AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1421550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1421550 MtrunA17_Chr7g0262811 98.077 104 2 0 1 104 1 104 2.50e-60 179
Msa1421550 MtrunA17_Chr1g0182681 68.000 50 14 2 1 49 1 49 4.45e-14 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGGTGGACTTGGTGGTTT+GGG 0.222354 tig0025135:+30416 Msa1421550:CDS
ACATTTGCTGGTGGTTATTC+AGG 0.231052 tig0025135:+30320 Msa1421550:CDS
CTTAGGTGGACTTGGTGGTT+TGG 0.237390 tig0025135:+30415 Msa1421550:CDS
CTTGGTGGTTTGGGAGGACT+TGG 0.272357 tig0025135:+30425 Msa1421550:CDS
TTAGGTGGTGGTGGTGGCTT+AGG 0.291571 tig0025135:+30398 Msa1421550:CDS
GGTGGAGCTGGTGGTGGTGT+TGG 0.293326 tig0025135:+30458 Msa1421550:CDS
GGTGGAATCGGTGGTGATTT+AGG 0.312961 tig0025135:+30380 Msa1421550:CDS
GGTGGTGTTGGTGGTGGAGC+TGG 0.316689 tig0025135:+30446 Msa1421550:CDS
GGAAACAATGGACTTCCTTT+TGG 0.322482 tig0025135:+30347 Msa1421550:CDS
TTGGGAGGACTTGGTGGTGT+TGG 0.324253 tig0025135:+30434 Msa1421550:CDS
GGTGGTGTTGGAGGTGGTGT+TGG 0.331290 tig0025135:+30470 Msa1421550:CDS
GCTGGTGGTTATTCAGGAAT+AGG 0.341133 tig0025135:+30326 Msa1421550:CDS
GTTGGAGGTGGTGTTGGAAC+TGG 0.344227 tig0025135:+30476 Msa1421550:CDS
CAAATGTCATGAAGTTCTTC+TGG 0.354882 tig0025135:-30304 None:intergenic
GGACTTGGTGGTGTTGGTGG+TGG 0.355251 tig0025135:+30440 Msa1421550:CDS
GGAGGACTTGGTGGTGTTGG+TGG 0.372674 tig0025135:+30437 Msa1421550:CDS
GCTGGTGGTGGTGTTGGAGG+TGG 0.373109 tig0025135:+30464 Msa1421550:CDS
AAGAACTTCATGACATTTGC+TGG 0.375624 tig0025135:+30308 Msa1421550:CDS
GGAGCTGGTGGTGGTGTTGG+AGG 0.379910 tig0025135:+30461 Msa1421550:CDS
GTTGGTGGTGGAGCTGGTGG+TGG 0.385227 tig0025135:+30452 Msa1421550:CDS
GGTGGTGTTGGAACTGGTGT+TGG 0.385912 tig0025135:+30482 Msa1421550:CDS
GGTGGAATTGGAGGTGGAAT+CGG 0.386910 tig0025135:+30368 Msa1421550:CDS
GGTGGTGGCTTAGGTGGACT+TGG 0.416312 tig0025135:+30407 Msa1421550:CDS
GGTGGTTTGGGAGGACTTGG+TGG 0.435056 tig0025135:+30428 Msa1421550:CDS
GGTGGTGGTGGTGGCTTAGG+TGG 0.452079 tig0025135:+30401 Msa1421550:CDS
GGTGTTGGTGGTGGAGCTGG+TGG 0.455563 tig0025135:+30449 Msa1421550:CDS
GGTGTTGGAACTGGTGTTGG+TGG 0.458137 tig0025135:+30485 Msa1421550:CDS
AAAGTGGTGTATGTTGTTGT+TGG 0.463389 tig0025135:+30217 Msa1421550:CDS
GGTGGCTTAGGTGGACTTGG+TGG 0.480958 tig0025135:+30410 Msa1421550:CDS
GGTGGACTTGGTGGTTTGGG+AGG 0.499205 tig0025135:+30419 Msa1421550:CDS
GGTGATTTAGGTGGTGGTGG+TGG 0.511257 tig0025135:+30392 Msa1421550:CDS
GTTGGTTCTTGCTCTTGTTG+TGG 0.516173 tig0025135:+30235 Msa1421550:CDS
ACCAACTGATGCTGGTTTGA+AGG 0.518003 tig0025135:+30280 Msa1421550:CDS
GAATATTGATCTTAAGGGAA+AGG 0.526279 tig0025135:-30515 None:intergenic
ATCGGTGGTGATTTAGGTGG+TGG 0.527781 tig0025135:+30386 Msa1421550:CDS
CCACCTCCAATTCCACCAAA+AGG 0.542402 tig0025135:-30362 None:intergenic
GGAATTGGAGGTGGAATCGG+TGG 0.552447 tig0025135:+30371 Msa1421550:CDS
GGTGGTGATTTAGGTGGTGG+TGG 0.559090 tig0025135:+30389 Msa1421550:CDS
AGAAATGTACCAACTGATGC+TGG 0.575990 tig0025135:+30272 Msa1421550:CDS
TATTCAGGAATAGGAAACAA+TGG 0.605549 tig0025135:+30335 Msa1421550:CDS
GGAATCGGTGGTGATTTAGG+TGG 0.612801 tig0025135:+30383 Msa1421550:CDS
GAGTGAGAGATATGGCAAAG+TGG 0.614546 tig0025135:+30201 None:intergenic
AACTTCATGACATTTGCTGG+TGG 0.621619 tig0025135:+30311 Msa1421550:CDS
TCCTTCAAACCAGCATCAGT+TGG 0.622405 tig0025135:-30281 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TATTCAGGAATAGGAAACAA+TGG + tig0025135:30335-30354 Msa1421550:CDS 30.0%
AAAGTGGTGTATGTTGTTGT+TGG + tig0025135:30217-30236 Msa1421550:CDS 35.0%
CAAATGTCATGAAGTTCTTC+TGG - tig0025135:30307-30326 None:intergenic 35.0%
AAGAACTTCATGACATTTGC+TGG + tig0025135:30308-30327 Msa1421550:CDS 35.0%
AGAAATGTACCAACTGATGC+TGG + tig0025135:30272-30291 Msa1421550:CDS 40.0%
! AACTTCATGACATTTGCTGG+TGG + tig0025135:30311-30330 Msa1421550:CDS 40.0%
! ACATTTGCTGGTGGTTATTC+AGG + tig0025135:30320-30339 Msa1421550:CDS 40.0%
!! GGAAACAATGGACTTCCTTT+TGG + tig0025135:30347-30366 Msa1421550:CDS 40.0%
!! AACAATGGACTTCCTTTTGG+TGG + tig0025135:30350-30369 Msa1421550:CDS 40.0%
! GTTGGTTCTTGCTCTTGTTG+TGG + tig0025135:30235-30254 Msa1421550:CDS 45.0%
!! ACCAACTGATGCTGGTTTGA+AGG + tig0025135:30280-30299 Msa1421550:CDS 45.0%
TCCTTCAAACCAGCATCAGT+TGG - tig0025135:30284-30303 None:intergenic 45.0%
GCTGGTGGTTATTCAGGAAT+AGG + tig0025135:30326-30345 Msa1421550:CDS 45.0%
! GGACTTCCTTTTGGTGGAAT+TGG + tig0025135:30356-30375 Msa1421550:CDS 45.0%
! CTTCCTTTTGGTGGAATTGG+AGG + tig0025135:30359-30378 Msa1421550:CDS 45.0%
!! TTAGGTGGACTTGGTGGTTT+GGG + tig0025135:30416-30435 Msa1421550:CDS 45.0%
CCACCTCCAATTCCACCAAA+AGG - tig0025135:30365-30384 None:intergenic 50.0%
! CCTTTTGGTGGAATTGGAGG+TGG + tig0025135:30362-30381 Msa1421550:CDS 50.0%
GGTGGAATTGGAGGTGGAAT+CGG + tig0025135:30368-30387 Msa1421550:CDS 50.0%
GGTGGAATCGGTGGTGATTT+AGG + tig0025135:30380-30399 Msa1421550:CDS 50.0%
GGAATCGGTGGTGATTTAGG+TGG + tig0025135:30383-30402 Msa1421550:CDS 50.0%
ATCGGTGGTGATTTAGGTGG+TGG + tig0025135:30386-30405 Msa1421550:CDS 50.0%
!! CTTAGGTGGACTTGGTGGTT+TGG + tig0025135:30415-30434 Msa1421550:CDS 50.0%
GGAATTGGAGGTGGAATCGG+TGG + tig0025135:30371-30390 Msa1421550:CDS 55.0%
! GGTGGTGATTTAGGTGGTGG+TGG + tig0025135:30389-30408 Msa1421550:CDS 55.0%
!! GGTGATTTAGGTGGTGGTGG+TGG + tig0025135:30392-30411 Msa1421550:CDS 55.0%
!! TTAGGTGGTGGTGGTGGCTT+AGG + tig0025135:30398-30417 Msa1421550:CDS 55.0%
! CTTGGTGGTTTGGGAGGACT+TGG + tig0025135:30425-30444 Msa1421550:CDS 55.0%
!! TTGGGAGGACTTGGTGGTGT+TGG + tig0025135:30434-30453 Msa1421550:CDS 55.0%
! GTTGGAGGTGGTGTTGGAAC+TGG + tig0025135:30476-30495 Msa1421550:CDS 55.0%
! GGTGGTGTTGGAACTGGTGT+TGG + tig0025135:30482-30501 Msa1421550:CDS 55.0%
! GGTGTTGGAACTGGTGTTGG+TGG + tig0025135:30485-30504 Msa1421550:CDS 55.0%
! GGTGGTGGCTTAGGTGGACT+TGG + tig0025135:30407-30426 Msa1421550:CDS 60.0%
! GGTGGCTTAGGTGGACTTGG+TGG + tig0025135:30410-30429 Msa1421550:CDS 60.0%
!! GGTGGACTTGGTGGTTTGGG+AGG + tig0025135:30419-30438 Msa1421550:CDS 60.0%
! GGTGGTTTGGGAGGACTTGG+TGG + tig0025135:30428-30447 Msa1421550:CDS 60.0%
!! GGAGGACTTGGTGGTGTTGG+TGG + tig0025135:30437-30456 Msa1421550:CDS 60.0%
!! GGACTTGGTGGTGTTGGTGG+TGG + tig0025135:30440-30459 Msa1421550:CDS 60.0%
! GGTGGTGTTGGAGGTGGTGT+TGG + tig0025135:30470-30489 Msa1421550:CDS 60.0%
!! GGTGGTGGTGGTGGCTTAGG+TGG + tig0025135:30401-30420 Msa1421550:CDS 65.0%
!! GGTGGTGTTGGTGGTGGAGC+TGG + tig0025135:30446-30465 Msa1421550:CDS 65.0%
!! GGTGTTGGTGGTGGAGCTGG+TGG + tig0025135:30449-30468 Msa1421550:CDS 65.0%
!! GTTGGTGGTGGAGCTGGTGG+TGG + tig0025135:30452-30471 Msa1421550:CDS 65.0%
!! GGTGGAGCTGGTGGTGGTGT+TGG + tig0025135:30458-30477 Msa1421550:CDS 65.0%
!! GGAGCTGGTGGTGGTGTTGG+AGG + tig0025135:30461-30480 Msa1421550:CDS 65.0%
!! GCTGGTGGTGGTGTTGGAGG+TGG + tig0025135:30464-30483 Msa1421550:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0025135 gene 30212 30526 30212 ID=Msa1421550;Name=Msa1421550
tig0025135 mRNA 30212 30526 30212 ID=Msa1421550-mRNA-1;Parent=Msa1421550;Name=Msa1421550-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|104
tig0025135 exon 30212 30526 30212 ID=Msa1421550-mRNA-1:exon:2155;Parent=Msa1421550-mRNA-1
tig0025135 CDS 30212 30526 30212 ID=Msa1421550-mRNA-1:cds;Parent=Msa1421550-mRNA-1
Gene Sequence

>Msa1421550

ATGGCAAAGTGGTGTATGTTGTTGTTGGTTCTTGCTCTTGTTGTGGCTACAACAAGTGCAAGAAATGTACCAACTGATGCTGGTTTGAAGGACCAGAAGAACTTCATGACATTTGCTGGTGGTTATTCAGGAATAGGAAACAATGGACTTCCTTTTGGTGGAATTGGAGGTGGAATCGGTGGTGATTTAGGTGGTGGTGGTGGCTTAGGTGGACTTGGTGGTTTGGGAGGACTTGGTGGTGTTGGTGGTGGAGCTGGTGGTGGTGTTGGAGGTGGTGTTGGAACTGGTGTTGGTGGTGTTCATCCTTTCCCTTAA

Protein sequence

>Msa1421550

MAKWCMLLLVLALVVATTSARNVPTDAGLKDQKNFMTFAGGYSGIGNNGLPFGGIGGGIGGDLGGGGGLGGLGGLGGLGGVGGGAGGGVGGGVGTGVGGVHPFP*