AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067346

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067346.t1 MTR_2g054750 88.571 140 4 1 1 140 1 128 1.14e-85 246
MS.gene067346.t1 MTR_4g113840 77.143 140 32 0 1 140 1 140 1.34e-79 231
MS.gene067346.t1 MTR_4g011190 44.286 140 67 1 6 134 5 144 1.35e-35 120
MS.gene067346.t1 MTR_3g107610 35.152 165 61 4 6 134 5 159 1.09e-27 100
MS.gene067346.t1 MTR_3g107610 33.333 147 48 4 6 114 5 139 6.44e-19 78.6
MS.gene067346.t1 MTR_3g107610 43.617 94 42 4 50 136 5 94 1.18e-13 64.7
MS.gene067346.t1 MTR_6g069400 29.104 134 73 4 1 134 265 376 1.49e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067346.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.05e-64 193
MS.gene067346.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.05e-64 193
MS.gene067346.t1 AT5G25490 37.576 165 66 5 6 137 5 165 1.30e-31 110
MS.gene067346.t1 AT5G25490 37.576 165 66 5 6 137 5 165 1.30e-31 110
MS.gene067346.t1 AT3G15680 41.558 154 67 6 6 136 5 158 6.28e-31 108
MS.gene067346.t1 AT3G15680 41.558 154 67 6 6 136 5 158 6.28e-31 108
MS.gene067346.t1 AT2G17975 31.013 158 77 7 6 137 7 158 7.02e-14 67.0
MS.gene067346.t1 AT2G17975 31.034 145 84 6 3 140 96 231 4.73e-11 58.9

Find 37 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTAGGGTATCCACAATTT+TGG 0.169674 2.3:+36489451 None:intergenic
CAGTTATATCTATAGGTTTC+TGG 0.204139 2.3:+36489414 None:intergenic
GGATCAGGGCCTCCAATCTT+AGG 0.228355 2.3:+36489435 None:intergenic
ACAGAACATACCAAAACTTT+TGG 0.258378 2.3:+36488599 None:intergenic
AATGGTTACTCTTGTGGATT+TGG 0.299384 2.3:-36489291 MS.gene067346:CDS
ATGGATGCCTCTGGTGGATA+TGG 0.313642 2.3:-36489261 MS.gene067346:CDS
TATCTATAGGTTTCTGGATC+AGG 0.325728 2.3:+36489420 None:intergenic
TGCAAAACACCCAAAAGTTT+TGG 0.338060 2.3:-36488609 MS.gene067346:intron
CAGAAACCTATAGATATAAC+TGG 0.359021 2.3:-36489413 MS.gene067346:CDS
TTCAGTCCAGTTATATCTAT+AGG 0.364972 2.3:+36489407 None:intergenic
TCTTCTTGAAATTTATATGC+TGG 0.441540 2.3:+36489484 None:intergenic
AATTGTGGATACCCTAAGAT+TGG 0.457887 2.3:-36489447 MS.gene067346:CDS
TGAGCTGGTCAGGAGGAGAT+TGG 0.487008 2.3:-36489521 MS.gene067346:CDS
ATCTATAGGTTTCTGGATCA+GGG 0.490676 2.3:+36489421 None:intergenic
GGTGGGAACATGGATGCCTC+TGG 0.491282 2.3:-36489270 MS.gene067346:CDS
ATATAACTGGACTGAAACCT+TGG 0.499509 2.3:-36489400 MS.gene067346:CDS
AACTGGACTGAAACCTTGGC+AGG 0.503471 2.3:-36489396 MS.gene067346:CDS
GATCAGGGCCTCCAATCTTA+GGG 0.508242 2.3:+36489436 None:intergenic
CTGAAACCTTGGCAGGGGAC+TGG 0.517119 2.3:-36489389 MS.gene067346:CDS
CTGGATGGAAAACTGGTGAC+TGG 0.527330 2.3:-36489218 MS.gene067346:CDS
AGCATATAAATTTCAAGAAG+AGG 0.527814 2.3:-36489482 MS.gene067346:CDS
TTGTGGATTTGGTGGGAACA+TGG 0.541127 2.3:-36489280 MS.gene067346:CDS
GGTTACTCTTGTGGATTTGG+TGG 0.558743 2.3:-36489288 MS.gene067346:CDS
GCATATAAATTTCAAGAAGA+GGG 0.572289 2.3:-36489481 MS.gene067346:CDS
CTGGTGACTGGATATGCACT+AGG 0.573750 2.3:-36489206 MS.gene067346:intron
TGTGGATACCCTAAGATTGG+AGG 0.581161 2.3:-36489444 MS.gene067346:CDS
AGGGATGCATGCCAAAATTG+TGG 0.584842 2.3:-36489462 MS.gene067346:CDS
TCATGTATCAGATATGGCTG+TGG 0.590303 2.3:-36488669 MS.gene067346:intron
GTTACTCTTGTGGATTTGGT+GGG 0.590561 2.3:-36489287 MS.gene067346:CDS
GGGAACATGGATGCCTCTGG+TGG 0.591219 2.3:-36489267 MS.gene067346:CDS
ACTGGACTGAAACCTTGGCA+GGG 0.594678 2.3:-36489395 MS.gene067346:CDS
GCAGGGGACTGGTATTGCAG+TGG 0.597750 2.3:-36489378 MS.gene067346:CDS
GCAATACCAGTCCCCTGCCA+AGG 0.605697 2.3:+36489383 None:intergenic
TATTGCAGTGGTATGAATTG+TGG 0.621087 2.3:-36489366 MS.gene067346:CDS
CTGGACTGAAACCTTGGCAG+GGG 0.627405 2.3:-36489394 MS.gene067346:CDS
AGAACAAGCTGTTATAGATG+TGG 0.633952 2.3:-36489324 MS.gene067346:CDS
ATCAGATCCATATCCACCAG+AGG 0.683350 2.3:+36489254 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTACAAAATATGTGATA+GGG + chr2.3:36489065-36489084 None:intergenic 15.0%
!! AATTAATTATATAAGCATCA+TGG + chr2.3:36489501-36489520 None:intergenic 15.0%
!! ATATAATTAATTCCTATTTC+AGG - chr2.3:36489509-36489528 MS.gene067346:CDS 15.0%
!! TAAATTACAAAATATGTGAT+AGG + chr2.3:36489066-36489085 None:intergenic 15.0%
!! AACATATCTATAATTAGACT+TGG - chr2.3:36489151-36489170 MS.gene067346:intron 20.0%
!! ACATATCTATAATTAGACTT+GGG - chr2.3:36489152-36489171 MS.gene067346:intron 20.0%
!! AGTCTAATTATAGATATGTT+TGG + chr2.3:36489151-36489170 None:intergenic 20.0%
!!! ATCACATATTTTGTAATTGA+GGG - chr2.3:36488869-36488888 MS.gene067346:intron 20.0%
! AGCATATAAATTTCAAGAAG+AGG - chr2.3:36488558-36488577 MS.gene067346:intron 25.0%
! CATATCTATAATTAGACTTG+GGG - chr2.3:36489153-36489172 MS.gene067346:intron 25.0%
! GCATATAAATTTCAAGAAGA+GGG - chr2.3:36488559-36488578 MS.gene067346:intron 25.0%
! TAATTAATTCCTATTTCAGG+TGG - chr2.3:36489512-36489531 MS.gene067346:CDS 25.0%
! TCTTCTTGAAATTTATATGC+TGG + chr2.3:36488559-36488578 None:intergenic 25.0%
!! CATCACATATTTTGTAATTG+AGG - chr2.3:36488868-36488887 MS.gene067346:intron 25.0%
!! TCACATATTTTGTAATTGAG+GGG - chr2.3:36488870-36488889 MS.gene067346:intron 25.0%
AGATGTGGTACATTGAAAAA+TGG - chr2.3:36488731-36488750 MS.gene067346:intron 30.0%
CAGAAACCTATAGATATAAC+TGG - chr2.3:36488627-36488646 MS.gene067346:CDS 30.0%
CAGTTATATCTATAGGTTTC+TGG + chr2.3:36488629-36488648 None:intergenic 30.0%
CGATAAATTTCAAATCTCCT+CGG + chr2.3:36489234-36489253 None:intergenic 30.0%
TTCAGTCCAGTTATATCTAT+AGG + chr2.3:36488636-36488655 None:intergenic 30.0%
TTGAAAAATGGTTACTCTTG+TGG - chr2.3:36488743-36488762 MS.gene067346:intron 30.0%
! ACAGAACATACCAAAACTTT+TGG + chr2.3:36489444-36489463 None:intergenic 30.0%
! CAGAACATACCAAAACTTTT+GGG + chr2.3:36489443-36489462 None:intergenic 30.0%
! CGAGGAGATTTGAAATTTAT+CGG - chr2.3:36489232-36489251 MS.gene067346:CDS 30.0%
! TTTTGTGTAAAAACAGGGTA+AGG - chr2.3:36488965-36488984 MS.gene067346:intron 30.0%
!!! TTACCCTGTTTTTACACAAA+AGG + chr2.3:36488966-36488985 None:intergenic 30.0%
AATGGTTACTCTTGTGGATT+TGG - chr2.3:36488749-36488768 MS.gene067346:intron 35.0%
AATTGTGGATACCCTAAGAT+TGG - chr2.3:36488593-36488612 MS.gene067346:intron 35.0%
AGAACAAGCTGTTATAGATG+TGG - chr2.3:36488716-36488735 MS.gene067346:intron 35.0%
ATATAACTGGACTGAAACCT+TGG - chr2.3:36488640-36488659 MS.gene067346:CDS 35.0%
CATACAATACACCAAATGGT+GGG - chr2.3:36488991-36489010 MS.gene067346:intron 35.0%
CTATAATTAGACTTGGGGAA+CGG - chr2.3:36489158-36489177 MS.gene067346:intron 35.0%
TATTGCAGTGGTATGAATTG+TGG - chr2.3:36488674-36488693 MS.gene067346:intron 35.0%
TGCTTCTCATGTATCAGATA+TGG - chr2.3:36489365-36489384 MS.gene067346:CDS 35.0%
! ACAGCCTTTTGTGTAAAAAC+AGG - chr2.3:36488959-36488978 MS.gene067346:intron 35.0%
! ATCTATAGGTTTCTGGATCA+GGG + chr2.3:36488622-36488641 None:intergenic 35.0%
! CAGCCTTTTGTGTAAAAACA+GGG - chr2.3:36488960-36488979 MS.gene067346:intron 35.0%
! TATCTATAGGTTTCTGGATC+AGG + chr2.3:36488623-36488642 None:intergenic 35.0%
! TGCAAAACACCCAAAAGTTT+TGG - chr2.3:36489431-36489450 MS.gene067346:CDS 35.0%
!! TCTTAGGGTATCCACAATTT+TGG + chr2.3:36488592-36488611 None:intergenic 35.0%
!! TGTTTTGCACTTGAAGCATT+CGG + chr2.3:36489420-36489439 None:intergenic 35.0%
!! TTACACAAAAGGCTGTTTTC+AGG + chr2.3:36488955-36488974 None:intergenic 35.0%
AAATATGTGATAGGGCAACC+CGG + chr2.3:36489057-36489076 None:intergenic 40.0%
CAATCTGAACCACCTGAAAT+AGG + chr2.3:36489524-36489543 None:intergenic 40.0%
GCATACAATACACCAAATGG+TGG - chr2.3:36488990-36489009 MS.gene067346:intron 40.0%
GCTGCATACAATACACCAAA+TGG - chr2.3:36488987-36489006 MS.gene067346:intron 40.0%
GTTGTTGTCATGTGACTGTA+AGG - chr2.3:36488915-36488934 MS.gene067346:intron 40.0%
TAAGCATCATGGATCTGATG+AGG + chr2.3:36489490-36489509 None:intergenic 40.0%
TCATGTATCAGATATGGCTG+TGG - chr2.3:36489371-36489390 MS.gene067346:CDS 40.0%
! CAGTTTTACAATTGTCTCCG+AGG - chr2.3:36489214-36489233 MS.gene067346:CDS 40.0%
! GTTACTCTTGTGGATTTGGT+GGG - chr2.3:36488753-36488772 MS.gene067346:intron 40.0%
AGGGATGCATGCCAAAATTG+TGG - chr2.3:36488578-36488597 MS.gene067346:intron 45.0%
ATCAGATCCATATCCACCAG+AGG + chr2.3:36488789-36488808 None:intergenic 45.0%
GGTTACTCTTGTGGATTTGG+TGG - chr2.3:36488752-36488771 MS.gene067346:intron 45.0%
GTCATGTGACTGTAAGGTCA+CGG - chr2.3:36488921-36488940 MS.gene067346:intron 45.0%
TCATGTGACTGTAAGGTCAC+GGG - chr2.3:36488922-36488941 MS.gene067346:intron 45.0%
TGTGGATACCCTAAGATTGG+AGG - chr2.3:36488596-36488615 MS.gene067346:intron 45.0%
TTGTAATTGAGGGGTGACCT+TGG - chr2.3:36488879-36488898 MS.gene067346:intron 45.0%
! AGTCACCAGTTTTCCATCCA+GGG + chr2.3:36488823-36488842 None:intergenic 45.0%
!! TTGTGGATTTGGTGGGAACA+TGG - chr2.3:36488760-36488779 MS.gene067346:intron 45.0%
AACTGGACTGAAACCTTGGC+AGG - chr2.3:36488644-36488663 MS.gene067346:CDS 50.0%
ACTGGACTGAAACCTTGGCA+GGG - chr2.3:36488645-36488664 MS.gene067346:CDS 50.0%
ATTGCAATTACCCCCCTGGA+TGG - chr2.3:36488807-36488826 MS.gene067346:intron 50.0%
CAACTTAACCAGTTGCGCCA+AGG + chr2.3:36488899-36488918 None:intergenic 50.0%
CTGGATGGAAAACTGGTGAC+TGG - chr2.3:36488822-36488841 MS.gene067346:intron 50.0%
CTGGTGACTGGATATGCACT+AGG - chr2.3:36488834-36488853 MS.gene067346:intron 50.0%
GATCAGGGCCTCCAATCTTA+GGG + chr2.3:36488607-36488626 None:intergenic 50.0%
TCTGATTGCAATTACCCCCC+TGG - chr2.3:36488803-36488822 MS.gene067346:intron 50.0%
! ATGGATGCCTCTGGTGGATA+TGG - chr2.3:36488779-36488798 MS.gene067346:intron 50.0%
! CAGTCACCAGTTTTCCATCC+AGG + chr2.3:36488824-36488843 None:intergenic 50.0%
! GTCACCAGTTTTCCATCCAG+GGG + chr2.3:36488822-36488841 None:intergenic 50.0%
! TCACCAGTTTTCCATCCAGG+GGG + chr2.3:36488821-36488840 None:intergenic 50.0%
CTGGACTGAAACCTTGGCAG+GGG - chr2.3:36488646-36488665 MS.gene067346:CDS 55.0%
GGATCAGGGCCTCCAATCTT+AGG + chr2.3:36488608-36488627 None:intergenic 55.0%
TACCCCCCTGGATGGAAAAC+TGG - chr2.3:36488815-36488834 MS.gene067346:intron 55.0%
TGAGCTGGTCAGGAGGAGAT+TGG - chr2.3:36488519-36488538 MS.gene067346:intron 55.0%
! CACCAGTTTTCCATCCAGGG+GGG + chr2.3:36488820-36488839 None:intergenic 55.0%
ACTGAAGCTCCCGCATACGC+AGG + chr2.3:36489031-36489050 None:intergenic 60.0%
ATGCGGGAGCTTCAGTGCAC+CGG - chr2.3:36489035-36489054 MS.gene067346:intron 60.0%
CATACGCAGGGTCTGGGTAG+GGG + chr2.3:36489018-36489037 None:intergenic 60.0%
CTACCCAGACCCTGCGTATG+CGG - chr2.3:36489018-36489037 MS.gene067346:intron 60.0%
CTGAAACCTTGGCAGGGGAC+TGG - chr2.3:36488651-36488670 MS.gene067346:CDS 60.0%
CTGAAGCTCCCGCATACGCA+GGG + chr2.3:36489030-36489049 None:intergenic 60.0%
GCAATACCAGTCCCCTGCCA+AGG + chr2.3:36488660-36488679 None:intergenic 60.0%
GCATACGCAGGGTCTGGGTA+GGG + chr2.3:36489019-36489038 None:intergenic 60.0%
GGGAACATGGATGCCTCTGG+TGG - chr2.3:36488773-36488792 MS.gene067346:intron 60.0%
GGTGGGAACATGGATGCCTC+TGG - chr2.3:36488770-36488789 MS.gene067346:intron 60.0%
TACCCAGACCCTGCGTATGC+GGG - chr2.3:36489019-36489038 MS.gene067346:intron 60.0%
TGGGTAGGGGTCCCACCATT+TGG + chr2.3:36489005-36489024 None:intergenic 60.0%
! GCAGGGGACTGGTATTGCAG+TGG - chr2.3:36488662-36488681 MS.gene067346:intron 60.0%
AGGGGTGACCTTGGCGCAAC+TGG - chr2.3:36488888-36488907 MS.gene067346:intron 65.0%
CGCATACGCAGGGTCTGGGT+AGG + chr2.3:36489020-36489039 None:intergenic 65.0%
CTCCCGCATACGCAGGGTCT+GGG + chr2.3:36489024-36489043 None:intergenic 65.0%
TGCGGGAGCTTCAGTGCACC+GGG - chr2.3:36489036-36489055 MS.gene067346:intron 65.0%
GCTCCCGCATACGCAGGGTC+TGG + chr2.3:36489025-36489044 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 36488518 36489544 36488518 ID=MS.gene067346
chr2.3 mRNA 36488518 36489544 36488518 ID=MS.gene067346.t1;Parent=MS.gene067346
chr2.3 exon 36489207 36489544 36489207 ID=MS.gene067346.t1.exon1;Parent=MS.gene067346.t1
chr2.3 CDS 36489207 36489544 36489207 ID=cds.MS.gene067346.t1;Parent=MS.gene067346.t1
chr2.3 exon 36488610 36488680 36488610 ID=MS.gene067346.t1.exon2;Parent=MS.gene067346.t1
chr2.3 CDS 36488610 36488680 36488610 ID=cds.MS.gene067346.t1;Parent=MS.gene067346.t1
chr2.3 exon 36488518 36488531 36488518 ID=MS.gene067346.t1.exon3;Parent=MS.gene067346.t1
chr2.3 CDS 36488518 36488531 36488518 ID=cds.MS.gene067346.t1;Parent=MS.gene067346.t1
Gene Sequence

>MS.gene067346

ATGAGCTGGTCAGGAGGAGATTGGATGTGCAATGCTTGCCAGCATATAAATTTCAAGAAGAGGGATGCATGCCAAAATTGTGGATACCCTAAGATTGGAGGCCCTGATCCAGAAACCTATAGATATAACTGGACTGAAACCTTGGCAGGGGACTGGTATTGCAGTGGTATGAATTGTGGAGCTCACAATTATGCTAGCAGAACAAGCTGTTATAGATGTGGTACATTGAAAAATGGTTACTCTTGTGGATTTGGTGGGAACATGGATGCCTCTGGTGGATATGGATCTGATTGCAATTACCCCCCTGGATGGAAAACTGGTGACTGGATATGCACTAGGTATTTTCACATCATCACATATTTTGTAATTGAGGGGTGACCTTGGCGCAACTGGTTAAGTTGTTGTCATGTGACTGTAAGGTCACGGGTTTAAGTCCTGAAAACAGCCTTTTGTGTAAAAACAGGGTAAGGCTGCATACAATACACCAAATGGTGGGACCCCTACCCAGACCCTGCGTATGCGGGAGCTTCAGTGCACCGGGTTGCCCTATCACATATTTTGTAATTTACTTCACTAAAATATTGCTGCATTTTCATGTACTGAAGTTGCTTTGCAAATTGCAACTACAAACCAAACATATCTATAATTAGACTTGGGGAACGGAGAAATTATTATTAATAAGAATGACACTAATGACAGTTTTACAATTGTCTCCGAGGAGATTTGAAATTTATCGGTTAAGACTACAAAGTCAACTCTCATCTCTGCGCTGACATAAAATAACTCGTTTCATTGTATTACATAAAAAGAAATATGAAATATCATAGAAATACATTTTTATTTTCTTTGCTTCTCATGTATCAGATATGGCTGTGGAGTGCACAATTATGCTAGCAGAGCCGAATGCTTCAAGTGCAAAACACCCAAAAGTTTTGGTATGTTCTGTTACTTAAAGTATATGCTATTCAACCTCATCAGATCCATGATGCTTATATAATTAATTCCTATTTCAGGTGGTTCAGATTGA
Protein sequence

>MS.gene067346.t1

MSWSGGDWMCNACQHINFKKRDACQNCGYPKIGGPDPETYRYNWTETLAGDWYCSGMNCGAHNYASRTSCYRCGTLKNGYSCGFGGNMDASGGYGSDCNYPPGWKTGDWICTRYGCGVHNYASRAECFKCKTPKSFGGSD