AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0113040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0113040 MtrunA17_Chr8g0334501 96.891 193 6 0 1 193 55 247 1.58e-138 394
Msa0113040 MtrunA17_Chr7g0245051 87.047 193 25 0 1 193 52 244 3.62e-126 363
Msa0113040 MtrunA17_Chr7g0245101 81.865 193 35 0 1 193 53 245 5.41e-118 342
Msa0113040 MtrunA17_Chr7g0271511 59.677 186 75 0 8 193 62 247 1.47e-81 248
Msa0113040 MtrunA17_Chr4g0040121 56.477 193 83 1 2 193 33 225 3.79e-80 244
Msa0113040 MtrunA17_Chr1g0193531 59.459 185 74 1 9 193 30 213 5.93e-80 243
Msa0113040 MtrunA17_Chr4g0020521 56.522 184 80 0 9 192 35 218 1.13e-79 243
Msa0113040 MtrunA17_Chr1g0193611 57.838 185 78 0 9 193 33 217 3.65e-79 241
Msa0113040 MtrunA17_Chr5g0404601 58.824 187 76 1 8 193 31 217 2.69e-78 240
Msa0113040 MtrunA17_Chr1g0193551 58.065 186 77 1 8 193 35 219 5.50e-78 238
Msa0113040 MtrunA17_Chr3g0141751 52.332 193 91 1 1 193 20 211 8.73e-77 235
Msa0113040 MtrunA17_Chr1g0193601 57.297 185 79 0 9 193 33 217 7.38e-76 233
Msa0113040 MtrunA17_Chr1g0193541 59.659 176 69 1 9 182 32 207 1.48e-75 232
Msa0113040 MtrunA17_Chr2g0324441 54.404 193 87 1 2 193 34 226 6.36e-74 229
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0113040 AT5G01930.1 80.628 191 37 0 3 193 42 232 7.48e-117 339
Msa0113040 AT3G10900.1 54.595 185 83 1 9 192 30 214 1.21e-74 230
Msa0113040 AT4G28320.1 55.080 187 83 1 8 193 41 227 3.32e-73 227
Msa0113040 AT2G20680.1 54.688 192 86 1 3 193 37 228 7.54e-73 226
Msa0113040 AT3G10890.1 51.630 184 89 0 9 192 32 215 1.78e-72 225
Msa0113040 AT5G66460.1 52.151 186 89 0 8 193 31 216 2.53e-72 225
Msa0113040 AT1G02310.1 51.596 188 84 3 8 193 29 211 1.00e-64 205
Msa0113040 AT1G02310.2 51.872 187 83 3 9 193 50 231 1.53e-64 205
Msa0113040 AT3G30540.1 42.391 184 69 1 9 192 30 176 2.53e-49 163

Find 52 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAATGGATTCAACACTTAT+TGG 0.246669 1_3:+28732184 Msa0113040:CDS
GTTGGCCATTCACTACAAAT+TGG 0.308540 1_3:-28732152 None:intergenic
CTCCTCTGGTGATACGTTAC+AGG 0.324607 1_3:+28732764 Msa0113040:CDS
TATTATCATTGGTTAACAAT+TGG 0.335350 1_3:+28732421 Msa0113040:CDS
ACTCACAAATATCACTTATA+AGG 0.349810 1_3:+28732686 Msa0113040:CDS
ATTCAACACTTATTGGTTGA+TGG 0.357211 1_3:+28732191 Msa0113040:CDS
ATTATCATTGGTTAACAATT+GGG 0.370572 1_3:+28732422 Msa0113040:CDS
GTATGACAGTTTGTAGGACT+TGG 0.375713 1_3:+28732280 Msa0113040:CDS
GGCCAACCTTTCTATGTCAA+TGG 0.396915 1_3:+28732168 Msa0113040:CDS
AATCAGACTCATATTATCAT+TGG 0.419663 1_3:+28732410 Msa0113040:CDS
GTCAAGTGGGGCAATGCTGC+TGG 0.420167 1_3:+28732471 Msa0113040:CDS
TTGAATCCATTGACATAGAA+AGG 0.430244 1_3:-28732174 None:intergenic
CAGTTGGTATGACAGTTTGT+AGG 0.445206 1_3:+28732274 Msa0113040:CDS
TTATGATGAAGTAGTATTCA+AGG 0.449801 1_3:+28732350 Msa0113040:CDS
GGAAACCAATTTGTAGTGAA+TGG 0.455801 1_3:+28732147 Msa0113040:CDS
GTTAACAATTGGGAGGCATA+TGG 0.457775 1_3:+28732432 Msa0113040:CDS
AGGACTTGGGCCTTCAATGA+TGG 0.488912 1_3:+28732294 Msa0113040:CDS
CGATGCACCTCTGACTCCTC+TGG 0.493066 1_3:+28732750 Msa0113040:CDS
TTTCACTCACCACAAAATCC+AGG 0.498414 1_3:-28732374 None:intergenic
GTGAAATGGAGGAAGATGAA+TGG 0.499830 1_3:+28732106 None:intergenic
TCTCCATTGACCATCATTGA+AGG 0.500587 1_3:-28732304 None:intergenic
TATGACAGTTTGTAGGACTT+GGG 0.504511 1_3:+28732281 Msa0113040:CDS
TGGCAGATGGTGCAAAAGAA+AGG 0.506336 1_3:+28732126 Msa0113040:CDS
TGAAGTAGTATTCAAGGCCC+TGG 0.508682 1_3:+28732356 Msa0113040:CDS
ATCCATTGACATAGAAAGGT+TGG 0.514039 1_3:-28732170 None:intergenic
TTGTAGTAGCCTCTGAGAGT+TGG 0.519117 1_3:-28732531 None:intergenic
GCAAAGCACAGTATGTCAAG+TGG 0.532392 1_3:+28732457 Msa0113040:CDS
GGGCCTTCAATGATGGTCAA+TGG 0.538506 1_3:+28732301 Msa0113040:CDS
CATCATCAGAGGTCAAGTTA+AGG 0.540046 1_3:-28732494 None:intergenic
CGGATGAGTCGACAAGAGGA+AGG 0.554210 1_3:+28732223 Msa0113040:CDS
AAAGTGATGGTGATTTCTGA+AGG 0.556976 1_3:-28732329 None:intergenic
CAAAGCACAGTATGTCAAGT+GGG 0.561874 1_3:+28732458 Msa0113040:CDS
TTCAAACATGCATCCTCAGT+TGG 0.569301 1_3:+28732258 Msa0113040:CDS
ATCATTGGTTAACAATTGGG+AGG 0.578607 1_3:+28732425 Msa0113040:CDS
AACTCTCAGAGGCTACTACA+AGG 0.578621 1_3:+28732533 Msa0113040:CDS
GACAAGAGGAAGGGTCACTC+AGG 0.585832 1_3:+28732233 Msa0113040:CDS
CGTATCACCAGAGGAGTCAG+AGG 0.597961 1_3:-28732757 None:intergenic
TTCACTCACCACAAAATCCA+GGG 0.604887 1_3:-28732373 None:intergenic
TTCTCACATCCAACTCTCAG+AGG 0.605503 1_3:+28732522 Msa0113040:CDS
ACTACTTCATCATAAAGTGA+TGG 0.615191 1_3:-28732342 None:intergenic
AACAATTGGGAGGCATATGG+TGG 0.626650 1_3:+28732435 Msa0113040:CDS
TTGGTTGATGGTATTTGCTG+CGG 0.640214 1_3:+28732203 Msa0113040:CDS
GCTGCGGATGAGTCGACAAG+AGG 0.648322 1_3:+28732219 Msa0113040:CDS
AAGTGATGGTGATTTCTGAA+GGG 0.650216 1_3:-28732328 None:intergenic
TCAAGGAACTTACCTTGACA+TGG 0.657148 1_3:-28732557 None:intergenic
CTACTACAAGGACCATGTCA+AGG 0.659291 1_3:+28732545 Msa0113040:CDS
GGATGAGTCGACAAGAGGAA+GGG 0.663089 1_3:+28732224 Msa0113040:CDS
ACAAACTGTCATACCAACTG+AGG 0.663360 1_3:-28732271 None:intergenic
GGAGGAAGATGAATGGCAGA+TGG 0.665469 1_3:+28732113 Msa0113040:CDS
AAAGCACAGTATGTCAAGTG+GGG 0.694927 1_3:+28732459 Msa0113040:CDS
TACCTGTAACGTATCACCAG+AGG 0.699288 1_3:-28732766 None:intergenic
GAGGAGTCAGAGGTGCATCG+AGG 0.724283 1_3:-28732747 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTAGTTTAAAAGAAAAAC+AGG - chr1_3:28732606-28732625 None:intergenic 15.0%
!!! GTTTTTCTTTTAAACTAATT+TGG + chr1_3:28732606-28732625 Msa0113040:intron 15.0%
!!! TATTATCATTGGTTAACAAT+TGG + chr1_3:28732421-28732440 Msa0113040:CDS 20.0%
!!! ATTATCATTGGTTAACAATT+GGG + chr1_3:28732422-28732441 Msa0113040:CDS 20.0%
! TTATGATGAAGTAGTATTCA+AGG + chr1_3:28732350-28732369 Msa0113040:CDS 25.0%
! AATCAGACTCATATTATCAT+TGG + chr1_3:28732410-28732429 Msa0113040:CDS 25.0%
!! AACAGGAAGAATTAAGTTTT+AGG - chr1_3:28732589-28732608 None:intergenic 25.0%
! GATCAATCAAGAAATAGTAT+AGG - chr1_3:28732634-28732653 None:intergenic 25.0%
! ACTCACAAATATCACTTATA+AGG + chr1_3:28732686-28732705 Msa0113040:CDS 25.0%
TTGAATCCATTGACATAGAA+AGG - chr1_3:28732177-28732196 None:intergenic 30.0%
! TCAATGGATTCAACACTTAT+TGG + chr1_3:28732184-28732203 Msa0113040:CDS 30.0%
! ATTCAACACTTATTGGTTGA+TGG + chr1_3:28732191-28732210 Msa0113040:CDS 30.0%
ACTACTTCATCATAAAGTGA+TGG - chr1_3:28732345-28732364 None:intergenic 30.0%
!!! TAAGTTTTAGGTACATCTCA+AGG - chr1_3:28732577-28732596 None:intergenic 30.0%
! AAGATCCAACAATTTTTGCT+TGG + chr1_3:28732709-28732728 Msa0113040:CDS 30.0%
! AGATCCAACAATTTTTGCTT+GGG + chr1_3:28732710-28732729 Msa0113040:CDS 30.0%
GGAAACCAATTTGTAGTGAA+TGG + chr1_3:28732147-28732166 Msa0113040:CDS 35.0%
ATCCATTGACATAGAAAGGT+TGG - chr1_3:28732173-28732192 None:intergenic 35.0%
TATGACAGTTTGTAGGACTT+GGG + chr1_3:28732281-28732300 Msa0113040:CDS 35.0%
! AAGTGATGGTGATTTCTGAA+GGG - chr1_3:28732331-28732350 None:intergenic 35.0%
! AAAGTGATGGTGATTTCTGA+AGG - chr1_3:28732332-28732351 None:intergenic 35.0%
! ATCATTGGTTAACAATTGGG+AGG + chr1_3:28732425-28732444 Msa0113040:CDS 35.0%
TGAGAAAAAGTCATCATCAG+AGG - chr1_3:28732508-28732527 None:intergenic 35.0%
GTTGGCCATTCACTACAAAT+TGG - chr1_3:28732155-28732174 None:intergenic 40.0%
!! TTGGTTGATGGTATTTGCTG+CGG + chr1_3:28732203-28732222 Msa0113040:CDS 40.0%
TTCAAACATGCATCCTCAGT+TGG + chr1_3:28732258-28732277 Msa0113040:CDS 40.0%
ACAAACTGTCATACCAACTG+AGG - chr1_3:28732274-28732293 None:intergenic 40.0%
! CAGTTGGTATGACAGTTTGT+AGG + chr1_3:28732274-28732293 Msa0113040:CDS 40.0%
GTATGACAGTTTGTAGGACT+TGG + chr1_3:28732280-28732299 Msa0113040:CDS 40.0%
TCTCCATTGACCATCATTGA+AGG - chr1_3:28732307-28732326 None:intergenic 40.0%
TTCACTCACCACAAAATCCA+GGG - chr1_3:28732376-28732395 None:intergenic 40.0%
TTTCACTCACCACAAAATCC+AGG - chr1_3:28732377-28732396 None:intergenic 40.0%
! GTTAACAATTGGGAGGCATA+TGG + chr1_3:28732432-28732451 Msa0113040:CDS 40.0%
CAAAGCACAGTATGTCAAGT+GGG + chr1_3:28732458-28732477 Msa0113040:CDS 40.0%
AAAGCACAGTATGTCAAGTG+GGG + chr1_3:28732459-28732478 Msa0113040:CDS 40.0%
CATCATCAGAGGTCAAGTTA+AGG - chr1_3:28732497-28732516 None:intergenic 40.0%
TCAAGGAACTTACCTTGACA+TGG - chr1_3:28732560-28732579 None:intergenic 40.0%
AGCTCCCAAGCAAAAATTGT+TGG - chr1_3:28732717-28732736 None:intergenic 40.0%
TGGCAGATGGTGCAAAAGAA+AGG + chr1_3:28732126-28732145 Msa0113040:CDS 45.0%
GGCCAACCTTTCTATGTCAA+TGG + chr1_3:28732168-28732187 Msa0113040:CDS 45.0%
TGAAGTAGTATTCAAGGCCC+TGG + chr1_3:28732356-28732375 Msa0113040:CDS 45.0%
! ATTCAAGGCCCTGGATTTTG+TGG + chr1_3:28732365-28732384 Msa0113040:CDS 45.0%
! AACAATTGGGAGGCATATGG+TGG + chr1_3:28732435-28732454 Msa0113040:CDS 45.0%
GCAAAGCACAGTATGTCAAG+TGG + chr1_3:28732457-28732476 Msa0113040:CDS 45.0%
TTCTCACATCCAACTCTCAG+AGG + chr1_3:28732522-28732541 Msa0113040:CDS 45.0%
! TTGTAGTAGCCTCTGAGAGT+TGG - chr1_3:28732534-28732553 None:intergenic 45.0%
AACTCTCAGAGGCTACTACA+AGG + chr1_3:28732533-28732552 Msa0113040:CDS 45.0%
CTACTACAAGGACCATGTCA+AGG + chr1_3:28732545-28732564 Msa0113040:CDS 45.0%
GGAGGAAGATGAATGGCAGA+TGG + chr1_3:28732113-28732132 Msa0113040:CDS 50.0%
GGATGAGTCGACAAGAGGAA+GGG + chr1_3:28732224-28732243 Msa0113040:CDS 50.0%
AGGACTTGGGCCTTCAATGA+TGG + chr1_3:28732294-28732313 Msa0113040:CDS 50.0%
GGGCCTTCAATGATGGTCAA+TGG + chr1_3:28732301-28732320 Msa0113040:CDS 50.0%
CGGATGAGTCGACAAGAGGA+AGG + chr1_3:28732223-28732242 Msa0113040:CDS 55.0%
GACAAGAGGAAGGGTCACTC+AGG + chr1_3:28732233-28732252 Msa0113040:CDS 55.0%
CGTATCACCAGAGGAGTCAG+AGG - chr1_3:28732760-28732779 None:intergenic 55.0%
GCTGCGGATGAGTCGACAAG+AGG + chr1_3:28732219-28732238 Msa0113040:CDS 60.0%
GTCAAGTGGGGCAATGCTGC+TGG + chr1_3:28732471-28732490 Msa0113040:CDS 60.0%
! GAGGAGTCAGAGGTGCATCG+AGG - chr1_3:28732750-28732769 None:intergenic 60.0%
CGATGCACCTCTGACTCCTC+TGG + chr1_3:28732750-28732769 Msa0113040:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 28732111 28732785 28732111 ID=Msa0113040;Name=Msa0113040
chr1_3 mRNA 28732111 28732785 28732111 ID=Msa0113040-mRNA-1;Parent=Msa0113040;Name=Msa0113040-mRNA-1;_AED=0.18;_eAED=0.18;_QI=0|0|0|1|1|1|2|0|193
chr1_3 exon 28732111 28732566 28732111 ID=Msa0113040-mRNA-1:exon:9481;Parent=Msa0113040-mRNA-1
chr1_3 exon 28732663 28732785 28732663 ID=Msa0113040-mRNA-1:exon:9482;Parent=Msa0113040-mRNA-1
chr1_3 CDS 28732111 28732566 28732111 ID=Msa0113040-mRNA-1:cds;Parent=Msa0113040-mRNA-1
chr1_3 CDS 28732663 28732785 28732663 ID=Msa0113040-mRNA-1:cds;Parent=Msa0113040-mRNA-1
Gene Sequence

>Msa0113040

ATGGAGGAAGATGAATGGCAGATGGTGCAAAAGAAAGGAAACCAATTTGTAGTGAATGGCCAACCTTTCTATGTCAATGGATTCAACACTTATTGGTTGATGGTATTTGCTGCGGATGAGTCGACAAGAGGAAGGGTCACTCAGGTGTTCAAACATGCATCCTCAGTTGGTATGACAGTTTGTAGGACTTGGGCCTTCAATGATGGTCAATGGAGAGCCCTTCAGAAATCACCATCACTTTATGATGAAGTAGTATTCAAGGCCCTGGATTTTGTGGTGAGTGAAACAAAGAAATACAAAATCAGACTCATATTATCATTGGTTAACAATTGGGAGGCATATGGTGGCAAAGCACAGTATGTCAAGTGGGGCAATGCTGCTGGCCTTAACTTGACCTCTGATGATGACTTTTTCTCACATCCAACTCTCAGAGGCTACTACAAGGACCATGTCAAGACTGTGCTCAGTAGAGTTAACACACTCACAAATATCACTTATAAGGAAGATCCAACAATTTTTGCTTGGGAGCTAATGAATGAGCCTCGATGCACCTCTGACTCCTCTGGTGATACGTTACAG
Protein sequence

>Msa0113040

MEEDEWQMVQKKGNQFVVNGQPFYVNGFNTYWLMVFAADESTRGRVTQVFKHASSVGMTVCRTWAFNDGQWRALQKSPSLYDEVVFKALDFVVSETKKYKIRLILSLVNNWEAYGGKAQYVKWGNAAGLNLTSDDDFFSHPTLRGYYKDHVKTVLSRVNTLTNITYKEDPTIFAWELMNEPRCTSDSSGDTLQ