AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene75959


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75959.t1 MTR_6g011450 73.203 153 34 1 47 192 423 575 3.05e-64 210
MS.gene75959.t1 MTR_6g011450 73.203 153 34 1 47 192 561 713 1.59e-63 210
MS.gene75959.t1 MTR_6g011470 70.073 137 13 1 55 191 1 109 1.34e-60 188
MS.gene75959.t1 MTR_4g073340 76.316 114 27 0 78 191 280 393 7.01e-56 184
MS.gene75959.t1 MTR_1g061130 34.848 66 43 0 115 180 829 894 5.42e-11 61.2
MS.gene75959.t1 MTR_1g061130 34.848 66 43 0 115 180 829 894 5.59e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75959.t1 AT4G04885 63.000 100 37 0 93 192 591 690 5.64e-36 133
MS.gene75959.t1 AT1G66500 37.654 162 68 7 54 183 124 284 1.20e-22 94.4
MS.gene75959.t1 AT5G43620 37.342 158 68 7 54 183 123 277 7.18e-21 89.4

Find 54 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACGAACCTTGAGAATATT+TGG 0.171658 6.4:+4620244 None:intergenic
GTTACAAATGCCATTTCTTT+TGG 0.240735 6.4:-4621325 None:intergenic
GTGACTGCTGTGCTCATCTT+TGG 0.248435 6.4:+4620150 None:intergenic
GGTTGTTGGCTTGACGTATT+AGG 0.261888 6.4:+4620465 None:intergenic
AAGAGTTGTTTCCGATTCTT+TGG 0.310522 6.4:+4620553 None:intergenic
ATCGCATATATAGGTGTCTT+TGG 0.354576 6.4:-4621177 MS.gene75959:CDS
TATGTAATTTGTGATTTATA+TGG 0.358933 6.4:-4620217 MS.gene75959:CDS
CCGATTCTTTGGTATGGAAT+AGG 0.359303 6.4:+4620564 None:intergenic
TATATAGGTGTCTTTGGAAC+CGG 0.377723 6.4:-4621171 MS.gene75959:CDS
GTCTTTGGAACCGGGCTATT+AGG 0.379584 6.4:-4621162 MS.gene75959:CDS
GGAATAGGAAGTGGCATAAC+AGG 0.392358 6.4:+4620579 None:intergenic
GGCATAACAGGTCGTGCATT+TGG 0.398786 6.4:+4620591 None:intergenic
TAACAGGTCGTGCATTTGGC+AGG 0.413669 6.4:+4620595 None:intergenic
TGCCCAAGGTGTTATCTCAT+TGG 0.416501 6.4:-4620406 MS.gene75959:CDS
AAATTAGAATATCCAACAAT+TGG 0.418071 6.4:+4620444 None:intergenic
AATATCCAACAATTGGTTGT+TGG 0.433148 6.4:+4620451 None:intergenic
TTTGCAGTAATCGCATATAT+AGG 0.434152 6.4:-4621186 MS.gene75959:intron
TTCCGACCTTTACCTCCAGC+TGG 0.442785 6.4:-4620531 MS.gene75959:CDS
TCAAATGTTAAGACTACTAC+AGG 0.446918 6.4:-4621291 MS.gene75959:intron
GATTCGGATGAGGTAGAATC+TGG 0.448129 6.4:+4620493 None:intergenic
ATTCTACCTCATCCGAATCT+TGG 0.451748 6.4:-4620489 MS.gene75959:CDS
TTGTTTCCGATTCTTTGGTA+TGG 0.469020 6.4:+4620558 None:intergenic
GCTCATCTTTGGATTTGAAT+CGG 0.471012 6.4:+4620161 None:intergenic
AGTAGAGCATGTGGGCCAGC+TGG 0.471650 6.4:+4620516 None:intergenic
TCAAGCCAACAACCAATTGT+TGG 0.475162 6.4:-4620456 MS.gene75959:CDS
CTTTGGTATGGAATAGGAAG+TGG 0.486169 6.4:+4620570 None:intergenic
CCTATTCCATACCAAAGAAT+CGG 0.490580 6.4:-4620564 MS.gene75959:CDS
GACGTATTAGGACCAAGATT+CGG 0.494335 6.4:+4620477 None:intergenic
TGTGGGCCAGCTGGAGGTAA+AGG 0.498674 6.4:+4620525 None:intergenic
ATTGATTTAGTTACCTTCGC+AGG 0.505170 6.4:+4620372 None:intergenic
CCACAAGTTGTGCATTGTCT+AGG 0.520332 6.4:+4620187 None:intergenic
CCTAGACAATGCACAACTTG+TGG 0.528311 6.4:-4620187 MS.gene75959:CDS
AGCACAGCAGTCACATGGAT+TGG 0.529243 6.4:-4620141 MS.gene75959:CDS
AGCCAATGAGATAACACCTT+GGG 0.530219 6.4:+4620404 None:intergenic
AACAGGTCGTGCATTTGGCA+GGG 0.540179 6.4:+4620596 None:intergenic
AAAGAAAGCGCCTAATAGCC+CGG 0.541200 6.4:+4621152 None:intergenic
CATCTTTGGATTTGAATCGG+TGG 0.563255 6.4:+4620164 None:intergenic
TTGATTTAGTTACCTTCGCA+GGG 0.565255 6.4:+4620373 None:intergenic
ACAGGTCGTGCATTTGGCAG+GGG 0.566169 6.4:+4620597 None:intergenic
ATTAGTTCACTCATTGCCCA+AGG 0.573674 6.4:-4620420 MS.gene75959:CDS
GAATATTTGGATCAAACTCA+AGG 0.580223 6.4:+4620257 None:intergenic
ATATAGGTGTCTTTGGAACC+GGG 0.582674 6.4:-4621170 MS.gene75959:CDS
AGATGAGCACAGCAGTCACA+TGG 0.587427 6.4:-4620146 MS.gene75959:CDS
GTTTGATCCAAATATTCTCA+AGG 0.588305 6.4:-4620251 MS.gene75959:CDS
AGAGCATGTGGGCCAGCTGG+AGG 0.611285 6.4:+4620519 None:intergenic
CAGGTCGTGCATTTGGCAGG+GGG 0.612021 6.4:+4620598 None:intergenic
GGCTAATCAAGCCCCTGCGA+AGG 0.612023 6.4:-4620385 MS.gene75959:intron
GGCCAGCTGGAGGTAAAGGT+CGG 0.612329 6.4:+4620529 None:intergenic
AGAATCTGGAGTAGAGCATG+TGG 0.640782 6.4:+4620507 None:intergenic
TTAGGACCAAGATTCGGATG+AGG 0.644974 6.4:+4620483 None:intergenic
TAGCCAATGAGATAACACCT+TGG 0.659744 6.4:+4620403 None:intergenic
TGATTTAGTTACCTTCGCAG+GGG 0.687811 6.4:+4620374 None:intergenic
GAATCTGGAGTAGAGCATGT+GGG 0.691664 6.4:+4620508 None:intergenic
ACTCACAAACTACTTGCGAG+AGG 0.695457 6.4:+4620075 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAATCATATTAACAACT+TGG + chr6.4:4620340-4620359 None:intergenic 15.0%
!!! ATTAATTCATTTGCAATTTT+TGG - chr6.4:4620761-4620780 MS.gene75959:intron 15.0%
!!! TATGTAATTTGTGATTTATA+TGG - chr6.4:4621185-4621204 MS.gene75959:intron 15.0%
!! AAATTAGAATATCCAACAAT+TGG + chr6.4:4620961-4620980 None:intergenic 20.0%
!! ACAGAATACAATAACAAAAT+TGG + chr6.4:4621108-4621127 None:intergenic 20.0%
!! AGTCTTAACATTTGAAAAAA+AGG + chr6.4:4620106-4620125 None:intergenic 20.0%
!! ATGTTTCTTGAACAAAAAAT+TGG + chr6.4:4620277-4620296 None:intergenic 20.0%
!!! AATATGATTTTAACTATGAC+CGG - chr6.4:4620347-4620366 MS.gene75959:intron 20.0%
!!! TTTAAGTTGTTCATAATAAC+TGG - chr6.4:4620145-4620164 MS.gene75959:CDS 20.0%
!!! TTTTTTGAAGTAATTTCATG+TGG + chr6.4:4620490-4620509 None:intergenic 20.0%
! ATAACTTATCCAATCATACT+CGG + chr6.4:4620711-4620730 None:intergenic 25.0%
! ATCATATTAACAACTTGGAA+AGG + chr6.4:4620335-4620354 None:intergenic 25.0%
! CAAAACATTAAAAGGAAAGA+AGG - chr6.4:4620433-4620452 MS.gene75959:CDS 25.0%
! TCATTTCGCAAAACATTAAA+AGG - chr6.4:4620425-4620444 MS.gene75959:CDS 25.0%
! TGTTATTGTATTCTGTTTGT+AGG - chr6.4:4621112-4621131 MS.gene75959:intron 25.0%
!! TTCTGTTTGTAGGATTTTAT+TGG - chr6.4:4621122-4621141 MS.gene75959:CDS 25.0%
!!! ATATGATTTTAACTATGACC+GGG - chr6.4:4620348-4620367 MS.gene75959:intron 25.0%
AAAAAGGAAGCCAAAAGAAA+TGG + chr6.4:4620090-4620109 None:intergenic 30.0%
AAATGAAGACTTAGGATACT+TGG + chr6.4:4620411-4620430 None:intergenic 30.0%
AAGTGAAGATGAAACTGATT+CGG + chr6.4:4620630-4620649 None:intergenic 30.0%
AATATCCAACAATTGGTTGT+TGG + chr6.4:4620954-4620973 None:intergenic 30.0%
ATCTATTCTGATGTTTCATG+TGG + chr6.4:4620558-4620577 None:intergenic 30.0%
GAATATTTGGATCAAACTCA+AGG + chr6.4:4621148-4621167 None:intergenic 30.0%
GTTTGATCCAAATATTCTCA+AGG - chr6.4:4621151-4621170 MS.gene75959:CDS 30.0%
TAGTAATGAGATCTGAGAAA+AGG + chr6.4:4620184-4620203 None:intergenic 30.0%
TATAATCCATGGGAAAATTC+AGG + chr6.4:4620605-4620624 None:intergenic 30.0%
TCAAATGTTAAGACTACTAC+AGG - chr6.4:4620111-4620130 MS.gene75959:CDS 30.0%
TTTGCAGTAATCGCATATAT+AGG - chr6.4:4620216-4620235 MS.gene75959:CDS 30.0%
! TGATTCGGATTATAATCCAT+GGG + chr6.4:4620615-4620634 None:intergenic 30.0%
!! GCTTACAGTTTTTAGACATA+CGG + chr6.4:4621301-4621320 None:intergenic 30.0%
!! TGTTGATGATGCCAATTAAT+GGG - chr6.4:4620377-4620396 MS.gene75959:intron 30.0%
!! TTGTTGATGATGCCAATTAA+TGG - chr6.4:4620376-4620395 MS.gene75959:intron 30.0%
AAGGAAAGAAGGAAATCTAG+AGG - chr6.4:4620444-4620463 MS.gene75959:CDS 35.0%
ACGCAATCAAGTAAAATGGA+AGG + chr6.4:4621084-4621103 None:intergenic 35.0%
ATCGCATATATAGGTGTCTT+TGG - chr6.4:4620225-4620244 MS.gene75959:CDS 35.0%
CCTATTCCATACCAAAGAAT+CGG - chr6.4:4620838-4620857 MS.gene75959:intron 35.0%
CTTCAGTCACATAACTTACT+TGG + chr6.4:4620305-4620324 None:intergenic 35.0%
GCTCATCTTTGGATTTGAAT+CGG + chr6.4:4621244-4621263 None:intergenic 35.0%
TATTTGACAGTCGAGATTAG+AGG - chr6.4:4620680-4620699 MS.gene75959:intron 35.0%
TGACGAACCTTGAGAATATT+TGG + chr6.4:4621161-4621180 None:intergenic 35.0%
TGGAAATGAACCCCATTAAT+TGG + chr6.4:4620391-4620410 None:intergenic 35.0%
TGGTACGCAATCAAGTAAAA+TGG + chr6.4:4621088-4621107 None:intergenic 35.0%
TGGTGATCTTTGCAATAGTT+TGG - chr6.4:4620781-4620800 MS.gene75959:intron 35.0%
TTGATTTAGTTACCTTCGCA+GGG + chr6.4:4621032-4621051 None:intergenic 35.0%
TTGTTTCCGATTCTTTGGTA+TGG + chr6.4:4620847-4620866 None:intergenic 35.0%
! AAGAGTTGTTTCCGATTCTT+TGG + chr6.4:4620852-4620871 None:intergenic 35.0%
! ATTGATTTAGTTACCTTCGC+AGG + chr6.4:4621033-4621052 None:intergenic 35.0%
! GTTTTGCGAAATGAAGACTT+AGG + chr6.4:4620419-4620438 None:intergenic 35.0%
! TGATTACCTGAATTTTCCCA+TGG - chr6.4:4620596-4620615 MS.gene75959:CDS 35.0%
!! CTGATTCGGATTATAATCCA+TGG + chr6.4:4620616-4620635 None:intergenic 35.0%
!! GTTGATGATGCCAATTAATG+GGG - chr6.4:4620378-4620397 MS.gene75959:intron 35.0%
!! TATATAGGTGTCTTTGGAAC+CGG - chr6.4:4620231-4620250 MS.gene75959:CDS 35.0%
AGCCAATGAGATAACACCTT+GGG + chr6.4:4621001-4621020 None:intergenic 40.0%
ATTAGTTCACTCATTGCCCA+AGG - chr6.4:4620982-4621001 MS.gene75959:intron 40.0%
ATTCTACCTCATCCGAATCT+TGG - chr6.4:4620913-4620932 MS.gene75959:intron 40.0%
CATCTTTGGATTTGAATCGG+TGG + chr6.4:4621241-4621260 None:intergenic 40.0%
CCGATTCTTTGGTATGGAAT+AGG + chr6.4:4620841-4620860 None:intergenic 40.0%
CTTTGGTATGGAATAGGAAG+TGG + chr6.4:4620835-4620854 None:intergenic 40.0%
GACGTATTAGGACCAAGATT+CGG + chr6.4:4620928-4620947 None:intergenic 40.0%
GCATCATCAACAATGTTACC+CGG + chr6.4:4620369-4620388 None:intergenic 40.0%
TAGCCAATGAGATAACACCT+TGG + chr6.4:4621002-4621021 None:intergenic 40.0%
TCAAGCCAACAACCAATTGT+TGG - chr6.4:4620946-4620965 MS.gene75959:intron 40.0%
TGATTTAGTTACCTTCGCAG+GGG + chr6.4:4621031-4621050 None:intergenic 40.0%
!! ATATAGGTGTCTTTGGAACC+GGG - chr6.4:4620232-4620251 MS.gene75959:CDS 40.0%
CCACAAGTTGTGCATTGTCT+AGG + chr6.4:4621218-4621237 None:intergenic 45.0%
CCTAGACAATGCACAACTTG+TGG - chr6.4:4621215-4621234 MS.gene75959:intron 45.0%
GATTCGGATGAGGTAGAATC+TGG + chr6.4:4620912-4620931 None:intergenic 45.0%
GGAATAGGAAGTGGCATAAC+AGG + chr6.4:4620826-4620845 None:intergenic 45.0%
TTAGGACCAAGATTCGGATG+AGG + chr6.4:4620922-4620941 None:intergenic 45.0%
! AGAATCTGGAGTAGAGCATG+TGG + chr6.4:4620898-4620917 None:intergenic 45.0%
! GAATCTGGAGTAGAGCATGT+GGG + chr6.4:4620897-4620916 None:intergenic 45.0%
! TGCCCAAGGTGTTATCTCAT+TGG - chr6.4:4620996-4621015 MS.gene75959:intron 45.0%
!! AAAGAAAGCGCCTAATAGCC+CGG + chr6.4:4620253-4620272 None:intergenic 45.0%
!! GAGGAGTATCCGAGTATGAT+TGG - chr6.4:4620699-4620718 MS.gene75959:intron 45.0%
!! GGTTGTTGGCTTGACGTATT+AGG + chr6.4:4620940-4620959 None:intergenic 45.0%
AACAGGTCGTGCATTTGGCA+GGG + chr6.4:4620809-4620828 None:intergenic 50.0%
AGATGAGCACAGCAGTCACA+TGG - chr6.4:4621256-4621275 MS.gene75959:intron 50.0%
AGCACAGCAGTCACATGGAT+TGG - chr6.4:4621261-4621280 MS.gene75959:intron 50.0%
GGCATAACAGGTCGTGCATT+TGG + chr6.4:4620814-4620833 None:intergenic 50.0%
GTGACTGCTGTGCTCATCTT+TGG + chr6.4:4621255-4621274 None:intergenic 50.0%
TAACAGGTCGTGCATTTGGC+AGG + chr6.4:4620810-4620829 None:intergenic 50.0%
!! GTCTTTGGAACCGGGCTATT+AGG - chr6.4:4620240-4620259 MS.gene75959:CDS 50.0%
ACAGGTCGTGCATTTGGCAG+GGG + chr6.4:4620808-4620827 None:intergenic 55.0%
TTCCGACCTTTACCTCCAGC+TGG - chr6.4:4620871-4620890 MS.gene75959:intron 55.0%
AGTAGAGCATGTGGGCCAGC+TGG + chr6.4:4620889-4620908 None:intergenic 60.0%
CAGGTCGTGCATTTGGCAGG+GGG + chr6.4:4620807-4620826 None:intergenic 60.0%
GGCCAGCTGGAGGTAAAGGT+CGG + chr6.4:4620876-4620895 None:intergenic 60.0%
GGCTAATCAAGCCCCTGCGA+AGG - chr6.4:4621017-4621036 MS.gene75959:intron 60.0%
TGTGGGCCAGCTGGAGGTAA+AGG + chr6.4:4620880-4620899 None:intergenic 60.0%
AGAGCATGTGGGCCAGCTGG+AGG + chr6.4:4620886-4620905 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 4620084 4621340 4620084 ID=MS.gene75959
chr6.4 mRNA 4620084 4621340 4620084 ID=MS.gene75959.t1;Parent=MS.gene75959
chr6.4 exon 4621292 4621340 4621292 ID=MS.gene75959.t1.exon1;Parent=MS.gene75959.t1
chr6.4 CDS 4621292 4621340 4621292 ID=cds.MS.gene75959.t1;Parent=MS.gene75959.t1
chr6.4 exon 4621119 4621201 4621119 ID=MS.gene75959.t1.exon2;Parent=MS.gene75959.t1
chr6.4 CDS 4621119 4621201 4621119 ID=cds.MS.gene75959.t1;Parent=MS.gene75959.t1
chr6.4 exon 4620386 4620625 4620386 ID=MS.gene75959.t1.exon3;Parent=MS.gene75959.t1
chr6.4 CDS 4620386 4620625 4620386 ID=cds.MS.gene75959.t1;Parent=MS.gene75959.t1
chr6.4 exon 4620084 4620290 4620084 ID=MS.gene75959.t1.exon4;Parent=MS.gene75959.t1
chr6.4 CDS 4620084 4620290 4620084 ID=cds.MS.gene75959.t1;Parent=MS.gene75959.t1
Gene Sequence

>MS.gene75959

ATGCCATTTCTTTTGGCTTCCTTTTTTTCAAATGTTAAGACTACTACAGGTTTGTTTCTACTTTAAGTTGTTCATAATAACTGGTGTGTTAATATTGCCTTTTCTCAGATCTCATTACTAATGTTTTTGATATTTGCAGTAATCGCATATATAGGTGTCTTTGGAACCGGGCTATTAGGCGCTTTCTTTTCCAATTTTTTGTTCAAGAAACATCATTTCCAAGTAAGTTATGTGACTGAAGAATGATACCTTTCCAAGTTGTTAATATGATTTTAACTATGACCGGGTAACATTGTTGATGATGCCAATTAATGGGGTTCATTTCCAAGTATCCTAAGTCTTCATTTCGCAAAACATTAAAAGGAAAGAAGGAAATCTAGAGGAACAATGATCTTCACATAAACCACATGAAATTACTTCAAAAAATTTCAACACAACGAAGAAAAGATAAATTTTTTAATTGTCAATAAGCCACATGAAACATCAGAATAGATTTTATTAATTGATGAATTTGATTACCTGAATTTTCCCATGGATTATAATCCGAATCAGTTTCATCTTCACTTTCAAAGTCATTATTTATAGCTTATAAAGTTTATTTGACAGTCGAGATTAGAGGAGTATCCGAGTATGATTGGATAAGTTATCATATTCATATACAATCACTTATTCGATGAATTAATTCATTTGCAATTTTTGGTGATCTTTGCAATAGTTTGGCCCCCTGCCAAATGCACGACCTGTTATGCCACTTCCTATTCCATACCAAAGAATCGGAAACAACTCTTTCCGACCTTTACCTCCAGCTGGCCCACATGCTCTACTCCAGATTCTACCTCATCCGAATCTTGGTCCTAATACGTCAAGCCAACAACCAATTGTTGGATATTCTAATTTGATTAGTTCACTCATTGCCCAAGGTGTTATCTCATTGGCTAATCAAGCCCCTGCGAAGGTAACTAAATCAATCGTTAGTTCAGTTTTTATATCACATTTTCCTTCCATTTTACTTGATTGCGTACCAATTTTGTTATTGTATTCTGTTTGTAGGATTTTATTGGCCTTGAGTTTGATCCAAATATTCTCAAGGTTCGTCATGAATATGTAATTTGTGATTTATATGGTGATTTTCCTAGACAATGCACAACTTGTGGCCACCGATTCAAATCCAAAGATGAGCACAGCAGTCACATGGATTGGCATGTGACAAAGAACCGTATGTCTAAAAACTGTAAGCAAAAGTCCTCTCGCAAGTAG

Protein sequence

>MS.gene75959.t1

MPFLLASFFSNVKTTTVIAYIGVFGTGLLGAFFSNFLFKKHHFQFGPLPNARPVMPLPIPYQRIGNNSFRPLPPAGPHALLQILPHPNLGPNTSSQQPIVGYSNLISSLIAQGVISLANQAPAKDFIGLEFDPNILKVRHEYVICDLYGDFPRQCTTCGHRFKSKDEHSSHMDWHVTKNRMSKNCKQKSSRK