AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000624.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000624.01.T01 MTR_1g011690 93.443 122 8 0 1 122 272 393 3.39e-77 239
MsG0180000624.01.T01 MTR_1g011700 83.607 122 20 0 1 122 240 361 1.99e-67 213
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000624.01.T01 AT5G11330 74.561 114 29 0 1 114 269 382 5.09e-55 181

Find 48 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCTCTTTCCTTGCTGACT+TGG 0.284884 1:-8791306 None:intergenic
TTGTCATGTTTGTGCTTCTA+AGG 0.298117 1:-8791105 None:intergenic
ATCCCTTGGAGAAGATATTC+TGG 0.324905 1:+8791032 MsG0180000624.01.T01:CDS
TGGATCAAAGGATCTCTATC+AGG 0.331457 1:-8791286 None:intergenic
CTAAGGTAGTGAGGCGTAGT+AGG 0.337106 1:-8791088 None:intergenic
GTTCTTCATGCAAGGCTTCT+CGG 0.373562 1:+8791238 MsG0180000624.01.T01:CDS
TAGGCAAATGCATAGAGAAA+TGG 0.381893 1:+8791146 MsG0180000624.01.T01:CDS
ATATTAGATGCAGCGGTGTT+AGG 0.401522 1:+8791127 MsG0180000624.01.T01:CDS
TGAAAAGCTTGAATCGGCTT+TGG 0.407533 1:+8791174 MsG0180000624.01.T01:CDS
TAATGAACATTCTTAAGTAC+TGG 0.416230 1:+8791907 MsG0180000624.01.T01:CDS
AGAACTTGCTTGGAAGTAAC+TGG 0.427168 1:-8791220 None:intergenic
TCCTTGCTGACTTGGATCAA+AGG 0.435046 1:-8791298 None:intergenic
AGGCAAATGCATAGAGAAAT+GGG 0.438389 1:+8791147 MsG0180000624.01.T01:CDS
TTGTAGAACGGACATTGATC+AGG 0.445098 1:+8791814 MsG0180000624.01.T01:CDS
TTCATGACCTTTGCTAACTC+AGG 0.460263 1:-8790968 None:intergenic
CGGTCGCATAAAACAAGGTC+TGG 0.461955 1:+8791258 MsG0180000624.01.T01:CDS
CCAAGCAAGTTCTTCATGCA+AGG 0.473413 1:+8791230 MsG0180000624.01.T01:CDS
CCTTGCATGAAGAACTTGCT+TGG 0.475601 1:-8791230 None:intergenic
TTCTTATCCACAGCATCATA+AGG 0.480398 1:+8791933 MsG0180000624.01.T01:CDS
ATTCTGGGACAATGTGGTAT+TGG 0.484504 1:+8791048 MsG0180000624.01.T01:CDS
CATATATGATAGTGATCCCT+TGG 0.487961 1:+8791018 MsG0180000624.01.T01:CDS
CTGTCTAATGTGTGAGGACG+AGG 0.493330 1:-8791708 None:intergenic
GGAAGCTGAAAAGCTTGAAT+CGG 0.497109 1:+8791168 MsG0180000624.01.T01:CDS
TGGGACAATGTGGTATTGGT+AGG 0.524425 1:+8791052 MsG0180000624.01.T01:CDS
TCATATATGAAATTTAAGAA+AGG 0.530399 1:-8791004 None:intergenic
TCCCTTGGAGAAGATATTCT+GGG 0.532438 1:+8791033 MsG0180000624.01.T01:CDS
TTATGATGCTGTGGATAAGA+AGG 0.532776 1:-8791931 None:intergenic
TAAGGTAGTGAGGCGTAGTA+GGG 0.552562 1:-8791087 None:intergenic
GGGACAATGTGGTATTGGTA+GGG 0.556947 1:+8791053 MsG0180000624.01.T01:CDS
ATCCAAGTCAGCAAGGAAAG+AGG 0.561259 1:+8791304 MsG0180000624.01.T01:CDS
GTCCCAGAATATCTTCTCCA+AGG 0.564956 1:-8791035 None:intergenic
TCCCAGAATATCTTCTCCAA+GGG 0.587316 1:-8791034 None:intergenic
GGACAATGTGGTATTGGTAG+GGG 0.607883 1:+8791054 MsG0180000624.01.T01:CDS
GGATCAAAGGATCTCTATCA+GGG 0.608135 1:-8791285 None:intergenic
CTTCTCGGTCGCATAAAACA+AGG 0.609601 1:+8791253 MsG0180000624.01.T01:CDS
TCCTTTGATCCAAGTCAGCA+AGG 0.611960 1:+8791297 MsG0180000624.01.T01:CDS
CATGACAATATTAGATGCAG+CGG 0.616705 1:+8791120 MsG0180000624.01.T01:CDS
AATGTCCGTTCTACAAAACA+AGG 0.617089 1:-8791807 None:intergenic
ACATTGATCAGGTCTTGTAT+CGG 0.620081 1:+8791825 MsG0180000624.01.T01:CDS
TTGGTGGCCTTATGATGCTG+TGG 0.628557 1:-8791940 None:intergenic
AAATCACTGTCTAATGTGTG+AGG 0.641880 1:-8791714 None:intergenic
ATGGATTCCTGAGTTAGCAA+AGG 0.642615 1:+8790961 MsG0180000624.01.T01:CDS
TTTGTGCTTCTAAGGTAGTG+AGG 0.645723 1:-8791097 None:intergenic
GAAGATATTCTGGGACAATG+TGG 0.671683 1:+8791042 MsG0180000624.01.T01:CDS
AAAGGTCATGAAAGAAACGA+AGG 0.680367 1:+8790979 MsG0180000624.01.T01:CDS
TTTCTGAAAGTAGAAGCTCA+CGG 0.705046 1:+8791666 MsG0180000624.01.T01:CDS
CGAGGTCTGTGCGGACACGA+AGG 0.707477 1:-8791690 None:intergenic
GTGTGAGGACGAGGTCTGTG+CGG 0.730763 1:-8791699 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCATATATGAAATTTAAGAA+AGG - Chr1:8791007-8791026 None:intergenic 15.0%
!! TTATTTGACAATTAAGATTA+TGG + Chr1:8791461-8791480 MsG0180000624.01.T01:intron 15.0%
!!! AATGTTCATTAAATTTTCAT+TGG - Chr1:8791898-8791917 None:intergenic 15.0%
!! TTACTTGAAATTGTAAAAGT+CGG + Chr1:8791532-8791551 MsG0180000624.01.T01:intron 20.0%
!! TTTGGAAAAAGAAAAGTAAA+CGG - Chr1:8791590-8791609 None:intergenic 20.0%
!!! TAGTTTTTGTTACACTAATA+AGG + Chr1:8791422-8791441 MsG0180000624.01.T01:intron 20.0%
! AAATTAGCATCACAATTTGA+AGG + Chr1:8791608-8791627 MsG0180000624.01.T01:intron 25.0%
! ACATCTTCAATTTGATTGTA+TGG + Chr1:8791393-8791412 MsG0180000624.01.T01:intron 25.0%
! GATAAATGTTGTTCATTTAC+GGG - Chr1:8791568-8791587 None:intergenic 25.0%
! GGATAAATGTTGTTCATTTA+CGG - Chr1:8791569-8791588 None:intergenic 25.0%
! TAATGAACATTCTTAAGTAC+TGG + Chr1:8791907-8791926 MsG0180000624.01.T01:CDS 25.0%
!! ACATTAGACAGTGATTTTAT+TGG + Chr1:8791720-8791739 MsG0180000624.01.T01:CDS 25.0%
!! TCAAATTGTGATGCTAATTT+TGG - Chr1:8791608-8791627 None:intergenic 25.0%
!!! ATTATCCTTGTTTTGTAGAA+CGG + Chr1:8791802-8791821 MsG0180000624.01.T01:CDS 25.0%
!!! TGATTTTATTGGTGTTGATT+CGG + Chr1:8791731-8791750 MsG0180000624.01.T01:CDS 25.0%
!! AATGAATGAGTTGAGTTTTG+AGG - Chr1:8791785-8791804 None:intergenic 30.0%
!! ATTTTCATTGGTGACACTTT+TGG - Chr1:8791886-8791905 None:intergenic 30.0%
!! TTTTCATTGGTGACACTTTT+GGG - Chr1:8791885-8791904 None:intergenic 30.0%
AAAGGTCATGAAAGAAACGA+AGG + Chr1:8790979-8790998 MsG0180000624.01.T01:CDS 35.0%
AAATCACTGTCTAATGTGTG+AGG - Chr1:8791717-8791736 None:intergenic 35.0%
AATGTCCGTTCTACAAAACA+AGG - Chr1:8791810-8791829 None:intergenic 35.0%
AATTGTCAAATAAACTGCCC+AGG - Chr1:8791454-8791473 None:intergenic 35.0%
ACCAAGAAGCAGAAAAAGTA+TGG + Chr1:8790942-8790961 MsG0180000624.01.T01:CDS 35.0%
AGGCAAATGCATAGAGAAAT+GGG + Chr1:8791147-8791166 MsG0180000624.01.T01:CDS 35.0%
CATGACAATATTAGATGCAG+CGG + Chr1:8791120-8791139 MsG0180000624.01.T01:CDS 35.0%
GTAACAGAAGCAAATGACAA+AGG - Chr1:8791375-8791394 None:intergenic 35.0%
TAGGCAAATGCATAGAGAAA+TGG + Chr1:8791146-8791165 MsG0180000624.01.T01:CDS 35.0%
TTATGATGCTGTGGATAAGA+AGG - Chr1:8791934-8791953 None:intergenic 35.0%
TTGTCATGTTTGTGCTTCTA+AGG - Chr1:8791108-8791127 None:intergenic 35.0%
! ACATTGATCAGGTCTTGTAT+CGG + Chr1:8791825-8791844 MsG0180000624.01.T01:CDS 35.0%
! CATATATGATAGTGATCCCT+TGG + Chr1:8791018-8791037 MsG0180000624.01.T01:CDS 35.0%
! TTTCTGAAAGTAGAAGCTCA+CGG + Chr1:8791666-8791685 MsG0180000624.01.T01:CDS 35.0%
!!! TCCATACTTTTTCTGCTTCT+TGG - Chr1:8790946-8790965 None:intergenic 35.0%
ATATTAGATGCAGCGGTGTT+AGG + Chr1:8791127-8791146 MsG0180000624.01.T01:CDS 40.0%
ATCCCTTGGAGAAGATATTC+TGG + Chr1:8791032-8791051 MsG0180000624.01.T01:CDS 40.0%
ATGGATTCCTGAGTTAGCAA+AGG + Chr1:8790961-8790980 MsG0180000624.01.T01:CDS 40.0%
GGAAGCTGAAAAGCTTGAAT+CGG + Chr1:8791168-8791187 MsG0180000624.01.T01:CDS 40.0%
GGATCAAAGGATCTCTATCA+GGG - Chr1:8791288-8791307 None:intergenic 40.0%
TCCCAGAATATCTTCTCCAA+GGG - Chr1:8791037-8791056 None:intergenic 40.0%
TCCCTTGGAGAAGATATTCT+GGG + Chr1:8791033-8791052 MsG0180000624.01.T01:CDS 40.0%
TGGATCAAAGGATCTCTATC+AGG - Chr1:8791289-8791308 None:intergenic 40.0%
TTCAGAAAACAGTGTCTGTG+CGG - Chr1:8791654-8791673 None:intergenic 40.0%
TTCATGACCTTTGCTAACTC+AGG - Chr1:8790971-8790990 None:intergenic 40.0%
TTGTAGAACGGACATTGATC+AGG + Chr1:8791814-8791833 MsG0180000624.01.T01:CDS 40.0%
! AGAACTTGCTTGGAAGTAAC+TGG - Chr1:8791223-8791242 None:intergenic 40.0%
! TGAAAAGCTTGAATCGGCTT+TGG + Chr1:8791174-8791193 MsG0180000624.01.T01:CDS 40.0%
!! ATTCTGGGACAATGTGGTAT+TGG + Chr1:8791048-8791067 MsG0180000624.01.T01:CDS 40.0%
!! GAAGATATTCTGGGACAATG+TGG + Chr1:8791042-8791061 MsG0180000624.01.T01:CDS 40.0%
!! TTTGTGCTTCTAAGGTAGTG+AGG - Chr1:8791100-8791119 None:intergenic 40.0%
ACACTAATAAGGCGATTGCC+TGG + Chr1:8791433-8791452 MsG0180000624.01.T01:intron 45.0%
ATCCAAGTCAGCAAGGAAAG+AGG + Chr1:8791304-8791323 MsG0180000624.01.T01:CDS 45.0%
CACTAATAAGGCGATTGCCT+GGG + Chr1:8791434-8791453 MsG0180000624.01.T01:intron 45.0%
CCAAGCAAGTTCTTCATGCA+AGG + Chr1:8791230-8791249 MsG0180000624.01.T01:CDS 45.0%
CTTCTCGGTCGCATAAAACA+AGG + Chr1:8791253-8791272 MsG0180000624.01.T01:CDS 45.0%
GTCCCAGAATATCTTCTCCA+AGG - Chr1:8791038-8791057 None:intergenic 45.0%
GTTCTTCATGCAAGGCTTCT+CGG + Chr1:8791238-8791257 MsG0180000624.01.T01:CDS 45.0%
TAAGGTAGTGAGGCGTAGTA+GGG - Chr1:8791090-8791109 None:intergenic 45.0%
TCCTTTGATCCAAGTCAGCA+AGG + Chr1:8791297-8791316 MsG0180000624.01.T01:CDS 45.0%
! CCTTGCATGAAGAACTTGCT+TGG - Chr1:8791233-8791252 None:intergenic 45.0%
!! GGACAATGTGGTATTGGTAG+GGG + Chr1:8791054-8791073 MsG0180000624.01.T01:CDS 45.0%
!! GGGACAATGTGGTATTGGTA+GGG + Chr1:8791053-8791072 MsG0180000624.01.T01:CDS 45.0%
!! TCATTGGTGACACTTTTGGG+AGG - Chr1:8791882-8791901 None:intergenic 45.0%
!! TCCTTGCTGACTTGGATCAA+AGG - Chr1:8791301-8791320 None:intergenic 45.0%
!! TGGGACAATGTGGTATTGGT+AGG + Chr1:8791052-8791071 MsG0180000624.01.T01:CDS 45.0%
CGGTCGCATAAAACAAGGTC+TGG + Chr1:8791258-8791277 MsG0180000624.01.T01:CDS 50.0%
CTAAGGTAGTGAGGCGTAGT+AGG - Chr1:8791091-8791110 None:intergenic 50.0%
CTGTCTAATGTGTGAGGACG+AGG - Chr1:8791711-8791730 None:intergenic 50.0%
! CTCCTCTTTCCTTGCTGACT+TGG - Chr1:8791309-8791328 None:intergenic 50.0%
!! AGCAAGGAAAGAGGAGTGTC+AGG + Chr1:8791313-8791332 MsG0180000624.01.T01:intron 50.0%
!! GCAAGGAAAGAGGAGTGTCA+GGG + Chr1:8791314-8791333 MsG0180000624.01.T01:intron 50.0%
GTGTGAGGACGAGGTCTGTG+CGG - Chr1:8791702-8791721 None:intergenic 60.0%
CGAGGTCTGTGCGGACACGA+AGG - Chr1:8791693-8791712 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 8790938 8791953 8790938 ID=MsG0180000624.01;Name=MsG0180000624.01
Chr1 mRNA 8790938 8791953 8790938 ID=MsG0180000624.01.T01;Parent=MsG0180000624.01;Name=MsG0180000624.01.T01;_AED=0.58;_eAED=0.58;_QI=0|0|0|0.5|1|1|2|0|228
Chr1 exon 8790938 8791329 8790938 ID=MsG0180000624.01.T01:exon:2243;Parent=MsG0180000624.01.T01
Chr1 exon 8791659 8791953 8791659 ID=MsG0180000624.01.T01:exon:2242;Parent=MsG0180000624.01.T01
Chr1 CDS 8790938 8791329 8790938 ID=MsG0180000624.01.T01:cds;Parent=MsG0180000624.01.T01
Chr1 CDS 8791659 8791953 8791659 ID=MsG0180000624.01.T01:cds;Parent=MsG0180000624.01.T01
Gene Sequence

>MsG0180000624.01.T01

ATGCACCAAGAAGCAGAAAAAGTATGGATTCCTGAGTTAGCAAAGGTCATGAAAGAAACGAAGGAACCTTTCTTAAATTTCATATATGATAGTGATCCCTTGGAGAAGATATTCTGGGACAATGTGGTATTGGTAGGGGAAGCAGCTCACCCTACTACGCCTCACTACCTTAGAAGCACAAACATGACAATATTAGATGCAGCGGTGTTAGGCAAATGCATAGAGAAATGGGAAGCTGAAAAGCTTGAATCGGCTTTGGAAGAGTATCAGTTCATTAGACTACCAGTTACTTCCAAGCAAGTTCTTCATGCAAGGCTTCTCGGTCGCATAAAACAAGGTCTGGTGCTCCCTGATAGAGATCCTTTGATCCAAGTCAGCAAGGAAAGAGGAGTACACTGTTTTCTGAAAGTAGAAGCTCACGGTCCTTCGTGTCCGCACAGACCTCGTCCTCACACATTAGACAGTGATTTTATTGGTGTTGATTCGGCACAAACAAGAGAAGATGAATATGTGCGCCTCAAAACTCAACTCATTCATTATCCTTGTTTTGTAGAACGGACATTGATCAGGTCTTGTATCGGCTGTATAGATAAGAATGACTGTGAGCTTCTACCTCCCAAAAGTGTCACCAATGAAAATTTAATGAACATTCTTAAGTACTGGTCCTTCTTATCCACAGCATCATAA

Protein sequence

>MsG0180000624.01.T01

MHQEAEKVWIPELAKVMKETKEPFLNFIYDSDPLEKIFWDNVVLVGEAAHPTTPHYLRSTNMTILDAAVLGKCIEKWEAEKLESALEEYQFIRLPVTSKQVLHARLLGRIKQGLVLPDRDPLIQVSKERGVHCFLKVEAHGPSCPHRPRPHTLDSDFIGVDSAQTREDEYVRLKTQLIHYPCFVERTLIRSCIGCIDKNDCELLPPKSVTNENLMNILKYWSFLSTAS*