AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32508

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32508.t1 MTR_5g080880 80.695 259 42 4 1 256 1 254 3.17e-136 387
MS.gene32508.t1 MTR_5g080870 68.093 257 45 5 1 257 1 220 3.26e-112 326
MS.gene32508.t1 MTR_7g063520 42.292 253 123 6 8 256 20 253 1.50e-57 184
MS.gene32508.t1 MTR_4g006560 32.075 159 100 3 100 256 83 235 1.42e-22 93.2
MS.gene32508.t1 MTR_1g013120 29.675 246 143 9 24 256 4 232 6.16e-21 88.6
MS.gene32508.t1 MTR_5g093000 27.451 204 113 7 74 257 26 214 3.27e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32508.t1 AT5G05990 37.453 267 141 7 5 256 3 258 1.82e-52 171
MS.gene32508.t1 AT3G55605 40.876 274 127 10 1 256 1 257 2.05e-49 163
MS.gene32508.t1 AT2G39795 42.132 197 104 3 63 256 60 249 2.37e-47 158
MS.gene32508.t1 AT5G02050 36.842 266 158 4 1 256 1 266 5.71e-45 152
MS.gene32508.t1 AT2G39790 30.213 235 143 5 31 257 19 240 3.78e-27 105
MS.gene32508.t1 AT1G15870 29.193 161 103 4 99 256 88 240 1.93e-20 87.4
MS.gene32508.t1 AT1G80720 30.052 193 117 7 68 256 10 188 5.33e-16 74.3
MS.gene32508.t1 AT1G80720 30.052 193 117 7 68 256 62 240 8.16e-16 75.1
MS.gene32508.t1 AT4G31930 29.630 162 99 5 100 255 80 232 5.12e-13 67.0

Find 45 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATTATCAACTATCTTAAA+TGG 0.175868 5.1:-62782803 None:intergenic
AGTGTTATTGTCTGATTTCC+TGG 0.252098 5.1:-62782824 None:intergenic
ATCAGACAATAACACTTAAA+AGG 0.289378 5.1:+62782831 MS.gene32508:CDS
TTATCAAGGTGAAGAAATTC+AGG 0.325526 5.1:+62782856 MS.gene32508:CDS
CCAAGTCAAGCACTTTCCTT+AGG 0.334931 5.1:+62782316 MS.gene32508:CDS
TGCAAGAAATTTACTGTGCT+TGG 0.359052 5.1:-62783552 None:intergenic
CAGCGAATAACCATCTCATC+TGG 0.375769 5.1:-62783043 None:intergenic
TTAGAAACCTTGACTGAAAG+TGG 0.404401 5.1:-62782980 None:intergenic
CTCTTATTTCTAAGTACTTG+TGG 0.408675 5.1:-62783521 None:intergenic
TGCAAGAGTACATGATCAAC+AGG 0.410602 5.1:+62783571 MS.gene32508:CDS
TTCAGTCAAGGTTTCTAAGA+AGG 0.418352 5.1:+62782985 MS.gene32508:CDS
CACAAGTACTTAGAAATAAG+AGG 0.434165 5.1:+62783522 MS.gene32508:CDS
GATTATCAACTATCTTAAAT+GGG 0.456111 5.1:-62782802 None:intergenic
TAATCATCAAAAGGATGATA+AGG 0.475586 5.1:+62782922 MS.gene32508:CDS
GAGAAAAGTCTCATCGGAGT+TGG 0.476774 5.1:-62782475 None:intergenic
CAGGAAAAGTAGAGACTACT+TGG 0.480599 5.1:+62783590 MS.gene32508:CDS
CAAGTCAAGCACTTTCCTTA+GGG 0.487750 5.1:+62782317 MS.gene32508:CDS
ATCGAAAATCACTTGTGCTC+AGG 0.490320 5.1:+62782509 MS.gene32508:CDS
GTCAAGGTTTCTAAGAAGGA+TGG 0.493043 5.1:+62782989 MS.gene32508:CDS
AGAAAAGTCTCATCGGAGTT+GGG 0.497268 5.1:-62782474 None:intergenic
CTCGTAGCGGTTGACGGCAG+CGG 0.497835 5.1:-62782400 None:intergenic
TTTAAGATAGTTGATAATCC+AGG 0.504200 5.1:+62782806 MS.gene32508:CDS
TGAACCCTCGTAGCGGTTGA+CGG 0.507166 5.1:-62782406 None:intergenic
AGAACATGATAATCATCAAA+AGG 0.514345 5.1:+62782913 MS.gene32508:CDS
ATCTTAAATGGGAAATTGCT+CGG 0.515748 5.1:-62782791 None:intergenic
GAAAGCACGGCGCGATGACC+CGG 0.519271 5.1:-62782378 None:intergenic
ACACTTAAAAGGACTTATCA+AGG 0.527097 5.1:+62782842 MS.gene32508:CDS
GTTTAGAGCGCGGAACTCAT+CGG 0.529531 5.1:-62782535 None:intergenic
AAGCATTCCACTTTCAGTCA+AGG 0.530679 5.1:+62782973 MS.gene32508:CDS
AACACATTTGAATTTCAAAG+AGG 0.535659 5.1:-62783014 None:intergenic
CGCTGCCGTCAACCGCTACG+AGG 0.550566 5.1:+62782401 MS.gene32508:CDS
GTTGACGGCAGCGGAAAGCA+CGG 0.551406 5.1:-62782391 None:intergenic
TGATTATCATGTTCTTCACC+AGG 0.551810 5.1:-62782905 None:intergenic
CCTAAGGAAAGTGCTTGACT+TGG 0.566876 5.1:-62782316 None:intergenic
TCAAGGTTTCTAAGAAGGAT+GGG 0.576019 5.1:+62782990 MS.gene32508:CDS
AATCTTGCAACAAGCAGCTG+CGG 0.606350 5.1:-62783096 None:intergenic
AGCGAATAACCATCTCATCT+GGG 0.609542 5.1:-62783042 None:intergenic
TAAACGGAGAAAAGTCTCAT+CGG 0.611707 5.1:-62782481 None:intergenic
GCTGCCGTCAACCGCTACGA+GGG 0.613894 5.1:+62782402 MS.gene32508:CDS
TGTTGCTTACCCAGATGAGA+TGG 0.638083 5.1:+62783033 MS.gene32508:CDS
TCAGAAGAAAAGTGAAACGT+AGG 0.644962 5.1:-62782435 None:intergenic
AAAGTAGAGACTACTTGGTG+TGG 0.647167 5.1:+62783595 MS.gene32508:CDS
AAGTGCTTGACTTGGAACGA+AGG 0.662607 5.1:-62782308 None:intergenic
GGAAGACGAAGTTTAGAGCG+CGG 0.683480 5.1:-62782545 None:intergenic
GAACAAATGAACCCTCGTAG+CGG 0.717050 5.1:-62782413 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATGTTGAAAATTTGATTT+TGG + chr5.1:62782747-62782766 MS.gene32508:intron 15.0%
!!! TGAGATTATGATTTTTAATT+TGG + chr5.1:62782880-62782899 MS.gene32508:CDS 15.0%
!! AATTGAAAGTAATACAAACA+GGG - chr5.1:62783420-62783439 None:intergenic 20.0%
!! ATGGTATGAAAATTTGAATT+TGG + chr5.1:62782692-62782711 MS.gene32508:intron 20.0%
!! GATTATCAACTATCTTAAAT+GGG - chr5.1:62782805-62782824 None:intergenic 20.0%
!! TAATTGAAAGTAATACAAAC+AGG - chr5.1:62783421-62783440 None:intergenic 20.0%
!!! AATTTGATTTTGGTTGATAT+AGG + chr5.1:62782757-62782776 MS.gene32508:intron 20.0%
!!! ATTTGATTTTGGTTGATATA+GGG + chr5.1:62782758-62782777 MS.gene32508:intron 20.0%
!!! TGATTTTCGATTCAATTAAA+CGG - chr5.1:62782500-62782519 None:intergenic 20.0%
! AACACATTTGAATTTCAAAG+AGG - chr5.1:62783017-62783036 None:intergenic 25.0%
! ACATCAGTGATGTTAAATAA+AGG + chr5.1:62783192-62783211 MS.gene32508:intron 25.0%
! AGAACATGATAATCATCAAA+AGG + chr5.1:62782913-62782932 MS.gene32508:CDS 25.0%
! AGAATAAAATAATCAGAACG+AGG - chr5.1:62783133-62783152 None:intergenic 25.0%
! ATCAGACAATAACACTTAAA+AGG + chr5.1:62782831-62782850 MS.gene32508:CDS 25.0%
! ATCATGAGTCTAGTAAATTA+AGG - chr5.1:62782569-62782588 None:intergenic 25.0%
! ATGTTAAATAAAGGCTATAG+TGG + chr5.1:62783201-62783220 MS.gene32508:intron 25.0%
! GGATTATCAACTATCTTAAA+TGG - chr5.1:62782806-62782825 None:intergenic 25.0%
! TAATCATCAAAAGGATGATA+AGG + chr5.1:62782922-62782941 MS.gene32508:CDS 25.0%
! TTTAATCATACCAGCTTATA+AGG - chr5.1:62782656-62782675 None:intergenic 25.0%
!! ATTTTCATACCATTACGAAA+TGG - chr5.1:62782685-62782704 None:intergenic 25.0%
!! TTTTCATACCATTACGAAAT+GGG - chr5.1:62782684-62782703 None:intergenic 25.0%
!!! ATGATTTTTAATTTGGTTCC+TGG + chr5.1:62782887-62782906 MS.gene32508:CDS 25.0%
!!! TTTAAGATAGTTGATAATCC+AGG + chr5.1:62782806-62782825 MS.gene32508:CDS 25.0%
AAAAAAGACCCATTTCGTAA+TGG + chr5.1:62782673-62782692 MS.gene32508:intron 30.0%
ACACTTAAAAGGACTTATCA+AGG + chr5.1:62782842-62782861 MS.gene32508:CDS 30.0%
ATCTTAAATGGGAAATTGCT+CGG - chr5.1:62782794-62782813 None:intergenic 30.0%
ATTGATCAGAAAAACTCAAC+CGG + chr5.1:62782359-62782378 MS.gene32508:CDS 30.0%
CACAAGTACTTAGAAATAAG+AGG + chr5.1:62783522-62783541 MS.gene32508:CDS 30.0%
TGAACTTATACCTTATAAGC+TGG + chr5.1:62782643-62782662 MS.gene32508:intron 30.0%
TTATCAAGGTGAAGAAATTC+AGG + chr5.1:62782856-62782875 MS.gene32508:CDS 30.0%
! GTGCATTCAATATTTGAAAC+CGG + chr5.1:62783165-62783184 MS.gene32508:intron 30.0%
! TGCATTCAATATTTGAAACC+GGG + chr5.1:62783166-62783185 MS.gene32508:intron 30.0%
!! CTCTTATTTCTAAGTACTTG+TGG - chr5.1:62783524-62783543 None:intergenic 30.0%
CCAATCTCAATTTCAAATCG+CGG - chr5.1:62783300-62783319 None:intergenic 35.0%
TAAACGGAGAAAAGTCTCAT+CGG - chr5.1:62782484-62782503 None:intergenic 35.0%
TCAGAAGAAAAGTGAAACGT+AGG - chr5.1:62782438-62782457 None:intergenic 35.0%
TCCAAATCCCTGGAAAAAAA+TGG - chr5.1:62783480-62783499 None:intergenic 35.0%
TGATTATCATGTTCTTCACC+AGG - chr5.1:62782908-62782927 None:intergenic 35.0%
TGCAAGAAATTTACTGTGCT+TGG - chr5.1:62783555-62783574 None:intergenic 35.0%
TTAGAAACCTTGACTGAAAG+TGG - chr5.1:62782983-62783002 None:intergenic 35.0%
TTGATCAGAAAAACTCAACC+GGG + chr5.1:62782360-62782379 MS.gene32508:CDS 35.0%
TTGCAGTTCAGAATCAGATT+GGG + chr5.1:62783373-62783392 MS.gene32508:intron 35.0%
! AGTGTTATTGTCTGATTTCC+TGG - chr5.1:62782827-62782846 None:intergenic 35.0%
! CGCGATTTGAAATTGAGATT+GGG + chr5.1:62783298-62783317 MS.gene32508:intron 35.0%
! GATTTGAAATTGAGATTGGG+TGG + chr5.1:62783301-62783320 MS.gene32508:intron 35.0%
! GCATTCAATATTTGAAACCG+GGG + chr5.1:62783167-62783186 MS.gene32508:intron 35.0%
! TCAAGGTTTCTAAGAAGGAT+GGG + chr5.1:62782990-62783009 MS.gene32508:CDS 35.0%
! TCAGAATCAGATTGGGATTT+TGG + chr5.1:62783380-62783399 MS.gene32508:intron 35.0%
! TTCAGTCAAGGTTTCTAAGA+AGG + chr5.1:62782985-62783004 MS.gene32508:CDS 35.0%
!!! AGATTCTGCCATTTTTTTCC+AGG + chr5.1:62783469-62783488 MS.gene32508:intron 35.0%
!!! ATTTTGGTTGATATAGGGTG+AGG + chr5.1:62782763-62782782 MS.gene32508:intron 35.0%
!!! GATTCTGCCATTTTTTTCCA+GGG + chr5.1:62783470-62783489 MS.gene32508:intron 35.0%
AAGCATTCCACTTTCAGTCA+AGG + chr5.1:62782973-62782992 MS.gene32508:CDS 40.0%
AGAAAAGTCTCATCGGAGTT+GGG - chr5.1:62782477-62782496 None:intergenic 40.0%
AGCGAATAACCATCTCATCT+GGG - chr5.1:62783045-62783064 None:intergenic 40.0%
ATCGAAAATCACTTGTGCTC+AGG + chr5.1:62782509-62782528 MS.gene32508:CDS 40.0%
CAAGTCAAGCACTTTCCTTA+GGG + chr5.1:62782317-62782336 MS.gene32508:CDS 40.0%
CAGGAAAAGTAGAGACTACT+TGG + chr5.1:62783590-62783609 MS.gene32508:CDS 40.0%
CCACTATAGCTGCTATGATA+TGG - chr5.1:62783229-62783248 None:intergenic 40.0%
CCATATCATAGCAGCTATAG+TGG + chr5.1:62783226-62783245 MS.gene32508:intron 40.0%
GTTGCAGTTCAGAATCAGAT+TGG + chr5.1:62783372-62783391 MS.gene32508:intron 40.0%
TAACATCACTGATGTAACCC+CGG - chr5.1:62783187-62783206 None:intergenic 40.0%
! AAAGTAGAGACTACTTGGTG+TGG + chr5.1:62783595-62783614 MS.gene32508:CDS 40.0%
! CCGCGATTTGAAATTGAGAT+TGG + chr5.1:62783297-62783316 MS.gene32508:intron 40.0%
! GTCAAGGTTTCTAAGAAGGA+TGG + chr5.1:62782989-62783008 MS.gene32508:CDS 40.0%
! TGCAAGAGTACATGATCAAC+AGG + chr5.1:62783571-62783590 MS.gene32508:CDS 40.0%
! TTTTTCCAGGGATTTGGATG+AGG + chr5.1:62783482-62783501 MS.gene32508:intron 40.0%
!!! GCCATTTTTTTCCAGGGATT+TGG + chr5.1:62783476-62783495 MS.gene32508:intron 40.0%
AATCTTGCAACAAGCAGCTG+CGG - chr5.1:62783099-62783118 None:intergenic 45.0%
CAGCGAATAACCATCTCATC+TGG - chr5.1:62783046-62783065 None:intergenic 45.0%
CCAAGTCAAGCACTTTCCTT+AGG + chr5.1:62782316-62782335 MS.gene32508:CDS 45.0%
GAACAAATGAACCCTCGTAG+CGG - chr5.1:62782416-62782435 None:intergenic 45.0%
GAGAAAAGTCTCATCGGAGT+TGG - chr5.1:62782478-62782497 None:intergenic 45.0%
GCTATAGCACCTTTGCATAG+CGG + chr5.1:62783252-62783271 MS.gene32508:intron 45.0%
GTTCAAACTCCGCTATGCAA+AGG - chr5.1:62783264-62783283 None:intergenic 45.0%
TCGCAGAAGAAAAAGCCCTA+AGG - chr5.1:62782335-62782354 None:intergenic 45.0%
TCTCTACAACCAAGCAGTAC+AGG - chr5.1:62783336-62783355 None:intergenic 45.0%
TGTTGCTAACCTGTACTGCT+TGG + chr5.1:62783324-62783343 MS.gene32508:intron 45.0%
! TGTTGCTTACCCAGATGAGA+TGG + chr5.1:62783033-62783052 MS.gene32508:CDS 45.0%
!! AAGTGCTTGACTTGGAACGA+AGG - chr5.1:62782311-62782330 None:intergenic 45.0%
!! CCTAAGGAAAGTGCTTGACT+TGG - chr5.1:62782319-62782338 None:intergenic 45.0%
! GGAAGACGAAGTTTAGAGCG+CGG - chr5.1:62782548-62782567 None:intergenic 50.0%
! GTTTAGAGCGCGGAACTCAT+CGG - chr5.1:62782538-62782557 None:intergenic 50.0%
CAACGCCTCATCCAAATCCC+TGG - chr5.1:62783490-62783509 None:intergenic 55.0%
TGAACCCTCGTAGCGGTTGA+CGG - chr5.1:62782409-62782428 None:intergenic 55.0%
GTTGACGGCAGCGGAAAGCA+CGG - chr5.1:62782394-62782413 None:intergenic 60.0%
CTCGTAGCGGTTGACGGCAG+CGG - chr5.1:62782403-62782422 None:intergenic 65.0%
GCTGCCGTCAACCGCTACGA+GGG + chr5.1:62782402-62782421 MS.gene32508:CDS 65.0%
! GAAAGCACGGCGCGATGACC+CGG - chr5.1:62782381-62782400 None:intergenic 65.0%
CGCTGCCGTCAACCGCTACG+AGG + chr5.1:62782401-62782420 MS.gene32508:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 62782291 62783650 62782291 ID=MS.gene32508
chr5.1 mRNA 62782291 62783650 62782291 ID=MS.gene32508.t1;Parent=MS.gene32508
chr5.1 exon 62782291 62782560 62782291 ID=MS.gene32508.t1.exon1;Parent=MS.gene32508.t1
chr5.1 CDS 62782291 62782560 62782291 ID=cds.MS.gene32508.t1;Parent=MS.gene32508.t1
chr5.1 exon 62782779 62783122 62782779 ID=MS.gene32508.t1.exon2;Parent=MS.gene32508.t1
chr5.1 CDS 62782779 62783122 62782779 ID=cds.MS.gene32508.t1;Parent=MS.gene32508.t1
chr5.1 exon 62783491 62783650 62783491 ID=MS.gene32508.t1.exon3;Parent=MS.gene32508.t1
chr5.1 CDS 62783491 62783650 62783491 ID=cds.MS.gene32508.t1;Parent=MS.gene32508.t1
Gene Sequence

>MS.gene32508

ATGGCGTTCAATTCAATCCTTCGTTCCAAGTCAAGCACTTTCCTTAGGGCTTTTTCTTCTGCGACTCAATTGATCAGAAAAACTCAACCGGGTCATCGCGCCGTGCTTTCCGCTGCCGTCAACCGCTACGAGGGTTCATTTGTTCCTACGTTTCACTTTTCTTCTGAAGCTGTCAAAAACGAACCCAACTCCGATGAGACTTTTCTCCGTTTAATTGAATCGAAAATCACTTGTGCTCAGGAAACCGATGAGTTCCGCGCTCTAAACTTCGTCTTCCTTAATTTACTAGACTCATGATTGTAGTAATAGAAACAATGTTTTTCTTTTTAATTTCATTAGCTAGACACAATTTTGAACTTATACCTTATAAGCTGGTATGATTAAAAAAGACCCATTTCGTAATGGTATGAAAATTTGAATTTGGTTGTTAATTATGATAATTATTATTATGTTGTGAAATGTTGAAAATTTGATTTTGGTTGATATAGGGTGAGGAAGTTCCGAGCAATTTCCCATTTAAGATAGTTGATAATCCAGGAAATCAGACAATAACACTTAAAAGGACTTATCAAGGTGAAGAAATTCAGGTTGAGATTATGATTTTTAATTTGGTTCCTGGTGAAGAACATGATAATCATCAAAAGGATGATAAGGATGATGAGAGTGAGAGAGCAACTCAATCAAGCATTCCACTTTCAGTCAAGGTTTCTAAGAAGGATGGGACCTCTTTGAAATTCAAATGTGTTGCTTACCCAGATGAGATGGTTATTCGCTGCTTGTTTATTAAGAATCGTGATGAACAGATCCGCAGCTGCTTGTTGCAAGATTTTCAGTATGTACCTCGTTCTGATTATTTTATTCTGTTTATAAATATGTGCATTCAATATTTGAAACCGGGGTTACATCAGTGATGTTAAATAAAGGCTATAGTGGTACCATATCATAGCAGCTATAGTGGTGCGCTATAGCACCTTTGCATAGCGGAGTTTGAACAAATAACTATTTTCCGCGATTTGAAATTGAGATTGGGTGGTGTTGCTAACCTGTACTGCTTGGTTGTAGAGACATGAAAAATATTGATGTTGCAGTTCAGAATCAGATTGGGATTTTGGAGCTTTTTGTAAAACCCTGTTTGTATTACTTTCAATTAATGTTGTAGCTTATACATTGTTTGATTGAGATTCTGCCATTTTTTTCCAGGGATTTGGATGAGGCGTTGCAAAAGTCATTCCACAAGTACTTAGAAATAAGAGGAATCAAACCAAGCACAGTAAATTTCTTGCAAGAGTACATGATCAACAGGAAAAGTAGAGACTACTTGGTGTGGTTGAATAAGCTCAAGAATTTCATTAAAGCATGA
Protein sequence

>MS.gene32508.t1

MAFNSILRSKSSTFLRAFSSATQLIRKTQPGHRAVLSAAVNRYEGSFVPTFHFSSEAVKNEPNSDETFLRLIESKITCAQETDEFRALNFGEEVPSNFPFKIVDNPGNQTITLKRTYQGEEIQVEIMIFNLVPGEEHDNHQKDDKDDESERATQSSIPLSVKVSKKDGTSLKFKCVAYPDEMVIRCLFIKNRDEQIRSCLLQDFQDLDEALQKSFHKYLEIRGIKPSTVNFLQEYMINRKSRDYLVWLNKLKNFIKA