AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene93852

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93852.t1 MTR_1g105305 93.467 199 13 0 1 199 1 199 3.00e-135 377
MS.gene93852.t1 MTR_5g005710 63.415 205 65 2 1 199 1 201 7.09e-95 275
MS.gene93852.t1 MTR_1g082770 36.943 157 96 3 20 173 20 176 9.46e-32 114
MS.gene93852.t1 MTR_7g113640 40.152 132 76 2 31 159 28 159 5.48e-31 112
MS.gene93852.t1 MTR_1g082830 36.170 141 88 2 31 169 47 187 1.48e-26 101
MS.gene93852.t1 MTR_1g082790 34.783 115 74 1 31 144 46 160 1.41e-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.gene93852.t1 AT3G06035 58.659 179 70 2 25 199 21 199 1.85e-72 218
MS.gene93852.t1 AT5G19250 67.123 146 48 0 31 176 28 173 4.25e-68 207
MS.gene93852.t1 AT1G54860 42.373 177 84 4 1 168 2 169 2.20e-47 154
MS.gene93852.t1 AT5G19240 44.767 172 89 3 23 192 20 187 2.57e-46 151
MS.gene93852.t1 AT5G19230 44.970 169 81 3 1 169 1 157 3.37e-40 135
MS.gene93852.t1 AT5G19230 44.970 169 81 3 1 169 1 157 3.37e-40 135

Find 42 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATTGACATTTAGCTAAA+AGG 0.190847 1.2:+78034901 None:intergenic
CCAAGTTCTCTCTATTCTTC+TGG 0.209568 1.2:-78035723 MS.gene93852:CDS
GTTATGCCTGCCTGTGTTCC+TGG 0.264326 1.2:-78034852 MS.gene93852:CDS
TCCAACTTTGGAATTCAAAT+TGG 0.272104 1.2:+78034659 None:intergenic
TGAGAGAGATAATCTTTATC+AGG 0.299934 1.2:-78035093 MS.gene93852:CDS
TGACATTTAGCTAAAAGGTT+TGG 0.301742 1.2:+78034906 None:intergenic
AGCTAAAAGGTTTGGGTAGT+TGG 0.318984 1.2:+78034914 None:intergenic
GTATTGGCTCAGAAGATAAC+TGG 0.333128 1.2:-78034746 MS.gene93852:CDS
GACATTTAGCTAAAAGGTTT+GGG 0.340607 1.2:+78034907 None:intergenic
CCAGAAGAATAGAGAGAACT+TGG 0.347419 1.2:+78035723 None:intergenic
GCAATAAATCATTCCAACTT+TGG 0.358521 1.2:+78034647 None:intergenic
TACATGGTTGATTCTTGAAT+TGG 0.360348 1.2:+78034985 None:intergenic
TCACCGTTATCACATTTAAC+TGG 0.363658 1.2:+78035661 None:intergenic
ATTGGCAGCATTAGAACTAT+AGG 0.374058 1.2:+78034677 None:intergenic
TTGGCAGCATTAGAACTATA+GGG 0.380106 1.2:+78034678 None:intergenic
CATCCTCTAGGTATCATAAC+AGG 0.398840 1.2:+78034595 None:intergenic
GCCAATTTGAATTCCAAAGT+TGG 0.400976 1.2:-78034660 MS.gene93852:CDS
GACACACAGTATACAGGAAT+TGG 0.421140 1.2:-78034768 MS.gene93852:CDS
TGCTCAATTCTCTTGTTAGC+TGG 0.427277 1.2:-78034627 MS.gene93852:CDS
CTCAACGACACACAGTATAC+AGG 0.481619 1.2:-78034774 MS.gene93852:CDS
TTGACCACTGACACTCCAAC+AGG 0.483770 1.2:-78034711 MS.gene93852:CDS
TTTGGGTAGTTGGAGAATTG+AGG 0.485525 1.2:+78034924 None:intergenic
ATTGGCTATTTCTGATACAA+AGG 0.497292 1.2:-78034883 MS.gene93852:CDS
TATCCAGTTAAATGTGATAA+CGG 0.502326 1.2:-78035664 MS.gene93852:intron
ACGAGGCTTGAAGCTAGGCC+AGG 0.504069 1.2:+78034834 None:intergenic
TGAAGCTAGGCCAGGAACAC+AGG 0.509872 1.2:+78034842 None:intergenic
GCTAGGCCAGGAACACAGGC+AGG 0.513127 1.2:+78034846 None:intergenic
GAGAATTGAGGTTCAGTACC+TGG 0.522201 1.2:+78034936 None:intergenic
GCTATTTCTGATACAAAGGA+TGG 0.531181 1.2:-78034879 MS.gene93852:CDS
CAGTATACAGGAATTGGTAT+TGG 0.536270 1.2:-78034762 MS.gene93852:CDS
GCACCTGTGGTATTTGTACA+TGG 0.542966 1.2:+78034969 None:intergenic
TCGTGAAGTTAGTGAGGACG+AGG 0.562843 1.2:+78034817 None:intergenic
TGAGGACGAGGCTTGAAGCT+AGG 0.566605 1.2:+78034829 None:intergenic
GTTTCCTGTTGGAGTGTCAG+TGG 0.576612 1.2:+78034707 None:intergenic
GAGATTTCGTGAAGTTAGTG+AGG 0.582648 1.2:+78034811 None:intergenic
GAGAGAGATAATCTTTATCA+GGG 0.592178 1.2:-78035092 MS.gene93852:CDS
TGGTACTGTATTAGCACCTG+TGG 0.607702 1.2:+78034956 None:intergenic
TGGCAGCATTAGAACTATAG+GGG 0.612217 1.2:+78034679 None:intergenic
ACAGGTGCTAATACAGTACC+AGG 0.621692 1.2:-78034954 MS.gene93852:CDS
CAGAAGAATAGAGAGAACTT+GGG 0.624874 1.2:+78035724 None:intergenic
CAACCATGTACAAATACCAC+AGG 0.631778 1.2:-78034972 MS.gene93852:CDS
GGCAGCATTAGAACTATAGG+GGG 0.666389 1.2:+78034680 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTGACCAATTCAAAATA+TGG + chr1.2:78034761-78034780 None:intergenic 20.0%
! ATTCATGAGATTAATGTCAT+AGG - chr1.2:78034826-78034845 MS.gene93852:CDS 25.0%
! ATTCATGAGATTAATGTCAT+TGG - chr1.2:78034826-78034845 MS.gene93852:CDS 25.0%
! TATCCAGTTAAATGTGATAA+CGG - chr1.2:78034677-78034696 MS.gene93852:CDS 25.0%
!!! TCTTAGACCATATTTTGAAT+TGG - chr1.2:78034751-78034770 MS.gene93852:CDS 25.0%
CCAATTGACATTTAGCTAAA+AGG + chr1.2:78035443-78035462 None:intergenic 30.0%
GACATTTAGCTAAAAGGTTT+GGG + chr1.2:78035437-78035456 None:intergenic 30.0%
GAGAGAGATAATCTTTATCA+GGG - chr1.2:78035249-78035268 MS.gene93852:intron 30.0%
GCAATAAATCATTCCAACTT+TGG + chr1.2:78035697-78035716 None:intergenic 30.0%
TGACATTTAGCTAAAAGGTT+TGG + chr1.2:78035438-78035457 None:intergenic 30.0%
TGAGAGAGATAATCTTTATC+AGG - chr1.2:78035248-78035267 MS.gene93852:intron 30.0%
TGCAGAAAAAACATTGAACA+GGG + chr1.2:78035226-78035245 None:intergenic 30.0%
TGTCAGTGAACAAAATGATT+TGG + chr1.2:78035120-78035139 None:intergenic 30.0%
TTTCAGCTTCATTGTGTATA+TGG + chr1.2:78035186-78035205 None:intergenic 30.0%
! TACATGGTTGATTCTTGAAT+TGG + chr1.2:78035359-78035378 None:intergenic 30.0%
!! ATTGGCTATTTCTGATACAA+AGG - chr1.2:78035458-78035477 MS.gene93852:intron 30.0%
!! CCTTTTAGCTAAATGTCAAT+TGG - chr1.2:78035440-78035459 MS.gene93852:intron 30.0%
!! TCCAACTTTGGAATTCAAAT+TGG + chr1.2:78035685-78035704 None:intergenic 30.0%
ATGCCTCTTAAAACATTCAC+TGG - chr1.2:78035019-78035038 MS.gene93852:CDS 35.0%
ATTGGCAGCATTAGAACTAT+AGG + chr1.2:78035667-78035686 None:intergenic 35.0%
CAGAAGAATAGAGAGAACTT+GGG + chr1.2:78034620-78034639 None:intergenic 35.0%
CAGTATACAGGAATTGGTAT+TGG - chr1.2:78035579-78035598 MS.gene93852:intron 35.0%
CTAAGCTTGAAATGAGTCAT+GGG + chr1.2:78034899-78034918 None:intergenic 35.0%
CTGCAGAAAAAACATTGAAC+AGG + chr1.2:78035227-78035246 None:intergenic 35.0%
GCCAATTTGAATTCCAAAGT+TGG - chr1.2:78035681-78035700 MS.gene93852:CDS 35.0%
TCACCGTTATCACATTTAAC+TGG + chr1.2:78034683-78034702 None:intergenic 35.0%
TTGGCAGCATTAGAACTATA+GGG + chr1.2:78035666-78035685 None:intergenic 35.0%
!! GCTATTTCTGATACAAAGGA+TGG - chr1.2:78035462-78035481 MS.gene93852:intron 35.0%
!! TGTCCAGTGAATGTTTTAAG+AGG + chr1.2:78035025-78035044 None:intergenic 35.0%
ACAGGGTAAGTGTAGTGTAA+TGG + chr1.2:78035209-78035228 None:intergenic 40.0%
AGCTAAAAGGTTTGGGTAGT+TGG + chr1.2:78035430-78035449 None:intergenic 40.0%
CAACCATGTACAAATACCAC+AGG - chr1.2:78035369-78035388 MS.gene93852:intron 40.0%
CCAAGTTCTCTCTATTCTTC+TGG - chr1.2:78034618-78034637 MS.gene93852:CDS 40.0%
CCAGAAGAATAGAGAGAACT+TGG + chr1.2:78034621-78034640 None:intergenic 40.0%
GACACACAGTATACAGGAAT+TGG - chr1.2:78035573-78035592 MS.gene93852:intron 40.0%
GAGATTTCGTGAAGTTAGTG+AGG + chr1.2:78035533-78035552 None:intergenic 40.0%
GCTAAGCTTGAAATGAGTCA+TGG + chr1.2:78034900-78034919 None:intergenic 40.0%
TGCTCAATTCTCTTGTTAGC+TGG - chr1.2:78035714-78035733 MS.gene93852:CDS 40.0%
TGGCAGCATTAGAACTATAG+GGG + chr1.2:78035665-78035684 None:intergenic 40.0%
TTGAGTAATGCACAGATGAC+AGG + chr1.2:78035050-78035069 None:intergenic 40.0%
TTTGGGTAGTTGGAGAATTG+AGG + chr1.2:78035420-78035439 None:intergenic 40.0%
! TCTCAGTTGTGACCTTTTTC+TGG - chr1.2:78035141-78035160 MS.gene93852:intron 40.0%
!! GGTCAGCTATTTTATCAGCA+AGG + chr1.2:78035338-78035357 None:intergenic 40.0%
!! GTATTGGCTCAGAAGATAAC+TGG - chr1.2:78035595-78035614 MS.gene93852:intron 40.0%
ACAGGTGCTAATACAGTACC+AGG - chr1.2:78035387-78035406 MS.gene93852:intron 45.0%
CTCAACGACACACAGTATAC+AGG - chr1.2:78035567-78035586 MS.gene93852:intron 45.0%
GAGAATTGAGGTTCAGTACC+TGG + chr1.2:78035408-78035427 None:intergenic 45.0%
GCACCTGTGGTATTTGTACA+TGG + chr1.2:78035375-78035394 None:intergenic 45.0%
GGCAGCATTAGAACTATAGG+GGG + chr1.2:78035664-78035683 None:intergenic 45.0%
TGGTACTGTATTAGCACCTG+TGG + chr1.2:78035388-78035407 None:intergenic 45.0%
TGTGCATGTGTGCCAGAAAA+AGG + chr1.2:78035156-78035175 None:intergenic 45.0%
TAGGGGGCAAAGTTTCCTGT+TGG + chr1.2:78035648-78035667 None:intergenic 50.0%
TCATCGCAGTCGCGAGATTA+GGG + chr1.2:78034973-78034992 None:intergenic 50.0%
TCGTGAAGTTAGTGAGGACG+AGG + chr1.2:78035527-78035546 None:intergenic 50.0%
TTCATCGCAGTCGCGAGATT+AGG + chr1.2:78034974-78034993 None:intergenic 50.0%
TTGACCACTGACACTCCAAC+AGG - chr1.2:78035630-78035649 MS.gene93852:intron 50.0%
! GTTTCCTGTTGGAGTGTCAG+TGG + chr1.2:78035637-78035656 None:intergenic 50.0%
GTTATGCCTGCCTGTGTTCC+TGG - chr1.2:78035489-78035508 MS.gene93852:intron 55.0%
TGAAGCTAGGCCAGGAACAC+AGG + chr1.2:78035502-78035521 None:intergenic 55.0%
TGAGGACGAGGCTTGAAGCT+AGG + chr1.2:78035515-78035534 None:intergenic 55.0%
ACGAGGCTTGAAGCTAGGCC+AGG + chr1.2:78035510-78035529 None:intergenic 60.0%
GCTAGGCCAGGAACACAGGC+AGG + chr1.2:78035498-78035517 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 78034608 78035755 78034608 ID=MS.gene93852
chr1.2 mRNA 78034608 78035755 78034608 ID=MS.gene93852.t1;Parent=MS.gene93852
chr1.2 exon 78035665 78035755 78035665 ID=MS.gene93852.t1.exon1;Parent=MS.gene93852.t1
chr1.2 CDS 78035665 78035755 78035665 ID=cds.MS.gene93852.t1;Parent=MS.gene93852.t1
chr1.2 exon 78034608 78035116 78034608 ID=MS.gene93852.t1.exon2;Parent=MS.gene93852.t1
chr1.2 CDS 78034608 78035116 78034608 ID=cds.MS.gene93852.t1;Parent=MS.gene93852.t1
Gene Sequence

>MS.gene93852

ATGGTGTTGCCCAAGTTCTCTCTATTCTTCTGGATTCTTTCTTCTTCATGTGTTATTCTCTTGATGAAATATCCAGTTAAATGTGATAACGGTGAGTATATTAACTGATCGTAAATTTTGTAATGATTTGATCATTTGCATTGTCTTAGACCATATTTTGAATTGGTCAAAATTCAGAATTTGTATCTACTGCAGTCACAATATGACGTTGTCATTGCATTCATGAGATTAATGTCATAGGATGACGTTGTCATTGCATTCATGAGATTAATGTCATTGGATGAAGATCCCATGACTCATTTCAAGCTTAGCAAATCAAAGCTAAGACAATAATGTGAGTTGTTCGATCTTTCATCAAACAACCCTAATCTCGCGACTGCGATGAACACATCATATATTTTAACAGTAAAAATGCCTCTTAAAACATTCACTGGACAGTCCTGTCATCTGTGCATTACTCAATTAGAAAGTTAGTTGACTAATAGCAGCATGTATTAAATAATAATGAACCAAATCATTTTGTTCACTGACAATCTCAGTTGTGACCTTTTTCTGGCACACATGCACATTCACAGCCATATACACAATGAAGCTGAAACCATTACACTACACTTACCCTGTTCAATGTTTTTTCTGCAGATGAGAGAGATAATCTTTATCAGGGTATCAACAAGTATCGAGCATCATTAAACTTGAAATCTCTCACAAAAAATAAAAATGCAGATTGCCTTGCTGATAAAATAGCTGACCAATTCAAGAATCAACCATGTACAAATACCACAGGTGCTAATACAGTACCAGGTACTGAACCTCAATTCTCCAACTACCCAAACCTTTTAGCTAAATGTCAATTGGCTATTTCTGATACAAAGGATGGAGCTGTTATGCCTGCCTGTGTTCCTGGCCTAGCTTCAAGCCTCGTCCTCACTAACTTCACGAAATCTCTCTACTCACAGAATCTCAACGACACACAGTATACAGGAATTGGTATTGGCTCAGAAGATAACTGGATTGTCGTTGTCTTGACCACTGACACTCCAACAGGAAACTTTGCCCCCTATAGTTCTAATGCTGCCAATTTGAATTCCAAAGTTGGAATGATTTATTGCTCAATTCTCTTGTTAGCTGGCAAAATTTTCCTGTTATGA
Protein sequence

>MS.gene93852.t1

MVLPKFSLFFWILSSSCVILLMKYPVKCDNDERDNLYQGINKYRASLNLKSLTKNKNADCLADKIADQFKNQPCTNTTGANTVPGTEPQFSNYPNLLAKCQLAISDTKDGAVMPACVPGLASSLVLTNFTKSLYSQNLNDTQYTGIGIGSEDNWIVVVLTTDTPTGNFAPYSSNAANLNSKVGMIYCSILLLAGKIFLL