AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0880042494.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880042494.01.T01 MTR_8g015220 63.077 65 23 1 37 101 242 305 2.09e-17 75.1
MsG0880042494.01.T01 MTR_8g102150 69.388 49 12 1 53 101 271 316 4.85e-15 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0880042494.01.T01 AT2G19800 88.889 36 4 0 66 101 282 317 1.62e-15 70.5
MsG0880042494.01.T01 AT1G14520 80.556 36 7 0 66 101 276 311 2.76e-14 67.0
MsG0880042494.01.T01 AT1G14520 80.556 36 7 0 66 101 276 311 2.76e-14 67.0
MsG0880042494.01.T01 AT4G26260 80.556 36 7 0 66 101 282 317 2.94e-14 67.0
MsG0880042494.01.T01 AT4G26260 80.556 36 7 0 66 101 283 318 2.95e-14 67.0
MsG0880042494.01.T01 AT1G14520 80.556 36 7 0 66 101 274 309 3.11e-14 66.6
MsG0880042494.01.T01 AT5G56640 77.778 36 8 0 66 101 279 314 2.68e-13 64.3
MsG0880042494.01.T01 AT5G56640 77.778 36 8 0 66 101 249 284 1.66e-12 61.6

Find 11 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCACCACTTCAGCTTTGC+AGG 0.279549 8:+9548154 None:intergenic
TCAATGAGGGAGATGTAGTA+TGG 0.376465 8:+9548339 None:intergenic
TCAATGAGGGAGATGTAGTA+TGG 0.376465 8:+9550102 None:intergenic
TAAGTCTGCAAAGAAAAGAT+TGG 0.428967 8:-9548466 MsG0880042494.01.T01:intron
AGTTAGAGTTGATGTTGAAA+AGG 0.459451 8:-9548367 MsG0880042494.01.T01:CDS
CTACATCTCCCTCATTGAAA+AGG 0.497519 8:-9548334 MsG0880042494.01.T01:intron
CTACATCTCCCTCATTGAAA+AGG 0.497519 8:-9550097 MsG0880042494.01.T01:intron
ACTTCCCTGCAAAGCTGAAG+TGG 0.537264 8:-9548159 MsG0880042494.01.T01:CDS
AGTGAGAGTTGATGTTGAAA+AGG 0.538804 8:-9550130 MsG0880042494.01.T01:CDS
TTGCTACAAGTGATTGAACA+TGG 0.595182 8:+9548414 None:intergenic
TTCACCACTTCAGCTTTGCA+GGG 0.603653 8:+9548155 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATAATAATAATAATAA+TGG + Chr8:9549857-9549876 None:intergenic 0.0%
!!! TTTTTTTTTTTTTTTTTTTA+TGG - Chr8:9548546-9548565 MsG0880042494.01.T01:intron 0.0%
!!! AAAATTATTTAAAGCAATTT+CGG - Chr8:9548734-9548753 MsG0880042494.01.T01:intron 10.0%
!! AAAAAAAACATATAAATCCA+AGG + Chr8:9548534-9548553 None:intergenic 15.0%
!! AAAAAAAACTTAATAACTCT+AGG + Chr8:9550155-9550174 None:intergenic 15.0%
!! GAAAAAAAAAAGGAAATAAA+AGG + Chr8:9548305-9548324 None:intergenic 15.0%
!!! AACTGATAGTTATTTTATTT+TGG - Chr8:9548902-9548921 MsG0880042494.01.T01:intron 15.0%
!!! ATTTTTACAACTAGAAAAAA+AGG + Chr8:9550076-9550095 None:intergenic 15.0%
!!! TTTTCTAGTTGTAAAAATTA+AGG - Chr8:9550078-9550097 MsG0880042494.01.T01:intron 15.0%
!! AGTAAAAACTTAATAACTCT+AGG + Chr8:9548371-9548390 None:intergenic 20.0%
!! ATATAATTAAAACAATCCTC+GGG - Chr8:9549658-9549677 MsG0880042494.01.T01:intron 20.0%
!! CATATAATTAAAACAATCCT+CGG - Chr8:9549657-9549676 MsG0880042494.01.T01:intron 20.0%
!! GTATATATTAGGGTTAAAAA+CGG - Chr8:9549726-9549745 MsG0880042494.01.T01:intron 20.0%
!! TCTAACGTTACATTAAAAAT+TGG + Chr8:9548987-9549006 None:intergenic 20.0%
!! TTAAAAATTGGATGAAAAGT+AGG + Chr8:9548975-9548994 None:intergenic 20.0%
!!! AAGCTATGTAGATTTTTTTT+TGG + Chr8:9548834-9548853 None:intergenic 20.0%
!!! AGTTTAGTTTATGAAGTAAA+GGG - Chr8:9548483-9548502 MsG0880042494.01.T01:intron 20.0%
!!! AGTTTTTATTATAAAGTTCC+TGG - Chr8:9548599-9548618 MsG0880042494.01.T01:intron 20.0%
!!! ATGTTGATTTATTGACATTT+AGG - Chr8:9549159-9549178 MsG0880042494.01.T01:intron 20.0%
!!! TAGTTTAGTTTATGAAGTAA+AGG - Chr8:9548482-9548501 MsG0880042494.01.T01:intron 20.0%
!!! TTTATGTGTTATTAACATCT+GGG + Chr8:9549351-9549370 None:intergenic 20.0%
!!! TTTTATGTGTTATTAACATC+TGG + Chr8:9549352-9549371 None:intergenic 20.0%
!!! TTTTCAGCTAGAAAAAAAAA+AGG + Chr8:9548315-9548334 None:intergenic 20.0%
! AAAAAATATGAACACCACAA+AGG + Chr8:9549211-9549230 None:intergenic 25.0%
! AAAAACAACTCCAAATTAGA+GGG + Chr8:9548636-9548655 None:intergenic 25.0%
! AAGTACTTTATAACCAACAA+TGG + Chr8:9549490-9549509 None:intergenic 25.0%
! ACTTTAGATTGAATATTCAC+CGG - Chr8:9548694-9548713 MsG0880042494.01.T01:intron 25.0%
! ATAACCTAACATCAAGAATT+GGG - Chr8:9549545-9549564 MsG0880042494.01.T01:intron 25.0%
! ATCTACTAGACGTATATATT+AGG - Chr8:9549715-9549734 MsG0880042494.01.T01:intron 25.0%
! CTAGCTGAAAAAAATTAACA+AGG - Chr8:9548324-9548343 MsG0880042494.01.T01:intron 25.0%
! TAAAAACAACTCCAAATTAG+AGG + Chr8:9548637-9548656 None:intergenic 25.0%
! TATAATTAAAACAATCCTCG+GGG - Chr8:9549659-9549678 MsG0880042494.01.T01:intron 25.0%
! TCTACTAGACGTATATATTA+GGG - Chr8:9549716-9549735 MsG0880042494.01.T01:intron 25.0%
! TGAAGTGGATATGTTTAATA+TGG - Chr8:9549128-9549147 MsG0880042494.01.T01:intron 25.0%
! TGGTTATGAACTTATGTATT+TGG - Chr8:9549016-9549035 MsG0880042494.01.T01:intron 25.0%
! TTAAATATTTGTCCACTTCA+AGG + Chr8:9548453-9548472 None:intergenic 25.0%
!! AAAGGAAATAAAAGCTTTTG+AGG + Chr8:9550058-9550077 None:intergenic 25.0%
!! TTATTTAAAGCAATTTCGGT+TGG - Chr8:9548738-9548757 MsG0880042494.01.T01:intron 25.0%
!! TTCAGTCTATTTTCTTTTTC+CGG + Chr8:9548716-9548735 None:intergenic 25.0%
!!! GGTTGTTTATTTTTTGTTGA+AGG - Chr8:9550099-9550118 MsG0880042494.01.T01:CDS 25.0%
!!! GTAACGTTAGATAATTTGTT+TGG - Chr8:9548996-9549015 MsG0880042494.01.T01:intron 25.0%
!!! GTTAGGTTATGTAATTTGTT+TGG + Chr8:9549535-9549554 None:intergenic 25.0%
AAGGGAATAAGCTATTAAGT+TGG - Chr8:9548501-9548520 MsG0880042494.01.T01:intron 30.0%
AATAACTCTAGGCAAAAACT+AGG + Chr8:9548360-9548379 None:intergenic 30.0%
AATTGGGTGAAAATTAGGTT+TGG - Chr8:9549561-9549580 MsG0880042494.01.T01:intron 30.0%
AGATACAAACTAAAGTGTAC+GGG + Chr8:9549254-9549273 None:intergenic 30.0%
AGGAAATAAAAGGTTTCTTG+AGG + Chr8:9548295-9548314 None:intergenic 30.0%
AGGGAATAAGCTATTAAGTT+GGG - Chr8:9548502-9548521 MsG0880042494.01.T01:intron 30.0%
ATAACTCTAGGCAAAAACTA+GGG + Chr8:9548359-9548378 None:intergenic 30.0%
ATATTCAAGACCCTCTAATT+TGG - Chr8:9548623-9548642 MsG0880042494.01.T01:intron 30.0%
ATGAAACACCAAAATAACGT+AGG - Chr8:9549610-9549629 MsG0880042494.01.T01:intron 30.0%
CATAACCTAACATCAAGAAT+TGG - Chr8:9549544-9549563 MsG0880042494.01.T01:intron 30.0%
GAGATACAAACTAAAGTGTA+CGG + Chr8:9549255-9549274 None:intergenic 30.0%
TAAGTCTGCAAAGAAAAGAT+TGG - Chr8:9549894-9549913 MsG0880042494.01.T01:intron 30.0%
TATAAACAACAACCGAGAAA+AGG - Chr8:9549421-9549440 MsG0880042494.01.T01:intron 30.0%
TATTAAGTAGGCCTCTAATT+TGG - Chr8:9549770-9549789 MsG0880042494.01.T01:intron 30.0%
TATTGACATTTAGGTCATAG+AGG - Chr8:9549168-9549187 MsG0880042494.01.T01:intron 30.0%
TCAAGAATTGGGTGAAAATT+AGG - Chr8:9549556-9549575 MsG0880042494.01.T01:intron 30.0%
TTCATCTAACTCCAAATTAG+AGG + Chr8:9549784-9549803 None:intergenic 30.0%
! AATTGTCACCTACGTTATTT+TGG + Chr8:9549621-9549640 None:intergenic 30.0%
! ACTTAACAAAGTACCATTGT+TGG - Chr8:9549474-9549493 MsG0880042494.01.T01:intron 30.0%
! TGGAATGTTACTTGAAAATG+TGG + Chr8:9549837-9549856 None:intergenic 30.0%
!! AGTTAGAGTTGATGTTGAAA+AGG - Chr8:9549993-9550012 MsG0880042494.01.T01:intron 30.0%
!! GTTAGTTTAAGTCCTTTTCT+CGG + Chr8:9549436-9549455 None:intergenic 30.0%
!!! TACGTTATTTTGGTGTTTCA+TGG + Chr8:9549611-9549630 None:intergenic 30.0%
!!! TGGAGTTGTTTTTAAGTTTC+TGG - Chr8:9548643-9548662 MsG0880042494.01.T01:intron 30.0%
AGGATGTTGAGAATCTGAAA+TGG - Chr8:9549809-9549828 MsG0880042494.01.T01:intron 35.0%
AGGCCTACTTAATATCTCTT+AGG + Chr8:9549764-9549783 None:intergenic 35.0%
CAATACACAAAGAACCTTTG+TGG - Chr8:9549194-9549213 MsG0880042494.01.T01:intron 35.0%
CACAAAGGTTCTTTGTGTAT+TGG + Chr8:9549196-9549215 None:intergenic 35.0%
GATACAAACTAAAGTGTACG+GGG + Chr8:9549253-9549272 None:intergenic 35.0%
TAACTCTAGGCAAAAACTAG+GGG + Chr8:9548358-9548377 None:intergenic 35.0%
TTCACCCAATTCTTGATGTT+AGG + Chr8:9549552-9549571 None:intergenic 35.0%
TTGCTACAAGTGATTGAACA+TGG + Chr8:9549949-9549968 None:intergenic 35.0%
TTGGAGTTAGATGAATGATG+AGG - Chr8:9549789-9549808 MsG0880042494.01.T01:intron 35.0%
! AGGGTTAAAAACGGAGTTTT+AGG - Chr8:9549735-9549754 MsG0880042494.01.T01:intron 35.0%
! GGGTTAAAAACGGAGTTTTA+GGG - Chr8:9549736-9549755 MsG0880042494.01.T01:intron 35.0%
!! AGTGAGAGTTGATGTTGAAA+AGG - Chr8:9548230-9548249 MsG0880042494.01.T01:intron 35.0%
!! GGTTAAAAACGGAGTTTTAG+GGG - Chr8:9549737-9549756 MsG0880042494.01.T01:intron 35.0%
!!! GTTAAAAACGGAGTTTTAGG+GGG - Chr8:9549738-9549757 MsG0880042494.01.T01:intron 35.0%
AAGCTGAAGTGGTGAAACAT+TGG - Chr8:9548425-9548444 MsG0880042494.01.T01:CDS 40.0%
ACTTCAACAACCGAAAAAGG+AGG + Chr8:9549114-9549133 None:intergenic 40.0%
AGCTACGAACTAAAGGGTTT+GGG + Chr8:9549328-9549347 None:intergenic 40.0%
CTACATCTCCCTCATTGAAA+AGG - Chr8:9548263-9548282 MsG0880042494.01.T01:intron 40.0%
GGGCCTAAGAGATATTAAGT+AGG - Chr8:9549758-9549777 MsG0880042494.01.T01:intron 40.0%
TAGAGGGTCTTGAATATTCC+AGG + Chr8:9548620-9548639 None:intergenic 40.0%
TCAATGAGGGAGATGTAGTA+TGG + Chr8:9548261-9548280 None:intergenic 40.0%
TCCACTTCAACAACCGAAAA+AGG + Chr8:9549117-9549136 None:intergenic 40.0%
TCTAGTAGATAAGTCCCAGA+GGG + Chr8:9549705-9549724 None:intergenic 40.0%
TTAGGTTTGGAGAGCAAATG+AGG - Chr8:9549574-9549593 MsG0880042494.01.T01:intron 40.0%
! AGGTGCTTACCTTTTCAATG+AGG + Chr8:9548275-9548294 None:intergenic 40.0%
! GGTGCTTACCTTTTCAATGA+GGG + Chr8:9548274-9548293 None:intergenic 40.0%
! TCGTGTAAGTCCTCCTTTTT+CGG - Chr8:9549101-9549120 MsG0880042494.01.T01:intron 40.0%
!! GGTTCACTGGTTTGAAAACT+TGG + Chr8:9548933-9548952 None:intergenic 40.0%
!!! TCCTTTTTCGGTTGTTGAAG+TGG - Chr8:9549113-9549132 MsG0880042494.01.T01:intron 40.0%
AAATAGGGAGTTAATCCCCG+AGG + Chr8:9549677-9549696 None:intergenic 45.0%
ACAAACTAAAGTGTACGGGG+AGG + Chr8:9549250-9549269 None:intergenic 45.0%
ATCTGGGAGCTACGAACTAA+AGG + Chr8:9549335-9549354 None:intergenic 45.0%
GAAACATTGGAGCCTTGAAG+TGG - Chr8:9548438-9548457 MsG0880042494.01.T01:CDS 45.0%
GAGCTACGAACTAAAGGGTT+TGG + Chr8:9549329-9549348 None:intergenic 45.0%
GGTTTGATGAGCAACTAGAG+TGG + Chr8:9548954-9548973 None:intergenic 45.0%
GTCTAGTAGATAAGTCCCAG+AGG + Chr8:9549706-9549725 None:intergenic 45.0%
TCCCAGAGGGATAGCAAATA+GGG + Chr8:9549692-9549711 None:intergenic 45.0%
TCTGGGAGCTACGAACTAAA+GGG + Chr8:9549334-9549353 None:intergenic 45.0%
TTCACCACTTCAGCTTTGCA+GGG + Chr8:9548421-9548440 None:intergenic 45.0%
TTTCACCACTTCAGCTTTGC+AGG + Chr8:9548422-9548441 None:intergenic 45.0%
!! ATTAAGTTGGGCAAGCACCT+TGG - Chr8:9548514-9548533 MsG0880042494.01.T01:intron 45.0%
!! TCCCTATTTGCTATCCCTCT+GGG - Chr8:9549688-9549707 MsG0880042494.01.T01:intron 45.0%
ACTTCCCTGCAAAGCTGAAG+TGG - Chr8:9548414-9548433 MsG0880042494.01.T01:CDS 50.0%
GAGCAACTAGAGTGGTTCAC+TGG + Chr8:9548946-9548965 None:intergenic 50.0%
GTCCCAGAGGGATAGCAAAT+AGG + Chr8:9549693-9549712 None:intergenic 50.0%
!! CTCCCTATTTGCTATCCCTC+TGG - Chr8:9549687-9549706 MsG0880042494.01.T01:intron 50.0%
Chromosome Type Strat End Strand Name
Chr8 gene 9548156 9550226 9548156 ID=MsG0880042494.01;Name=MsG0880042494.01
Chr8 mRNA 9548156 9550226 9548156 ID=MsG0880042494.01.T01;Parent=MsG0880042494.01;Name=MsG0880042494.01.T01;_AED=0.50;_eAED=0.58;_QI=0|0|0|1|1|1|3|0|101
Chr8 exon 9550098 9550226 9550098 ID=MsG0880042494.01.T01:exon:2559;Parent=MsG0880042494.01.T01
Chr8 exon 9548335 9548484 9548335 ID=MsG0880042494.01.T01:exon:2558;Parent=MsG0880042494.01.T01
Chr8 exon 9548156 9548182 9548156 ID=MsG0880042494.01.T01:exon:2557;Parent=MsG0880042494.01.T01
Chr8 CDS 9550098 9550226 9550098 ID=MsG0880042494.01.T01:cds;Parent=MsG0880042494.01.T01
Chr8 CDS 9548335 9548484 9548335 ID=MsG0880042494.01.T01:cds;Parent=MsG0880042494.01.T01
Chr8 CDS 9548156 9548182 9548156 ID=MsG0880042494.01.T01:cds;Parent=MsG0880042494.01.T01
Gene Sequence

>MsG0880042494.01.T01

ATGTTTTCTCTAACTTTAAACTTCTTCTACATTTCAATCAATTGTAGCAAATATGATCTCTACAGCAAGAGCAAAGTGAGAGTTGATGTTGAAAAGGTGAAACCATACTACATCTCCCTCATTGAAAAGTCTGCAAAGAAAAGATTGGTAAATGTTTTCTCTAACATTAAAATTCTTCCATGTTCAATCACTTGTAGCAAATATGATCTCTACAGCAAGAGCAAAGTTAGAGTTGATGTTGAAAAGGTGAAACCATACTACATCTCCCTCATTGAAAAGTACTTCCCTGCAAAGCTGAAGTGGTGA
Protein sequence

>MsG0880042494.01.T01

MFSLTLNFFYISINCSKYDLYSKSKVRVDVEKVKPYYISLIEKSAKKRLVNVFSNIKILPCSITCSKYDLYSKSKVRVDVEKVKPYYISLIEKYFPAKLKW*