-8755189 None:intergenic 35.0%
GATGAAGAAAGAAATTGTGG+AGG + chr2_2:8755241-8755260 Msa0235890:CDS 35.0%
ATGTTCATCAAATCCAAAGC+AGG + chr2_2:8755310-8755329 Msa0235890:CDS 35.0%
!! GAATCTCTAAAATCCTGCTT+TGG - chr2_2:8755326-8755345 None:intergenic 35.0%
GATTAGTAAGGCAGAAGAAA+TGG + chr2_2:8755373-8755392 Msa0235890:CDS 35.0%
AGAAGAAATGGAAGAGTTGT+TGG + chr2_2:8755385-8755404 Msa0235890:CDS 35.0%
! TCAAAGTATTTAGGCAGGTA+TGG + chr2_2:8755453-8755472 Msa0235890:CDS 35.0%
GTTAGATCAGAAATGCAATG+CGG + chr2_2:8755503-8755522 Msa0235890:CDS 35.0%
TCTTCTTCTTCTACTTCTTC+TGG + chr2_2:8754522-8754541 Msa0235890:CDS 35.0%
CCAATATCAAAACATGAAGG+TGG - chr2_2:8754642-8754661 None:intergenic 35.0%
!!! CCACCTTCATGTTTTGATAT+TGG + chr2_2:8754639-8754658 Msa0235890:CDS 35.0%
CCACCAATATCAAAACATGA+AGG - chr2_2:8754645-8754664 None:intergenic 35.0%
!!! CCTTCATGTTTTGATATTGG+TGG + chr2_2:8754642-8754661 Msa0235890:CDS 35.0%
! CTTGGTGTACAAATTGTTCT+TGG - chr2_2:8754933-8754952 None:intergenic 35.0%
! GCAAAAGAATGTGTTGTTCT+TGG - chr2_2:8754951-8754970 None:intergenic 35.0%
AGACTCAAGAAAAACAAAGG+AGG + chr2_2:8755108-8755127 Msa0235890:CDS 35.0%
GGAAACCAAAGAAAGTTTCA+AGG + chr2_2:8755129-8755148 Msa0235890:CDS 35.0%
TTCACCCTTGAAACTTTCTT+TGG - chr2_2:8755137-8755156 None:intergenic 35.0%
!! TTCACCAAGATTGGTTTCAA+AGG + chr2_2:8755163-8755182 Msa0235890:CDS 35.0%
!! TCAACCTTTGAAACCAATCT+TGG - chr2_2:8755170-8755189 None:intergenic 35.0%
GATGAAGAAAGAAATTGTGG+AGG + chr2_2:8755241-8755260 Msa0235890:CDS 35.0%
ATGTTCATCAAATCCAAAGC+AGG + chr2_2:8755310-8755329 Msa0235890:CDS 35.0%
!! GAATCTCTAAAATCCTGCTT+TGG - chr2_2:8755326-8755345 None:intergenic 35.0%
GATTAGTAAGGCAGAAGAAA+TGG + chr2_2:8755373-8755392 Msa0235890:CDS 35.0%
AGAAGAAATGGAAGAGTTGT+TGG + chr2_2:8755385-8755404 Msa0235890:CDS 35.0%
! TCAAAGTATTTAGGCAGGTA+TGG + chr2_2:8755453-8755472 Msa0235890:CDS 35.0%
GTTAGATCAGAAATGCAATG+CGG + chr2_2:8755503-8755522 Msa0235890:CDS 35.0%
GATGATGCTGATGAAGAAGA+AGG - chr2_2:8754501-8754520 None:intergenic 40.0%
! CTTCTTCTGGTCCTTTTTCT+TGG + chr2_2:8754535-8754554 Msa0235890:CDS 40.0%
! ATTTGAGAGGAAAGCACAAC+AGG + chr2_2:8754833-8754852 Msa0235890:CDS 40.0%
GATGATGCTGATGAAGAAGA+AGG - chr2_2:8754501-8754520 None:intergenic 40.0%
! CTTCTTCTGGTCCTTTTTCT+TGG + chr2_2:8754535-8754554 Msa0235890:CDS 40.0%
! ATTTGAGAGGAAAGCACAAC+AGG + chr2_2:8754833-8754852 Msa0235890:CDS 40.0%
!! GAGGAAAGCACAACAGGTTT+TGG + chr2_2:8754839-8754858 Msa0235890:CDS 45.0%
!! GAGGAAAGCACAACAGGTTT+TGG + chr2_2:8754839-8754858 Msa0235890:CDS 45.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 8754474 8755538 8754474 ID=Msa0235890;Name=Msa0235890
chr2_2 mRNA 8754474 8755538 8754474 ID=Msa0235890-mRNA-1;Parent=Msa0235890;Name=Msa0235890-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|354
chr2_2 exon 8754474 8755538 8754474 ID=Msa0235890-mRNA-1:exon:3769;Parent=Msa0235890-mRNA-1
chr2_2 CDS 8754474 8755538 8754474 ID=Msa0235890-mRNA-1:cds;Parent=Msa0235890-mRNA-1
Gene Sequence

>Msa0235890

ATGATGAAGTGGGGTGCAAAAAAACCTTCTTCTTCATCAGCATCATCATCTTCTTCTTCTACTTCTTCTGGTCCTTTTTCTTGGCTTTCTAAGTTGAAACATATGAGAATCAATTCAGATTCAAATCATGCAAAAATATTGAAACAGAAAGAAAAGAAGAATTCTCCACCTTCATGTTTTGATATTGGTGGAAAATATGGTAACAAAAGTGGAAGAAAACAAGGTATAGTCAAGTTAAAAGAGGAGGATATTATTGGCTTAGAAGATCAAAGAAAAACGGTGAATGATAAGAAGGGTTTGATGAAGATTGATGAGTATGAATATGATAGAGAAAAGGAATATGAAAATATAAGGAGAAGATTTGAGAGGAAAGCACAACAGGTTTTGGAAGAACAATTATTGAAATTAGAAAGAGAAGCAAAAGAAGTAGAAGATGTTAAATTTGAATATGAATCTCCAAGAACAATTTGTACACCAAGAACAACACATTCTTTTGCTTCTTCTAATGCAGATTTGACGAAGAATTCTTCTAGCTTAAGAAATATTCGTTTTGAGAAAAGTGAAATTGCATCATCTCAGAAGAAACAAAGTTATGAGAAGCATAGTTTGAAAAAACATGAAGAGTTGAAGGTAAAGACTCAAGAAAAACAAAGGAGGAAACCAAAGAAAGTTTCAAGGGTGAAAATATATTCACCAAGATTGGTTTCAAAGGTTGAAATATGCAGAATAAAAGCATTAGAAGAAATGAGGAACAAAGCAAAACAAAAGATGAAGAAAGAAATTGTGGAGGAAATTATTAGTACTAAACCAGAATTAGATAGTTTTGCTGTGATTAAATGTTCATCAAATCCAAAGCAGGATTTTAGAGATTCAATGATTGAGATGATTGAAGAGAAACAGATTAGTAAGGCAGAAGAAATGGAAGAGTTGTTGGCATGTTATTTGACTTTGAATGCTGATGAATATCATGATCTCATAATCAAAGTATTTAGGCAGGTATGGTTTGATATGAGTCAATATGGTTTAGGTGTTAGATCAGAAATGCAATGCGGTTTCTATGAATGA

Protein sequence

>Msa0235890

MMKWGAKKPSSSSASSSSSSTSSGPFSWLSKLKHMRINSDSNHAKILKQKEKKNSPPSCFDIGGKYGNKSGRKQGIVKLKEEDIIGLEDQRKTVNDKKGLMKIDEYEYDREKEYENIRRRFERKAQQVLEEQLLKLEREAKEVEDVKFEYESPRTICTPRTTHSFASSNADLTKNSSSLRNIRFEKSEIASSQKKQSYEKHSLKKHEELKVKTQEKQRRKPKKVSRVKIYSPRLVSKVEICRIKALEEMRNKAKQKMKKEIVEEIISTKPELDSFAVIKCSSNPKQDFRDSMIEMIEEKQISKAEEMEELLACYLTLNADEYHDLIIKVFRQVWFDMSQYGLGVRSEMQCGFYE*