AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09931


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09931.t1 MTR_5g011800 95.652 230 9 1 4 233 1 229 7.36e-163 449
MS.gene09931.t1 MTR_5g011820 89.700 233 23 1 1 233 1 232 9.24e-154 426
MS.gene09931.t1 MTR_4g102220 58.898 236 80 6 4 233 1 225 4.85e-80 239
MS.gene09931.t1 MTR_4g024370 51.055 237 104 5 4 233 1 232 1.79e-74 226
MS.gene09931.t1 MTR_4g024370 51.055 237 104 5 4 233 1 232 1.79e-74 226
MS.gene09931.t1 MTR_6g060390 29.130 230 137 9 8 232 4 212 1.19e-22 92.4
MS.gene09931.t1 MTR_6g060440 29.565 230 134 10 8 232 4 210 8.15e-22 90.1
MS.gene09931.t1 MTR_7g117380 28.384 229 150 7 8 232 3 221 3.45e-19 83.2
MS.gene09931.t1 MTR_1g076800 25.764 229 147 8 7 232 3 211 7.06e-19 82.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09931.t1 AT2G45360 52.381 231 93 5 4 233 1 215 6.91e-73 221
MS.gene09931.t1 AT3G60780 50.215 233 98 6 4 233 1 218 1.25e-69 213
MS.gene09931.t1 AT1G62840 47.718 241 98 8 4 233 1 224 2.53e-55 176
MS.gene09931.t1 AT1G12320 43.723 231 102 7 4 229 1 208 4.46e-45 150

Find 66 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGGGGATGTTCACTTTATT+AGG 0.233385 5.1:-5228616 MS.gene09931:CDS
TTTATTTCTAAGATGGATTC+TGG 0.260989 5.1:-5228827 MS.gene09931:CDS
TATGAGTTAGTTGCTCTCTC+TGG 0.291619 5.1:+5229262 None:intergenic
TTTGATTGGAATAGATTTCT+TGG 0.340143 5.1:-5228942 MS.gene09931:CDS
ATGGCGGAGCGTGGTGGCGC+GGG 0.351116 5.1:-5228798 MS.gene09931:CDS
AGATGGATTCTGGTTATATA+TGG 0.373750 5.1:-5228817 MS.gene09931:CDS
TGGTATGTCACCGGAAGTTT+TGG 0.381944 5.1:-5228993 MS.gene09931:CDS
ATTTCTTGGTTGTTGATTCT+CGG 0.396616 5.1:-5228928 MS.gene09931:CDS
TGAAAGACATGAAACTTGTT+TGG 0.407611 5.1:-5229288 MS.gene09931:CDS
TGTTCGGTCAGTATTTCTTC+CGG 0.416161 5.1:-5228762 MS.gene09931:CDS
GAAGTGATGGATGGTTTGAT+TGG 0.429509 5.1:-5228956 MS.gene09931:CDS
ATGAGTTAGTTGCTCTCTCT+GGG 0.435811 5.1:+5229263 None:intergenic
AAGCATGTTGATCAACGATC+AGG 0.439670 5.1:-5228635 MS.gene09931:CDS
TCCGATCTTGACCGTTCATC+AGG 0.440907 5.1:+5229040 None:intergenic
AGAATCCGGTGCGGCGGAGC+TGG 0.456364 5.1:-5229194 MS.gene09931:CDS
GGCGGAGCTGGTATCCTCTA+TGG 0.456798 5.1:-5229182 MS.gene09931:CDS
TGGATAAACCAACACTCGTT+GGG 0.457594 5.1:+5229104 None:intergenic
GGGGATCACGACGACTTGTT+CGG 0.470863 5.1:-5228778 MS.gene09931:CDS
ACCTGTGTGACCGCTTGCTA+TGG 0.473046 5.1:+5229084 None:intergenic
AGTATTTCTTCCGGTGGGGA+AGG 0.473923 5.1:-5228753 MS.gene09931:CDS
TTCTCTAGGAAGGTGATTGA+TGG 0.483897 5.1:+5229213 None:intergenic
TGTTACGGCGATGAAGCATA+AGG 0.490118 5.1:-5228684 MS.gene09931:CDS
AATCACCTTCCTAGAGAATC+CGG 0.490375 5.1:-5229208 MS.gene09931:CDS
AAGGTGATTGATGGTAGTTA+TGG 0.490442 5.1:+5229222 None:intergenic
GACGTGCTGTTCATAATAGA+TGG 0.491292 5.1:-5228661 MS.gene09931:CDS
CGGTCAGTATTTCTTCCGGT+GGG 0.491351 5.1:-5228758 MS.gene09931:CDS
GGTTCTCCTACCAAAACTTC+CGG 0.492682 5.1:+5228983 None:intergenic
TGGCGGAGCGTGGTGGCGCG+GGG 0.493800 5.1:-5228797 MS.gene09931:CDS
TATGGCGGAGCGTGGTGGCG+CGG 0.506489 5.1:-5228799 MS.gene09931:CDS
CTGGTATCCTCTATGGCAGC+AGG 0.510352 5.1:-5229175 MS.gene09931:CDS
TGGTGGTGACAACTCTGTTA+CGG 0.515438 5.1:-5228699 MS.gene09931:CDS
CTTGCAAAGTTGAGTAGTAA+AGG 0.517171 5.1:-5228878 MS.gene09931:CDS
AAACCATCCATCACTTCCTC+CGG 0.520767 5.1:+5228962 None:intergenic
AACAGAGTTGTCACCACCAC+CGG 0.522950 5.1:+5228703 None:intergenic
GGATACCAGCTCCGCCGCAC+CGG 0.538075 5.1:+5229189 None:intergenic
GTTACGGCGATGAAGCATAA+GGG 0.543192 5.1:-5228683 MS.gene09931:CDS
AGGAGAACCGGAGGAAGTGA+TGG 0.549491 5.1:-5228969 MS.gene09931:CDS
TCCTGATGAACGGTCAAGAT+CGG 0.549497 5.1:-5229041 MS.gene09931:CDS
GGTGGGGAAGGGAATTCATA+TGG 0.556013 5.1:-5228741 MS.gene09931:CDS
ATGGATAAACCAACACTCGT+TGG 0.556717 5.1:+5229103 None:intergenic
TCGGTCAGTATTTCTTCCGG+TGG 0.561365 5.1:-5228759 MS.gene09931:CDS
GTATTTCTTCCGGTGGGGAA+GGG 0.563160 5.1:-5228752 MS.gene09931:CDS
AGCATGTTGATCAACGATCA+GGG 0.563826 5.1:-5228634 MS.gene09931:CDS
TCCTAGAGAATCCGGTGCGG+CGG 0.565345 5.1:-5229200 MS.gene09931:CDS
GGAGTTATCCCAACGAGTGT+TGG 0.567790 5.1:-5229112 MS.gene09931:CDS
GTTCCATCCTGCTGCCATAG+AGG 0.581085 5.1:+5229168 None:intergenic
ATATGAATTCCCTTCCCCAC+CGG 0.588515 5.1:+5228743 None:intergenic
TCCGCCGCACCGGATTCTCT+AGG 0.590144 5.1:+5229199 None:intergenic
CTCAGCTGATAGTAGAAACA+TGG 0.594393 5.1:-5229144 MS.gene09931:CDS
GGGAGAAGCTGGTATGTCAC+CGG 0.594972 5.1:-5229002 MS.gene09931:CDS
TTATATATGGCGGAGCGTGG+TGG 0.612287 5.1:-5228804 MS.gene09931:CDS
CCGCACCGGATTCTCTAGGA+AGG 0.614758 5.1:+5229203 None:intergenic
GAACCGGAGGAAGTGATGGA+TGG 0.618455 5.1:-5228965 MS.gene09931:CDS
TCCATAGCAAGCGGTCACAC+AGG 0.622700 5.1:-5229085 MS.gene09931:CDS
GGTCAGTATTTCTTCCGGTG+GGG 0.623177 5.1:-5228757 MS.gene09931:CDS
TGGTTATATATGGCGGAGCG+TGG 0.623341 5.1:-5228807 MS.gene09931:CDS
TATCCTCTATGGCAGCAGGA+TGG 0.630751 5.1:-5229171 MS.gene09931:CDS
TGTGCATAGTTCCTGATGAA+CGG 0.633781 5.1:-5229051 MS.gene09931:CDS
ATAGCAAGCGGTCACACAGG+TGG 0.636263 5.1:-5229082 MS.gene09931:CDS
TGGATTCTGGTTATATATGG+CGG 0.643639 5.1:-5228814 MS.gene09931:CDS
GCATGTTGATCAACGATCAG+GGG 0.659538 5.1:-5228633 MS.gene09931:CDS
GTTGGTTTATCCATAGCAAG+CGG 0.671936 5.1:-5229094 MS.gene09931:CDS
TGAGTTAGTTGCTCTCTCTG+GGG 0.683268 5.1:+5229264 None:intergenic
ATAGTAGAAACATGGTCACA+CGG 0.693003 5.1:-5229136 MS.gene09931:CDS
CCTTCCTAGAGAATCCGGTG+CGG 0.793946 5.1:-5229203 MS.gene09931:CDS
GTAGAAACATGGTCACACGG+CGG 0.823354 5.1:-5229133 MS.gene09931:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGCTAATTTTATTTCTAAGA+TGG - chr5.1:5229065-5229084 MS.gene09931:CDS 20.0%
! TTTGATTGGAATAGATTTCT+TGG - chr5.1:5228957-5228976 MS.gene09931:CDS 25.0%
!!! TTTATTTCTAAGATGGATTC+TGG - chr5.1:5229072-5229091 MS.gene09931:CDS 25.0%
! AATTCATATGGCACACTTTT+CGG - chr5.1:5229170-5229189 MS.gene09931:CDS 30.0%
! AGATGGATTCTGGTTATATA+TGG - chr5.1:5229082-5229101 MS.gene09931:CDS 30.0%
! TGAAAGACATGAAACTTGTT+TGG - chr5.1:5228611-5228630 MS.gene09931:CDS 30.0%
!! ATTTCTTGGTTGTTGATTCT+CGG - chr5.1:5228971-5228990 MS.gene09931:CDS 30.0%
!!! AAGATTTTACAAGAGTGTTG+AGG - chr5.1:5228998-5229017 MS.gene09931:CDS 30.0%
ATAGTAGAAACATGGTCACA+CGG - chr5.1:5228763-5228782 MS.gene09931:CDS 35.0%
ATCGGAGTATGCAAAAAACA+TGG - chr5.1:5228876-5228895 MS.gene09931:CDS 35.0%
CTTGCAAAGTTGAGTAGTAA+AGG - chr5.1:5229021-5229040 MS.gene09931:CDS 35.0%
TCGGAGTATGCAAAAAACAT+GGG - chr5.1:5228877-5228896 MS.gene09931:CDS 35.0%
! AAGGTGATTGATGGTAGTTA+TGG + chr5.1:5228680-5228699 None:intergenic 35.0%
! TGGATTCTGGTTATATATGG+CGG - chr5.1:5229085-5229104 MS.gene09931:CDS 35.0%
AAGCATGTTGATCAACGATC+AGG - chr5.1:5229264-5229283 MS.gene09931:CDS 40.0%
AATCACCTTCCTAGAGAATC+CGG - chr5.1:5228691-5228710 MS.gene09931:CDS 40.0%
AGCATGTTGATCAACGATCA+GGG - chr5.1:5229265-5229284 MS.gene09931:CDS 40.0%
ATGAGTTAGTTGCTCTCTCT+GGG + chr5.1:5228639-5228658 None:intergenic 40.0%
ATGGATAAACCAACACTCGT+TGG + chr5.1:5228799-5228818 None:intergenic 40.0%
CAGGGGATGTTCACTTTATT+AGG - chr5.1:5229283-5229302 MS.gene09931:CDS 40.0%
CTCAGCTGATAGTAGAAACA+TGG - chr5.1:5228755-5228774 MS.gene09931:CDS 40.0%
TATGAGTTAGTTGCTCTCTC+TGG + chr5.1:5228640-5228659 None:intergenic 40.0%
TGGATAAACCAACACTCGTT+GGG + chr5.1:5228798-5228817 None:intergenic 40.0%
TGTGCATAGTTCCTGATGAA+CGG - chr5.1:5228848-5228867 MS.gene09931:CDS 40.0%
TGTTCGGTCAGTATTTCTTC+CGG - chr5.1:5229137-5229156 MS.gene09931:CDS 40.0%
! GACGTGCTGTTCATAATAGA+TGG - chr5.1:5229238-5229257 MS.gene09931:CDS 40.0%
! GTTGGTTTATCCATAGCAAG+CGG - chr5.1:5228805-5228824 MS.gene09931:CDS 40.0%
! TTCTCTAGGAAGGTGATTGA+TGG + chr5.1:5228689-5228708 None:intergenic 40.0%
!! GAAGTGATGGATGGTTTGAT+TGG - chr5.1:5228943-5228962 MS.gene09931:CDS 40.0%
AAACCATCCATCACTTCCTC+CGG + chr5.1:5228940-5228959 None:intergenic 45.0%
ATATGAATTCCCTTCCCCAC+CGG + chr5.1:5229159-5229178 None:intergenic 45.0%
GCAAAAAACATGGGAGAAGC+TGG - chr5.1:5228886-5228905 MS.gene09931:CDS 45.0%
GCATGTTGATCAACGATCAG+GGG - chr5.1:5229266-5229285 MS.gene09931:CDS 45.0%
GGTTCTCCTACCAAAACTTC+CGG + chr5.1:5228919-5228938 None:intergenic 45.0%
GTTACGGCGATGAAGCATAA+GGG - chr5.1:5229216-5229235 MS.gene09931:CDS 45.0%
TCCTGATGAACGGTCAAGAT+CGG - chr5.1:5228858-5228877 MS.gene09931:CDS 45.0%
TGAGTTAGTTGCTCTCTCTG+GGG + chr5.1:5228638-5228657 None:intergenic 45.0%
TGTTACGGCGATGAAGCATA+AGG - chr5.1:5229215-5229234 MS.gene09931:CDS 45.0%
! TGGTATGTCACCGGAAGTTT+TGG - chr5.1:5228906-5228925 MS.gene09931:CDS 45.0%
! TGGTGGTGACAACTCTGTTA+CGG - chr5.1:5229200-5229219 MS.gene09931:CDS 45.0%
!! ATGTCACCGGAAGTTTTGGT+AGG - chr5.1:5228910-5228929 MS.gene09931:CDS 45.0%
!! GGAAGTTTTGGTAGGAGAAC+CGG - chr5.1:5228918-5228937 MS.gene09931:CDS 45.0%
AACAGAGTTGTCACCACCAC+CGG + chr5.1:5229199-5229218 None:intergenic 50.0%
AGTATTTCTTCCGGTGGGGA+AGG - chr5.1:5229146-5229165 MS.gene09931:CDS 50.0%
CGGTCAGTATTTCTTCCGGT+GGG - chr5.1:5229141-5229160 MS.gene09931:CDS 50.0%
GGAGTTATCCCAACGAGTGT+TGG - chr5.1:5228787-5228806 MS.gene09931:CDS 50.0%
GGTCAGTATTTCTTCCGGTG+GGG - chr5.1:5229142-5229161 MS.gene09931:CDS 50.0%
GGTGGGGAAGGGAATTCATA+TGG - chr5.1:5229158-5229177 MS.gene09931:CDS 50.0%
GTAGAAACATGGTCACACGG+CGG - chr5.1:5228766-5228785 MS.gene09931:CDS 50.0%
GTATTTCTTCCGGTGGGGAA+GGG - chr5.1:5229147-5229166 MS.gene09931:CDS 50.0%
TATCCTCTATGGCAGCAGGA+TGG - chr5.1:5228728-5228747 MS.gene09931:CDS 50.0%
TCCGATCTTGACCGTTCATC+AGG + chr5.1:5228862-5228881 None:intergenic 50.0%
TCGGTCAGTATTTCTTCCGG+TGG - chr5.1:5229140-5229159 MS.gene09931:CDS 50.0%
! TGGTTATATATGGCGGAGCG+TGG - chr5.1:5229092-5229111 MS.gene09931:CDS 50.0%
! TTATATATGGCGGAGCGTGG+TGG - chr5.1:5229095-5229114 MS.gene09931:CDS 50.0%
!! AGTTTTGGTAGGAGAACCGG+AGG - chr5.1:5228921-5228940 MS.gene09931:CDS 50.0%
AGGAGAACCGGAGGAAGTGA+TGG - chr5.1:5228930-5228949 MS.gene09931:CDS 55.0%
ATAGCAAGCGGTCACACAGG+TGG - chr5.1:5228817-5228836 MS.gene09931:CDS 55.0%
CCTTCCTAGAGAATCCGGTG+CGG - chr5.1:5228696-5228715 MS.gene09931:CDS 55.0%
CTGGTATCCTCTATGGCAGC+AGG - chr5.1:5228724-5228743 MS.gene09931:CDS 55.0%
GGGAGAAGCTGGTATGTCAC+CGG - chr5.1:5228897-5228916 MS.gene09931:CDS 55.0%
GTTCCATCCTGCTGCCATAG+AGG + chr5.1:5228734-5228753 None:intergenic 55.0%
TCCATAGCAAGCGGTCACAC+AGG - chr5.1:5228814-5228833 MS.gene09931:CDS 55.0%
! ACCTGTGTGACCGCTTGCTA+TGG + chr5.1:5228818-5228837 None:intergenic 55.0%
! ATGGCACACTTTTCGGCTGC+CGG - chr5.1:5229177-5229196 MS.gene09931:CDS 55.0%
! GAACCGGAGGAAGTGATGGA+TGG - chr5.1:5228934-5228953 MS.gene09931:CDS 55.0%
! GGGGATCACGACGACTTGTT+CGG - chr5.1:5229121-5229140 MS.gene09931:CDS 55.0%
GGCGGAGCTGGTATCCTCTA+TGG - chr5.1:5228717-5228736 MS.gene09931:CDS 60.0%
TCCTAGAGAATCCGGTGCGG+CGG - chr5.1:5228699-5228718 MS.gene09931:CDS 60.0%
! CCGCACCGGATTCTCTAGGA+AGG + chr5.1:5228699-5228718 None:intergenic 60.0%
TCCGCCGCACCGGATTCTCT+AGG + chr5.1:5228703-5228722 None:intergenic 65.0%
! CACTTTTCGGCTGCCGGTGG+TGG - chr5.1:5229183-5229202 MS.gene09931:CDS 65.0%
! GCACACTTTTCGGCTGCCGG+TGG - chr5.1:5229180-5229199 MS.gene09931:CDS 65.0%
AGAATCCGGTGCGGCGGAGC+TGG - chr5.1:5228705-5228724 MS.gene09931:CDS 70.0%
GGATACCAGCTCCGCCGCAC+CGG + chr5.1:5228713-5228732 None:intergenic 70.0%
! TATGGCGGAGCGTGGTGGCG+CGG - chr5.1:5229100-5229119 MS.gene09931:CDS 70.0%
! ATGGCGGAGCGTGGTGGCGC+GGG - chr5.1:5229101-5229120 MS.gene09931:CDS 75.0%
!! TGGCGGAGCGTGGTGGCGCG+GGG - chr5.1:5229102-5229121 MS.gene09931:CDS 80.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 5228610 5229311 5228610 ID=MS.gene09931
chr5.1 mRNA 5228610 5229311 5228610 ID=MS.gene09931.t1;Parent=MS.gene09931
chr5.1 exon 5228610 5229311 5228610 ID=MS.gene09931.t1.exon1;Parent=MS.gene09931.t1
chr5.1 CDS 5228610 5229311 5228610 ID=cds.MS.gene09931.t1;Parent=MS.gene09931.t1
Gene Sequence

>MS.gene09931

ATGAAAGACATGAAACTTGTTTGGTCCCCAGAGAGAGCAACTAACTCATACATAGACACAGTTGAAGCCATAACTACCATCAATCACCTTCCTAGAGAATCCGGTGCGGCGGAGCTGGTATCCTCTATGGCAGCAGGATGGAACGCTCAGCTGATAGTAGAAACATGGTCACACGGCGGAGTTATCCCAACGAGTGTTGGTTTATCCATAGCAAGCGGTCACACAGGTGGAAGACACGTGTGCATAGTTCCTGATGAACGGTCAAGATCGGAGTATGCAAAAAACATGGGAGAAGCTGGTATGTCACCGGAAGTTTTGGTAGGAGAACCGGAGGAAGTGATGGATGGTTTGATTGGAATAGATTTCTTGGTTGTTGATTCTCGGAGAAAAGATTTTACAAGAGTGTTGAGGCTTGCAAAGTTGAGTAGTAAAGGTGCTGTGTTGATATGTAAGAATGCTAATTTTATTTCTAAGATGGATTCTGGTTATATATGGCGGAGCGTGGTGGCGCGGGGATCACGACGACTTGTTCGGTCAGTATTTCTTCCGGTGGGGAAGGGAATTCATATGGCACACTTTTCGGCTGCCGGTGGTGGTGACAACTCTGTTACGGCGATGAAGCATAAGGGACGTGCTGTTCATAATAGATGGATTAAGCATGTTGATCAACGATCAGGGGATGTTCACTTTATTAGGAAATGA

Protein sequence

>MS.gene09931.t1

MKDMKLVWSPERATNSYIDTVEAITTINHLPRESGAAELVSSMAAGWNAQLIVETWSHGGVIPTSVGLSIASGHTGGRHVCIVPDERSRSEYAKNMGEAGMSPEVLVGEPEEVMDGLIGIDFLVVDSRRKDFTRVLRLAKLSSKGAVLICKNANFISKMDSGYIWRSVVARGSRRLVRSVFLPVGKGIHMAHFSAAGGGDNSVTAMKHKGRAVHNRWIKHVDQRSGDVHFIRK