AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71465

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71465.t1 MTR_1g089830 59.146 164 29 1 1 164 1 126 1.52e-57 177
MS.gene71465.t1 MTR_1g045040 54.601 163 41 2 1 163 1 130 1.62e-44 143
MS.gene71465.t1 MTR_1g075130 73.494 83 18 1 86 168 7 85 8.90e-28 99.8
MS.gene71465.t1 MTR_8g089170 36.585 164 83 3 3 160 4 152 3.80e-26 97.4
MS.gene71465.t1 MTR_8g089130 35.503 169 86 4 3 163 4 157 1.68e-24 93.6
MS.gene71465.t1 MTR_8g039350 70.455 44 13 0 3 46 14 57 5.14e-15 66.2
MS.gene71465.t1 MTR_4g028990 43.478 92 45 3 73 164 13 97 2.32e-13 62.8
MS.gene71465.t1 MTR_5g013370 53.846 52 23 1 4 55 13 63 6.14e-11 60.1
MS.gene71465.t1 MTR_5g013370 53.846 52 23 1 4 55 13 63 8.61e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTTGTGGTTTACATTTCA+AGG 0.339580 1.3:+53637947 MS.gene71465:CDS
ATTGGTGTCGGCATCTCTAT+TGG 0.346524 1.3:-53638916 None:intergenic
ATTGGTGTCGGCGTCTCTAT+TGG 0.349108 1.3:-53638934 None:intergenic
CCACAAGCGTTACACAATAT+TGG 0.380139 1.3:-53637933 None:intergenic
TTTCAACAGAAACTCAAGTT+TGG 0.389578 1.3:+53637889 MS.gene71465:CDS
AATCTTTCAAACCAAACTTC+AGG 0.411413 1.3:+53638062 MS.gene71465:CDS
CCAAGCAATGAGATAGGTCT+TGG 0.425187 1.3:+53639063 MS.gene71465:CDS
CACAATATTGGCGTCTCGTA+TGG 0.440494 1.3:-53637921 None:intergenic
TCAAACAACAAAATATCGTC+AGG 0.502407 1.3:-53639021 None:intergenic
TCTTGGATGCATTCGTCTAA+AGG 0.502885 1.3:+53639080 MS.gene71465:CDS
TTTATACCAAGCAATGAGAT+AGG 0.511374 1.3:+53639057 MS.gene71465:CDS
CCAATATTGTGTAACGCTTG+TGG 0.532300 1.3:+53637933 MS.gene71465:CDS
GAAACTCAAGTTTGGCGCAA+AGG 0.544030 1.3:+53637897 MS.gene71465:CDS
CCAAGACCTATCTCATTGCT+TGG 0.545705 1.3:-53639063 None:intergenic
GGTTTACATTTCAAGGCGAA+AGG 0.567422 1.3:+53637954 MS.gene71465:CDS
AATAGAGACGCCGACACCAA+TGG 0.575440 1.3:+53638936 MS.gene71465:CDS
GTCGGCGTCTCTATTGGTGT+CGG 0.578211 1.3:-53638928 None:intergenic
TCTTCGGGAGATAGTTAGCA+AGG 0.579240 1.3:-53637980 None:intergenic
AAAAGCGTTCATTTGTAGAG+AGG 0.581892 1.3:+53638869 MS.gene71465:CDS
GGAAACTCATCCATTGGTGT+CGG 0.599667 1.3:-53638946 None:intergenic
AGCCCTGCAAAATCAGTCAT+CGG 0.602139 1.3:+53638004 MS.gene71465:CDS
GATACTTCTACAGATCAAGA+TGG 0.615323 1.3:+53639108 MS.gene71465:CDS
CTTCGGGAGATAGTTAGCAA+GGG 0.642252 1.3:-53637979 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAGATGATATAAATTGA+AGG - chr1.3:53638164-53638183 None:intergenic 15.0%
!! AATAGATGATATAAATTGAA+GGG - chr1.3:53638163-53638182 None:intergenic 15.0%
!! TTAAAATATGAAACTTCATT+TGG - chr1.3:53638537-53638556 None:intergenic 15.0%
!!! ACATTGTAAGAATATTTTTA+AGG + chr1.3:53638348-53638367 MS.gene71465:intron 15.0%
!!! ATTGTAAGAATATTTTTAAG+GGG + chr1.3:53638350-53638369 MS.gene71465:intron 15.0%
!!! CATTGTAAGAATATTTTTAA+GGG + chr1.3:53638349-53638368 MS.gene71465:intron 15.0%
!!! AATTTTTATTACCTGAAGTT+TGG - chr1.3:53638076-53638095 None:intergenic 20.0%
! ACAAATATCTCCATAAATGT+AGG - chr1.3:53638631-53638650 None:intergenic 25.0%
! CGATTGAAAATGAAAATGTT+GGG + chr1.3:53638268-53638287 MS.gene71465:intron 25.0%
! GTGGGAAAAATACAAATTTA+TGG + chr1.3:53638827-53638846 MS.gene71465:CDS 25.0%
! TCGATTGAAAATGAAAATGT+TGG + chr1.3:53638267-53638286 MS.gene71465:intron 25.0%
!! AATAACTTGTGCTTTACATT+TGG - chr1.3:53638134-53638153 None:intergenic 25.0%
!! ATGGGTATTGTTATAATTCA+GGG + chr1.3:53638381-53638400 MS.gene71465:intron 25.0%
!! CTTTACATTTGGTGAAATAT+GGG - chr1.3:53638123-53638142 None:intergenic 25.0%
!! TTTACATTTGGTGAAATATG+GGG - chr1.3:53638122-53638141 None:intergenic 25.0%
AATCTTTCAAACCAAACTTC+AGG + chr1.3:53638062-53638081 MS.gene71465:CDS 30.0%
AATGACAACTAAAGAAGAGT+TGG + chr1.3:53638659-53638678 MS.gene71465:intron 30.0%
ACTCATAAGTAGTGTAGAAT+GGG + chr1.3:53638295-53638314 MS.gene71465:intron 30.0%
ACTCTATATGCCTACATTTA+TGG + chr1.3:53638618-53638637 MS.gene71465:intron 30.0%
CACATTAGCTAGTATTCTTA+TGG + chr1.3:53638718-53638737 MS.gene71465:intron 30.0%
CTAGCTAATGTGTAACTATA+AGG - chr1.3:53638710-53638729 None:intergenic 30.0%
TCAAACAACAAAATATCGTC+AGG - chr1.3:53639024-53639043 None:intergenic 30.0%
TTTATACCAAGCAATGAGAT+AGG + chr1.3:53639057-53639076 MS.gene71465:CDS 30.0%
TTTCAACAGAAACTCAAGTT+TGG + chr1.3:53637889-53637908 MS.gene71465:CDS 30.0%
! CATGGGTATTGTTATAATTC+AGG + chr1.3:53638380-53638399 MS.gene71465:intron 30.0%
! GCTTTACATTTGGTGAAATA+TGG - chr1.3:53638124-53638143 None:intergenic 30.0%
! TATAGACTAAGAAGCTTTTG+TGG - chr1.3:53638970-53638989 None:intergenic 30.0%
! TGGGTATTGTTATAATTCAG+GGG + chr1.3:53638382-53638401 MS.gene71465:intron 30.0%
!! ATTTTAAGTAGACACAGCAT+TGG + chr1.3:53638550-53638569 MS.gene71465:intron 30.0%
!! ATTTTTCCTTTTCTAGTGCA+TGG + chr1.3:53638180-53638199 MS.gene71465:intron 30.0%
!! TTTTAAGGGGTACAATTCAT+GGG + chr1.3:53638363-53638382 MS.gene71465:intron 30.0%
!! TTTTTAAGGGGTACAATTCA+TGG + chr1.3:53638362-53638381 MS.gene71465:intron 30.0%
!! TTTTTCCTTTTCTAGTGCAT+GGG + chr1.3:53638181-53638200 MS.gene71465:intron 30.0%
!!! ACAAATGAACGCTTTTTTTG+AGG - chr1.3:53638865-53638884 None:intergenic 30.0%
!!! CAGATGTTTTTTCAATGTCA+AGG - chr1.3:53638031-53638050 None:intergenic 30.0%
!!! CATTAGTACCTTATTTTCTC+AGG + chr1.3:53638805-53638824 MS.gene71465:intron 30.0%
GACTCATAAGTAGTGTAGAA+TGG + chr1.3:53638294-53638313 MS.gene71465:intron 35.0%
GATACTTCTACAGATCAAGA+TGG + chr1.3:53639108-53639127 MS.gene71465:CDS 35.0%
TAAAACCCATGCACTAGAAA+AGG - chr1.3:53638189-53638208 None:intergenic 35.0%
! TCGTTGCAATGTGGATTAAA+GGG + chr1.3:53638500-53638519 MS.gene71465:intron 35.0%
! TTTTCCCACCTGAGAAAATA+AGG - chr1.3:53638816-53638835 None:intergenic 35.0%
! TTTTGTGGAAACTCATCCAT+TGG - chr1.3:53638955-53638974 None:intergenic 35.0%
!! AAAAGCGTTCATTTGTAGAG+AGG + chr1.3:53638869-53638888 MS.gene71465:CDS 35.0%
!!! AGTACCTTATTTTCTCAGGT+GGG + chr1.3:53638809-53638828 MS.gene71465:intron 35.0%
!!! TAGTACCTTATTTTCTCAGG+TGG + chr1.3:53638808-53638827 MS.gene71465:intron 35.0%
ATAAGTAGTGTAGAATGGGC+AGG + chr1.3:53638299-53638318 MS.gene71465:intron 40.0%
CCAATATTGTGTAACGCTTG+TGG + chr1.3:53637933-53637952 MS.gene71465:CDS 40.0%
CCACAAGCGTTACACAATAT+TGG - chr1.3:53637936-53637955 None:intergenic 40.0%
CGCTTGTGGTTTACATTTCA+AGG + chr1.3:53637947-53637966 MS.gene71465:CDS 40.0%
GGTTTACATTTCAAGGCGAA+AGG + chr1.3:53637954-53637973 MS.gene71465:CDS 40.0%
TCTTGGATGCATTCGTCTAA+AGG + chr1.3:53639080-53639099 MS.gene71465:CDS 40.0%
! ACGCTGCTAAAGTTTTCTAC+GGG - chr1.3:53638427-53638446 None:intergenic 40.0%
! CACGCTGCTAAAGTTTTCTA+CGG - chr1.3:53638428-53638447 None:intergenic 40.0%
! GTCGTTGCAATGTGGATTAA+AGG + chr1.3:53638499-53638518 MS.gene71465:intron 40.0%
!! GTGCATGGGTTTTAATGTAG+CGG + chr1.3:53638195-53638214 MS.gene71465:intron 40.0%
!! GTGGATTAAAGGGTGTTTGA+GGG + chr1.3:53638510-53638529 MS.gene71465:intron 40.0%
!! TGTGGATTAAAGGGTGTTTG+AGG + chr1.3:53638509-53638528 MS.gene71465:intron 40.0%
AGCCCTGCAAAATCAGTCAT+CGG + chr1.3:53638004-53638023 MS.gene71465:CDS 45.0%
CACAATATTGGCGTCTCGTA+TGG - chr1.3:53637924-53637943 None:intergenic 45.0%
CCAAGACCTATCTCATTGCT+TGG - chr1.3:53639066-53639085 None:intergenic 45.0%
CCAAGCAATGAGATAGGTCT+TGG + chr1.3:53639063-53639082 MS.gene71465:CDS 45.0%
CTTCGGGAGATAGTTAGCAA+GGG - chr1.3:53637982-53638001 None:intergenic 45.0%
GAAACTCAAGTTTGGCGCAA+AGG + chr1.3:53637897-53637916 MS.gene71465:CDS 45.0%
GGAAACTCATCCATTGGTGT+CGG - chr1.3:53638949-53638968 None:intergenic 45.0%
TCTTCGGGAGATAGTTAGCA+AGG - chr1.3:53637983-53638002 None:intergenic 45.0%
TGAGAGTTGTCGTTGCAATG+TGG + chr1.3:53638491-53638510 MS.gene71465:intron 45.0%
! CGCTGCTAAAGTTTTCTACG+GGG - chr1.3:53638426-53638445 None:intergenic 45.0%
! TGATTTTGCAGGGCTCTCTT+CGG - chr1.3:53637999-53638018 None:intergenic 45.0%
!! ATTGGTGTCGGCATCTCTAT+TGG - chr1.3:53638919-53638938 None:intergenic 45.0%
!! GTCCGATGACTGATTTTGCA+GGG - chr1.3:53638009-53638028 None:intergenic 45.0%
AATAGAGACGCCGACACCAA+TGG + chr1.3:53638936-53638955 MS.gene71465:CDS 50.0%
! GATTTTGCAGGGCTCTCTTC+GGG - chr1.3:53637998-53638017 None:intergenic 50.0%
!! ATTGGTGTCGGCGTCTCTAT+TGG - chr1.3:53638937-53638956 None:intergenic 50.0%
!! GGTCCGATGACTGATTTTGC+AGG - chr1.3:53638010-53638029 None:intergenic 50.0%
GTCGGCGTCTCTATTGGTGT+CGG - chr1.3:53638931-53638950 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 53637885 53639134 53637885 ID=MS.gene71465
chr1.3 mRNA 53637885 53639134 53637885 ID=MS.gene71465.t1;Parent=MS.gene71465
chr1.3 exon 53637885 53638083 53637885 ID=MS.gene71465.t1.exon1;Parent=MS.gene71465.t1
chr1.3 CDS 53637885 53638083 53637885 ID=cds.MS.gene71465.t1;Parent=MS.gene71465.t1
chr1.3 exon 53638827 53639134 53638827 ID=MS.gene71465.t1.exon2;Parent=MS.gene71465.t1
chr1.3 CDS 53638827 53639134 53638827 ID=cds.MS.gene71465.t1;Parent=MS.gene71465.t1
Gene Sequence

>MS.gene71465

ATGGTTTCAACAGAAACTCAAGTTTGGCGCAAAGGACCATACGAGACGCCAATATTGTGTAACGCTTGTGGTTTACATTTCAAGGCGAAAGGAACCCTTGCTAACTATCTCCCGAAGAGAGCCCTGCAAAATCAGTCATCGGACCTTGACATTGAAAAAACATCTGAAAGTAATGCAAATCTTTCAAACCAAACTTCAGGTAATAAAAATTGCAATAAGTTAATTAAATGTTCACCCCATATTTCACCAAATGTAAAGCACAAGTTATTCATTTTCCCTTCAATTTATATCATCTATTTTTCCTTTTCTAGTGCATGGGTTTTAATGTAGCGGTTGAGAAAGTCATTGTTGCTTAATTTTTTGAAATATCTAAATAAATTTATCGATTGAAAATGAAAATGTTGGGTATGACTCATAAGTAGTGTAGAATGGGCAGGACAAGCAAGACAAGTGAGCAAGAAAGACATTGTAAGAATATTTTTAAGGGGTACAATTCATGGGTATTGTTATAATTCAGGGGTATTGATTTCTTGCAATACCCCGTAGAAAACTTTAGCAGCGTGTTTTGATTTCTTTGATTTCTTGCATAACTTAAAGATGATTCTATGAGAGTTGTCGTTGCAATGTGGATTAAAGGGTGTTTGAGGGACCAAATGAAGTTTCATATTTTAAGTAGACACAGCATTGGATTTTGAATTAATTATATTGTTGTGCATTATAAAACGTACATACAACTCTATATGCCTACATTTATGGAGATATTTGTGCTAATACAATGACAACTAAAGAAGAGTTGGTATAAGATTGATCGATCAATCTTAGCCTTATAGTTACACATTAGCTAGTATTCTTATGGTAATACAAATAAATGATTATTCATTAATATGTAGCGTGTATGATGTATAAATATTTTTTTTTATCATTAGTACCTTATTTTCTCAGGTGGGAAAAATACAAATTTATGGAACGTCAAAATTCCTCAAAAAAAGCGTTCATTTGTAGAGAGGCATTCATCGACTGTGATGCAGACACCAATAGAGATGCCGACACCAATAGAGACGCCGACACCAATGGATGAGTTTCCACAAAAGCTTCTTAGTCTATATGAATCTGAGAAAGAAGAAAATGAATCATCTCCTGACGATATTTTGTTGTTTGAGAAAATGAACAACTTTATACCAAGCAATGAGATAGGTCTTGGATGCATTCGTCTAAAGGCAGATGATACTTCTACAGATCAAGATGGTTAA
Protein sequence

>MS.gene71465.t1

MVSTETQVWRKGPYETPILCNACGLHFKAKGTLANYLPKRALQNQSSDLDIEKTSESNANLSNQTSGGKNTNLWNVKIPQKKRSFVERHSSTVMQTPIEMPTPIETPTPMDEFPQKLLSLYESEKEENESSPDDILLFEKMNNFIPSNEIGLGCIRLKADDTSTDQDG