AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG009601

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009601 MtrunA17_Chr2g0315211 99.306 288 2 0 1 288 36 323 0.0 587
MsaG009601 MtrunA17_Chr2g0315201 71.528 288 75 1 1 288 36 316 2.91e-141 400
MsaG009601 MtrunA17_Chr5g0403631 39.355 310 134 10 3 286 41 322 2.85e-29 113
MsaG009601 MtrunA17_Chr3g0141401 38.255 298 138 14 3 286 47 312 2.15e-28 110
MsaG009601 MtrunA17_Chr1g0154651 35.640 289 97 11 3 288 46 248 9.53e-25 99.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009601 AT1G78700.1 67.224 299 78 8 1 288 36 325 2.45e-123 355
MsaG009601 AT4G18890.1 57.679 293 75 9 1 288 36 284 1.26e-94 281
MsaG009601 AT4G18890.2 52.988 251 69 9 43 288 2 208 8.91e-64 200
MsaG009601 AT1G75080.2 37.349 332 111 14 3 288 55 335 1.79e-38 138
MsaG009601 AT1G75080.1 37.349 332 111 14 3 288 55 335 1.79e-38 138
MsaG009601 AT1G19350.3 38.182 330 107 15 3 286 76 354 1.37e-36 134
MsaG009601 AT1G19350.5 37.879 330 108 15 3 286 54 332 1.72e-36 133
MsaG009601 AT1G19350.1 37.879 330 108 15 3 286 54 332 1.72e-36 133
MsaG009601 AT1G19350.6 37.879 330 108 15 3 286 54 332 1.72e-36 133
MsaG009601 AT1G19350.4 37.879 330 108 15 3 286 54 332 1.72e-36 133
MsaG009601 AT3G50750.1 37.755 294 100 10 3 283 46 269 2.56e-32 120
MsaG009601 AT4G36780.1 45.455 187 70 7 3 176 48 215 2.60e-25 102

Find 116 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGACCCAGATTGGTTTGC+TGG 0.249683 2:-62221885 MsaT009601.1:CDS
CTACAAATCCATTTGGCTTC+AGG 0.253790 2:-62221812 MsaT009601.1:CDS
CCTCCCAGTCAGCTTTCCTC+TGG 0.324519 2:+62221991 None:intergenic
GAGAGGATCCATGAAGATTC+TGG 0.328306 2:-62221612 MsaT009601.1:CDS
CACTACTTACCTGGTCTTTG+AGG 0.341054 2:+62221560 None:intergenic
CTGATCCCAGCAAACCAATC+TGG 0.350204 2:+62221879 None:intergenic
AGGGAATTTCCATCACCATT+AGG 0.370323 2:+62222149 None:intergenic
CATCTGATCCAGAATCTTCA+TGG 0.372743 2:+62221604 None:intergenic
GCATGGGATGAGCGCGGGCT+AGG 0.380817 2:+62222179 None:intergenic
TTCTCCGGTTTGAGAATGTA+TGG 0.382953 2:-62224857 None:intergenic
CAGATTGGTTTGCTGGGATC+AGG 0.383352 2:-62221878 MsaT009601.1:CDS
CTCCCAGTCAGCTTTCCTCT+GGG 0.391858 2:+62221992 None:intergenic
TACAAATCCATTTGGCTTCA+GGG 0.393154 2:-62221811 MsaT009601.1:CDS
AAGGAAGAAGAGCCAGGACT+TGG 0.403188 2:+62222203 None:intergenic
GAGGATCAGTCTACTCGTCC+TGG 0.410691 2:-62221972 MsaT009601.1:CDS
AGAGCCAGGACTTGGGTTGT+AGG 0.415820 2:+62222211 None:intergenic
ATTTCAGATGAATTTGCCTT+TGG 0.420372 2:-62221672 MsaT009601.1:CDS
TCTACTCGTCCTGGGTGGGG+TGG 0.421075 2:-62221963 MsaT009601.1:CDS
CTACTCGTCCTGGGTGGGGT+GGG 0.424088 2:-62221962 MsaT009601.1:CDS
CTAGTCGCTACAAATCCATT+TGG 0.424358 2:-62221819 MsaT009601.1:CDS
TGGAAGCAGTGCAGTTGGTT+TGG 0.426703 2:-62221652 MsaT009601.1:CDS
GAGCTAAGTGGAGGAGTGAC+AGG 0.433832 2:+62222032 None:intergenic
AATATATAGCTGCGGAAGCT+TGG 0.439819 2:+62222076 None:intergenic
TTGACCCAGATTGGTTTGCT+GGG 0.448546 2:-62221884 MsaT009601.1:CDS
ACCAATCTGGGTCAAGAACT+TGG 0.450542 2:+62221892 None:intergenic
ACCTCTTCCCTGAAGCCAAA+TGG 0.452419 2:+62221804 None:intergenic
TCCCATGCTGTAAATCCTAA+TGG 0.453038 2:-62222164 MsaT009601.1:CDS
GCCAAGTTCTTGACCCAGAT+TGG 0.457814 2:-62221893 MsaT009601.1:CDS
TAGGAGGAGTGGAGGAAGGC+TGG 0.458194 2:+62221925 None:intergenic
TGTTCTCCAGCTTTAGCTGC+AGG 0.458482 2:-62221732 MsaT009601.1:CDS
TCCTCCACTCCTCCTAGCCC+TGG 0.459964 2:-62221918 MsaT009601.1:CDS
TCATTGTTATCGCAATGTTT+CGG 0.469180 2:+62224821 None:intergenic
GAACATGTCCCACTTTGTCC+AGG 0.469503 2:+62221750 None:intergenic
GGGTCAAGAACTTGGCGACC+AGG 0.476781 2:+62221900 None:intergenic
TCCATTTGGCTTCAGGGAAG+AGG 0.481397 2:-62221805 MsaT009601.1:CDS
CTCTGGGGTGATCGAGCAGT+TGG 0.483752 2:+62222008 None:intergenic
AGAACTTGGCGACCAGGGCT+AGG 0.484854 2:+62221906 None:intergenic
AGTTGGTTTGGTGAAGCCTT+GGG 0.485013 2:-62221640 MsaT009601.1:CDS
GGATCAGGATGCCCCACAGC+GGG 0.486389 2:-62221863 MsaT009601.1:CDS
GCCTTTGGAAGCAGTGCAGT+TGG 0.487429 2:-62221657 MsaT009601.1:CDS
CACCCCAGAGGAAAGCTGAC+TGG 0.487819 2:-62221995 MsaT009601.1:CDS
GCGGAACGCATGGATGTGAT+AGG 0.488603 2:-62222287 MsaT009601.1:CDS
AGGAGAAGTTTGCCCGCTGT+GGG 0.488942 2:+62221851 None:intergenic
CATGGGATGAGCGCGGGCTA+GGG 0.493897 2:+62222180 None:intergenic
TCAGAGCCTGCAGCTAAAGC+TGG 0.499118 2:+62221726 None:intergenic
GATTCCCGCATGTGGACCCC+TGG 0.499359 2:-62221768 MsaT009601.1:CDS
ATGCAAGCCTGCGGAACGCA+TGG 0.500040 2:-62222297 MsaT009601.1:CDS
AAAGCTCTTTGTAATGAAGC+TGG 0.501704 2:-62224791 MsaT009601.1:CDS
CTCTTTGTAATGAAGCTGGT+TGG 0.502741 2:-62224787 MsaT009601.1:CDS
ACTTGGGTTGTAGGAAGCAC+AGG 0.505215 2:+62222220 None:intergenic
GCTTCCTACAACCCAAGTCC+TGG 0.505291 2:-62222215 MsaT009601.1:CDS
GATGATTTAGAGCTCACTCT+TGG 0.505956 2:-62221585 MsaT009601.1:CDS
TGGATCCTCTCTCCTTCCCA+AGG 0.506658 2:+62221624 None:intergenic
CAGTTGGTTTGGTGAAGCCT+TGG 0.507522 2:-62221641 MsaT009601.1:CDS
TCAGTCTACTCGTCCTGGGT+GGG 0.507843 2:-62221967 MsaT009601.1:CDS
GCGACCAGGGCTAGGAGGAG+TGG 0.508618 2:+62221914 None:intergenic
TTACGATACGTTGTACCATC+AGG 0.508951 2:+62224755 None:intergenic
GGATGAGCGCGGGCTAGGGA+AGG 0.515742 2:+62222184 None:intergenic
ACCCCAGAGGAAAGCTGACT+GGG 0.516090 2:-62221994 MsaT009601.1:CDS
CAGTCTACTCGTCCTGGGTG+GGG 0.517746 2:-62221966 MsaT009601.1:CDS
CTAGGGAAGGAAGAAGAGCC+AGG 0.519399 2:+62222197 None:intergenic
ATCACATCCATGCGTTCCGC+AGG 0.519528 2:+62222290 None:intergenic
AGGAGTGACAGGAGCACTGA+TGG 0.525130 2:+62222043 None:intergenic
TGATCCCAGCAAACCAATCT+GGG 0.525877 2:+62221880 None:intergenic
CACCATTAGGATTTACAGCA+TGG 0.525920 2:+62222162 None:intergenic
GTGATAGGTGGTTCTGCAAT+GGG 0.525969 2:-62222272 MsaT009601.1:CDS
TCTGAAATAGCTTCAGACAT+TGG 0.527497 2:+62221687 None:intergenic
TTGTCCAGGGGTCCACATGC+GGG 0.536824 2:+62221764 None:intergenic
TAGGAGAAGTTTGCCCGCTG+TGG 0.548726 2:+62221850 None:intergenic
GGGCTAGGAGGAGTGGAGGA+AGG 0.549534 2:+62221921 None:intergenic
AGGATCAGTCTACTCGTCCT+GGG 0.551485 2:-62221971 MsaT009601.1:CDS
ATGGAAATTCCCTCATTCCA+TGG 0.555829 2:-62222139 MsaT009601.1:CDS
GCTGTAAATCCTAATGGTGA+TGG 0.562331 2:-62222158 MsaT009601.1:CDS
TAGCTGCGGAAGCTTGGAAG+AGG 0.564442 2:+62222082 None:intergenic
ACCAGGGCTAGGAGGAGTGG+AGG 0.565432 2:+62221917 None:intergenic
ATCAGTCTACTCGTCCTGGG+TGG 0.572626 2:-62221968 MsaT009601.1:CDS
TTTGTCCAGGGGTCCACATG+CGG 0.572765 2:+62221763 None:intergenic
AACATGTCCCACTTTGTCCA+GGG 0.573471 2:+62221751 None:intergenic
CGAGCAGTTGGAGAGCTAAG+TGG 0.574747 2:+62222020 None:intergenic
ACCATTAGGATTTACAGCAT+GGG 0.576979 2:+62222163 None:intergenic
TCTCCGGTTTGAGAATGTAT+GGG 0.580133 2:-62224856 None:intergenic
AGGAAGAAGAGCCAGGACTT+GGG 0.580376 2:+62222204 None:intergenic
ACCAACTGCACTGCTTCCAA+AGG 0.582208 2:+62221656 None:intergenic
TCCCAGTCAGCTTTCCTCTG+GGG 0.589485 2:+62221993 None:intergenic
TTACAGCATGGGATGAGCGC+GGG 0.592384 2:+62222174 None:intergenic
TGTGATAGGTGGTTCTGCAA+TGG 0.592423 2:-62222273 MsaT009601.1:CDS
GGTTGGATCGTTGAGCCTGA+TGG 0.594077 2:-62224770 MsaT009601.1:CDS
ATGTGGACCCCTGGACAAAG+TGG 0.596230 2:-62221759 MsaT009601.1:CDS
GGTCAAGAACTTGGCGACCA+GGG 0.596349 2:+62221901 None:intergenic
GGTTTGGTGAAGCCTTGGGA+AGG 0.598437 2:-62221636 MsaT009601.1:CDS
TGATGGTACAACGTATCGTA+AGG 0.599548 2:-62224753 MsaT009601.1:intron
CAAATGGATTTGTAGCGACT+AGG 0.599882 2:+62221820 None:intergenic
GGAGAAGTTTGCCCGCTGTG+GGG 0.600569 2:+62221852 None:intergenic
TGAAGCCTTGGGAAGGAGAG+AGG 0.605206 2:-62221629 MsaT009601.1:CDS
CTCTTGGTACCTCAAAGACC+AGG 0.612700 2:-62221569 MsaT009601.1:intron
GTGGCAGTGATTCCCGCATG+TGG 0.613531 2:-62221776 MsaT009601.1:CDS
TACTGCTGCCCACCCCACCC+AGG 0.630033 2:+62221954 None:intergenic
ATTTGTAGCGACTAGGCTGA+AGG 0.634933 2:+62221827 None:intergenic
ACTTGGCGACCAGGGCTAGG+AGG 0.641842 2:+62221909 None:intergenic
TGTGGACCCCTGGACAAAGT+GGG 0.642302 2:-62221758 MsaT009601.1:CDS
CTGACATGGTAAGATGAACA+CGG 0.642363 2:+62222245 None:intergenic
TTTCAAGGGATGCAAGCCTG+CGG 0.653639 2:-62222306 MsaT009601.1:intron
GTAGCGACTAGGCTGAAGGT+AGG 0.654465 2:+62221831 None:intergenic
GCAGTTGGAGAGCTAAGTGG+AGG 0.657333 2:+62222023 None:intergenic
TTTACAGCATGGGATGAGCG+CGG 0.658189 2:+62222173 None:intergenic
CCGCAGCTATATATTCACAC+TGG 0.658262 2:-62222068 MsaT009601.1:CDS
AGGAAGCACAGGGACTGACA+TGG 0.663416 2:+62222231 None:intergenic
CTTGGGTTGTAGGAAGCACA+GGG 0.669094 2:+62222221 None:intergenic
CCAGAGGAAAGCTGACTGGG+AGG 0.670133 2:-62221991 MsaT009601.1:CDS
ACATGTCCCACTTTGTCCAG+GGG 0.671696 2:+62221752 None:intergenic
TGACATGGTAAGATGAACAC+GGG 0.677171 2:+62222246 None:intergenic
CTGATGATGATCCAGATGAG+AGG 0.693997 2:+62222108 None:intergenic
GAACGCATGGATGTGATAGG+TGG 0.705174 2:-62222284 MsaT009601.1:CDS
CCAGTGTGAATATATAGCTG+CGG 0.708057 2:+62222068 None:intergenic
GGGATCAGGATGCCCCACAG+CGG 0.711509 2:-62221864 MsaT009601.1:CDS
CAACTGCTCGATCACCCCAG+AGG 0.741309 2:-62222007 MsaT009601.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 62221455 62224864 62221455 ID=MsaG009601
Chr2 mRNA 62221455 62224864 62221455 ID=MsaT009601.1;Parent=MsaG009601
Chr2 exon 62221455 62221473 62221455 ID=MsaT009601.1.exon3;Parent=MsaT009601.1
Chr2 CDS 62221455 62221473 62221455 ID=cds.MsaT009601.1;Parent=MsaT009601.1
Chr2 exon 62221570 62222321 62221570 ID=MsaT009601.1.exon2;Parent=MsaT009601.1
Chr2 CDS 62221570 62222321 62221570 ID=cds.MsaT009601.1;Parent=MsaT009601.1
Chr2 exon 62224754 62224864 62224754 ID=MsaT009601.1.exon1;Parent=MsaT009601.1
Chr2 CDS 62224754 62224864 62224754 ID=cds.MsaT009601.1;Parent=MsaT009601.1
Gene Sequence

>MsaT009601.1

ATGTATGGGAACTATAAGCTTCCGAAACATTGCGATAACAATGAAGTTCTCAAAGCTCTTTGTAATGAAGCTGGTTGGATCGTTGAGCCTGATGGTACAACGTATCGTAAGGGATGCAAGCCTGCGGAACGCATGGATGTGATAGGTGGTTCTGCAATGGGAAGCCCGTGTTCATCTTACCATGTCAGTCCCTGTGCTTCCTACAACCCAAGTCCTGGCTCTTCTTCCTTCCCTAGCCCGCGCTCATCCCATGCTGTAAATCCTAATGGTGATGGAAATTCCCTCATTCCATGGCTCAAAAACCTCTCATCTGGATCATCATCAGCATCCTCTTCCAAGCTTCCGCAGCTATATATTCACACTGGCTCCATCAGTGCTCCTGTCACTCCTCCACTTAGCTCTCCAACTGCTCGATCACCCCAGAGGAAAGCTGACTGGGAGGATCAGTCTACTCGTCCTGGGTGGGGTGGGCAGCAGTACTCTTTCCAGCCTTCCTCCACTCCTCCTAGCCCTGGTCGCCAAGTTCTTGACCCAGATTGGTTTGCTGGGATCAGGATGCCCCACAGCGGGCAAACTTCTCCTACCTTCAGCCTAGTCGCTACAAATCCATTTGGCTTCAGGGAAGAGGTTTTCTGTGGCAGTGATTCCCGCATGTGGACCCCTGGACAAAGTGGGACATGTTCTCCAGCTTTAGCTGCAGGCTCTGATCATAATGCTGACATACCAATGTCTGAAGCTATTTCAGATGAATTTGCCTTTGGAAGCAGTGCAGTTGGTTTGGTGAAGCCTTGGGAAGGAGAGAGGATCCATGAAGATTCTGGATCAGATGATTTAGAGCTCACTCTTGGTACCTCAAAGACCAGAAATAAAAATTTAACCTGA
Protein sequence

>MsaT009601.1

MYGNYKLPKHCDNNEVLKALCNEAGWIVEPDGTTYRKGCKPAERMDVIGGSAMGSPCSSYHVSPCASYNPSPGSSSFPSPRSSHAVNPNGDGNSLIPWLKNLSSGSSSASSSKLPQLYIHTGSISAPVTPPLSSPTARSPQRKADWEDQSTRPGWGGQQYSFQPSSTPPSPGRQVLDPDWFAGIRMPHSGQTSPTFSLVATNPFGFREEVFCGSDSRMWTPGQSGTCSPALAAGSDHNADIPMSEAISDEFAFGSSAVGLVKPWEGERIHEDSGSDDLELTLGTSKTRNKNLT*