AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480019349.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480019349.01.T01 MTR_4g029130 87.368 190 19 1 1 185 1 190 1.39e-106 303
MsG0480019349.01.T01 MTR_7g072540 52.406 187 75 4 1 176 1 184 4.05e-46 151
MsG0480019349.01.T01 MTR_5g083970 53.608 97 38 2 11 101 15 110 7.50e-24 94.0
MsG0480019349.01.T01 MTR_3g072360 47.872 94 42 1 11 97 19 112 5.49e-14 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTTGCAGTTCCATTTGTT+TGG 0.199775 4:-18806449 MsG0480019349.01.T01:CDS
GGTCGTCTCCGAGGTAATTT+TGG 0.262457 4:+18806191 None:intergenic
AAAATCTTCCAAGTATCTTT+TGG 0.274979 4:-18806310 MsG0480019349.01.T01:CDS
TGTTGCAGTTCCATTTGTTT+GGG 0.310743 4:-18806448 MsG0480019349.01.T01:CDS
GTCTTTAGAGAATGTGTGTT+TGG 0.374019 4:+18806407 None:intergenic
CCAACTTCTACTTTGTGCTT+TGG 0.382263 4:-18806090 MsG0480019349.01.T01:CDS
AATGTGTGTTTGGGAGTTCC+AGG 0.387249 4:+18806417 None:intergenic
TCTGAAAGATGGGTGACAAT+TGG 0.414182 4:+18806476 None:intergenic
CACGCCTCTTGTAGTTACTT+TGG 0.419541 4:+18806034 None:intergenic
AAGCAATGCCAAAAGATACT+TGG 0.426442 4:+18806302 None:intergenic
GATAAGAAGGTGGAGGTGTA+AGG 0.431589 4:+18806373 None:intergenic
GTAACTACAAGAGGCGTGTA+AGG 0.469845 4:-18806029 MsG0480019349.01.T01:CDS
ATAAGAAGGTGGAGGTGTAA+GGG 0.477682 4:+18806374 None:intergenic
TCTTTAGAGAATGTGTGTTT+GGG 0.478199 4:+18806408 None:intergenic
GCAACAGAAACTCTGAAAGA+TGG 0.487509 4:+18806465 None:intergenic
GGTTGAGATTCCCAAACAAA+TGG 0.489006 4:+18806438 None:intergenic
TTCAGGGGTGAAAATGAAGA+TGG 0.498666 4:-18806123 MsG0480019349.01.T01:CDS
TAAGAAGGTGGAGGTGTAAG+GGG 0.511212 4:+18806375 None:intergenic
CCAAAGCACAAAGTAGAAGT+TGG 0.519370 4:+18806090 None:intergenic
AAATTACCTCGGAGACGACC+AGG 0.521658 4:-18806188 MsG0480019349.01.T01:CDS
CAACAGAAACTCTGAAAGAT+GGG 0.528072 4:+18806466 None:intergenic
TTTCAGCAGACTACTTTCAA+AGG 0.534157 4:-18806505 MsG0480019349.01.T01:CDS
TTTGTTTGGGAATCTCAACC+TGG 0.562667 4:-18806435 MsG0480019349.01.T01:CDS
CGTTCGATCAGCTCGAACAG+TGG 0.567340 4:-18806060 MsG0480019349.01.T01:CDS
GCATTGTTGAAATGATAAGA+AGG 0.591984 4:+18806360 None:intergenic
GAAGGTGGAGGTGTAAGGGG+AGG 0.592725 4:+18806378 None:intergenic
TTGATGACAATGAAAACGAA+GGG 0.593187 4:+18806223 None:intergenic
ATTGATGACAATGAAAACGA+AGG 0.623463 4:+18806222 None:intergenic
AGATTCTTCCAAAATTACCT+CGG 0.631820 4:-18806199 MsG0480019349.01.T01:CDS
GCTTCCAAAGTAACTACAAG+AGG 0.633252 4:-18806038 MsG0480019349.01.T01:CDS
GCTAACCCTGGTCGTCTCCG+AGG 0.638752 4:+18806182 None:intergenic
TTGTTGAAATGATAAGAAGG+TGG 0.647192 4:+18806363 None:intergenic
TTGAAATGATAAGAAGGTGG+AGG 0.647831 4:+18806366 None:intergenic
AAACGAAGGGTATGACGATG+AGG 0.665324 4:+18806236 None:intergenic
AATTACCTCGGAGACGACCA+GGG 0.689091 4:-18806187 MsG0480019349.01.T01:CDS
TGACGATGAGGACAAAGACG+AGG 0.731325 4:+18806248 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAAGAAAAATCTTAAGCTT+TGG - Chr4:18806428-18806447 MsG0480019349.01.T01:CDS 25.0%
!! AAAATCTTCCAAGTATCTTT+TGG - Chr4:18806277-18806296 MsG0480019349.01.T01:CDS 25.0%
!!! AAGATTTTGAGTGCTTTTTT+TGG + Chr4:18806265-18806284 None:intergenic 25.0%
!!! CTTTTTTTGGTTCTTTTTGT+TGG + Chr4:18806252-18806271 None:intergenic 25.0%
AGATTCTTCCAAAATTACCT+CGG - Chr4:18806388-18806407 MsG0480019349.01.T01:CDS 30.0%
GCATTGTTGAAATGATAAGA+AGG + Chr4:18806230-18806249 None:intergenic 30.0%
TGCTTCAAAAACTAAACTTC+AGG - Chr4:18806303-18806322 MsG0480019349.01.T01:CDS 30.0%
TTGTTGAAATGATAAGAAGG+TGG + Chr4:18806227-18806246 None:intergenic 30.0%
! ATTGATGACAATGAAAACGA+AGG + Chr4:18806368-18806387 None:intergenic 30.0%
! TCTTTAGAGAATGTGTGTTT+GGG + Chr4:18806182-18806201 None:intergenic 30.0%
! TTGATGACAATGAAAACGAA+GGG + Chr4:18806367-18806386 None:intergenic 30.0%
!!! TGGATCTTCTTTTGATTTCA+GGG - Chr4:18806448-18806467 MsG0480019349.01.T01:CDS 30.0%
!!! TTGGATCTTCTTTTGATTTC+AGG - Chr4:18806447-18806466 MsG0480019349.01.T01:CDS 30.0%
AAGCAATGCCAAAAGATACT+TGG + Chr4:18806288-18806307 None:intergenic 35.0%
TGTTGCAGTTCCATTTGTTT+GGG - Chr4:18806139-18806158 MsG0480019349.01.T01:CDS 35.0%
TTGAAATGATAAGAAGGTGG+AGG + Chr4:18806224-18806243 None:intergenic 35.0%
TTTCAGCAGACTACTTTCAA+AGG - Chr4:18806082-18806101 MsG0480019349.01.T01:CDS 35.0%
! CAACAGAAACTCTGAAAGAT+GGG + Chr4:18806124-18806143 None:intergenic 35.0%
! GTCTTTAGAGAATGTGTGTT+TGG + Chr4:18806183-18806202 None:intergenic 35.0%
!!! GGATCTTCTTTTGATTTCAG+GGG - Chr4:18806449-18806468 MsG0480019349.01.T01:CDS 35.0%
CCAAAGCACAAAGTAGAAGT+TGG + Chr4:18806500-18806519 None:intergenic 40.0%
CCAACTTCTACTTTGTGCTT+TGG - Chr4:18806497-18806516 MsG0480019349.01.T01:CDS 40.0%
CTGTTGCAGTTCCATTTGTT+TGG - Chr4:18806138-18806157 MsG0480019349.01.T01:CDS 40.0%
GCTTCCAAAGTAACTACAAG+AGG - Chr4:18806549-18806568 MsG0480019349.01.T01:CDS 40.0%
GGTTGAGATTCCCAAACAAA+TGG + Chr4:18806152-18806171 None:intergenic 40.0%
TCTGAAAGATGGGTGACAAT+TGG + Chr4:18806114-18806133 None:intergenic 40.0%
TTCAGGGGTGAAAATGAAGA+TGG - Chr4:18806464-18806483 MsG0480019349.01.T01:CDS 40.0%
TTTGTTTGGGAATCTCAACC+TGG - Chr4:18806152-18806171 MsG0480019349.01.T01:CDS 40.0%
! ATAAGAAGGTGGAGGTGTAA+GGG + Chr4:18806216-18806235 None:intergenic 40.0%
! GATTTTTCTTCTGCTAACCC+TGG + Chr4:18806420-18806439 None:intergenic 40.0%
! GCAACAGAAACTCTGAAAGA+TGG + Chr4:18806125-18806144 None:intergenic 40.0%
AATGTGTGTTTGGGAGTTCC+AGG + Chr4:18806173-18806192 None:intergenic 45.0%
CACGCCTCTTGTAGTTACTT+TGG + Chr4:18806556-18806575 None:intergenic 45.0%
! AAACGAAGGGTATGACGATG+AGG + Chr4:18806354-18806373 None:intergenic 45.0%
! GATAAGAAGGTGGAGGTGTA+AGG + Chr4:18806217-18806236 None:intergenic 45.0%
! GTAACTACAAGAGGCGTGTA+AGG - Chr4:18806558-18806577 MsG0480019349.01.T01:CDS 45.0%
! TAAGAAGGTGGAGGTGTAAG+GGG + Chr4:18806215-18806234 None:intergenic 45.0%
AAATTACCTCGGAGACGACC+AGG - Chr4:18806399-18806418 MsG0480019349.01.T01:CDS 50.0%
AATTACCTCGGAGACGACCA+GGG - Chr4:18806400-18806419 MsG0480019349.01.T01:CDS 50.0%
TGACGATGAGGACAAAGACG+AGG + Chr4:18806342-18806361 None:intergenic 50.0%
! GGTCGTCTCCGAGGTAATTT+TGG + Chr4:18806399-18806418 None:intergenic 50.0%
CGTTCGATCAGCTCGAACAG+TGG - Chr4:18806527-18806546 MsG0480019349.01.T01:CDS 55.0%
! GAAGGTGGAGGTGTAAGGGG+AGG + Chr4:18806212-18806231 None:intergenic 60.0%
GCTAACCCTGGTCGTCTCCG+AGG + Chr4:18806408-18806427 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr4 gene 18806026 18806583 18806026 ID=MsG0480019349.01;Name=MsG0480019349.01
Chr4 mRNA 18806026 18806583 18806026 ID=MsG0480019349.01.T01;Parent=MsG0480019349.01;Name=MsG0480019349.01.T01;_AED=0.41;_eAED=0.41;_QI=0|-1|0|1|-1|0|1|0|185
Chr4 exon 18806026 18806583 18806026 ID=MsG0480019349.01.T01:exon:10987;Parent=MsG0480019349.01.T01
Chr4 CDS 18806026 18806583 18806026 ID=MsG0480019349.01.T01:cds;Parent=MsG0480019349.01.T01
Chr4 mRNA 18806292 18806537 18806292 ID=MsG0480019349.01.T02;Parent=MsG0480019349.01;Name=MsG0480019349.01.T02;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|0|1|0|81
Chr4 exon 18806292 18806537 18806292 ID=MsG0480019349.01.T02:exon:10988;Parent=MsG0480019349.01.T02
Chr4 CDS 18806292 18806537 18806292 ID=MsG0480019349.01.T02:cds;Parent=MsG0480019349.01.T02
Gene Sequence

>MsG0480019349.01.T02

ATGACAAGTTTTTCAGCAGACTACTTTCAAAGGAAAATTCCAATTGTCACCCATCTTTCAGAGTTTCTGTTGCAGTTCCATTTGTTTGGGAATCTCAACCTGGAACTCCCAAACACACATTCTCTAAAGACATTATTCCTCCCCTTACACCTCCACCTTCTTATCATTTCAACAATGCCAACAAAAAGAACCAAAAAAAGCACTCAAAATCTTCCAAGTATCTTTTGGCATTGCTTCAAAAACTAA

>MsG0480019349.01.T01

ATGTTCAATTCAACATGTGAGAAGAGTGTTCTTCAAATCAAACAAGATGACAAGTTTTTCAGCAGACTACTTTCAAAGGAAAATTCCAATTGTCACCCATCTTTCAGAGTTTCTGTTGCAGTTCCATTTGTTTGGGAATCTCAACCTGGAACTCCCAAACACACATTCTCTAAAGACATTATTCCTCCCCTTACACCTCCACCTTCTTATCATTTCAACAATGCCAACAAAAAGAACCAAAAAAAGCACTCAAAATCTTCCAAGTATCTTTTGGCATTGCTTCAAAAACTAAACTTCAGGAAGAACAATCAGTCCTCGTCTTTGTCCTCATCGTCATACCCTTCGTTTTCATTGTCATCAATAGATTCTTCCAAAATTACCTCGGAGACGACCAGGGTTAGCAGAAGAAAAATCTTAAGCTTTGGATCTTCTTTTGATTTCAGGGGTGAAAATGAAGATGGAAATGATTCACCAACTTCTACTTTGTGCTTTGGAATTCATCGTTCGATCAGCTCGAACAGTGGCTTCCAAAGTAACTACAAGAGGCGTGTAAGGTAA

Protein sequence

>MsG0480019349.01.T02

MTSFSADYFQRKIPIVTHLSEFLLQFHLFGNLNLELPNTHSLKTLFLPLHLHLLIISTMPTKRTKKSTQNLPSIFWHCFKN*

>MsG0480019349.01.T01

MFNSTCEKSVLQIKQDDKFFSRLLSKENSNCHPSFRVSVAVPFVWESQPGTPKHTFSKDIIPPLTPPPSYHFNNANKKNQKKHSKSSKYLLALLQKLNFRKNNQSSSLSSSSYPSFSLSSIDSSKITSETTRVSRRKILSFGSSFDFRGENEDGNDSPTSTLCFGIHRSISSNSGFQSNYKRRVR*