AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016916.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016916.01.T01 MTR_3g098170 70.803 137 25 2 8 129 24 160 3.01e-62 187
MsG0380016916.01.T01 MTR_3g098140 61.538 143 34 2 8 129 14 156 1.14e-55 171
MsG0380016916.01.T01 MTR_3g098180 63.910 133 33 2 12 129 26 158 1.67e-54 168
MsG0380016916.01.T01 MTR_3g098160 58.108 148 42 3 2 129 18 165 3.04e-53 165
MsG0380016916.01.T01 MTR_3g098130 60.902 133 37 2 12 129 31 163 4.90e-52 162
MsG0380016916.01.T01 MTR_3g098130 60.902 133 37 2 12 129 69 201 7.06e-52 163
MsG0380016916.01.T01 MTR_3g098100 54.348 138 47 3 8 129 18 155 5.75e-46 146
MsG0380016916.01.T01 MTR_3g098120 58.779 131 45 3 8 129 66 196 1.52e-43 141
MsG0380016916.01.T01 MTR_3g098170 56.989 93 25 2 8 85 24 116 8.19e-28 99.8
MsG0380016916.01.T01 MTR_3g098160 48.958 96 34 2 2 82 18 113 1.29e-23 89.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016916.01.T01 AT1G04290 51.852 135 49 3 3 122 15 148 2.48e-38 127
MsG0380016916.01.T01 AT1G04290 40.000 95 41 3 3 82 15 108 1.85e-12 60.1

Find 22 sgRNAs with CRISPR-Local

Find 131 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTGACAAAGGGAAGATATT+TGG 0.225921 3:+89379994 None:intergenic
CTGTTGTAAGCGTAGAGTTC+AGG 0.371032 3:-89380057 MsG0380016916.01.T01:CDS
GCGGTCGCAATTCCCGCCGC+TGG 0.372294 3:-89381182 MsG0380016916.01.T01:CDS
GCTGGGTTTCCGTTGGATAC+AGG 0.382257 3:-89381164 MsG0380016916.01.T01:CDS
AATCTTAGCAGGCCTGCGTT+TGG 0.424003 3:-89381928 MsG0380016916.01.T01:CDS
TTGGAAGCTCTAATCTTAGC+AGG 0.446169 3:-89381939 MsG0380016916.01.T01:CDS
CGGTCGCAATTCCCGCCGCT+GGG 0.475967 3:-89381181 MsG0380016916.01.T01:CDS
TCCCGCCGCTGGGTTTCCGT+TGG 0.479717 3:-89381171 MsG0380016916.01.T01:CDS
CGTTTGGATCTTATACAACC+TGG 0.540006 3:-89381912 MsG0380016916.01.T01:CDS
TCCAACGGAAACCCAGCGGC+GGG 0.543153 3:+89381170 None:intergenic
CTTTCCTACTCGTAGAACCT+TGG 0.550825 3:+89380087 None:intergenic
CAAGGTTCTACGAGTAGGAA+AGG 0.577693 3:-89380086 MsG0380016916.01.T01:CDS
AGCATGAGACATTGATCTCG+AGG 0.588082 3:+89381135 None:intergenic
GGAGATTGAGATTGATACCA+AGG 0.588778 3:-89380104 MsG0380016916.01.T01:CDS
ATCCAACGGAAACCCAGCGG+CGG 0.629370 3:+89381169 None:intergenic
GCATGAGACATTGATCTCGA+GGG 0.635278 3:+89381136 None:intergenic
TGACTACATCAAATCATCGA+TGG 0.639192 3:-89381985 MsG0380016916.01.T01:CDS
GATACCAAGGTTCTACGAGT+AGG 0.640264 3:-89380091 MsG0380016916.01.T01:CDS
AGGGAAACTCCTGTATCCAA+CGG 0.642836 3:+89381155 None:intergenic
ATTGAGCAAACGATACGACC+AGG 0.645306 3:+89381894 None:intergenic
GTTGTATAAGATCCAAACGC+AGG 0.664561 3:+89381916 None:intergenic
TGTATCCAACGGAAACCCAG+CGG 0.724693 3:+89381166 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAACATGTAAAAAATTGAA+AGG + Chr3:89381720-89381739 None:intergenic 15.0%
!!! AATTTTCCTTTCTAATTATA+TGG + Chr3:89380248-89380267 None:intergenic 15.0%
!!! ATTTTCCTTTCTAATTATAT+GGG + Chr3:89380247-89380266 None:intergenic 15.0%
!! AAGTTTCAATGAATGATTAA+TGG + Chr3:89381601-89381620 None:intergenic 20.0%
!! ACTAATTTACATGTTCTATT+TGG + Chr3:89380968-89380987 None:intergenic 20.0%
!! ATTTAGTCTAGACTAATAAA+GGG - Chr3:89381435-89381454 MsG0380016916.01.T01:intron 20.0%
!! CAAATTTAATACAAAAAACC+AGG + Chr3:89381786-89381805 None:intergenic 20.0%
!! CATTGAAGTAAATATAGTAT+TGG + Chr3:89380209-89380228 None:intergenic 20.0%
!! TATGACAATTACAATTAGAA+AGG + Chr3:89381150-89381169 None:intergenic 20.0%
!! TATTTAGTCTAGACTAATAA+AGG - Chr3:89381434-89381453 MsG0380016916.01.T01:intron 20.0%
!! TTCTAATTGTAATTGTCATA+CGG - Chr3:89381150-89381169 MsG0380016916.01.T01:CDS 20.0%
!!! AAACGAAAAATTAGTGTTTT+AGG + Chr3:89381352-89381371 None:intergenic 20.0%
!!! AACGAAAAATTAGTGTTTTA+GGG + Chr3:89381351-89381370 None:intergenic 20.0%
!!! GATATCAAATTGATAATTAG+AGG - Chr3:89381744-89381763 MsG0380016916.01.T01:intron 20.0%
!!! TTTTGAATTAGAATGACATT+TGG - Chr3:89381113-89381132 MsG0380016916.01.T01:intron 20.0%
!!! TTTTTTTGTTTAATTCCCTA+TGG - Chr3:89381834-89381853 MsG0380016916.01.T01:intron 20.0%
! ACCAAATGTCATTCTAATAA+AGG - Chr3:89380272-89380291 MsG0380016916.01.T01:intron 25.0%
! CATTTCCCATATAATTAGAA+AGG - Chr3:89380239-89380258 MsG0380016916.01.T01:intron 25.0%
! GCAATGAAATAAACTAACAT+TGG + Chr3:89380884-89380903 None:intergenic 25.0%
! TCATAAAAAAGAGTTTGTCT+AGG + Chr3:89381493-89381512 None:intergenic 25.0%
! TCCTTTATTAGAATGACATT+TGG + Chr3:89380276-89380295 None:intergenic 25.0%
! TGAACATAGTAACATACATT+GGG - Chr3:89380407-89380426 MsG0380016916.01.T01:intron 25.0%
! TTGAACATAGTAACATACAT+TGG - Chr3:89380406-89380425 MsG0380016916.01.T01:intron 25.0%
!! AAAACTATTTTACACTGTCA+CGG - Chr3:89381013-89381032 MsG0380016916.01.T01:intron 25.0%
!! ACATGTTCTATTTGGTAATT+AGG + Chr3:89380960-89380979 None:intergenic 25.0%
!! TATTAGTCTAGACTAAATAC+AGG + Chr3:89381433-89381452 None:intergenic 25.0%
!!! TTTCATTGTTTTGTATGACA+TGG - Chr3:89380989-89381008 MsG0380016916.01.T01:intron 25.0%
AAAAAGAGAAGGAACGATAA+CGG - Chr3:89380454-89380473 MsG0380016916.01.T01:intron 30.0%
AATAAAGGACTAAAAGCCAT+AGG - Chr3:89380287-89380306 MsG0380016916.01.T01:intron 30.0%
AATGAATCCTCTCTACATAT+AGG + Chr3:89381187-89381206 None:intergenic 30.0%
AGAAGAATGGAAAAAAGAGA+AGG - Chr3:89380443-89380462 MsG0380016916.01.T01:intron 30.0%
AGAATCAGTGAAGAGATATT+TGG - Chr3:89380481-89380500 MsG0380016916.01.T01:intron 30.0%
ATAAAGGACTAAAAGCCATA+GGG - Chr3:89380288-89380307 MsG0380016916.01.T01:intron 30.0%
ATAGGGACATTGCATAATAT+AGG - Chr3:89380305-89380324 MsG0380016916.01.T01:intron 30.0%
ATGATTAACGATAACACAAG+AGG + Chr3:89380913-89380932 None:intergenic 30.0%
ATTAGAGCTTCCAAAAACTT+GGG + Chr3:89380033-89380052 None:intergenic 30.0%
GAACATAGTAACATACATTG+GGG - Chr3:89380408-89380427 MsG0380016916.01.T01:intron 30.0%
GAATTAGCATATGTGCTTAA+TGG + Chr3:89381045-89381064 None:intergenic 30.0%
GCTAATTGAATATGAGAATG+AGG - Chr3:89381528-89381547 MsG0380016916.01.T01:intron 30.0%
TATATTATGCAATGTCCCTA+TGG + Chr3:89380306-89380325 None:intergenic 30.0%
TCATAATTATAAGTAGTCCG+TGG + Chr3:89380379-89380398 None:intergenic 30.0%
TGATTAACGATAACACAAGA+GGG + Chr3:89380912-89380931 None:intergenic 30.0%
TTCTCATATTCAATTAGCAG+TGG + Chr3:89381526-89381545 None:intergenic 30.0%
TTGCATAATATAGGTAGAGA+CGG - Chr3:89380314-89380333 MsG0380016916.01.T01:intron 30.0%
! AAATACAGGTTCGTTTTCTT+GGG + Chr3:89381419-89381438 None:intergenic 30.0%
! TAAATACAGGTTCGTTTTCT+TGG + Chr3:89381420-89381439 None:intergenic 30.0%
! TCATGCTAACCAATGTTTTT+GGG - Chr3:89380116-89380135 MsG0380016916.01.T01:intron 30.0%
! TGAATTTTCTCCCAAGTTTT+TGG - Chr3:89380020-89380039 MsG0380016916.01.T01:CDS 30.0%
!!! AATGTTTTTGGGGTGAAAAA+AGG - Chr3:89380127-89380146 MsG0380016916.01.T01:intron 30.0%
!!! TTCTTCTTGCTTTTTGATGA+TGG - Chr3:89380669-89380688 MsG0380016916.01.T01:intron 30.0%
!!! TTTTTTCACCCCAAAAACAT+TGG + Chr3:89380128-89380147 None:intergenic 30.0%
ACTGACAAAGGGAAGATATT+TGG + Chr3:89381987-89382006 None:intergenic 35.0%
AGAGTTCAGGAAGAAAAAGA+CGG - Chr3:89381934-89381953 MsG0380016916.01.T01:CDS 35.0%
ATGAAAGGTTCCAGAAACTT+GGG + Chr3:89380545-89380564 None:intergenic 35.0%
ATTCCCTATGGCTTATGTAA+TGG - Chr3:89381846-89381865 MsG0380016916.01.T01:intron 35.0%
CTACCATTACATAAGCCATA+GGG + Chr3:89381852-89381871 None:intergenic 35.0%
GAAAAGTGAAGGAAGAAGAA+TGG - Chr3:89380430-89380449 MsG0380016916.01.T01:intron 35.0%
GATTAGAGCTTCCAAAAACT+TGG + Chr3:89380034-89380053 None:intergenic 35.0%
GTTGTATGAGATTCAATCGT+AGG + Chr3:89380577-89380596 None:intergenic 35.0%
TGACTACATCAAATCATCGA+TGG - Chr3:89379993-89380012 MsG0380016916.01.T01:CDS 35.0%
TGCATAATATAGGTAGAGAC+GGG - Chr3:89380315-89380334 MsG0380016916.01.T01:intron 35.0%
TGTGAAACCTATATGTAGAG+AGG - Chr3:89381177-89381196 MsG0380016916.01.T01:CDS 35.0%
TGTTCATTGAGAAAACGACA+CGG + Chr3:89380604-89380623 None:intergenic 35.0%
! CAAAAACATTGGTTAGCATG+AGG + Chr3:89380117-89380136 None:intergenic 35.0%
! CTCATGCTAACCAATGTTTT+TGG - Chr3:89380115-89380134 MsG0380016916.01.T01:intron 35.0%
! GGAATATGACATTCTTTTCC+TGG - Chr3:89381765-89381784 MsG0380016916.01.T01:intron 35.0%
! TACATCACTGTTAGCTTAGT+GGG + Chr3:89381655-89381674 None:intergenic 35.0%
!! CATGCTAACCAATGTTTTTG+GGG - Chr3:89380117-89380136 MsG0380016916.01.T01:intron 35.0%
ATGGCTTATGTAATGGTAGG+AGG - Chr3:89381853-89381872 MsG0380016916.01.T01:intron 40.0%
CATAATATAGGTAGAGACGG+GGG - Chr3:89380317-89380336 MsG0380016916.01.T01:intron 40.0%
CATACATTGGGGAAAAGTGA+AGG - Chr3:89380419-89380438 MsG0380016916.01.T01:intron 40.0%
CCTACCATTACATAAGCCAT+AGG + Chr3:89381853-89381872 None:intergenic 40.0%
CCTATGGCTTATGTAATGGT+AGG - Chr3:89381850-89381869 MsG0380016916.01.T01:intron 40.0%
CGATTGAATCTCATACAACC+TGG - Chr3:89380578-89380597 MsG0380016916.01.T01:intron 40.0%
CGTTTGGATCTTATACAACC+TGG - Chr3:89380066-89380085 MsG0380016916.01.T01:CDS 40.0%
GAGTTCAGGAAGAAAAAGAC+GGG - Chr3:89381935-89381954 MsG0380016916.01.T01:CDS 40.0%
GATGAAAGGTTCCAGAAACT+TGG + Chr3:89380546-89380565 None:intergenic 40.0%
GCATAATATAGGTAGAGACG+GGG - Chr3:89380316-89380335 MsG0380016916.01.T01:intron 40.0%
GGAGATTGAGATTGATACCA+AGG - Chr3:89381874-89381893 MsG0380016916.01.T01:CDS 40.0%
GTTGTATAAGATCCAAACGC+AGG + Chr3:89380065-89380084 None:intergenic 40.0%
! AAATGTGTGAGTTCTAGCCA+CGG - Chr3:89380359-89380378 MsG0380016916.01.T01:intron 40.0%
! ACATCACTGTTAGCTTAGTG+GGG + Chr3:89381654-89381673 None:intergenic 40.0%
! GCTAGAACTCACACATTTTG+GGG + Chr3:89380357-89380376 None:intergenic 40.0%
! GGCTAGAACTCACACATTTT+GGG + Chr3:89380358-89380377 None:intergenic 40.0%
! GGGCATCGTTTATAAAGTGA+AGG + Chr3:89381331-89381350 None:intergenic 40.0%
! GTACATCACTGTTAGCTTAG+TGG + Chr3:89381656-89381675 None:intergenic 40.0%
! TGGCTAGAACTCACACATTT+TGG + Chr3:89380359-89380378 None:intergenic 40.0%
! TTGGAAGCTCTAATCTTAGC+AGG - Chr3:89380039-89380058 MsG0380016916.01.T01:CDS 40.0%
!! GGAGAAAAGAGAAGCATCAA+CGG - Chr3:89380502-89380521 MsG0380016916.01.T01:intron 40.0%
AAAGGTTCCAGAAACTTGGG+AGG + Chr3:89380542-89380561 None:intergenic 45.0%
AGAGTACGAACGAGTAAACG+TGG + Chr3:89380632-89380651 None:intergenic 45.0%
AGCATGAGACATTGATCTCG+AGG + Chr3:89380846-89380865 None:intergenic 45.0%
AGGGAAACTCCTGTATCCAA+CGG + Chr3:89380826-89380845 None:intergenic 45.0%
AGTACGAACGAGTAAACGTG+GGG + Chr3:89380630-89380649 None:intergenic 45.0%
ATTGAGCAAACGATACGACC+AGG + Chr3:89380087-89380106 None:intergenic 45.0%
CAAGGTTCTACGAGTAGGAA+AGG - Chr3:89381892-89381911 MsG0380016916.01.T01:CDS 45.0%
CACATCCACCAGAGTAACAA+TGG + Chr3:89380770-89380789 None:intergenic 45.0%
CGAATTTCCTCCCAAGTTTC+TGG - Chr3:89380532-89380551 MsG0380016916.01.T01:intron 45.0%
CTGTTGTAAGCGTAGAGTTC+AGG - Chr3:89381921-89381940 MsG0380016916.01.T01:CDS 45.0%
CTTTCCTACTCGTAGAACCT+TGG + Chr3:89381894-89381913 None:intergenic 45.0%
GACGCCCTTGAGCAAAAATT+TGG + Chr3:89381961-89381980 None:intergenic 45.0%
GAGTACGAACGAGTAAACGT+GGG + Chr3:89380631-89380650 None:intergenic 45.0%
GATACCAAGGTTCTACGAGT+AGG - Chr3:89381887-89381906 MsG0380016916.01.T01:CDS 45.0%
GCATGAGACATTGATCTCGA+GGG + Chr3:89380845-89380864 None:intergenic 45.0%
TCAAGTAAGCACTTGCACGT+TGG - Chr3:89380742-89380761 MsG0380016916.01.T01:intron 45.0%
! ACGGGCCAAATTTTTGCTCA+AGG - Chr3:89381953-89381972 MsG0380016916.01.T01:CDS 45.0%
! CATTGTTACTCTGGTGGATG+TGG - Chr3:89380768-89380787 MsG0380016916.01.T01:intron 45.0%
! CGGGCCAAATTTTTGCTCAA+GGG - Chr3:89381954-89381973 MsG0380016916.01.T01:CDS 45.0%
!! CATTGGCTTGTCAGTGTGAT+TGG - Chr3:89381286-89381305 MsG0380016916.01.T01:intron 45.0%
!! GTGATTGGTGTCAGCATAGT+TGG - Chr3:89381301-89381320 MsG0380016916.01.T01:intron 45.0%
!!! ACTCACACATTTTGGGGTGT+CGG + Chr3:89380351-89380370 None:intergenic 45.0%
!! GTTAATTAATTAATTAATTT+AGG + Chr3:89380713-89380732 None:intergenic 5.0%
!!! ATTTTTTTAATAATATTCAT+TGG - Chr3:89381269-89381288 MsG0380016916.01.T01:intron 5.0%
AATCTTAGCAGGCCTGCGTT+TGG - Chr3:89380050-89380069 MsG0380016916.01.T01:CDS 50.0%
ATTGAGAAAACGACACGGCC+AGG + Chr3:89380599-89380618 None:intergenic 50.0%
CTGGAACCTTTCATCTTGCG+TGG - Chr3:89380551-89380570 MsG0380016916.01.T01:intron 50.0%
GTACGAACGAGTAAACGTGG+GGG + Chr3:89380629-89380648 None:intergenic 50.0%
TGTATCCAACGGAAACCCAG+CGG + Chr3:89380815-89380834 None:intergenic 50.0%
! GTTACTCTGGTGGATGTGGT+AGG - Chr3:89380772-89380791 MsG0380016916.01.T01:intron 50.0%
!! CGTTGGTGCCATTGTTACTC+TGG - Chr3:89380759-89380778 MsG0380016916.01.T01:intron 50.0%
!! TGGTGCCATTGTTACTCTGG+TGG - Chr3:89380762-89380781 MsG0380016916.01.T01:intron 50.0%
!!! CTCACACATTTTGGGGTGTC+GGG + Chr3:89380350-89380369 None:intergenic 50.0%
!!! TCACACATTTTGGGGTGTCG+GGG + Chr3:89380349-89380368 None:intergenic 50.0%
CGTAGGCCACGCAAGATGAA+AGG + Chr3:89380560-89380579 None:intergenic 55.0%
GCTGGGTTTCCGTTGGATAC+AGG - Chr3:89380814-89380833 MsG0380016916.01.T01:intron 55.0%
! TCTGGTGGATGTGGTAGGAG+CGG - Chr3:89380777-89380796 MsG0380016916.01.T01:intron 55.0%
ATCCAACGGAAACCCAGCGG+CGG + Chr3:89380812-89380831 None:intergenic 60.0%
TCCAACGGAAACCCAGCGGC+GGG + Chr3:89380811-89380830 None:intergenic 65.0%
CGGTCGCAATTCCCGCCGCT+GGG - Chr3:89380797-89380816 MsG0380016916.01.T01:intron 70.0%
TCCCGCCGCTGGGTTTCCGT+TGG - Chr3:89380807-89380826 MsG0380016916.01.T01:intron 70.0%
GCGGTCGCAATTCCCGCCGC+TGG - Chr3:89380796-89380815 MsG0380016916.01.T01:intron 75.0%
Chromosome Type Strat End Strand Name
Chr3 gene 89379985 89382015 89379985 ID=MsG0380016916.01;Name=MsG0380016916.01
Chr3 mRNA 89379985 89382015 89379985 ID=MsG0380016916.01.T01;Parent=MsG0380016916.01;Name=MsG0380016916.01.T01;_AED=0.50;_eAED=0.53;_QI=0|0|0|1|0|0|3|0|129
Chr3 exon 89381862 89382015 89381862 ID=MsG0380016916.01.T01:exon:12327;Parent=MsG0380016916.01.T01
Chr3 exon 89381115 89381206 89381115 ID=MsG0380016916.01.T01:exon:12326;Parent=MsG0380016916.01.T01
Chr3 exon 89379985 89380128 89379985 ID=MsG0380016916.01.T01:exon:12325;Parent=MsG0380016916.01.T01
Chr3 CDS 89381862 89382015 89381862 ID=MsG0380016916.01.T01:cds;Parent=MsG0380016916.01.T01
Chr3 CDS 89381115 89381206 89381115 ID=MsG0380016916.01.T01:cds;Parent=MsG0380016916.01.T01
Chr3 CDS 89379985 89380128 89379985 ID=MsG0380016916.01.T01:cds;Parent=MsG0380016916.01.T01
Gene Sequence

>MsG0380016916.01.T01

ATGGTAGATGACTACATCAAATCATCGATGGTAGATGAATTTTCTCCCAAGTTTTTGGAAGCTCTAATCTTAGCAGGCCTGCGTTTGGATCTTATACAACCTGGTCGTATCGTTTGCTCAATGAAGACACCTCATGCTAACCAATGTTTTTGGGGAGCGGTCGCAATTCCCGCCGCTGGGTTTCCGTTGGATACAGGAGTTTCCCTCGAGATCAATGTCTCATGCTTCGATGCTGCTTATGCCAATGAGGAGATTGAGATTGATACCAAGGTTCTACGAGTAGGAAAGGCTATAGCTGTTGTAAGCGTAGAGTTCAGGAAGAAAAAGACGGGCCAAATTTTTGCTCAAGGGCGTCATACCAAATATCTTCCCTTTGTCAGTAAAATGTGA
Protein sequence

>MsG0380016916.01.T01

MVDDYIKSSMVDEFSPKFLEALILAGLRLDLIQPGRIVCSMKTPHANQCFWGAVAIPAAGFPLDTGVSLEINVSCFDAAYANEEIEIDTKVLRVGKAIAVVSVEFRKKKTGQIFAQGRHTKYLPFVSKM*