AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680030317.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680030317.01.T01 MTR_6g004440 88.136 118 13 1 10 126 197 314 1.43e-72 219
MsG0680030317.01.T01 MTR_3g076970 54.237 118 53 1 10 126 235 352 3.71e-41 139
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680030317.01.T01 AT5G50180 56.780 118 50 1 10 126 229 346 4.87e-43 144
MsG0680030317.01.T01 AT5G40540 61.538 117 41 3 10 122 138 254 3.85e-38 129
MsG0680030317.01.T01 AT5G40540 61.538 117 41 3 10 122 159 275 6.10e-38 129
MsG0680030317.01.T01 AT5G40540 61.538 117 41 3 10 122 235 351 3.26e-37 129
MsG0680030317.01.T01 AT3G27560 57.627 118 43 3 10 120 235 352 1.87e-35 125

Find 42 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTCTTCCACATTGGCTTTC+GGG 0.175062 6:-532225 MsG0680030318.01.T01:intron
CTGTCTTCCACATTGGCTTT+CGG 0.211052 6:-532226 MsG0680030318.01.T01:intron
CTAAAATTCGGCCTATCATT+TGG 0.291837 6:-532046 MsG0680030318.01.T01:intron
GCACTTGTACCAGGAGATTC+TGG 0.337848 6:-532169 MsG0680030318.01.T01:intron
TTTCTCATCCCCGTTGGGTA+TGG 0.348326 6:+531162 MsG0680030317.01.T01:CDS
CCCAGTGCTGAAGATCTTCC+TGG 0.351946 6:+531983 MsG0680030317.01.T01:CDS
GATGGCTTCATCTGAGAATA+TGG 0.358500 6:+532138 MsG0680030317.01.T01:CDS
TGTATGATTTCACTAAAATT+CGG 0.393164 6:-532058 MsG0680030318.01.T01:intron
TTCAATTTCTCATCCCCGTT+GGG 0.397321 6:+531157 MsG0680030317.01.T01:CDS
TACCATTTCGCTATTAGAAC+CGG 0.412194 6:+532102 MsG0680030317.01.T01:CDS
GCCATCCGCATTGGAACAAC+CGG 0.433409 6:-532121 MsG0680030318.01.T01:three_prime_UTR
TTGGGTATGGGTAGGGTAAC+GGG 0.433745 6:+531175 MsG0680030317.01.T01:CDS
TTACCCTACCCATACCCAAC+GGG 0.448493 6:-531171 MsG0680030318.01.T01:intron
TTCTCATCCCCGTTGGGTAT+GGG 0.462345 6:+531163 MsG0680030317.01.T01:CDS
ATGTTTCGACGAGACGACTC+TGG 0.468042 6:+532196 MsG0680030317.01.T01:CDS
GTTGGGTATGGGTAGGGTAA+CGG 0.481814 6:+531174 MsG0680030317.01.T01:CDS
AACCGGTTCTAATAGCGAAA+TGG 0.489838 6:-532104 MsG0680030318.01.T01:intron
GCCAGGAAGATCTTCAGCAC+TGG 0.492910 6:-531984 MsG0680030318.01.T01:intron
AAATCATACAGATGCTCCTT+CGG 0.494850 6:+532071 MsG0680030317.01.T01:CDS
GGAAAGAGGATCCAAATGAT+AGG 0.498052 6:+532035 MsG0680030317.01.T01:CDS
ATGTGGAAGACAGGTTCAAA+GGG 0.506061 6:+532236 MsG0680030317.01.T01:CDS
CCAGGAAGATCTTCAGCACT+GGG 0.509306 6:-531983 MsG0680030318.01.T01:intron
GTTCAATTTCTCATCCCCGT+TGG 0.512048 6:+531156 MsG0680030317.01.T01:CDS
TTTGAACCTGTCTTCCACAT+TGG 0.512154 6:-532233 MsG0680030318.01.T01:intron
CATCCCCGTTGGGTATGGGT+AGG 0.518749 6:+531167 MsG0680030317.01.T01:CDS
GTCTTCCACATTGGCTTTCG+GGG 0.519836 6:-532224 MsG0680030318.01.T01:intron
CGAAAGCCAATGTGGAAGAC+AGG 0.526697 6:+532227 MsG0680030317.01.T01:CDS
AATGTGGAAGACAGGTTCAA+AGG 0.531304 6:+532235 MsG0680030317.01.T01:CDS
TCAGATGAAGCCATCCGCAT+TGG 0.535963 6:-532130 MsG0680030318.01.T01:three_prime_UTR
ACAATCATAGCTAAATCGCC+AGG 0.545242 6:-532001 MsG0680030318.01.T01:intron
AACATTAATGCACTTGTACC+AGG 0.546040 6:-532178 MsG0680030318.01.T01:intron
ATCCCCGTTGGGTATGGGTA+GGG 0.549063 6:+531168 MsG0680030317.01.T01:CDS
ACCGGTTGTTCCAATGCGGA+TGG 0.555137 6:+532120 MsG0680030317.01.T01:CDS
CTATGATTGTAACATCATGC+TGG 0.562663 6:+532014 MsG0680030317.01.T01:CDS
TGTAACATCATGCTGGAAAG+AGG 0.566604 6:+532021 MsG0680030317.01.T01:CDS
GTATTGCCACCAGAATCTCC+TGG 0.622877 6:+532160 MsG0680030317.01.T01:CDS
AAATGGTAGAGAGATACCGA+AGG 0.647571 6:-532087 MsG0680030318.01.T01:intron
GTTACCCTACCCATACCCAA+CGG 0.659888 6:-531172 MsG0680030318.01.T01:intron
AGAAACCCCGAAAGCCAATG+TGG 0.669643 6:+532219 MsG0680030317.01.T01:CDS
TAGAACCGGTTGTTCCAATG+CGG 0.695897 6:+532116 MsG0680030317.01.T01:CDS
CTTGTACCAGGAGATTCTGG+TGG 0.699320 6:-532166 MsG0680030318.01.T01:intron
TACCCTACCCATACCCAACG+GGG 0.727048 6:-531170 MsG0680030318.01.T01:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAACACAAAATTAT+TGG - Chr6:531803-531822 MsG0680030318.01.T01:intron 10.0%
!!! ATTCTGAAATAATAAAAATA+TGG - Chr6:531957-531976 MsG0680030318.01.T01:intron 10.0%
!! AGTTAAATTATGATTATAGT+CGG - Chr6:531456-531475 MsG0680030318.01.T01:intron 15.0%
!! TAAAAAAAACACAAAACTAA+CGG + Chr6:531671-531690 MsG0680030317.01.T01:intron 15.0%
!!! TTTGTGACAAAAATATTTTA+AGG + Chr6:531520-531539 MsG0680030317.01.T01:intron 15.0%
!!! TTTTATTATTTCAGAATACA+AGG + Chr6:531960-531979 MsG0680030317.01.T01:CDS 15.0%
!! AAACACAAAATTATTGGTAT+TGG - Chr6:531797-531816 MsG0680030318.01.T01:intron 20.0%
!! CTTTGTAAAAATATTGGTAT+TGG - Chr6:531647-531628 MsG0680030318.01.T01:intron 20.0%
!! TGTATGATTTCACTAAAATT+CGG - Chr6:532061-532080 MsG0680030318.01.T01:intron 20.0%
!! TTTAATAGAAAGTTAACAGA+GGG + Chr6:531821-531840 MsG0680030317.01.T01:intron 20.0%
!!! ACTTTTTTTTTGTTTGGAAT+TGG - Chr6:531879-531898 MsG0680030318.01.T01:intron 20.0%
!!! TTTTAATAGAAAGTTAACAG+AGG + Chr6:531820-531839 MsG0680030317.01.T01:intron 20.0%
! CTTGCACTTTGTAAAAATAT+TGG - Chr6:531854-531873 MsG0680030318.01.T01:intron 25.0%
! TTAAGGTTTAAATGTGTCAT+TGG + Chr6:531537-531556 MsG0680030317.01.T01:intron 25.0%
!! ATTGTTGTGAAGTTACATTT+TGG + Chr6:531357-531376 MsG0680030317.01.T01:intron 25.0%
!!! AATATTTTTACAAAGTGCAG+GGG + Chr6:531739-531758 MsG0680030317.01.T01:intron 25.0%
!!! CAAAATTTTATGAAAGTGCA+GGG + Chr6:531913-531932 MsG0680030317.01.T01:intron 25.0%
!!! CAATATTTTTACAAAGTGCA+AGG + Chr6:531738-531757 MsG0680030317.01.T01:intron 25.0%
!!! CAATATTTTTACAAAGTGCA+GGG + Chr6:531738-531757 MsG0680030317.01.T01:intron 25.0%
!!! CAATATTTTTACAAAGTGCA+GGG - Chr6:531757-531738 MsG0680030318.01.T01:intron 25.0%
!!! CTTTCATAAAATTTTGGCAT+TGG - Chr6:531909-531928 MsG0680030318.01.T01:intron 25.0%
AAGTATATGAGAATTGGGTA+TGG + Chr6:531199-531218 MsG0680030317.01.T01:intron 30.0%
AGACGTATATGGTTTCTATT+TGG + Chr6:531411-531430 MsG0680030317.01.T01:intron 30.0%
AGTATATGAGAATTGGGTAT+GGG + Chr6:531200-531219 MsG0680030317.01.T01:intron 30.0%
CCTGCACTTTGTAAAAATAT+TGG + Chr6:531622-531641 MsG0680030317.01.T01:intron 30.0%
CCTGCACTTTGTAAAAATAT+TGG - Chr6:531641-531622 MsG0680030318.01.T01:intron 30.0%
GACGTATATGGTTTCTATTT+GGG + Chr6:531412-531431 MsG0680030317.01.T01:intron 30.0%
! CCAAACAAAAAAAAAGTGCA+GGG + Chr6:531882-531901 MsG0680030317.01.T01:intron 30.0%
! CCTGCACTTTCATAAAATTT+TGG - Chr6:531915-531934 MsG0680030318.01.T01:intron 30.0%
! TCCAAACAAAAAAAAAGTGC+AGG + Chr6:531881-531900 MsG0680030317.01.T01:intron 30.0%
!! ATATTTTTACAAAGTGCAGG+GGG + Chr6:531740-531759 MsG0680030317.01.T01:intron 30.0%
!! CCAAAATTTTATGAAAGTGC+AGG + Chr6:531912-531931 MsG0680030317.01.T01:intron 30.0%
!! CCAATATTTTTACAAAGTGC+AGG + Chr6:531737-531756 MsG0680030317.01.T01:intron 30.0%
!! CCAATATTTTTACAAAGTGC+AGG - Chr6:531756-531737 MsG0680030318.01.T01:intron 30.0%
!!! CACTTTTTTTTGTTTGGCAT+TGG + Chr6:531597-531616 MsG0680030317.01.T01:intron 30.0%
AAAGCTACTTGAGACGTATA+TGG + Chr6:531400-531419 MsG0680030317.01.T01:intron 35.0%
AAATCATACAGATGCTCCTT+CGG + Chr6:532071-532090 MsG0680030317.01.T01:CDS 35.0%
AACATTAATGCACTTGTACC+AGG - Chr6:532181-532200 MsG0680030318.01.T01:intron 35.0%
ACGGGTAAGTATATGAGAAT+TGG + Chr6:531193-531212 MsG0680030317.01.T01:intron 35.0%
CGGGTAAGTATATGAGAATT+GGG + Chr6:531194-531213 MsG0680030317.01.T01:intron 35.0%
CTAAAATTCGGCCTATCATT+TGG - Chr6:532049-532068 MsG0680030318.01.T01:intron 35.0%
CTATGATTGTAACATCATGC+TGG + Chr6:532014-532033 MsG0680030317.01.T01:CDS 35.0%
GTATATGAGAATTGGGTATG+GGG + Chr6:531201-531220 MsG0680030317.01.T01:intron 35.0%
TACCATTTCGCTATTAGAAC+CGG + Chr6:532102-532121 MsG0680030317.01.T01:CDS 35.0%
TTCCAACGTAATGTATGCTT+TGG - Chr6:531290-531309 MsG0680030318.01.T01:intron 35.0%
! CAAAATCTGATGAAAGTGCA+GGG - Chr6:531564-531583 MsG0680030318.01.T01:intron 35.0%
!! CTTTCATCAGATTTTGGCAT+TGG + Chr6:531568-531587 MsG0680030317.01.T01:intron 35.0%
!!! CCCTGCACTTTTTTTTTGTT+TGG - Chr6:531885-531904 MsG0680030318.01.T01:intron 35.0%
!!! TCGCTGCACTTTTTTTTGTT+TGG + Chr6:531591-531610 MsG0680030317.01.T01:intron 35.0%
AAATGGTAGAGAGATACCGA+AGG - Chr6:532090-532109 MsG0680030318.01.T01:intron 40.0%
AATGTGGAAGACAGGTTCAA+AGG + Chr6:532235-532254 MsG0680030317.01.T01:CDS 40.0%
ACAATCATAGCTAAATCGCC+AGG - Chr6:532004-532023 MsG0680030318.01.T01:intron 40.0%
ATGTGGAAGACAGGTTCAAA+GGG + Chr6:532236-532255 MsG0680030317.01.T01:CDS 40.0%
GATGGCTTCATCTGAGAATA+TGG + Chr6:532138-532157 MsG0680030317.01.T01:CDS 40.0%
GGAAAGAGGATCCAAATGAT+AGG + Chr6:532035-532054 MsG0680030317.01.T01:CDS 40.0%
GTCCAAAGCATACATTACGT+TGG + Chr6:531285-531304 MsG0680030317.01.T01:intron 40.0%
TGTAACATCATGCTGGAAAG+AGG + Chr6:532021-532040 MsG0680030317.01.T01:CDS 40.0%
TTCAATTTCTCATCCCCGTT+GGG + Chr6:531157-531176 MsG0680030317.01.T01:CDS 40.0%
TTTGAACCTGTCTTCCACAT+TGG - Chr6:532236-532255 MsG0680030318.01.T01:intron 40.0%
! AACCGGTTCTAATAGCGAAA+TGG - Chr6:532107-532126 MsG0680030318.01.T01:three_prime_UTR 40.0%
! AATGTATGCTTTGGACCTTG+TGG - Chr6:531281-531300 MsG0680030318.01.T01:intron 40.0%
! ATGTATGCTTTGGACCTTGT+GGG - Chr6:531280-531299 MsG0680030318.01.T01:intron 40.0%
! CCAAAATCTGATGAAAGTGC+AGG - Chr6:531565-531584 MsG0680030318.01.T01:intron 40.0%
! CCTGCACTTTCATCAGATTT+TGG + Chr6:531562-531581 MsG0680030317.01.T01:intron 40.0%
! CTGCTGCTTGAAGTTTACTA+AGG + Chr6:531496-531515 MsG0680030317.01.T01:intron 40.0%
AAGTAGAGCAGACTTGAGGT+CGG + Chr6:531310-531329 MsG0680030317.01.T01:intron 45.0%
AGTTCTTAGGCATGGCAATG+GGG - Chr6:531257-531276 MsG0680030318.01.T01:intron 45.0%
ATGAGAATTGGGTATGGGGA+TGG + Chr6:531205-531224 MsG0680030317.01.T01:intron 45.0%
GAGTTCTTAGGCATGGCAAT+GGG - Chr6:531258-531277 MsG0680030318.01.T01:intron 45.0%
GGAAAAGTAGAGCAGACTTG+AGG + Chr6:531306-531325 MsG0680030317.01.T01:intron 45.0%
GTTCAATTTCTCATCCCCGT+TGG + Chr6:531156-531175 MsG0680030317.01.T01:CDS 45.0%
TAGAACCGGTTGTTCCAATG+CGG + Chr6:532116-532135 MsG0680030317.01.T01:CDS 45.0%
TCAAGCAGCAGTGAATTCAG+TGG - Chr6:531487-531506 MsG0680030318.01.T01:intron 45.0%
TGAGAATTGGGTATGGGGAT+GGG + Chr6:531206-531225 MsG0680030317.01.T01:intron 45.0%
!! ATATTGGTATTGGTGCCACG+TGG - Chr6:531724-531743 MsG0680030318.01.T01:intron 45.0%
!! CTGTCTTCCACATTGGCTTT+CGG - Chr6:532229-532248 MsG0680030318.01.T01:intron 45.0%
!! TGTCTTCCACATTGGCTTTC+GGG - Chr6:532228-532247 MsG0680030318.01.T01:intron 45.0%
AGAAACCCCGAAAGCCAATG+TGG + Chr6:532219-532238 MsG0680030317.01.T01:CDS 50.0%
ATGTTTCGACGAGACGACTC+TGG + Chr6:532196-532215 MsG0680030317.01.T01:CDS 50.0%
CATGCCTAAGAACTCCCACA+AGG + Chr6:531263-531282 MsG0680030317.01.T01:intron 50.0%
CCACGTGGCGTGAAATGATT+GGG - Chr6:531709-531728 MsG0680030318.01.T01:intron 50.0%
CCAGGAAGATCTTCAGCACT+GGG - Chr6:531986-532005 MsG0680030318.01.T01:intron 50.0%
CGAAAGCCAATGTGGAAGAC+AGG + Chr6:532227-532246 MsG0680030317.01.T01:CDS 50.0%
CTTGTACCAGGAGATTCTGG+TGG - Chr6:532169-532188 MsG0680030318.01.T01:intron 50.0%
CTTGTGGGAGTTCTTAGGCA+TGG - Chr6:531265-531284 MsG0680030318.01.T01:intron 50.0%
GAGAATTGGGTATGGGGATG+GGG + Chr6:531207-531226 MsG0680030317.01.T01:intron 50.0%
GCACTTGTACCAGGAGATTC+TGG - Chr6:532172-532191 MsG0680030318.01.T01:intron 50.0%
GGAGTTCTTAGGCATGGCAA+TGG - Chr6:531259-531278 MsG0680030318.01.T01:intron 50.0%
GTATTGCCACCAGAATCTCC+TGG + Chr6:532160-532179 MsG0680030317.01.T01:CDS 50.0%
GTTACCCTACCCATACCCAA+CGG - Chr6:531175-531194 MsG0680030318.01.T01:intron 50.0%
GTTGGGTATGGGTAGGGTAA+CGG + Chr6:531174-531193 MsG0680030317.01.T01:CDS 50.0%
TCAGATGAAGCCATCCGCAT+TGG - Chr6:532133-532152 MsG0680030318.01.T01:three_prime_UTR 50.0%
TGGACCTTGTGGGAGTTCTT+AGG - Chr6:531270-531289 MsG0680030318.01.T01:intron 50.0%
TTACCCTACCCATACCCAAC+GGG - Chr6:531174-531193 MsG0680030318.01.T01:intron 50.0%
TTCTCATCCCCGTTGGGTAT+GGG + Chr6:531163-531182 MsG0680030317.01.T01:CDS 50.0%
TTGGGTATGGGTAGGGTAAC+GGG + Chr6:531175-531194 MsG0680030317.01.T01:CDS 50.0%
TTTCTCATCCCCGTTGGGTA+TGG + Chr6:531162-531181 MsG0680030317.01.T01:CDS 50.0%
! AAAACTAACGGAGTGCCACG+TGG + Chr6:531683-531702 MsG0680030317.01.T01:intron 50.0%
!! GTCTTCCACATTGGCTTTCG+GGG - Chr6:532227-532246 MsG0680030318.01.T01:intron 50.0%
ACCGGTTGTTCCAATGCGGA+TGG + Chr6:532120-532139 MsG0680030317.01.T01:CDS 55.0%
ATCCCCGTTGGGTATGGGTA+GGG + Chr6:531168-531187 MsG0680030317.01.T01:CDS 55.0%
CCCAATCATTTCACGCCACG+TGG + Chr6:531706-531725 MsG0680030317.01.T01:intron 55.0%
CGTGAAATGATTGGGCCACG+TGG - Chr6:531701-531720 MsG0680030318.01.T01:intron 55.0%
GCCACGTGGCGTGAAATGAT+TGG - Chr6:531710-531729 MsG0680030318.01.T01:intron 55.0%
GCCAGGAAGATCTTCAGCAC+TGG - Chr6:531987-532006 MsG0680030318.01.T01:intron 55.0%
GCCATCCGCATTGGAACAAC+CGG - Chr6:532124-532143 MsG0680030318.01.T01:three_prime_UTR 55.0%
TACCCTACCCATACCCAACG+GGG - Chr6:531173-531192 MsG0680030318.01.T01:intron 55.0%
TCTTAGGCATGGCAATGGGG+CGG - Chr6:531254-531273 MsG0680030318.01.T01:intron 55.0%
! CCCAGTGCTGAAGATCTTCC+TGG + Chr6:531983-532002 MsG0680030317.01.T01:CDS 55.0%
CATCCCCGTTGGGTATGGGT+AGG + Chr6:531167-531186 MsG0680030317.01.T01:CDS 60.0%
CTTAGGCATGGCAATGGGGC+GGG - Chr6:531253-531272 MsG0680030318.01.T01:intron 60.0%
TTAGGCATGGCAATGGGGCG+GGG - Chr6:531252-531271 MsG0680030318.01.T01:intron 60.0%
CATGGCAATGGGGCGGGGTG+GGG - Chr6:531247-531266 MsG0680030318.01.T01:intron 70.0%
GCATGGCAATGGGGCGGGGT+GGG - Chr6:531248-531267 MsG0680030318.01.T01:intron 70.0%
CAATGGGGCGGGGTGGGGAC+AGG - Chr6:531242-531261 MsG0680030318.01.T01:intron 75.0%
GGCATGGCAATGGGGCGGGG+TGG - Chr6:531249-531268 MsG0680030318.01.T01:intron 75.0%
Chromosome Type Strat End Strand Name
Chr6 gene 531151 532288 531151 ID=MsG0680030317.01;Name=MsG0680030317.01
Chr6 mRNA 531151 532288 531151 ID=MsG0680030317.01.T01;Parent=MsG0680030317.01;Name=MsG0680030317.01.T01;_AED=0.55;_eAED=0.55;_QI=0|0|0|0.5|0|0|2|0|126
Chr6 exon 531151 531196 531151 ID=MsG0680030317.01.T01:exon:2125;Parent=MsG0680030317.01.T01
Chr6 exon 531954 532288 531954 ID=MsG0680030317.01.T01:exon:2126;Parent=MsG0680030317.01.T01
Chr6 CDS 531151 531196 531151 ID=MsG0680030317.01.T01:cds;Parent=MsG0680030317.01.T01
Chr6 CDS 531954 532288 531954 ID=MsG0680030317.01.T01:cds;Parent=MsG0680030317.01.T01
Gene Sequence

>MsG0680030317.01.T01

ATGAGGTTCAATTTCTCATCCCCGTTGGGTATGGGTAGGGTAACGGCCATATTTTTATTATTTCAGAATACAAGGCCCAGTGCTGAAGATCTTCCTGGCGATTTAGCTATGATTGTAACATCATGCTGGAAAGAGGATCCAAATGATAGGCCGAATTTTAGTGAAATCATACAGATGCTCCTTCGGTATCTCTCTACCATTTCGCTATTAGAACCGGTTGTTCCAATGCGGATGGCTTCATCTGAGAATATGGTATTGCCACCAGAATCTCCTGGTACAAGTGCATTAATGTTTCGACGAGACGACTCTGGAGAAACCCCGAAAGCCAATGTGGAAGACAGGTTCAAAGGGTATTTCTTCTGCTTCAATCAGTGTTATTGA
Protein sequence

>MsG0680030317.01.T01

MRFNFSSPLGMGRVTAIFLLFQNTRPSAEDLPGDLAMIVTSCWKEDPNDRPNFSEIIQMLLRYLSTISLLEPVVPMRMASSENMVLPPESPGTSALMFRRDDSGETPKANVEDRFKGYFFCFNQCY*