AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49963

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49963.t1 MTR_1g105305 94.472 199 11 0 1 199 1 199 2.65e-137 382
MS.gene49963.t1 MTR_5g005710 63.902 205 64 2 1 199 1 201 6.58e-96 277
MS.gene49963.t1 MTR_1g082770 36.943 157 96 3 20 173 20 176 1.02e-31 114
MS.gene49963.t1 MTR_7g113640 38.889 144 84 3 19 159 17 159 4.14e-31 112
MS.gene49963.t1 MTR_1g082830 36.170 141 88 2 31 169 47 187 1.55e-26 101
MS.gene49963.t1 MTR_1g082790 34.783 115 74 1 31 144 46 160 1.47e-18 79.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49963.t1 AT3G06035 58.659 179 70 2 25 199 21 199 3.16e-72 217
MS.gene49963.t1 AT5G19250 61.078 167 63 1 24 188 19 185 1.85e-68 207
MS.gene49963.t1 AT1G54860 41.808 177 85 4 1 168 2 169 1.02e-46 152
MS.gene49963.t1 AT5G19240 45.349 172 88 3 23 192 20 187 2.16e-46 152
MS.gene49963.t1 AT5G19230 45.562 169 80 3 1 169 1 157 3.90e-41 138
MS.gene49963.t1 AT5G19230 45.562 169 80 3 1 169 1 157 3.90e-41 138

Find 42 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATTGACATTTAGCTAAA+AGG 0.190847 1.1:+75324770 None:intergenic
CCAAGTTCTCTCTATTCTTC+TGG 0.209568 1.1:-75325592 MS.gene49963:CDS
GTTATGCCTGCCTGTGTTCC+TGG 0.264326 1.1:-75324721 MS.gene49963:CDS
TCCAACTTTGGAAATCAAAT+TGG 0.265283 1.1:+75324528 None:intergenic
TGAGAGAGATAATCTTTATC+AGG 0.299934 1.1:-75324962 MS.gene49963:CDS
TGACATTTAGCTAAAAGGTT+TGG 0.301742 1.1:+75324775 None:intergenic
AGCTAAAAGGTTTGGGTAGT+TGG 0.318984 1.1:+75324783 None:intergenic
GTATTGGCTCAGAAGATAAC+TGG 0.333128 1.1:-75324615 MS.gene49963:CDS
GACATTTAGCTAAAAGGTTT+GGG 0.340607 1.1:+75324776 None:intergenic
CCAGAAGAATAGAGAGAACT+TGG 0.347419 1.1:+75325592 None:intergenic
GCAATAAATCATTCCAACTT+TGG 0.358521 1.1:+75324516 None:intergenic
TACATGGTTGATTCTTGAAT+TGG 0.360348 1.1:+75324854 None:intergenic
ATTGGCAGCATTAGAACTAT+AGG 0.374058 1.1:+75324546 None:intergenic
GCCAATTTGATTTCCAAAGT+TGG 0.375408 1.1:-75324529 MS.gene49963:CDS
TTGGCAGCATTAGAACTATA+GGG 0.380106 1.1:+75324547 None:intergenic
CATCCTCTAGGTATCATAAC+AGG 0.398840 1.1:+75324464 None:intergenic
TCACCGTCATCACATTTAAC+TGG 0.400596 1.1:+75325530 None:intergenic
GACACACAGTATACAGGAAT+TGG 0.421140 1.1:-75324637 MS.gene49963:CDS
TGCTCAATTCTCTTGTTAGC+TGG 0.427277 1.1:-75324496 MS.gene49963:CDS
CTCAACGACACACAGTATAC+AGG 0.481619 1.1:-75324643 MS.gene49963:CDS
TTGACCACTGACACTCCAAC+AGG 0.483770 1.1:-75324580 MS.gene49963:CDS
TTTGGGTAGTTGGAGAATTG+AGG 0.485525 1.1:+75324793 None:intergenic
ATTGGCTATTTCTGATACAA+AGG 0.497292 1.1:-75324752 MS.gene49963:CDS
ACGAGGCTTGAAGCTAGGCC+AGG 0.504069 1.1:+75324703 None:intergenic
TGAAGCTAGGCCAGGAACAC+AGG 0.509872 1.1:+75324711 None:intergenic
GCTAGGCCAGGAACACAGGC+AGG 0.513127 1.1:+75324715 None:intergenic
GAGAATTGAGGTTCAGTACC+TGG 0.522201 1.1:+75324805 None:intergenic
GCTATTTCTGATACAAAGGA+TGG 0.531181 1.1:-75324748 MS.gene49963:CDS
CAGTATACAGGAATTGGTAT+TGG 0.536270 1.1:-75324631 MS.gene49963:CDS
GCACCTGTGGTATTTGTACA+TGG 0.542966 1.1:+75324838 None:intergenic
TCGTGAAGTTAGTGAGGACG+AGG 0.562843 1.1:+75324686 None:intergenic
TGAGGACGAGGCTTGAAGCT+AGG 0.566605 1.1:+75324698 None:intergenic
GTTTCCTGTTGGAGTGTCAG+TGG 0.576612 1.1:+75324576 None:intergenic
GAGATTTCGTGAAGTTAGTG+AGG 0.582648 1.1:+75324680 None:intergenic
GAGAGAGATAATCTTTATCA+GGG 0.592178 1.1:-75324961 MS.gene49963:CDS
TATCCAGTTAAATGTGATGA+CGG 0.600716 1.1:-75325533 MS.gene49963:intron
TGGTACTGTATTAGCACCTG+TGG 0.607702 1.1:+75324825 None:intergenic
TGGCAGCATTAGAACTATAG+GGG 0.612217 1.1:+75324548 None:intergenic
ACAGGTGCTAATACAGTACC+AGG 0.621692 1.1:-75324823 MS.gene49963:CDS
CAGAAGAATAGAGAGAACTT+GGG 0.624874 1.1:+75325593 None:intergenic
CAACCATGTACAAATACCAC+AGG 0.631778 1.1:-75324841 MS.gene49963:CDS
GGCAGCATTAGAACTATAGG+GGG 0.666389 1.1:+75324549 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTGACCAATACAAAATA+TGG + chr1.1:75324630-75324649 None:intergenic 20.0%
! ATTCATGAGATTAATGTCAT+TGG - chr1.1:75324695-75324714 MS.gene49963:CDS 25.0%
!! TCTTAGACCATATTTTGTAT+TGG - chr1.1:75324620-75324639 MS.gene49963:CDS 25.0%
CCAATTGACATTTAGCTAAA+AGG + chr1.1:75325312-75325331 None:intergenic 30.0%
GACATTTAGCTAAAAGGTTT+GGG + chr1.1:75325306-75325325 None:intergenic 30.0%
GAGAGAGATAATCTTTATCA+GGG - chr1.1:75325118-75325137 MS.gene49963:intron 30.0%
GCAATAAATCATTCCAACTT+TGG + chr1.1:75325566-75325585 None:intergenic 30.0%
TATCCAGTTAAATGTGATGA+CGG - chr1.1:75324546-75324565 MS.gene49963:CDS 30.0%
TGACATTTAGCTAAAAGGTT+TGG + chr1.1:75325307-75325326 None:intergenic 30.0%
TGAGAGAGATAATCTTTATC+AGG - chr1.1:75325117-75325136 MS.gene49963:intron 30.0%
TGCAGAAAAAACATTGAACA+GGG + chr1.1:75325095-75325114 None:intergenic 30.0%
TGTCAGTGAACAAAATGATT+TGG + chr1.1:75324989-75325008 None:intergenic 30.0%
TTTCAGCTTCATTGTGTATA+TGG + chr1.1:75325055-75325074 None:intergenic 30.0%
! TACATGGTTGATTCTTGAAT+TGG + chr1.1:75325228-75325247 None:intergenic 30.0%
! TCCAACTTTGGAAATCAAAT+TGG + chr1.1:75325554-75325573 None:intergenic 30.0%
!! ATTGGCTATTTCTGATACAA+AGG - chr1.1:75325327-75325346 MS.gene49963:intron 30.0%
!! CCTTTTAGCTAAATGTCAAT+TGG - chr1.1:75325309-75325328 MS.gene49963:intron 30.0%
ATGCCTCTTAAAACATTCAC+TGG - chr1.1:75324888-75324907 MS.gene49963:CDS 35.0%
ATTGGCAGCATTAGAACTAT+AGG + chr1.1:75325536-75325555 None:intergenic 35.0%
CAGAAGAATAGAGAGAACTT+GGG + chr1.1:75324489-75324508 None:intergenic 35.0%
CAGTATACAGGAATTGGTAT+TGG - chr1.1:75325448-75325467 MS.gene49963:intron 35.0%
CTAAGCTTGAAATGAGTCAT+GGG + chr1.1:75324768-75324787 None:intergenic 35.0%
CTGCAGAAAAAACATTGAAC+AGG + chr1.1:75325096-75325115 None:intergenic 35.0%
TTGGCAGCATTAGAACTATA+GGG + chr1.1:75325535-75325554 None:intergenic 35.0%
! GCCAATTTGATTTCCAAAGT+TGG - chr1.1:75325550-75325569 MS.gene49963:CDS 35.0%
!! GCTATTTCTGATACAAAGGA+TGG - chr1.1:75325331-75325350 MS.gene49963:intron 35.0%
!! TGTCCAGTGAATGTTTTAAG+AGG + chr1.1:75324894-75324913 None:intergenic 35.0%
ACAGGGTAAGTGTAGTGTAA+TGG + chr1.1:75325078-75325097 None:intergenic 40.0%
AGCTAAAAGGTTTGGGTAGT+TGG + chr1.1:75325299-75325318 None:intergenic 40.0%
CAACCATGTACAAATACCAC+AGG - chr1.1:75325238-75325257 MS.gene49963:intron 40.0%
CCAAGTTCTCTCTATTCTTC+TGG - chr1.1:75324487-75324506 MS.gene49963:CDS 40.0%
CCAGAAGAATAGAGAGAACT+TGG + chr1.1:75324490-75324509 None:intergenic 40.0%
GACACACAGTATACAGGAAT+TGG - chr1.1:75325442-75325461 MS.gene49963:intron 40.0%
GAGATTTCGTGAAGTTAGTG+AGG + chr1.1:75325402-75325421 None:intergenic 40.0%
GCTAAGCTTGAAATGAGTCA+TGG + chr1.1:75324769-75324788 None:intergenic 40.0%
TCACCGTCATCACATTTAAC+TGG + chr1.1:75324552-75324571 None:intergenic 40.0%
TGCTCAATTCTCTTGTTAGC+TGG - chr1.1:75325583-75325602 MS.gene49963:CDS 40.0%
TGGCAGCATTAGAACTATAG+GGG + chr1.1:75325534-75325553 None:intergenic 40.0%
TTGAGTAATGCACAGATGAC+AGG + chr1.1:75324919-75324938 None:intergenic 40.0%
TTTGGGTAGTTGGAGAATTG+AGG + chr1.1:75325289-75325308 None:intergenic 40.0%
! TCTCAGTTGTGACCTTTTTC+TGG - chr1.1:75325010-75325029 MS.gene49963:intron 40.0%
!! GGTCAGCTATTTTATCAGCA+AGG + chr1.1:75325207-75325226 None:intergenic 40.0%
!! GTATTGGCTCAGAAGATAAC+TGG - chr1.1:75325464-75325483 MS.gene49963:intron 40.0%
ACAGGTGCTAATACAGTACC+AGG - chr1.1:75325256-75325275 MS.gene49963:intron 45.0%
CTCAACGACACACAGTATAC+AGG - chr1.1:75325436-75325455 MS.gene49963:intron 45.0%
GAGAATTGAGGTTCAGTACC+TGG + chr1.1:75325277-75325296 None:intergenic 45.0%
GCACCTGTGGTATTTGTACA+TGG + chr1.1:75325244-75325263 None:intergenic 45.0%
GGCAGCATTAGAACTATAGG+GGG + chr1.1:75325533-75325552 None:intergenic 45.0%
TGGTACTGTATTAGCACCTG+TGG + chr1.1:75325257-75325276 None:intergenic 45.0%
TGTGCATGTGTGCCAGAAAA+AGG + chr1.1:75325025-75325044 None:intergenic 45.0%
TAGGGGGCAAAGTTTCCTGT+TGG + chr1.1:75325517-75325536 None:intergenic 50.0%
TCATCGCAGTCGCGAGATTA+GGG + chr1.1:75324842-75324861 None:intergenic 50.0%
TCGTGAAGTTAGTGAGGACG+AGG + chr1.1:75325396-75325415 None:intergenic 50.0%
TTCATCGCAGTCGCGAGATT+AGG + chr1.1:75324843-75324862 None:intergenic 50.0%
TTGACCACTGACACTCCAAC+AGG - chr1.1:75325499-75325518 MS.gene49963:intron 50.0%
! GTTTCCTGTTGGAGTGTCAG+TGG + chr1.1:75325506-75325525 None:intergenic 50.0%
GTTATGCCTGCCTGTGTTCC+TGG - chr1.1:75325358-75325377 MS.gene49963:intron 55.0%
TGAAGCTAGGCCAGGAACAC+AGG + chr1.1:75325371-75325390 None:intergenic 55.0%
TGAGGACGAGGCTTGAAGCT+AGG + chr1.1:75325384-75325403 None:intergenic 55.0%
ACGAGGCTTGAAGCTAGGCC+AGG + chr1.1:75325379-75325398 None:intergenic 60.0%
GCTAGGCCAGGAACACAGGC+AGG + chr1.1:75325367-75325386 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 75324477 75325624 75324477 ID=MS.gene49963
chr1.1 mRNA 75324477 75325624 75324477 ID=MS.gene49963.t1;Parent=MS.gene49963
chr1.1 exon 75325534 75325624 75325534 ID=MS.gene49963.t1.exon1;Parent=MS.gene49963.t1
chr1.1 CDS 75325534 75325624 75325534 ID=cds.MS.gene49963.t1;Parent=MS.gene49963.t1
chr1.1 exon 75324477 75324985 75324477 ID=MS.gene49963.t1.exon2;Parent=MS.gene49963.t1
chr1.1 CDS 75324477 75324985 75324477 ID=cds.MS.gene49963.t1;Parent=MS.gene49963.t1
Gene Sequence

>MS.gene49963

ATGGTGTTGCCCAAGTTCTCTCTATTCTTCTGGATTCTTTCTTCTTCATGTGTTATTCTCTTGATGAAATATCCAGTTAAATGTGATGACGGTGAGTATATTAACTGATCGTAAATTTTGTAATGATTTGATCATTTGCATTGTCTTAGACCATATTTTGTATTGGTCAAAATTCAGAATTTGTATCTACTGCAGTCACAATATGACGTTGTCATTGCATTCATGAGATTAATGTCATTGGATGACGTTGTCATTGCATTCATGAGATTAATGTCATTGGATGAAGATCCCATGACTCATTTCAAGCTTAGCAAATCAAAGCTAAGACAATAATGTGAGTTGTTCGATCTTTCATCAAACAACCCTAATCTCGCGACTGCGATGAACGCATCATATATTTTAACAGTAAAAATGCCTCTTAAAACATTCACTGGACAGTCCTGTCATCTGTGCATTACTCAATTAGAAAGTTAGTTGACTAATAGCAGCATGTATTAAATAATAATGAACCAAATCATTTTGTTCACTGACAATCTCAGTTGTGACCTTTTTCTGGCACACATGCACATTCACAGCCATATACACAATGAAGCTGAAACCATTACACTACACTTACCCTGTTCAATGTTTTTTCTGCAGATGAGAGAGATAATCTTTATCAGGGTATCAACAAGTATCGAGCATCATTAAACTTGAAATCTCTCACAAAAAATAAAAATGCAGATTGCCTTGCTGATAAAATAGCTGACCAATTCAAGAATCAACCATGTACAAATACCACAGGTGCTAATACAGTACCAGGTACTGAACCTCAATTCTCCAACTACCCAAACCTTTTAGCTAAATGTCAATTGGCTATTTCTGATACAAAGGATGGAGCTGTTATGCCTGCCTGTGTTCCTGGCCTAGCTTCAAGCCTCGTCCTCACTAACTTCACGAAATCTCTCTACTCACAGAATCTCAACGACACACAGTATACAGGAATTGGTATTGGCTCAGAAGATAACTGGATTGTCGTTGTCTTGACCACTGACACTCCAACAGGAAACTTTGCCCCCTATAGTTCTAATGCTGCCAATTTGATTTCCAAAGTTGGAATGATTTATTGCTCAATTCTCTTGTTAGCTGGCAAAATTTTCCTGTTATGA
Protein sequence

>MS.gene49963.t1

MVLPKFSLFFWILSSSCVILLMKYPVKCDDDERDNLYQGINKYRASLNLKSLTKNKNADCLADKIADQFKNQPCTNTTGANTVPGTEPQFSNYPNLLAKCQLAISDTKDGAVMPACVPGLASSLVLTNFTKSLYSQNLNDTQYTGIGIGSEDNWIVVVLTTDTPTGNFAPYSSNAANLISKVGMIYCSILLLAGKIFLL