AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1338040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1338040 MtrunA17_Chr4g0075391 97.959 147 3 0 1 147 1 147 2.02e-104 295
Msa1338040 MtrunA17_Chr4g0013081 47.761 67 35 0 79 145 312 378 1.45e-15 72.4
Msa1338040 MtrunA17_Chr5g0432531 44.776 67 37 0 79 145 184 250 4.77e-14 67.4
Msa1338040 MtrunA17_Chr7g0244571 47.619 63 33 0 83 145 283 345 7.48e-14 67.4
Msa1338040 MtrunA17_Chr1g0177881 43.750 64 36 0 83 146 104 167 1.06e-12 62.4
Msa1338040 MtrunA17_Chr2g0284471 36.842 76 43 1 83 153 249 324 1.74e-12 63.5
Msa1338040 MtrunA17_Chr8g0379681 42.373 59 34 0 83 141 260 318 2.07e-11 60.5
Msa1338040 MtrunA17_Chr4g0025901 39.062 64 39 0 83 146 101 164 3.30e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1338040 AT4G04025.1 53.289 152 57 3 4 141 22 173 2.02e-44 144
Msa1338040 AT5G01840.1 45.161 62 34 0 87 148 204 265 1.71e-13 66.2
Msa1338040 AT1G06920.1 41.573 89 47 2 58 141 215 303 2.20e-13 66.2
Msa1338040 AT2G30400.1 46.269 67 32 1 79 145 254 316 2.23e-13 66.2
Msa1338040 AT5G58360.1 37.234 94 47 3 60 145 199 288 8.57e-13 64.7
Msa1338040 AT4G18830.1 41.270 63 37 0 83 145 284 346 1.40e-12 64.3

Find 21 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGACATGTAGAGAGAAAA+AGG 0.217537 tig0001538:+37444 Msa1338040:CDS
ATGATCCAAGAGAGGATTTC+AGG 0.230726 tig0001538:+37525 Msa1338040:CDS
GAAGATCTTTCGCATCTTGA+AGG 0.366336 tig0001538:-37580 None:intergenic
GAGAGTTCTTCTTCTGTCTC+TGG 0.413981 tig0001538:+37341 Msa1338040:CDS
AAATCTCAAGTATAAGACTA+TGG 0.438492 tig0001538:-37646 None:intergenic
AAAAGGGAGAAGAGGAGAGA+AGG 0.442296 tig0001538:+37461 Msa1338040:CDS
GACTCCCTGAAATCCTCTCT+TGG 0.457320 tig0001538:-37530 None:intergenic
TCTTATCATGTAAATGTCAA+TGG 0.460946 tig0001538:+37693 Msa1338040:CDS
GTTCTTCTTCTGTCTCTGGT+AGG 0.472904 tig0001538:+37345 Msa1338040:CDS
GGATTTCAGGGAGTCTATGA+TGG 0.485788 tig0001538:+37538 Msa1338040:CDS
CTATTATATGTCGATGAACT+CGG 0.518436 tig0001538:+37616 Msa1338040:CDS
TGATCCAAGAGAGGATTTCA+GGG 0.524133 tig0001538:+37526 Msa1338040:CDS
ATATAGTGTTTCTTCTTCAG+AGG 0.569609 tig0001538:+37313 Msa1338040:CDS
GTCAAGTCTCTCTTGCACCA+TGG 0.576800 tig0001538:-37396 None:intergenic
AAAACAACAAAGAGGATGCA+AGG 0.595456 tig0001538:+37268 Msa1338040:CDS
AAAACCTCAAAACAACAAAG+AGG 0.609556 tig0001538:+37260 Msa1338040:CDS
TGTGCTAGTGTAGAAACAGA+AGG 0.614020 tig0001538:-37371 None:intergenic
TTCTACACTAGCACATGCCA+TGG 0.653332 tig0001538:+37379 Msa1338040:CDS
GTGTTCTTATGATCCAAGAG+AGG 0.658417 tig0001538:+37517 Msa1338040:CDS
GTGCTAGTGTAGAAACAGAA+GGG 0.663929 tig0001538:-37370 None:intergenic
TCTGTTGCTACTGCAACACA+AGG 0.676898 tig0001538:-37291 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAGTTTTTCTCTTATCATT+TGG - tig0001538:37421-37440 None:intergenic 25.0%
! AAATCTCAAGTATAAGACTA+TGG - tig0001538:37649-37668 None:intergenic 25.0%
!! TATACTTGAGATTTTTCATG+AGG + tig0001538:37655-37674 Msa1338040:CDS 25.0%
! TCTTATCATGTAAATGTCAA+TGG + tig0001538:37693-37712 Msa1338040:CDS 25.0%
AAAACCTCAAAACAACAAAG+AGG + tig0001538:37260-37279 Msa1338040:CDS 30.0%
ATATAGTGTTTCTTCTTCAG+AGG + tig0001538:37313-37332 Msa1338040:CDS 30.0%
TAGACATGTAGAGAGAAAAA+GGG + tig0001538:37445-37464 Msa1338040:CDS 30.0%
CTATTATATGTCGATGAACT+CGG + tig0001538:37616-37635 Msa1338040:CDS 30.0%
AAAACAACAAAGAGGATGCA+AGG + tig0001538:37268-37287 Msa1338040:CDS 35.0%
CTAGACATGTAGAGAGAAAA+AGG + tig0001538:37444-37463 Msa1338040:CDS 35.0%
!!! GCATCCTCTTTGTTGTTTTG+AGG - tig0001538:37267-37286 None:intergenic 40.0%
GTGCTAGTGTAGAAACAGAA+GGG - tig0001538:37373-37392 None:intergenic 40.0%
TGTGCTAGTGTAGAAACAGA+AGG - tig0001538:37374-37393 None:intergenic 40.0%
TAGAGAGAAAAAGGGAGAAG+AGG + tig0001538:37453-37472 Msa1338040:CDS 40.0%
GTGTTCTTATGATCCAAGAG+AGG + tig0001538:37517-37536 Msa1338040:CDS 40.0%
ATGATCCAAGAGAGGATTTC+AGG + tig0001538:37525-37544 Msa1338040:CDS 40.0%
TGATCCAAGAGAGGATTTCA+GGG + tig0001538:37526-37545 Msa1338040:CDS 40.0%
GAAGATCTTTCGCATCTTGA+AGG - tig0001538:37583-37602 None:intergenic 40.0%
TCTGTTGCTACTGCAACACA+AGG - tig0001538:37294-37313 None:intergenic 45.0%
GAGAGTTCTTCTTCTGTCTC+TGG + tig0001538:37341-37360 Msa1338040:CDS 45.0%
GTTCTTCTTCTGTCTCTGGT+AGG + tig0001538:37345-37364 Msa1338040:CDS 45.0%
TTCTACACTAGCACATGCCA+TGG + tig0001538:37379-37398 Msa1338040:CDS 45.0%
AAAAGGGAGAAGAGGAGAGA+AGG + tig0001538:37461-37480 Msa1338040:CDS 45.0%
GGATTTCAGGGAGTCTATGA+TGG + tig0001538:37538-37557 Msa1338040:CDS 45.0%
GTCAAGTCTCTCTTGCACCA+TGG - tig0001538:37399-37418 None:intergenic 50.0%
GACTCCCTGAAATCCTCTCT+TGG - tig0001538:37533-37552 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0001538 gene 37257 37718 37257 ID=Msa1338040;Name=Msa1338040
tig0001538 mRNA 37257 37718 37257 ID=Msa1338040-mRNA-1;Parent=Msa1338040;Name=Msa1338040-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|153
tig0001538 exon 37257 37718 37257 ID=Msa1338040-mRNA-1:exon:1451;Parent=Msa1338040-mRNA-1
tig0001538 CDS 37257 37718 37257 ID=Msa1338040-mRNA-1:cds;Parent=Msa1338040-mRNA-1
Gene Sequence

>Msa1338040

ATGAAAACCTCAAAACAACAAAGAGGATGCAAGGCCTTGTGTTGCAGTAGCAACAGATATAGTGTTTCTTCTTCAGAGGAAGCAGAGAGTTCTTCTTCTGTCTCTGGTAGGTTCCCTTCTGTTTCTACACTAGCACATGCCATGGTGCAAGAGAGACTTGACCAAATGATAAGAGAAAAACTTGAAGCTAGACATGTAGAGAGAAAAAGGGAGAAGAGGAGAGAAGGAACTAAGTTTGTTGTAATGTTAGCAACAGAAAAGTGTTCTTATGATCCAAGAGAGGATTTCAGGGAGTCTATGATGGAGATGATAACAGTGAATCGCCTTCAAGATGCGAAAGATCTTCGTAGTTTATTGAACTATTATATGTCGATGAACTCGGAAGAATACCATAGTCTTATACTTGAGATTTTTCATGAGGTTTGTACTAATTTGTTCTTATCATGTAAATGTCAATGGTAA
Protein sequence

>Msa1338040

MKTSKQQRGCKALCCSSNRYSVSSSEEAESSSSVSGRFPSVSTLAHAMVQERLDQMIREKLEARHVERKREKRREGTKFVVMLATEKCSYDPREDFRESMMEMITVNRLQDAKDLRSLLNYYMSMNSEEYHSLILEIFHEVCTNLFLSCKCQW*